I just don’t know enough paleontology
I just read this post by John Hawks this morning over my morning coffee. I totally agree with this sentence:
Many years ago, I got used to the fact that paleontologists and geneticists live in separate realities.
and I find this quite disturbing.
I’m one of the geneticists trying to figure out the ancestry of apes and trying to date the speciation events, and I just cannot read the paleontology papers. Well, I can read them, but I really don’t understand them, so I often end up just scanning for estimates of speciation times without being able to judge how they come about.
Just last week I tried to figure out the divergence time between humans and orangutans to relate it to the estimates we get in the orangutan genome project.
For example, following a reference from another paper I read this one that, according to the first paper was supposed to give a lower bound on the speciation of 18 million years ago. First I just scanned the PDF for “18″ but the units where “18″ appear are mm so not exactly what I was looking for. So I tried actually understanding the paper… I probably failed, ’cause as far as I understand it it gives an upper bound of 20 million years ago.
Scanning the supplemental information of the first paper I then found that they use the 18 mya both as an upper and a lower bound, depending on which table you look at, and that just makes it that more confusing.
As a side remark, here I agree with John Hawks again:
After quoting from their online supplement (once again, grumbling that the essential details are hidden online where nobody reads them!)
I hope that it is an upper bound, since a lower bound would be very inconsistent with our genetic estimate, but I just wish I could be sure I understood the paper…
–
238-242=-4
August 26th, 2009 at 7:31 am
I’ll get to that problem in due time (I’m writing a textbook chapter, so I’m being systematic).
For a quickie, the lower bound on orang-human split ought to be closer to 11 million years, and an upper bound would be around 14. The lower bound comes from putting Sivapithecus on the orang clade, which is well-accepted, though not universally so. The upper bound is the first appearance of great apes in Eurasia — David Begun calls this the “Griphopithecus” dispersal. The disagreements are whether Dryopithecus — very well attested in Middle Miocene Europe — is on the African ape clade already, or if it is a stem great ape.
And after writing that paragraph, I can already tell that’s as understandable as Latin. Oh, well, it’s late!
Morotopithecus is irrelevant to the human-orang divergence. It could be a stem great ape, but more probably it preceded the gibbon-great ape divergence.
August 26th, 2009 at 8:18 am
Well, I understood some of it at least, and I am very happy with those bounds :-)
August 26th, 2009 at 1:30 pm
Upper bounds are an abomination introduced for mathematical convenience!! They have no basis in scientific evidence.
Lower bounds, on the other hand, are based in evidence. That evidence may be wrong or misinterpreted, but there is evidence there. For example, IF we accept Sahelanthropus as being on the human lineage (and not on the chimpanzee lineage) and IF the Sahelanthropus fossils date to ~7 Ma, then that is a lower bound based in evidence, because under these assumptions the human lineage MUST have diverged from the chimpanzee by then. (I’m not necessarily arguing one way or the other for Sahelanthropus, but it is evidence that could form the basis for a lower bound estimate).
There is no similar “MUST” for any upper bound that is useful. Assuming most (if not all) known life evolved on Earth, then all primate lineages MUST have diverged after the formation of the Earth (not a useful upper bound). It strains the limits of credulity that a human lineage (separate from chimpanzees) could have existed in the Cretaceous and not left any fossil trace between then and 5-7 Ma (again, not a useful upper bound). As one tries to bring an upper bound down to a value where it is useful and actually imposes a boundary, the credulity criterion becomes very weak and there is NO evidence-based criterion. “First appearance” is a useless value – we know for certain that many lineages have existed for long periods of time before their first appearance in the fossil record (gibbons are a good example of this in the hominoids).
August 26th, 2009 at 3:20 pm
As one tries to bring an upper bound down to a value where it is useful and actually imposes a boundary, the credulity criterion becomes very weak and there is NO evidence-based criterion.
Why not argue the same for lower bounds? How do you know, really, that the first appearance of a species was not really a collateral? How do you know the polarity of features, really? It’s only the limits of credulity on parsimony that argue for phylogenetic relationships at all.
August 26th, 2009 at 3:44 pm
Yes – it is the limits on credulity that allow any scientific inference. However, any upper bound for which one can legitimately believe on the basis of evidence provides no useful constraint.
For a human lineage divergence from chimpanzees, anyone with any kind of reasonable knowledge of the evidence could not (in my opinion) possibly push the lower bound of this divergence closer to the present than 4 Ma or so.
However, for an upper bound, I’d say that 20 Ma is probably absolutely safe (but completely useless). So then, how about 15? 10? 7? By the time that number gets near a value that is useful, it is no longer reasonable to use it – and there is no evidence that reasonably supports it (where reasonably = you could convince the majority of your scientific peers). What evidence would you use to support a useful upper bound for the human-chimpanzee divergence?
August 26th, 2009 at 4:16 pm
Sorry, I don’t get why this is a problem specific to upper bounds. I mean, doesn’t the same argument goes for lower bounds as well? A lower bound of 100kya is safe, but what about 4.5mya?
Of course, the tighter the bounds, the higher the risk that they are wrong, I just don’t see why this is more of a problem for upper bounds than lower bounds?
Sorry if I’m being thick here…
August 26th, 2009 at 4:43 pm
The available fossil evidence is actually meaningful for a lower bound in a way that it is not for an upper bound.
Because I think we’re all reasonably conversant with the broad outlines of the fossil and genetic evidence, I’m sticking with the human-chimpanzee divergence for the example here.
So, first, the lower bound. Yes, 100 Ka is certainly safe, but there are huge numbers of fossils almost universally assigned to the hominin clade found in deposits earlier than 100 Ka. As one pushes that date earlier, the number of near-universally accepted hominin fossils decreases until one gets to a point where the evidence no longer supports an earlier lower bound. You and I may differ as to where that point is, but we are fundamentally basing that lower bound on the first appearance of a fossil for which we accept the hypothesis that it is more closely related to humans than chimpanzees. For you that might be Ardipithecus at ~5 Ma, for me that might be Orrorin at ~6 Ma, and for someone else that might be Sahelanthropus at ~7 Ma; but the fundamental reasoning is the same in all cases.
There is no equivalent for the upper bound. What could it possibly be? The first appearance of a fossil on the gorilla lineage? (I’m not really up on my gorilla fossils, so this will all be “what if?”).
* What if the first near-universally accepted gorilla lineage fossil appears at 2 Ma? This obviously provides no information on the upper bound of the human-chimpanzee divergence – there’s a long absence of fossil information for the gorilla lineage.
* What if the first near-universally accepted gorilla lineage fossil appears at 10 Ma? If you accept this hypothesis, this still provides no significant information on the upper bound. Is that gorilla-lineage fossil from an animal that died and was fossilized IMMEDIATELY after the gorilla-(human,chimpanzee) split or from an animal that lived 8 million years after that split? (as in the first what if?)
If you had a fossil from a species from the human-chimpanzee lineage after it split from the gorilla lineage, it might seem that the date of this fossil could be useful for setting a lower bound, but often is not. If the fossil belongs to the ACTUAL ANCESTRAL SPECIES of humans and chimpanzees, then it could provide an upper bound. However, we generally cannot be certain that this is the case. It certainly could, and odds are, probably does belong to a side branch that left no living descendents (an extinct stem lineage). In that case, it provides no evidence for an upper bound. That stem lineage could have diverged from the common human-chimpanzee-stem lineage ancestor at any time.
Fossils that are on one of the descendant lineages of the split you are trying to date give information on a lower bound for that split, but fossils on separate evolutionary lineages don’t really tell you much.
August 26th, 2009 at 4:45 pm
Er. “useful for setting AN UPPER bound” not “useful for setting a lower bound” towards the end of the first sentence in the second to last paragraph.
August 26th, 2009 at 5:05 pm
Ok, I think I get your point, but just to clarify: the argument is basically that for lower bounds we just need a fossil we can agree is only on one of the lineages leading to humans or chimps, respectively, and then we know that the speciation happened earlier than that. Yes? And that the problem with upper bounds is that we need to then have a fossil that we can agree is ancestral to both species and those are harder to identify?
The latter is something I have a bit of a problem seeing, but then I do not know any paleontology so I will take your word for that. I guess it boils down to what you say about the actual ancestral species vs side branches.
I guess if we find a human-looking (for whatever that means) fossil we don’t know if it is ancestral to humans or a side branch either, but if it is sufficiently close to human we would still expect it to have a shared branch with actual humans not shared with chimps.
Am I getting this right?
It makes sense in my head, so I hope it is not too far off :)
August 26th, 2009 at 6:06 pm
It seems to me that you’ve more or less got my point.
For what it’s worth, we do not know if ANY of the known fossil hominins are directly ancestral to living humans, just that (based on morphological analysis) that they are more closely related to humans than chimpanzees – and that’s all we need for the calibration point. That is, any member of the descendant clade after the split; they don’t have to be directly ancestral to living humans to provide a valid lower bound for the human-chimpanzee split.
Many paleontologists would argue that it is somewhere between enormously difficult to effectively impossible to identify whether a particular fossil is directly ancestral to a later lineage or is a closely related side branch. A strict cladist would argue that one should NEVER take the position that the actual ancestor is known.
In addition, the odds of any given fossil group being directly ancestral to a later lineage depends on one’s understanding of the bushiness of the larger group in question. So if you believe the evidence suggests that there have been relatively few hominoid lineages alive at any given time, that increases the odds that any individual fossil belongs to a group that is directly ancestral to later lineages. However, if you believe the evidence suggests that there have often been quite a number of hominoid lineages alive at any given time, then that decreases the likelihood that any particular fossil belongs to a group directly ancestral to later forms.
August 26th, 2009 at 6:24 pm
Good to hear that I am finally getting the point :)
I also see the point about any given fossil being ancestral to humans. A priori I would find it extremely unlikely that any fossil we dig up is ancestral to any living human – based just on how unlikely fossilization is in the first place – but I don’t have any good intuition about how likely it is that it was part of a species that eventually led to humans.
August 27th, 2009 at 9:13 am
In regard to recognized fairly certain ancestors of the non-human African apes fossil evidence from the Pleistocene is hard to come by. There’s just very little of it that’s been found. Making the nature of the divergence problematic especially in terms of locomotion. If one grants that gorilla and chimp knuckle walking COULD be parallel evolution (I know of NO comparative studies) then it’s as easy to derive knuckle walking from upright bipedalism as the other way around. Personally. I find much of the prevalent theory based squarely in crown of creation ethnocentrism, or human ‘species-ism’ if you prefer, rather than sound science. The critical fossil links if they exist will have to come from forested west Africa, difficult ground indeed for paleontological or archaeological survey. Other than an interestingly human cast, this is one of the more significant aspects of Sahelanthropus. It indicates in a round about way that the relevant ground pounders, are circuitously working around to where they really need to explore. It’s a challenge. Imagine telling the National Geographical Society or some similar funding source that your intended survey is liable to find little or nothing due to the nature of the ground that most neds to be covered.
August 28th, 2009 at 7:21 am
In addition, the odds of any given fossil group being directly ancestral to a later lineage depends on one’s understanding of the bushiness of the larger group in question. So if you believe the evidence suggests that there have been relatively few hominoid lineages alive at any given time, that increases the odds that any individual fossil belongs to a group that is directly ancestral to later lineages.
At some point, the hypothesis that we haven’t found the ancestors becomes incompatible with reasonable hypotheses about the origins of branches by vicariance, dispersal, ecological specialization, or the like. Or reasonable assessments about sampling density and the likelihood of missing the true ancestors at every locality.
I don’t disagree that an “upper bound” is subject to parsimony and credulity. I just don’t think the situation is any better for “lower bounds”. The comments above lay out a 3-million-year fudge factor in the lower bound on the human-chimpanzee divergence, a period during which we have a reasonably good fossil record.
My idea of an upper bound for the human-chimpanzee divergence — based on fossils alone — is between 10 and 13 million years. Also a three-million-year span.
I think we can pin down the orang-human divergence with narrower bounds, because there are biogeographic constraints getting apes into Asia and good phylogenetic signs that the initial dispersal of great apes into Eurasia was accomplished by stem great apes. But the upper bound is only as good as the hypothesis.