Late Miocene fossil apes from Africa

Time for some attention to the Miocene apes. I've neglected them for the last few years, and there have been some interesting finds. I don't mean the stuff that most people find interesting -- near-complete skeletons, or discovery of rare postcranial elements. There've been some of those, but they're European. No, I mean interesting as in African, which means potential ancestors of humans, gorillas or chimpanzees. Or all three.

This is a part of the fossil record that potentially can confirm (or disconfirm) details of the genetic comparisons between living apes. We have an increasingly detailed model for the speciation of humans and chimpanzees from their chuman ancestors. That model has been built from the complete genomes of humans, chimpanzees and macaques, and the partial genomes of the other apes. But there are potential reasons for uncertainty in the timing and duration of speciations among these living hominoids. What we need is a fossil record.

And now we have just a tiny bit of one.

Chororapithecus

I wrote about Chororapithecus two years ago on its announcement ("Did Gen Suwa just save paleoanthropology?", "More on Chororapithecus"). It's a small set of 10-million-year-old teeth from Ethiopia that look a lot like you'd expect an early gorilla to look. I don't have any new news about it, but I was reading back through the paper by Gen Suwa and colleagues (2007) and once again ran across this shocking paragraph:

Acceptance of Chororapithecus as a basal member of the gorilla clade would push back the gorilla species split to >10.5 Myr ago. Because this is a minimum date established from a meagre fossil record, the actual divergence would have predated this by an unknown time gap. From the currently available evidence, we consider that a species split of ~20 Myr ago for Pongo, 12 Myr ago for Gorilla, and 9 Myr ago for Pan are all probable estimates (see Supplementary Information). We consider that the early divergence hypothesis is congruent with both fossil and molecular data, and should be further evaluated using both sides of the evidence (Suwa et al. 2007:924).

I found that so astounding when reading it this time, that I had to go back and check what I'd written two years ago. And, blog be praised, I took good notes on it. After quoting from their online supplement (once again, grumbling that the essential details are hidden online where nobody reads them!), I concluded:

Well, that's a tricky bit of argument. We might believe that African apes never left Africa and that all the dryopithecines are therefore on the orangutan line. At least, that makes some biogeographic sense. But it's hard to argue that any of these dates are "congruent" with genetic evidence as we currently understand it. Many of the recent methods don't make any prior assumptions about "calibrated" divergence times like the orangutan-human divergence. Worse, Hobolth et al. (2007) found a human-chimp speciation time of 4 million years even considering an orangutan-human divergence of 18 million years.
The "shorter generation lengths" explanation doesn't help much -- after all, if we infer that the current great ape lineages existed as early as 20 million years ago, then almost all of the divergence time is occupied by long-generation-length species. Much faster evolution in Old World monkeys should show a strong signal of acceleration in that lineage (with a higher number of derived substitutions), and we don't see it.
If we believe these interpretations of the genes, a 10-million-year-old gorilla did not exist. Chororapithecus was something else.

Many years ago, I got used to the fact that paleontologists and geneticists live in separate realities. But this one is a real mind-bender. How somebody can blithely write that a date could be consistent with genetic estimates when the date is actually twice as old as any genetic estimate -- it's just astounding. And that we have to push all of this around for three teeth.

OK, so why am I re-reading this now? Well, Chororapithecus no longer has the only three teeth. So, it's time for a little review of the rest of the fossil record of African Late Miocene apes.

Nakalipithecus

The most substantial sample belongs to Nakalipithecus, reported by Yutaka Kunimatsu and colleagues in 2007. I didn't review that paper at the time, because it came out at the same time as our acceleration paper, so I was a little busy. The Nakalipithecus and Chororapithecus papers came out too close together for there to have been systematic comparisons of the two apes. Based on the papers -- and the brief account by Kunimatsu et al. (2007) -- the Nakalipithecus dentition is more comparable to Ouranopithecus than to gorillas.

In addition, Kunimatsu and colleagues mentioned a "large mystery ape" (my phrase, not theirs) represented by a single premolar. They wrote that this ape is more primitive and very different from Nakalipithecus or hominins. From an upper premolar, I find this idea hard to interpret -- maybe it looks like a Proconsul? They don't picture it or give measurements, so I'd say it's a genuine mystery. Maybe they are hoping to turn up more examples before they publish.

A mixed bag from Kenya and Niger

Martin Pickford and Brigitte Senut (2005) reported four ape teeth from three sites in Kenya. Three of the teeth, dating to around the same age as Orrorin, 5.9 million years ago, represent a gorilla-sized ape whose teeth look quite a bit like you'd expect an early gorilla to look, if a bit smaller.

Strangely, neither Suwa and colleagues (2007) nor Kunimatsu and colleagues (2007) mentioned these ancient gorilla-like teeth. You'd think somebody would have pointed this out. The upper molar fragment from Kapsomin looks an awful lot like the Chororapithecus holotype -- the two papers show the anatomy in profile, and the break in the Kapsomin specimen allows comparison of the enamel thickness, which is very comparable. The lower molar from Cheboit, on the other hand, doesn't look very much like the Chororapithecus lower molar, even though both are supposed to be M3. The Chororapithecus specimen looks more like a gorilla M3 -- elongated and narrower at the distal end, looking triangular in occlusal view. But the three examples of Nakalipithecus lower M3 do look like the Cheboit tooth -- all are more rectangular in occlusal shape than the triangular Chororapithecus example, two of them have a slightly lingually displaced hypoconulid. The difference is size -- the Nakalipithecus teeth are bigger, well within the gorilla range, while the Cheboit and Kapsomin teeth are at the bottom end or below that range.

Pickford and Senut (2005) also described an older molar from Ngarora, some 12.5 million years old. I think you could probably find a reasonable match for this tooth among samples of Dryopithecus -- it's the size of a chimpanzee molar but doesn't share any derived features. The authors suggest that the specimen may be an early member of the chimpanzee clade, which would require pushing the Pan-Homo divergence back before 12.5 million years ago. That's the same argument we saw above from Suwa and colleagues (2007).

Part of the reason I'm bringing this up now is a new paper by Martin Pickford and colleagues (2009), describing an ape mandible fragment from Niger. This is not the first publication on the fossil; they previously presented it in the South African Journal of Science (2008). It is a museum specimen collected in 1964 by oil geologists, and the precise locality was not recorded. The associated faunal collection allowed Pickford and colleagues to place it in the Late Miocene, but only broadly between 11 and 5 million years ago. The mandible only preserves a segment of the body around and including the roots of a first molar -- it's the right size and robustness to be a chimpanzee, but again there are no derived features, not even any occlusal anatomy on the molar. Perhaps it's Sahelanthropus' sinister twin.

I'll just mention Samburupithecus, another element of the Late Miocene African fossil ape inventory. Pickford and Ishida (1998) interpreted it as relatively derived compared to Kenyapithecus, and possibly an ancestor or outgroup to the African ape-hominin clade. At 9.5 million years old, it would predate the divergence of gorillas from the chimp-human clade, on the current molecular chronology.

Where do they fit?

OK, so after all these ape dental and mandibular remains, we come back to the question that got me started. Do any of these apes compel us to revisit the current DNA chronology?

Let's review the problem: DNA comparisons suggest that humans and chimpanzees diverged less than 5 million years ago, and gorillas a shade before that, within the last 7 million years. Against that chronology, we have three samples of fossils that are arguably hominins, from earlier than 5 million years ago (Sahelanthropus, Orrorin, and Ardipithecus kadabba), two large fossil East African apes, known from teeth, which have been compared with gorillas, and several specimens that may belong either to a gorilla-sized or chimpanzee-sized ape.

It is tempting to play "what-if" games with the chronology -- what if we changed the date of the human-chimp ancestor, for example; would the large hominoids work as members of a gorilla clade? But that's really very misleading. The genealogy of a single gene locus can be pushed around on the assumption of a different rate calibration. Models for multiple loci involving lineage sorting -- the models that we now test using genome-wide data -- involve trade-offs between speciation time, population history, rate heterogeneity, and branch lengths.

I think before I can answer the question, I will need to review two more issues:

  1. What are the real constraints and confidence intervals on the genetic estimates? Just how far is it fair to push them?

  2. Do we face any similar problems with the Asian apes? What about the cercopithecoids? If a single chronology works for these other lineages, the argument is less credible for a special chronological exception for the African ape-hominin (that would be hominine) clade.

So, the next post in this series will cover genetic estimates of human-chimpanzee divergence times.

References:

Bernor RL. 2007. New apes fill the gap. Proc Nat Acad Sci USA 104:19661-19662. doi:10.1073/pnas.0710109105

Kunimatsu Y and 13 others. 2007. A new Late Miocene great ape from Kenya and its implications for the origins of African great apes and humans. Proc Nat Acad Sci USA 104:19220-19225. doi:10.1073/pnas.0706190104

Suwa G, Kono RT, Katoh S, Asfaw B, Beyene Y. 2007. A new species of great ape from the late Miocene epoch in Ethiopia. Nature 448:921-924. doi:10.1038/nature06113

Pickford M, Ishida H. 1998. Interpretation of Samburupithecus, an Upper Miocene hominoid from Kenya. C R Acad Sci Paris 326:299-306.

Pickford M, Senut B. 2005. Hominoid teeth with chimpanzee- and gorilla-like features from the Miocene of Kenya: Implications for the chronology of ape-human divergence and biogeography of Miocene hominoids. Anthropol Sci 113:95-102. doi:10.1537/ase.04S014

Pickford M, Senut B, Morales J, Braga J. 2008. First hominoid from the Miocene of Niger. S Afr J Sci 104:337-339.

Pickford M, Coppens Y, Senut S, Morales J, Braga J. 2009. Late Miocene hominoid from Niger. C R Palevol 8:413-425. doi:10.1016/j.crpv.2008.11.003