Worst year in review

As we’re wrapping up what may be the worst year in recent global memory, especially geopolitically, let’s take a moment to review some more positive things that came up at Lawnchair in 2016.

Headed home

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Alternate subtitle: Go West
This was a quiet year on the blog, with only 18 posts compared with the roughly thirty per year in 2014-2015. The major reason for the silence was that I moved from Kazakhstan back to the US to join the Anthropology Department at Vassar College in New York. With all the movement there was  less time to blog. Much of the second half of 2016 was spent setting up the Biological Anthropology Lab at Vassar, which will focus on “virtual” anthropology, including 3D surface scanning…

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Cast of early Homo cranium KNM-ER 1470 and 3D surface scan made in the lab using an Artec Spider.

… and 3D printing.

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gibbon endocast, created from a CT scan using Avizo software and printed on a Zortrax M200.

This first semester stateside I reworked my ‘Intro to Bio Anthro’ and ‘Race’ courses, which I think went pretty well being presented to an American audience for the first time. The latter class examines human biological variation, situating empirical observations in modern and historical social contexts. This is an especially important class today as 2016 saw a rise in nationalist and racist movements across the globe. Just yesterday Sarah Zhang published an essay in The Atlantic titled, “Will the Alt-right peddle a new kind of racist genetics?” It’s a great read, and I’m pleased to say that in the Race class this semester, we addressed all of the various social and scientific issues that came up in that piece. Admittedly though, I’m dismayed that this scary question has to be raised at this point in time, but it’s important for scholars to address and publicize given our society’s tragically short and selective memory.

So the first semester went well, and next semester I’ll be teaching a seminar focused on Homo naledi and a mid-level course on the prehistory of Central Asia. The Homo naledi class will be lots of fun, as we’ll used 3D printouts of H. naledi and other hominin species to address questions in human evolution. The Central Asia class will be good prep for when I return to Kazakhstan next summer to continue the hunt for human fossils in the country.

Osteology is still everywhere

A recurring segment over the years has been “Osteology Everywhere,” in which I recount how something I’ve seen out and about reminds me of a certain bone or fossil. Five of the blog 18 posts this year were OAs, and four of these were fossiliferous: I saw …

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Anatomy terminology hidden in 3D block letters,

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Hominin canines in Kazakhstani baursaki cakes,

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The Ardipithecus ramidus ilium in Almaty,

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Homo naledi juvenile femur head in nutmeg,

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And a Homo erectus cranium on a Bangkok sidewalk. As I’m teaching a fossil-focused seminar next semester, OA will probably become increasingly about fossils, and I’ll probably get my students involved in the fun as well.

New discoveries and enduring questions

The most-read post on the blog this year was about the recovery of the oldest human Nuclear DNA, from the 450,000 year old Sima de los Huesos fossils. My 2013 prediction that nuclear DNA would conflict with mtDNA by showing these hominins to be closer to Neandertals than Denisovans was shown to be correct.

giphy

These results are significant in part because they demonstrate one way that new insights can be gained from fossils that have been known for years. But more intriguingly, the ability of researchers to extract DNA from exceedingly old fossils suggests that this is only the tip of the iceberg.

The other major discoveries I covered this year were the capuchin monkeys who made stone tools and the possibility that living humans and extinct Neandertals share a common pattern of brain development.

Pride & Predator

An unrelated image from 2016 that makes me laugh.

The comparison between monkey-made and anthropogenic stone tools drives home the now dated fact that humans aren’t the only rock-modifiers. But the significance for the evolution of human tool use is less clear cut – what are the parallels (if any) in the motivation and modification of rocks between hominins and capuchins, who haven’t shared a common ancestor for tens of millions of years? I’m sure we’ll hear more on that in the coming years.

In the case of whether Neandertal brain development is like that of humans, I pointed out that new study’s results differ from previous research probably because of differences samples and methods. The only way to reconcile this issue is for the two teams of researchers, one based in Zurich and the other in Leipzig, to come together or for a third party to try their hand at the analysis. Maybe we’ll see this in 2017, maybe not.

There were other cool things in 2016 that I just didn’t get around to writing about, such as the publication of new Laetoli footprints with accompanying free 3D scans, new papers on Homo naledi that are in press in the Journal of Human Evolution, and new analysis of old Lucy (Australopithecus afarensis) fossils suggesting that she spent a lifetime climbing trees but may have sucked at it. But here’s hoping that 2017 tops 2016, on the blog, in the fossil record, and basically on Earth in general.

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mtDNA sucks for inferring hominin relationships

Ancient DNA studies keep on delivering awesome findings about human evolution. Continuing this trend, Matthias Meyer and colleagues report today in Nature nuclear DNA (nDNA) sequenced from  ~430,000 year old humans from the Sima de los Huesos (SH) site in Spain. SH is badass not only because the name translates as “pit of bones,” but also because the pit has yielded hordes of fossils comprising at least 28 people (Bermudez de Castro et al., 2004), and some of these bones preserve the oldest human DNA yet recovered (Meyer et al., 2013).

Point 1 in Northern Spain, is Sima de los Huesos. The rest of the points are other sites where hominin fossils preserve ancient DNA. Figure 1. From Meyer et al. 2013.

Point 1 in Northern Spain, is Sima de los Huesos. The rest of the points are other sites where hominin fossils preserve ancient DNA. Figure 1. From Meyer et al. 2013.

Anatomically, the SH hominins have been interpreted as “pre-Neandertals,” having many, but not all, of the characteristics of geologically younger fossils we know as Neandertals. Mitochondrial DNA (mtDNA) obtained from one of the SH femurs was found, surprisingly,to be more similar to Densivan than to Neandertal mtDNA (Meyer et al., 2013), not what would be expected if the SH hominins were early members of the Neandertal lineage. Meyer et al. interpreted this to mean that perhaps the SH hominins were ancestral to both Neandertals and Denisovans, though they noted that nDNA would be necessary to uncover the true relationships between these fossil groups.

Writing about the SH mtDNA in 2013, I noted that mtDNA has failed to reflect hominin relationships before. The distinctiveness of Denisovan mtDNA initially led to the idea that they branched off before the Neandertal-modern human population divergence (Kraus et al. 2010), and therefore that humans and Neandertals formed a clade. Later, nDNA proved Denisovans and Neandertals to be more closely related to one another than to humans (Reich et al., 2010). Then I’m all like, “Hopefully we’ll be able to get human nuclear DNA from Sima de los Huesos. When we do, I predict we’ll see the same kind of twist as with the Denisova DNA, with SH being more similar to Neandertals.”

I made that prediction right before telling Josh Baskin he’d be big.

And lo, Meyer et al. (2016) managed to wring a little bit more DNA out of this sample, and what do they find: “nuclear DNA sequences from two specimens … show that the Sima de los Huesos hominins were related to Neandertals rather than Denisovans” (from the paper abstract).

This is not a surprising outcome. The SH hominins look like Neandertals, and mtDNA acts a single genetic locus – the gene tree is unlikely to reflect the species tree. What’s more, this is similar to the story mtDNA told about human and Neandertal admixture. The lack of Neandertal mtDNA in any living (or fossil) humans was taken to reflect a lack of admixture between early humans and derelict Neandertals, but more recent nDNA analysis have clearly shown that our ancestors couldn’t help but become overcome with lust at the sight of Neandertals (and Denisovans) in Eurasia.

So here ancient DNA corroborates the anatomy that suggested the SH hominins were early members of the Neandertal lineage. This new study also raises the question as to what’s going on with mtDNA lineages – Meyer et al. suggest that the SH mtDNA was characteristic of early Neandertals, later to be replaced by the mtDNA lineage possessed by known Neandertals. They suggest an African origin for this new mtDNA, though I don’t see what that has to be the case. It also raises the question whether the difference in early (SH) vs. later Neandertal mtDNA reflects local population turnover/replacement, or a selective sweep of an adaptive mtDNA variant. Either way, Meyer et al. have done a remarkable job of making astounding discoveries from highly degraded, very short bits of super old DNA. I can’t wait to see what ancient DNA surprises are yet to come.

ResearchBlogging.orgReferences
Bermudez de Castro, JM., Martinón-Torres, M., Lozano, M., Sarmiento, S., & Muela, A. (2004). Paleodemography of the Atapuerca: Sima De Los Huesos Hominin Sample: A Revision and New Approaches to the Paleodemography of the European Middle Pleistocene Population Journal of Anthropological Research, 60 (1), 5-26 DOI: 10.1086/jar.60.1.3631006

Krause, J., Fu, Q., Good, J., Viola, B., Shunkov, M., Derevianko, A., & Pääbo, S. (2010). The complete mitochondrial DNA genome of an unknown hominin from southern Siberia Nature, 464 (7290), 894-897 DOI: 10.1038/nature08976

Meyer, M., Fu, Q., Aximu-Petri, A., Glocke, I., Nickel, B., Arsuaga, J., Martínez, I., Gracia, A., de Castro, J., Carbonell, E., & Pääbo, S. (2013). A mitochondrial genome sequence of a hominin from Sima de los Huesos Nature, 505 (7483), 403-406 DOI: 10.1038/nature12788

Meyer, M., Arsuaga, J., de Filippo, C., Nagel, S., Aximu-Petri, A., Nickel, B., Martínez, I., Gracia, A., de Castro, J., Carbonell, E., Viola, B., Kelso, J., Prüfer, K., & Pääbo, S. (2016). Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins Nature DOI: 10.1038/nature17405

Reich, D., Green, R., Kircher, M., Krause, J., Patterson, N., Durand, E., Viola, B., Briggs, A., Stenzel, U., Johnson, P., Maricic, T., Good, J., Marques-Bonet, T., Alkan, C., Fu, Q., Mallick, S., Li, H., Meyer, M., Eichler, E., Stoneking, M., Richards, M., Talamo, S., Shunkov, M., Derevianko, A., Hublin, J., Kelso, J., Slatkin, M., & Pääbo, S. (2010). Genetic history of an archaic hominin group from Denisova Cave in Siberia Nature, 468 (7327), 1053-1060 DOI: 10.1038/nature09710

Denisova the Menace

Johannes Krause and colleagues reported yesterday in Nature‘s advance online publication, on a new hominin mitochondrial DNA (mtDNA) genome. The genetic material is derived from a finger bone which lacks diagnostic morphology, from a southern Siberian site called Denisova dating to between 30 – 50 thousand years ago. Of note, the authors describe that the mtDNA is about twice as different from humans as any neandertal mtDNA is from modern humans. If the human-neandertal mtDNA divergence is accurately estimated at around 450 thousand years ago, that means this mystery specimen’s mtDNA lineage diverged from the human-neandertal line around 1 million years ago.

This is really interesting, because also around 40 thousand years ago, but from a site some 100 km to the west of Denisova, bones that were morphologically non-diagnostic yielded mtDNA basically identical to Neandertals.
Does this speak to the presence of at least 3 human species running around the Old World around 40 thousand years ago? Not necessarily. Most claims of a speciose recent human fossil record are based on cranial morphology. For example, modern human skulls are fairly different from “classic” neandertal skulls of western Europe (which is why the Skhul and Qafzeh hominins which display characteristics of both groups are so interesting). However, the mtDNA we have of most of these specimens comes from non-diagnostic specimens. The first Neandertal mtDNA studied came from a piece of tibia (shin bone); this bone is basically non-diagnostic morphologically between recent hominins, and the site it came from (Vindija, Croatia) has both human and Neandertal remains. The Denisova finger, similarly, is non-diagnostic in morphology so far as I can tell, and the archaeological layer contains both Middle and Upper Paleolithic cultural materials: we have no idea what these mtDNA bearers looked like.
I think people thinking “new species at Denisova” (NB: Krause and colleagues never make this claim!) would be shocked if it turns out that the Denisova remains, or those from which the Vindija specimens came, were morphologically modern humans, but this is entirely possible.
Humans today are not so diverse genetically as superficial appearances may suggest to many people. I wouldn’t be surprised if humans simply displayed more genetic diversity in the past. It is certainly interesting just how different the Denisova genome is from both humans and Neandertals. What exactly this difference means is just not clear. It is further interesting to note that the coding regions of the Denisova mtDNA show signs of strong purifying selection. Assumptions of neutrality are so important for genetic studies that I think people often forget that mtDNA actually serves functions necessary to survival, and is not actually neutral. Maybe this ancient mtDNA lineage lasted so long because the mitochondria provided some selective advantage, hence the purifying selection? Who knows?!
The authors make a funny deduction that I can’t quite follow, that because the Denisova specimen’s mtDNA diverged from humans-neandertals some 1 million years ago, “it was distinct from the initial radiation of H[omo] erectus that first left Africa 1.9 million years ago, and perhaps also from the taxon H. heidelbergensis,” which is the name given to mainly European but also African fossils between 1 and 0.5 million years ago. I just don’t follow this. We don’t know what mtDNA diversity was like at any of these times, so there is no reason to think that this specimen’s ancestors were from some undocumented dispersal from Africa. The implicit assumption is that mtDNA lineages arise sporadically and discretely from Africa and then spread to different parts of the world, repeatedly over the course of human evolution. If there’s gene flow all around from the get-go, then the Denisova specimen simply represents an especially ancient mtDNA lineage – not necessarily an ancient population (recall that mtDNA is only inherited from mothers).
Oh well, should be interesting to see the nuclear DNA from this specimen, surely to be described in the near future…
Reference
Krause J, Fu Q, Good JM, Viola B, Shunkov MV, Derevianko AP, Paabo S. 2010. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature, in press.

Long-term effects of hybridization in primates

One of my research interests is hybridization in primates, and the possible role it played in hominin evolution. It’s a sticky subject, so it’s always fun to find good papers on real-life examples of hybridization between different primate ‘species.’ In this vein, Burrell et al. <!–[if supportFields]> ADDIN EN.CITE Burrell200975375317Burrell, Andrew S.Jolly, Clifford J.Tosi, Anthony J.Disotell, Todd R.Mitochondrial evidence for the hybrid origin of the kipunji, Rungwecebus kipunji (Primates: Papionini)Molecular Phylogenetics and EvolutionMolecular Phylogenetics and Evolution340-348512KipunjiBaboonRungwecebusLophocebusPapioHybrid speciationMangabey2009http://www.sciencedirect.com/science/article/B6WNH-4VNKGV7-4/2/1fc25562a43afdf7c3fafda3bcfaceb7 <![endif]–>(2009)<!–[if supportFields]><![endif]–> report that the kipunji—a highly endangered papionin monkey from a small area in Tanzania—has an mtDNA haplotype from its yellow baboon (Papio cynocephalus) neighbors. Morphologically, the (living) monkey looks more like mangabeys (Lophocebus), though it has some baboon-like affinities, too.The authors posit that the most likely reason for this is inter-generic hybridization in the past, between Papio cynocephalus (yellow baboons) and Lophocebus sp. (mangabey monkeys).

The authors suggest a scenario in which in a marginal environment, Lophocebus (or Cercocebus?) males mated with some P. cynocephalus females. The hybrids, then, back-crossed into the respective parent species—thus baboon mtDNA was brought into a mangabey population. From here, the habitat favored nuclear genes of mangabeys, hence the overall mangabey appearance. Even though mtDNA is often (by necessity) assumed to be selectively neutral for phylogenetic studies such as these, it is not inconceivable that the baboon mtDNA persisted in the population because of selection, too.

The authors note that the test of the hybrid-origin hypothesis will come from nuclear DNA. If the kipunji truly represents the meshing of two genera’s genomes, then it should have a large amount of mangabey nuclear DNA. However, if the nuclear genome is all Papio that would mean that the kipunji’s ancestors were baboons whose morphology (and niche?) converged on that of mangabeys. Even this outcome would be a bit incredible, given the apparent pervasiveness of homoplasy within the papionins. In fact, the few nuclear genes known for the specimen either cluster in Papio, or are phylogenetically ambiguous. But for the moment, mtDNA and morphology support hybrid-origins. This is especially remarkable, since hybridization between genera, above the species level, leading to a stable taxon has not been documented before.

It is unclear whether the kipunji represents an instance of hybrid (or “secondary”) speciation, in which hybrids thrive in an environment while individuals of the parental species don’t, or just an intense case of gene transfer between species (I suppose if you’re getting a whole mitochondrial genome, it’s not really introgression). Nevertheless, the paper provides an amazing example of the potential evolutionary significance of hybridization in primates. Nice.

References

<!–[if supportFields]> ADDIN EN.REFLIST <![endif]–>Burrell AS, Jolly CJ, Tosi AJ, and Disotell TR. 2009. Mitochondrial evidence for the hybrid origin of the kipunji, Rungwecebus kipunji (Primates: Papionini). Molecular Phylogenetics and Evolution 51(2):340-348.

Cryptic Variation and Ice Man

This fortnight’s Current Biology has some interesting articles, two of which caught my attention. First is a “Quick Guide” to cryptic variation, which is genetic variation that goes unnoticed under most circumstances. Also published is the mtDNA sequence of the 5,000 year old Tyrolean Ice Man (a.k.a. Ötzi; this paper actually came out right before Halloween, so I suppose I was too excited about the holiday to write about it then).

First, “cryptic variation.” The authors describe cryptic variation as, “unexpressed, bottled-up genetic potential. … expressed under abnormal conditions such as in a new environment or a different genetic background” (Gibson and Reed 2008). Sounds impossible, because one quickly asks, how can we study ‘cryptic variation’ if it refers to something that is phenotypically unexpressed? But it has been documented in plants and Drosophila, the work-horse-fly of biology. As an example, the authors cite the condition of Antennapedia in Drosophila, in which a mutation causing legs to grow in place of flies’ antennae. When placed into the genomes of different species of Drosophila, this mutation produces different phenotypes. This indicates that variation can be affected by interactions among genes, a phenomenon known as epistasis.

A related phenomenon is ‘canalization,’ which is the evolution of phenotypic ‘buffering’ that prevents variation from arising during development. [For a good synthesis of the concept of canalization, evidence for it, and an application in anthropology, check out Hallgrimsson et al.’s Yearbook paper (Hallgrímsson et al. 2002)] Basically, it seems that enough stabilizing selection can ensure that an individual’s phenotype will develop to a given form in spite of various environmental or internal stresses (i.e. climate and the external environment, or the genetic environment of an organism). This suppression of phenotypic variation can allow ‘cryptic’ genetic variation to accumulate, to be suddenly expressed in a future generation because of certain circumstances. The authors point out that this is possibly problematic because this is not how genes are supposed to work, as far as we know. I think this is an interesting, and potentially very important, avenue of paleoanthropological research, specifically regarding the possibility of hybridization. I’ve written elsewhere, as have others, about the possibility and implications of hybridization on human evolution. Could hybridizing hominin lineages have ‘released’ some type of cryptic variation? An interesting idea, but as always it’s fairly pointless unless it can be tested. And at the moment I cannot think of a way, but I’ll work on it…

In the mean time, researchers have sequenced the mtDNA of the Tyrolean Ice Man. This poor chap, unfortunately for him but fortunately for science, died and ended up in a glacier between Italy and Austria that preserved his soft-tissue very well, some 5000 years ago. What did the study find? Turns out Ice Man’s mtDNA is part of haplogroup K, but has two specific mutations that make his unlike any living mtDNA haplogroup. I seem to remember reading recently about another ancient mtDNA sequence that is unlike anything modern known in modern humans… Oh yes, the 38 ky old Neandertal from Vindija (Green et al. 2008)! If a 5,000 year-old Italian could have belonged to an extinct mtDNA lineage, what does this mean for a similarly ‘extinct’ 38ky old Neandertal? Not a whole lot, but it does underscore how easily mitochondrial lineages can be lost, and it cautions against using the single Neandertal’s mtDNA to argue against their contribution to the modern Homo sapiens gene pool.

Additionally it highlights some of the limitations of genetic studies. Genetic studies like this are limited to the current database of sequences. Ötzi was compared to a sample of some 2000 individuals’ genomes. But there’s always a chance that Ötzi’s ‘extinct’ mitochondrial haplogroup is present but has not yet been sampled. This reminds me of a recent Q&A in Nature entitled, “The pitfalls of tracing your ancestry.” Here, Charmaine Royal of Duke University described issues that arise when people try to trace their ancestry with genetic testing. Here’s what Royal said that has bearing on Otzi, and other ancient genomes:

“The general limitation, I’d say, of all of these tests, is that they can’t pinpoint with 100% accuracy who your ancestors may or may not be. Some people are concerned that the biogeographical ancestry test reifies the notion of race. This is the notion that there are four or five parental groups from which we all came and there are discrete boundaries between these groups. But our genetic research has shown that those boundaries don’t exist.

In lineage testing, where someone is wanting to know which tribe or region in Africa they came from, the information that’s given is based on the present day populations. The names of those groups and those locations have changed over time and so people getting that information about present day Africans and extrapolating to who their pre-middle-passage ancestors may have been — that may not necessarily be accurate. So, those limitations need to be clarified.

Another limitation is that the outcomes of ancestry tests are very much dependent on what is already in a database — who a client’s DNA can be matched to. If a database is not comprehensive some potential matches will be missing, and nobody has a complete database. That’s a major limitation, probably one of the biggest.”

Royal also discusses some interesting issues of when genome testing goes wrong—that is, when people’s genetic results about their identity don’t conform to what they’d expected, how they identify themselves. The piece does a good job illustrating the complex nature of cultural identity and genetic affinity. In the same vein, paternity testing creates the same issues: how one’s social identity/reality can be ripped asunder by a genetic test. So, while genetics and genomics are incredibly valuable scientific avenues, it’s always fun to point out their limitations and adverse effects. Anyway, paleogenomics and cryptic variation are interesting topics that will hopefully continue to be developed and incorporated into Anthropology in the coming years.

References
Gibson G, and Reed LK. 2008. Cryptic genetic variation. Current Biology 18(21):R989-R990.
Green RE, Malaspinas A-S, Krause J, Briggs AW, Johnson PLF, Uhler C, Meyer M, Good JM, Maricic T, Stenzel U and others. 2008. A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing. Cell 134(3):416-426.
Hallgrímsson B, Willmore K, and Hall BK. 2002. Canalization, developmental stability, and morphological integration in primate limbs. American Journal of Physical Anthropology 119(S35):131-158.

More Neandertal mtDNA stuff…

Has anyone read Hawk’s latest blog about Neandertal mtDNA? He answers some emailer’s questions and goes on a long explanation.

His “Drift” section has me confused. If someone could read what Hawks wrote, and then maybe explain the concept to me like I’m a college freshman who barely understands this stuff, that would be excellent. Basically, I don’t understand how his explanation shows that drift probably didn’t happen. Instead it seems like a lot of mathematical mumbo-jumbo, ending with Hawks stating that “contamination” might just be proof that neandertals and humans shared DNA. I’m concerned because I’m not even sure which part of it I find confusing: the concept of drift, the population genetics involved, what mtDNA tells us, or all three!

His other explanations make sense, if I assume his Drift-stuff is true. Please help!

Neandertal mtDNA genome sequenced

A neandertal mtDNA genome has been sequenced <!–[if supportFields]> ADDIN EN.CITE Green200840440417Green, Richard E.Malaspinas, Anna-SapfoKrause, JohannesBriggs, Adrian W.Johnson, Philip L. F.Uhler, CarolineMeyer, MatthiasGood, Jeffrey M.Maricic, TomislavStenzel, UdoPrüfer, KaySiebauer, MichaelBurbano, Hernán A.Ronan, MichaelRothberg, Jonathan M.Egholm, MichaelRudan, PavaoBrajkovic, DejanaKucan, ZeljkoGusic, IvanWikström, MårtenLaakkonen, LiisaKelso, JanetSlatkin, MontgomeryPääbo, SvanteA Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput SequencingCellCell416-4261343CHEMBIODNAECO_EVOL2008http://www.sciencedirect.com/science/article/B6WSN-4T5BPWS-C/2/f0b90ab2a8efae1fa309863a20f37464 <![endif]–>(Green et al. 2008)<!–[if supportFields]><![endif]–>, the specimen coming from the Croatian site of Vindija, some 38 kya. The paper’s verdict: “Neandertal mtDNA falls outside the range of variation of modern humans.” So though they don’t explicitly say it, it sounds like the conclusion is that, based on mtDNA, neandertals were a separate species from the humans that inhabit the globe today. Is this the end of the story? Hardly.

First, a technical note. The team used the “high-throughput 454 sequencing technique”, and since I am not a geneticist and could barely understand what the technique involves when I looked into it, all I can gather is that the method creates more sequence copies than traditional PCR (polymerase chain reaction). Perhaps a colleague can enlighten me and other readers on this technique? Also, the team took strong precautions that pretty much ensured that the sample wasn’t (significantly) contaminated with modern human mtDNA. Cool beans, the future today.

Anyway, what’s important is that this complete sequence (from a single individual) allows researchers to do whole mtDNA comparisons of neandertals with modern humans, to try to answer a riddle that is hotly debated in Paleoanthropology—whither Neandertals? Was there admixture between the archaic humans endemic to Eurasia (Neandertals) and the immigrating modern humans coming from Africa?

Now, in general I don’t care that much about neandertals. In my mind, they’re just a form of H. sapiens, albeit probably a homely form. But what I do care about (lately) are patterns of speciation in primates and human origins, so the question of modern-human-neandertal admixture is an interesting one to me. Green and colleagues inferred from the Vindija mtDNA that humans and neandertals were distinct (i.e. probably separate species)—a level of separation I don’t know I can agree with. When the team compared sequence differences between the neandertal and 53 modern humans from around the globe, they found that there are more differences between the neandertal and each human than there are between any pair of humans. This is in contrast to previous studies that looked only at the HRVI and HRVII regions of mtDNA, which found more overlap (less difference) between humans and neandertals. So this underscores the importance of using whole genomes for analysis, rather than a few genes.

Next the team estimated the human-neandertal divergence, assuming a molecular clock with a HomoPan divergence of 6-8 mya. This yielded a divergence date of 660,000 years, with the 95% confidence interval of 800,000 to 520,00 years. I suppose this is not too unreasonable. Some 600 kya is roughly the time when H. heidelbergensis is running around Europe and Africa. Their HomoPan divergence estimate is not so much to my liking, however. They based this estimate on the fossil record, 8 mya being based on the ~7 my-old Sahelanthropus tchadensis cranium and 6 mya based on the ~6 my-old Orrorin tugenensis material. I might have just stuck with the 6 mya divergence, because Sahelanthropus is not convincingly a hominin or “pre-hominin,” really it’s not convincingly anything but an ape. And 5-6 mya is when we start seeing fossils that really look like hominins, be it the Orrorin femora or the dental and mandibular fossils from E. Africa.

Now, as I asked before, is this the end of the story? No. For starters, this paper only looks at mtDNA, which is only maternally inherited. So we could deduce from this paper that perhaps no neandertal females interbred with modern humans. What will be more informative is a look at nuclear DNA—which the team hopes to have sequenced by the end of this year. Moreover, this single neandertal falls outside the range of variation of modern humans. There are several human mtDNA haplotypes—different lineages of mtDNA (again, I’m not a geneticist, so I don’t know how many or how different—a little help, anyone?). From this single individual we cannot get a good picture of neandertal mtDNA variation (haplotypes). Plausibly if we had more samples of mtDNA from archaic humans (are there any from any Upper Paleolithic modern humans?) we may well see the gap between humans and this neandertal bridged. Of course, on the other hand, we might not. So this paper demonstrates considerable difference between human and neandertal mtDNA, but the case is anything but closed.

Also, as paper commentator A. Clark noted, there are many genes in modern human nuclear DNA that appear to be over 1 my old <!–[if supportFields]> ADDIN EN.CITE Clark200840340317Clark, Andrew G.Genome Sequences from Extinct RelativesCellCell388-38913432008http://www.sciencedirect.com/science/article/B6WSN-4T5BPWS-8/2/ea3c7ee1a50fed191e907fcecd1cf481 <![endif]–>(Clark 2008)<!–[if supportFields]><![endif]–>, and this may suggest that modern humans and archaic populations (including neandertals) may have interbred at least sporadically. He notes, “The long period of coexistence of modern humans and Neanderthals, as well as the great depth of common ancestry of modern human nuclear genes, make it quite plausible that there was opportunity for interbreeding . . . If there had been admixture, say 100,000 years ago, giving modern humans small segregating pieces of our genome with Neanderthal ancestry, it would be nearly impossible to identify them as such, even with full genome sequences.” When two populations intermingle, their offsprings’ genomes will not necessarily simply be a mix of ½ one parent, ½ the other. Rather, often only adaptive genes are able to ‘sneak’ into the other population’s gene pool—a phenomenon known as introgression. It looks like the human FOXP2 gene may well be an example of introgression, and in fact may have introgressed from an archaic population into modern humans <!–[if supportFields]> ADDIN EN.CITE Coop200826526517Coop, GrahamBullaughey, KevinLuca, FrancescaPrzeworski, MollyThe Timing of Selection at the Human FOXP2 GeneMolecular Biology and EvolutionMol Biol EvolMolecular Biology and EvolutionMol Biol Evol1257-12592572008<![endif]–>(Coop et al. 2008)<!–[if supportFields]><![endif]–>. On an interesting aside, geneticist Chung-I Wu has formulated the “genic species concept,” in which species are formed when they can still interbreed and exchange genetic material, but adaptive regions are not exchanged; obviously this intriguing concept is also controversial <!–[if supportFields]> ADDIN EN.CITE Noor200240540517Noor, Mohamed A. F.Is the biological species concept showing its age?Trends in Ecology & EvolutionTrends in Ecology & Evolution153-154174species conceptsspeciationreproductive isolationadaptationhybridizationbiological species concept2002http://www.sciencedirect.com/science/article/B6VJ1-45BCHTS-1/2/befbc7badc90a2be01430b6c1390afd0 <![endif]–>(Noor 2002)<!–[if supportFields]><![endif]–>.

A final point to consider that didn’t come up in Green et al.’s paper is the growing body of evidence that human evolution is accelerating, and has been for the past 40 ky, but especially in the past 10-20 ky <!–[if supportFields]> ADDIN EN.CITE Hawks20071117Hawks, JohnWang, Eric T.Cochran, Gregory M.Harpending, Henry C.Moyzis, Robert K.Recent acceleration of human adaptive evolutionProceedings of the National Academy of SciencesProc Nat Acad SciProceedings of the National Academy of SciencesProc Nat Acad Sci20753-2075810452

20753

Adaptive evolutionhuman evolutionlinkage disequilibriumdemography2007December 26, 2007<![endif]–>(Hawks et al. 2007)<!–[if supportFields]><![endif]–>. This is interesting as the neandertal specimen is 38 ky-old, and other neandertal DNA has come from even older specimens (Krause et al. 2007). I’m not sure at the moment how to interpret this in the context of mtDNA and recent sequencing of neandertal mtDNA. But it should be very important when the team (or someone else) analyzes ancient nuclear DNA, especially given that neandertals (arguably) ‘disappeared’ before human adaptive evolution really began to sprint.

This is an exciting time for anthropological genetics. Techniques are being developed for the extraction and analysis of ancient DNA, which will help shed light on the nature of the emergence of modern humans, and their interactions with archaic populations. At the same time, I am always wary of papers in genetics because of the numbers of assumptions/parameters required by their models.

<!–[if supportFields]> ADDIN EN.REFLIST <![endif]–>Clark AG (2008) Genome Sequences from Extinct Relatives. Cell 134(3):388-389

Coop G, Bullaughey K, Luca F, Przeworski M (2008) The Timing of Selection at the Human FOXP2 Gene. Mol Biol Evol 25(7):1257-1259

Green RE, Malaspinas A-S, Krause J, Briggs AW, Johnson PLF, Uhler C, Meyer M, Good JM, Maricic T, Stenzel U, Prüfer K, Siebauer M, Burbano HA, Ronan M, Rothberg JM, Egholm M, Rudan P, Brajkovic D, Kucan Z, Gusic I, Wikström M, Laakkonen L, Kelso J, Slatkin M, Pääbo S (2008) A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing. Cell 134(3):416-426

Hawks J, Wang ET, Cochran GM, Harpending HC, Moyzis RK (2007) Recent acceleration of human adaptive evolution. Proceedings of the National Academy of Sciences 104(52):20753-20758

Krause J, Lalueza-Fox C, Orlando L, Enard W, Green RE, Burbano HA, Hublin J-J, Hänni C, Fortea J, de la Rasilla M, Bertranpetit J, Rosas A, Pääbo S (2007) The derived FOXP2 variant of modern humans was shared with neandertals. Current Biology 17

Noor MAF (2002) Is the biological species concept showing its age? Trends in Ecology & Evolution 17(4):153-154<!–[if supportFields]><![endif]–>