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Friday, May 28, 2010

Ardipithecus ramidus paleoenvironment: Not a paradigm shift after all

The current issue of Science contains two letters addressing Ardipithecus ramidus ("Ardi") as described by White’s team in Science last October. Both have a similar message: contrary to the claims made by authors of October’s Ardi papers, Ardipithecus and its surrounding environments do not change everything we know about the origins of exclusively human ancestors. Esteban Sarmiento addresses the skeletal evidence of Ardi itself and raises many of the issues I raised when I blogged about it.

But what I didn’t address at the time was the environment. White and colleagues reconstructed Ardi’s environment as a fairly humid and closed woodland. This, they argued, overturns the conventional ‘wisdom’ that hominids originated in a savannah environment.

However, Cerling and colleagues present their reinterpretation of the data presented by White and colleagues, and reach the opposite conclusion. They find, rather, that all lines of evidence point to a relatively more open (i.e. grassland) habitat for Ardi. First of all, ancient soil analyses give a strong signal that Ardi’s habitats contained a very large C4 plant component – plants like grasses rather than woody vegetation like trees. Even compared to other hominid sites, Aramis appears to have one of the highest C4 (i.e. grass) biomasses. Second, the water deficit value of Aramis (1500 mm) is completely consistent with a dry woodland in a riparian (river) environment. In fact, the Aramis value “is similar to values in some of the hottest and driest parts of eastern Africa today,” Cerling and colleagues note. Third, there are more species of grazing (on grass) than browsing (on leaves) hooved animals at Aramis. Finally, Cerling and others argue that the way other data were presented or interpreted by the Ardi team were misleading and/or downplayed the evidence for a more open, grassy environment.

So where did Ardipithecus live - an open grassy environment, or a more closed and forested one? What does its reconstructed habitat mean for hominid origins? This is an important question, because as I've argued before it's not too clear that Ardi is actually a hominid, or whether it is a hominid that had already diverged from later hominids that were ancestral to us humans. The apparent misrepresentation of Ardi's environment, and the stress placed on hominid traits for which there is no direct or unambiguous evidence (i.e. lumbar curvature inferred even though no lumbar vertebrae or a sacrum are known for Ardi), suggests that all the hype around Ardipithecus is just that - hype. Indeed, a sexy find that 'overturns everything we know about hominid origins' is bound to garner glorious funding.

References

Cerling T et al. 2010. Comment on the Paleoenvironment of Ardipithecus ramidus. Science 328: 1105-d.

Sarmiento E. 2010. Comment on the Paleobiology and Classification of Ardipithecus ramidus. Science 328: 1105-b

Thursday, May 20, 2010

Wanted: Catchier Titles

This past year I finally got around to being productive. I wrote a paper with J. Francis Thackeray, and we presented it as a poster at this year's American Association of Physical Anthropology meeting in Albuquerque. I also presented a small study about global patterns of human cranial trait covariation at a graduate student conference here at the University of Michigan. I'm overall pleased with the final products, but I'm really kicking myself in the buttocks over the titles:

"One or two species: a morphometric comparison of robust australopithecines from Swartkrans and Kromdraai"
"Conspecificity of South African robust australopithecines"
"Population-specific patterns of variation and studies of integration" (which was originally "variation and covariation within and among human populations," sounds like a real page-turner, I know)

Translation: boooooring! So one goal I have for the future is to come up with catchier titles for my projects. I mean, almost anything would be more interesting than the titles I used. How about something like "Putting broken faces to work" for the first two, and "Different Cov(x,y) for different folks." These may not be too good, but they're certainly better than my original titles. Once armed with fancier titles, then all I'll need is a good dissertation onto which to slap a good title.

Thursday, May 6, 2010

Neandertal Nuclear Genome: Multiregional Evolution is the new Out of Africa

Green and colleagues announced the Neandertal nuclear genome in tomorrow's issue of the journal Science. Hitherto only complete mitochondrial DNA (mtDNA) genomes had been recovered. These are only inherited maternally, and the genetic differences between the Neandertal mtDNA and that of modern humans seemed to suggest that Neandertals and humans didn't mix, that is that they were replaced by "anatomically modern humans" (whatever that phrase means). mtDNA is special as far as genetic stuff goes - only inherited maternally, so only tells about one strain out of a slew of ancestors; doesn't recombine; as a result, selection acting on a part results on selection of the entire mitochondrial genome; oh and it's certainly not selectively neutral.

So should we have been wary when it was suggested by mtDNA that neandertals and humans were separate species (recall the issue was even crazier with the Denisova mtDNA specimen...)?

YES - HUMANS AND NEANDERTALS EXCHANGED GENES (but just Eurasian humans...)

This is a big deal, because for the past several decades researchers have debated the nature of modern human origins. On morphological and shaky mtDNA evidence, several researchers have argued that modern humans emerged from a small African population, which then spread throughout the world between 100-200 thousand years ago and replaced all other 'archaic' human populations. Intuitively this doesn't make sense, and today's neandertal announcement renders the Out of Africa with Replacement model for human origins absolutely untenable.

So, were Neandertals and (even then-modern) humans the same species? Yes! If Neandertals were a different species, we would expect all humans to be equally genetically divergent from neandertals. But this is not what Green and colleagues found. Rather, the genomes of a French person, a Chinese person, and a Papua New Guinean were actually more similar to the Neandertal genomes than the two African human representatives were to the Neandertals. Such disparate divergences mean we're dealing with genetic variation within a species, rather than between species.

In fact, the authors estimate that about 1-4% of modern, non-African genomes are derived from Neandertals. Plagnol and Wall (2006) estimated around 5% of human genes come from 'archaic' humans, so it is good to see corroborating evidence from two sources. It is interesting, however, that earlier candidates for introgression from archaics, such as the microcephalin haplogroup D, do not appear to have come from Neandertals (maybe another archaic population, then?).

The authors were also able to use these neandertal and modern human genomes to estimate regions of the human genome that have been under recent and accelerated evolution, including:
  • SPAG17 is associated with sperm motility - is this evidence for sperm competition and recent sexual selection?
  • Regions in which, among modern humans, mutations are associated with social-cognitive diseases like schizophrenia and autism
  • RUNX2, again where misexpression in humans is associated with dysgenesis of frontal bone (forehead), shoulder and rib-cage shape morphology
Interesting...

I think the only things I would have loved to have seen in this study are simple logistical issues, things that are probably simply not practical at the moment because of technological constraints. First, I'd love to see a much larger set of modern human reference genomes. The study included only 2 human nuclear genomes from sub-Saharan Africa, 1 from Europe, 1 from China and 1 from Papua New Guinea. Yes, this samples variation from all over the world, but it's 5 out of nearly 7 billion genomes out there today. At the moment, however, it's just not that easy to acquire and handle genomic data for many individuals.

Second, I'd like to see nuclear genome comparisons using Upper Paleolithic modern humans - 'modern human' contemporaries of Neandertals. The Denisova mtDNA was surprising because, at some 40 ka, its genome was about twice as different from modern humans as the neandertal mtDNA sequences were. Just what kind of genetic diversity are we looking at in ancient (anatomically both 'archaic' and 'modern') humans?

Green and colleagues should be lauded because of how meticulously they went about this project. They took major pains to circumvent issues of contamination, they maximized the DNA they could obtain in spite of preservation issues, they came up with some clever tests. And their results are really interesting.

References
Green RE et al. 2010. A draft sequence of the Neandertal genome. Science 328: 710 - 722.

Plagnol V and Wall JD. 2006. Possible Ancestral Structure in Human Populations. PLoS Genetics 2(7): e105