DONE!

I always wanted to finish University before the construction of the new Building for the Institute was done.
I missed the mark by 13 months.

I'm done with University

Not in a "I'm so fed up that I quit and started a career as an eccentric artist" kind of way, although I came pretty close to this state several times in the last two years. I'm done in the sense that I have finished everything that is required of me to get my degree.

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.

(Not) always worth mentioning: Bipedalism in fossils

News of potentially bipedal fossils always seem to be interesting. However there are different kinds of bipedalisms and not everyone of them is worth mentioning.

Some random question:

I read a very interesesting paper yesterday which really made think about anumber of things. But instead of sharing all these rather confusing thoughts with you, I'm just going to throw a random question in here, mostly because I'm interesed in the opinions of other people on this topic. Also because I'm rather confused right now and this might help me in overcoming it.

Anyways, the question is as follows:

Where does the causal foundation of (morphologic) characters lay, in ontogeny or in phylogeny?

I hope I was able to formulate it in a proper matter, if not let me know and I try to explain it better. Also let me know what you think the answer to this question is.

And also, if you're interested in the article which caused my confusion, here it is:

Vergara-Sillva, F. (2009). Pattern Cladistics and the Realism-Antirelaism debate in the Philosophy of biology. Acta Biotheor,57. S. 269-294.

The road towards madness: Thesis Devlog part 2: I actually did something last month

A lot of stuff happened in during the last month, and most of it was quite positive.

I was able to clear out most of the obstruction that were preventing me from getting started on my thesis. In fact, I spent the last two weeks in the Senckenberg-Museum in Frankfurt, acquiring my first Data for my Thesis, so technically I already started working on it.

I’ve never visited a collection before so I was really excited to take a look “behind the scenes” of a museum, especially the Senckenberg. I was born in the Area around Frankfurt, and I visited the Senckenberg quite a lot when I was a child and I still have very fond memories of those visits, Funnily enough most parts of the upper floors of the museum haven’t changed a bit since I was a kid. This place also partially responsible for getting interested me in Paleoanthropology a few years back. Well it was a lecture of Bernard Wood which I visited, but it was hosted by the Senckenberg.

Anyways, as I said I never visited a collection before that, so I was really excited to get this opportunity. I just love old stuff and Collections are always a great place for that. I had skulls on my desk which were acquired during the 1840s, a time when nobody besides Darwin and some other few people ever thought about natural selection, where the first Neanderthal was still to be discovered and where people could become respectable biologists by simply walking through the jungle with a Rifle in their hand, occasionally shooting in the trees and collecting all the dead stuff which fell in front of their feet.

I often stopped my work wondering who also might have held this object in their hand and what they might’ve done with it.

I also stopped my work from time to time to wonder what I was looking for. I wasn’t really trained to this kind of work I’m supposed to do right now. Sure I know to navigate myself on a human skull and I know how a primate skull basically looks like. But identifying smaller structures on skulls of non-adult primates? That’s quite difficult. So the first few days where mostly spent with me trying to navigate myself around this stuff. Funnily enough, large portions of the more challenging parts of this thesis will involve me having to learn the appropriate skills while doing the actual work, which is quite interesting.

I learned a lot of stuff in the last few weeks and I also regained huge parts of my motivation for science in general. There were quite a few things which got me down in the past few months, most of them dealt with the more ‘administrative’ parts of science and less with the actual work. I was even thinking about whether or not I’m suited for this kind of work. Honestly I still don’t know if I really am, but what I’m sure about is that I don’t care about that. Either I will be able to do things the way I want, or I won’t do it. If I would wanted to get an easy job, I would’ve gone into engineering and not Anthropology in the first place.

At some point I might write about this in more detail, but what I will promise right now is that, as soon as I’m allowed to, I will simply put my Thesis somewhere up where everybody will have access to it. If my time allows it, I will even try and translate the whole thing into English. I want to do this, because I think that, even if this thing is a complete mess, someone else might find something of value in it. And be it as an example of what you should never do while writing a Thesis. The alternative was either putting this thing in my shelf and letting it gather dust, or publishing my results in some obscure Journal which no one is ever going to read anyway. Ideas are the forces that drive scientific innovation and I strongly believe that the more Ideas you have to discuss the better you’re able to really get some kind of scientific progress.

The road towards madness: Thesis Devlog part 1: "Get started fool!"

(In the vague hope of creating some kind of regularity in my writing, as well as to give myself some space where I could organise my thought, I decided to start a “Development-Blog” (or “Devlog” as it is called among us cool people) for my Thesis. I intend to write this once per month and I will present you what I have done so far and what I want to accomplish in the next few weeks. Watch as I make dumb mistake after dumb mistake and how the stress of this work will make me go insane as the year porgresses).


I’m sitting at my Thesis for quite some time by now. Well, “sitting” isn’t really the appropriate term. I circling around it, like a dog who isn’t sure if he should really lay down on the carpet or not. It goes without saying that this isn’t a really satisfying state of affairs, for three reasons:


1. This is the last thing I need to do to graduate from University.


2. I don’t have anything better to do.


3. I only have time until January 2013 to graduate before I have to re-do my Psychology-finals, which I already took in 2010.


So despite being more or less unprepared for the work that lies ahead of me, I decided to simply jump into the fray and hope for the best.
But before I start to tell you what kind of stuff I need to do, let me quickly tell you what exactly my Thesis is about.
The goal of my Thesis is to compare phylogenetic trees of the relationships between great Apes and Humans from different ontogenetic stages with each other. I want to do this mostly because it’s interesting to see how certain Traits are affected by ontogenetic processes and how those traits effect phylogenetic trees. Also this was the first Idea where none of my Professors told me that it is too big, too expensive, or just stupid.

So far my plans are to do this study with the following taxa:


Papio


Pongo


Pan


Homo


You probably have noticed that there are no Gorillas in my species sample. That’s because my advisor told that it would probably be better for my results if I exclude them. As I tried to show a few months ago, there are some problems when it comes to the reliability of phylogenetic trees who try to resolve the relationships between Gorillas, Chimpanzees and Humans. Excluding the Gorillas from my sample helps me to avoid that this “trichotomy-problem” is somehow effecting my results.
I’m not very happy about this, since it also limits my possibilities of drawing more wider ranging conclusions from my thesis.
But fortunately, nobody is expecting me to make some kind of ground breaking work. all I have to make sure is that my study is well executed on a technical level and that I don’t make any factual mistakes.


What I need to organise right now is where I get my sample from, where I’m going to get my measuring tools from and how I’m going to pay for this stuff.


The first question fortunately is quite easy to answer, since there are some rather big collections at several museums in the german-speaking area. So far I plan to go to the Senckenberg-Museum in Frankfurt (which is right around the corner), the Museum of the Institute of anthropology of the University of Zürich and the Museum of natural history in Berlin.
I hope that I’m able to collect all my data until June, but this means that I need to make sure I get access to those collections within the next few months.


The next point bothers me a little bit. I need to collect some osteometric data for my Thesis but funnily enough my Institute doesn’t seem to own the appropriate tools for these kind of work anymore. This strange because we still have rooms full of old skeletons where nobody knows where they’re from, but no means of analysing them in a proper manner.
Fortunately I think I know where I could get those tools from, but those things are fairly expensive, which brings me to the last problem.


Spending several weeks in different towns to have a look at primate skulls is a fun thing to do, but it costs money. I still need a place to sleep and something to eat from time to time. My initial plan was to apply for a grant which our biology department offers for students who are about to graduate. Unfortunately I needed a letter of recommendation from my advisor for this, something he refused to do because he wanted to see other projects to be supported. This grant would have been enough for me to ravel to each and every museum I desired without having to worry about how I’m going to pay my bills. I still get mad about this, although there’s really nothing a can do about this. Instead I decided to apply for a different grant, which doesn’t need the approval of my advisor, I still need to the application for this and I hope I’m able to do this by the end of this week. As an alternative route I took a side very boring side job and try to save as much money as I can. Luckily enough, my Institute will still pay for the stuff I directly need to do my work e.g. those expensive measuring tools, computer programs etc.


Essentially I was able to sort out most of the aforementioned points, the only thing I need to do right now, is to get going. The most important thing right now is to fix the time when I have to visit the different collections as well as to find out if there are really no tools in this Institute. I also try to get my application for this grant ready and I hope I can give you some more information on that sometime later this week.
I think that’s it for now, let’s just hope things will go as planned (which they probably won’t).

Apes (and other primates) on the internet -The digital morphology museum

I’m a huge fan of Internet Databases, such as the Nespos Database, where you can get access to CT-Scans of original fossils as well as recent specimens for your work.. However what always bothers me is that all those databases aren’t completely open to the public. For example to get access to the Nespos Database, you need to explain why you need access to it, you need to be a member of an academic institution and you need to pay for a membership.
These things make it rather difficult, if for example biology teachers want to use these materials during their courses (which would be a really great thing).
This is why I was really excited, when I read on Lawn Chair Anthropology about the “Digital morphology museum” of the university of Kyoto. Here you can take a look at their whole stock of CT and MRT-Scans of a bunch of different Primate specimens and, after a small registration process, you can even download these Scans for free.


Right now I’m thinking about something for which I can use this Database. Perhaps some kind of online course? I don’t know but I’ll come up with something.


If you want to take a look for yourself, you can do it right here.

A lot of trees here...

Those few and lucky people who read this blog on a more regular basis probably have realised that  a lot of the stuff I wrote recently dealt in some manner with phylogenetic trees.
On one hand this does not seem to be very suprising since taxonomic questions always were some kind of focus of this blog. However the other reason for this is because I finally found a suitable topic for my M.A. Thesis (yaaaay!). I won't write about the exact topic as of yet simply because I still need to write it down properly, but if you're interested, just look at the comments under this Post, it's mentioned in one of them.

I plan on covering the whole process of me writing the thesis, analysing my data and whatever else I need to do on this Blog. This is going to be my first real scientific work so it might be interesting to see what kind of stupid mistakes I make and in what kind of pitfalls and Problem I might run into. Also, I want to use this blog as a Plattform where I can write down some of the ideas I get while working on my thesis. In fact this is why I wrote my last post and there's another one coming soon.

In other news: This week I'm in Frankfurt at the Senckenberg-Museum to attend a congress about the ecology and organisms of the eocene. Since I'm mostly interested in primates and I don't have that much knowledge about fossil invertebrates and I also have to prepare my Thesis (yaaaay!), I will probably visit the conference only on Friday, since this is the "primate day".
Of course, good ol' "Ida" will be a big topic on this day and from what I can tell from the abstracts, I'm pretty sure the discussions are going to be very "interesting".

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)

The debate that should not be: Some thoughts about creationism, intelligent design and other "alternative explanations"

If you blog about human evolution there’s one topic which is really hard to avoid. I’m of course speaking about creationism, or “intelligent design” or some other kind of unscientific explanation about human evolution. So far I tried to avoid this topic as best as I could, since I don’t feel competent enough to actually write something about it. However, last week I received an Email from one of my German readers which forced into writing something about it. 

I don’t want to talk about the exact content of the email or about the (rather short) debate I had with the person who wrote me this Email. What I want to talk about is my point of view on this whole issue and why I think we shouldn’t even have these kinds of debates.
It goes without saying that this text only represents my opinion so don’t interpret the stuff I’m going to write as some kind of general explanation about this topic.
I’m going to split this Post into three different parts to make it a little bit easier to follow my line of argument.


1. Why Sciences and Religion shouldn’t interfere with each other.
To understand this point, first of all we need to define what we understand under the term “God”. This probably is a topic for not one but several posts itself, but for the sake of my argument, let’s put as simple as possible.
“God” is an entity which almighty and which isn’t completely detectable. The first premise directly leads to the latter, because if an entity is almighty then it also has power over those parts of reality which we can’t perceive.
Now, if we want to build a scientific hypothesis, we have to make sure that we can actually falsify it (if you want to know why, I wrote something about it here). But how can we falsify something which isn’t completely detectable? The simple answer is: We can’t.
Therefore, if we try to explain our world due to the work of a non detectable entity, we’re leaving the scientific framework.
The scientific method is not suited for those questions. You simply can’t prove or disprove God due to scientific methods. Or to put it more bluntly: “God doesn’t matter in Science”
This does not mean however, that each scientist is an atheist. You can believe in whatever you want, as long as you don’t try to mix up both “worlds”. Every attempt to do otherwise ends in a logical fallacy.

2. Why, in my opinion, Science produces reliable statements about our world.
Some of the more “advanced” criticisms of evolutionary theory try to show that the theory itself or the scientific method itself is somehow erroneous in some manner.
The interesting thing about the different perspectives on the world, whether they are scientific or more metaphysical is, that all of them need some kind of basic assumptions to actually work. If you don’t make those assumptions you will, at some point during your argument, come to a stage where your own arguments become circular.
But which are those basic assumptions for a scientific world-view?

The first assumption is that we live in a world which consists of laws.
-If there are no laws in nature, then we won’t be able to make any reliable statements about it.

The second assumption is that we’re able to recognize these laws.
-Science is a cognitive process. If we weren’t able to recognize any of these laws, than we couldn’t do any kind of science.


These basic assumptions are the fundamental aspects on which every other scientific theory is build upon and it’s the only context in which they make any kind of sense. The question, whether or not I “believe” in evolution isn’t a real question. It’s simply the explanation which, in the framework I presented here, makes the most plausible. The “question of faith” doesn’t ask itself if you look at separate scientific theories, it’s only important if you look at the basic assumptions of Science. And so far I haven’t found anything which convinced me that those basic assumptions are wrong.
However, this does not answer the question, whether or not science can answer every question. Unfortunately we will never receive a message which says: Achievement get! Explain every law of nature!” Or to say it with the words of Gerhard Vollmer:

"The degree of consistency between our theoretical knowledge of the world and the real world remains unknown to us, even if it's complete."

[From: Vollmer G. (1975) Evolutionäre Erkenntnistheorie Hirzel, Stuttgart, Leipzig, p. 137, (probably horribly) translated])

Ok, after we set the stage for the debate, let’s move on to the original point of this post.


3. What’s that stuff got to do with creationism?
The first point of my argument shows that it’s completely impossible to prove or disprove God within a scientific framework. Therefore any kind of “theory” which tries something like that is making a logical fallacy. This works in both directions. You can’t explain any kind of natural law with the work of God, as well as you can’t demonstrate that God doesn’t exist.


The second point shows that it’s not the question whether or not someone believes in a certain scientific theory, because its validity is the result of the scientific framework. Not “believing” in a certain theory means omitting any kind of ability to recognize laws in nature and therefore this person leaves the scientific framework. Any kind of argument which follows after this point is subject of my first line of argument.


Now about the debate on creationism: Both of my arguments show that any kind of argument which is brought up by these people is not part of the scientific framework. This means that their arguments don’t matter in a scientific discussion. But it also means that you’ll never be able to use purely scientific arguments if you want to debate with them. Someone who isn’t convinced that we’re able to recognize laws in nature will never be convinced by scientific arguments, simply because he doesn’t believe them.

In my opinion the only thing you can try to do is to show, that there are no conflicts between scientific and metaphysical (e.g. religious) views on the world, as long as both sided try to stay within their specific framework. Both sides have completely different premises and thus there is no reason for a conflict. Those conflicts only occur if one side tries to interfere with the other, but as I demonstrated, this is logically false.
Trying to debate this stuff on this level is pretty difficult, since you’re leaving the scientific framework and enter a purely philosophical one and I think this is the reason why this whole debate does not take place on this level. This and also because I think there isn’t much public interest in these kinds of debates. The public tends to direct its attention to the loudest participants and those aren’t often the most competent when it comes to actual discussions.


Anyway, this is my opinion about this whole story. I have to admit that I'm not very comfortable with this post. Firstly because I think I left some important questions unanswered and secondly because I’m not very confident that my English is actually good enough for this topic, in fact I’m pretty sure it isn’t. So, if you don’t understand some of my arguments, please tell me and I’ll try to clarify things. Furthermore I would really like to know how other people think about this debate.

Where to put Australopithecus sediba?

It took me some time to decide what I should do with Australopithecus sediba on this Blog, in the end I decided to concentrate on the aspects I at least know a little bit of, one of them is taxonomy.


I had to reconstruct a bunch of phylogenetic trees in the last few months and I found  some free online tools which enabled me to do this without using any fancy (and expensive) Computer Programs. The only disadvantage of these resources is that they were originally made for molecular data sets. This made my work a little bit more complicated since I had to modify my morphological datasets in a way that these programs were able to work with them. I won’t talk about the exact process right now; instead I want to show you some of the stuff I did with Australopithecus sediba.
First of all, let’s have a look at a classic tree which illustrates the phylogenetic relationships among the genus Homo. I took the tree from Strait et al. (1997) for this particular example:

Strait et al. (1997)

There’s nothing really special about this tree, sure you could discuss whether or not the shown phylogeny represent the true relationships of these fossils, but discussing this stuff always tends to get boring, since you have to look at the characters and you need to discuss the validity of each of them
To make things a little more interesting, I took the character matrix from Strait et al. and included Australopithecus sediba. The characters for Australopithecus sediba were taken from the initial description of this Fossil (Berger et al., 2010). This is the tree you get, when you run this modified matrix through an Analysis:

Same character matrix but with A. sediba.

Sediba ruined everything!
What in the first tree looked like a nice and clear relationship is now collapsed into something completely indifferent.
To make things clear, the taxonomic position of Homo habilis and Homo rudolfensis never was pretty clear. In fact, the latter species was established, because the initial hypodigm (the total sum of all fossils which describe a species) of Homo habilis was so diverse in its morphology that it was split up into two separate species. The “new” species was then called Homo rudolfensis. I won’t talk up the exact reasons why this was the case, since it would make this post too long, but I will eventually come back to this topic in another post.


Let’s go back to Australopithecus sediba for the moment. It’s not only that the fossil practically ruins the common taxonomic picture of relationships of early homo, it’s also very young. Right now, Australopithecus sediba is dated at about 1.9 million years, this is very young, if you keep in mind that there are fossils of Homo habilis and Homo rudolfensis which are much older then 2 million years. There are also possible fossils from Homo ergaster/erectus which are only slightly younger then the sediba fossils. Now add the about 1.7-1.8 million year old remains from Dmanisi/Georgia to this mess and you can see how complicated this whole story starts to look.
Fortunately the tree I showed you at the beginning of this post isn’t completely useless since it shows that Australopithecus sediba falls somewhere within the relationship of Homo ergaster/erectus, Homo rudolfensis and Homo habilis.


So let’s have look at the possible relationships and the possible consequences of each scenario:






Scenario if A. sediba would share a LCA with the Genus Homo


In this scenario, Australopithecus sediba would share a last common ancestor with the Genus Homo. The only problem which arises from this tree is that you have to discuss what you should do with the Homo rudolfensis and habilis fossils which pre-date the emergence of Australopithecus sediba in the fossil record.






All other scenarios basically ruin our contemporary picture of the Genus Homo:



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Two of the possible relationships if A. sediba would be place somewhere within the Genus Homo

 No matter which scenario we look at, none of them shows the Genus Homo as a monophyletic group. This means that either we have to include Australopithecus sediba within the genus Homo which I’m not very fond of since it would lead to an even weaker definition of it. Or we have to exclude Homo habilis and/or Homo rudolfensis from the genus Homo. The Genus Homo would then begin with Homo ergaster/Homo erectus and everything before that species would be either inside the genus Australopithecus or in a complete new genus.
Personally, I have no Idea what I should make out of this stuff. Right now everything seems to contradict itself and I think we need to have much more knowledge about this certain period of time. This means of course more fossils from this period but also more research on the already known fossils.
What I think we can safely right now is that the emergence of the genus Homo didn’t happen in a gradualistic fashion where one species slowly evolved into the next one. I think what we have here is a series of, possible independent, speciation events. This would explain why we have that many species that look similar to another but who overlap in spatial as well as temporal aspects and whose phylogenetic relationships are completely unclear. I have some more thoughts on this matter and I will write another Post where I go into much more detail. For now, all I can say is that, although Australopithecus sediba completely ruins the contemporary phylogeny, it might help us to really understand what happened back then.








References:
 Berger, L., de Ruiter, D., Churchill, S., Schmid, P., Carlson, K., Dirks, P., Kibii, J. (2010). Australopithecus sediba: A New Species of Homo-Like Australopith from South Africa Science, 328 (5975), 195-204 DOI: 10.1126/science.1184944
Strait, D., Grine, F., Moniz, M. (1997). A reappraisal of early hominid phylogeny Journal of Human Evolution, 32 (1), 17-82 DOI: 10.1006/jhev.1996.0097