Leopard horse: Fossils, phenotypes and genotypes

I wish I were talking about some beastly horse-big-cat hybrid, or at least a carnivorous horse. Instead… a ton of anthropology-related papers came out today in PNAS, and possibly the coolest one is a study that compares the DNA of Pleistocene fossil and modern horses with different coat colors/patterns, and then ties this in with Paleolithic cave art. A crazy confluence of four-field anthropology right there.

Modern horses and their depictions in Late Pleistocene French caves (Pruvost et al. 2011)
Melanie Pruvost and colleagues (in press) noted that the depiction of spotted horses at the site of Pech-Merle (they give 24 kya) could mean one of two things: (1) either the early human painters were depicting horses they actually saw on the landscape at the time, or (2) they were just being fanciful and frivolous, creative and carefree with their cavern canvas. Now, some modern horse breeds have a similar spotted, “leopard” phenotype, and a genetic basis for this is understood. So Pruvost and pals examined DNA from fossil horse bones from European sites dating to 20 – 2 kya to see if these mottled mares roamed the lands of the cave-painters. Sure enough, several samples show evidence for the mutation causing leopard spots.

This is pretty cool for evolutionary biology and paleontology. A major question in biology is how an individual’s genes (genotype) relate to overall appearance/behavior (phenotype). To a certain extent, physical variation between organisms arises from genetic variation, so when we see things evolve through the fossil record, this ought to correspond with some genetic changes as well. But linking genes to appearances isn’t so easy (especially for extinct animals). Pruvost and colleagues’ study is a step in this direction, though. Plus, the recent sequencing of the fossil Neandertal (Green et al. 2010) and Denisovan (Reich et al. 2010) genomes makes it possible to try to figure out if/how humans’ unique physical traits reflect our genes. In fact, even before these genomes were fully sequenced, Carles Lalueza-Fox and team (2007) identified a mutation on Neandertals’ MC1R gene, strongly suggesting the Neandertals sampled had light skin and red hair.

But the genetic basis for skeletal phenotypes is harder to discern. For example, Green et al. (2010) identified the unique human version of the RUNX2 gene as having come under strong natural selection since the disappearance of Neandertals. The authors noted that because mutations of RUNX2 in humans are associated with a cleidocranial dysplasia affecting the form of the skull and shoulders, and because humans and Neandertals differ in some aspects of their skulls and shoulders, then RUNX2 variation between humans and Neandertals is likely related to visible differences in their skeletons. But that’s about as much as could be said at the moment – RUNX2 is involved in bony development of the entire skeleton, interacting with other various genes in various places during ontogeny. So while it’s tempting, it’s still a little early to link RUNX2, or pretty much any other development-related gene, with physical differences between humans and our fossil relatives. But one day!

ResearchBlogging.org
A Neandertal’s ruddy locks have never preserved in the fossil record, but its bones are very well known. In an ironic twist, we may have a better understanding of the genetic basis of variation in a soft-tissue (for which there are no fossils), than we do for the skeleton (for which we have lots of fossils).

And maybe one day I’ll get that leopard horse I was hoping for.

References
Green, R., Krause, J., Briggs, A., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M., Hansen, N., Durand, E., Malaspinas, A., Jensen, J., Marques-Bonet, T., Alkan, C., Prufer, K., Meyer, M., Burbano, H., Good, J., Schultz, R., Aximu-Petri, A., Butthof, A., Hober, B., Hoffner, B., Siegemund, M., Weihmann, A., Nusbaum, C., Lander, E., Russ, C., Novod, N., Affourtit, J., Egholm, M., Verna, C., Rudan, P., Brajkovic, D., Kucan, Z., Gusic, I., Doronichev, V., Golovanova, L., Lalueza-Fox, C., de la Rasilla, M., Fortea, J., Rosas, A., Schmitz, R., Johnson, P., Eichler, E., Falush, D., Birney, E., Mullikin, J., Slatkin, M., Nielsen, R., Kelso, J., Lachmann, M., Reich, D., & Paabo, S. (2010). A Draft Sequence of the Neandertal Genome Science, 328 (5979), 710-722 DOI: 10.1126/science.1188021

Pruvost, M., Bellone, R., Benecke, N., Sandoval-Castellanos, E., Cieslak, M., Kuznetsova, T., Morales-Muniz, A., O’Connor, T., Reissmann, M., Hofreiter, M., & Ludwig, A. (2011). Genotypes of predomestic horses match phenotypes painted in Paleolithic works of cave art Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1108982108

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

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01/01/2011: Looking forward and backward, so fast you may barf

2010 was a big year for anthropology and lawn-chair-anthropologists. There was laughter and crying, and maybe also some yelling. And smiling. Let’s take a look back at some of the big events of the past year.

  1. Ancient DNA. What a great year for ancient human DNA! In April, Krause and colleagues (2010) announced the sequencing of mitochondrial DNA from a ~50,000 year old girl from Denisova in Siberia. This sequence was twice as divergent from humans as Neandertal mtDNA, which really shocked a lot of people. Then just a week or so ago Reich and colleagues (2010) announced nuclear DNA from the site. The big news was that these ancient humans contributed genes to modern day Melanesians, but not other modern humans sampled. In May, Green and the Pääbo lab announced a draft sequence of the Neandertal nuclear genome. Like with the Denisova story, Neandertal mtDNA is fairly distinct from that of modern humans, and the nuclear genome revealed contribution to some modern humans but not to others. Basically, ancient DNA came out supporting the multiregional model of modern human origins.
  2. Malapa hominids. Lee Berger and researchers announced a new fossil site, Malapa, in South Africa. This site yielded 2 partial skeletons (and others forthcoming), including a very well-preserved skull of a subadult. Superficially the thing looked to me like Australopithecus africanus, though the authors argue that it shows some features derived toward the condition of early Homo. But at an estimated 1.9-1.7 million years old, it’s a little too young to have anything to do with the origin of Homo – not to mention its small 400 cubic centimeter cranial capacity. I really don’t know what to do with Malapa yet.
  3. Woranso-Mille Australopithecus afarensis. This site dates to around 3.6 million years ago, so it’s roughly contemporaneous with Laetoli afarensis, or intermediate in age between Laetoli and later afarensis sites like Maka and Hadar. Haile-Selassie and colleagues described a partial skeleton from the site. This male includes part of the pelvis, which didn’t get much coverage. But it has a 1st rib, scapula and clavicle, indicating a fairly human-like (rather than ape-like) torso shape. So even for how well we know A. afarensis, we’re always learning more about our ancestor.
  4. Saadanius hijazensis and catarrhines. I didn’t blog about this one at the time as I was getting ready to hit the field. But this was exciting because Iyad Zalmout and friends here at UM discovered and analyzed it. Saadanius was found in ~29 million year old deposits in Saudi Arabia, right around the estimated time of origins of apes. The fossil looks like an Aegyptopithecus to my untrained eye, but apparently may be similar to the last common ancestor of apes and old world monkeys.
  5. Field work. I had my first (of hopefully more!) field season at Dmanisi in Georgia. Paleoanthropology would be nothing without fossils, so an important aspect of the job I’d like to do more of is increasing the fossil record. Dmanisi is an amazing place for this, being among the oldest human sites outside Africa, and the interesting ‘intermediacy’ of the Dmanisi hominids between early Homo and more classic H. erectus. We found some great stuff last year, and I anticipate the site will produce more great fossils in the future. Who knows, maybe more fossiliferous deposits will be found in nearby regions?
So it was a helluva year, 2010. What excitement will 2011 bring? Here are some things I’d like to, or expect to, see this year:
  1. More ancient DNA – the surprise that many researchers got from Denisova and Neandertal ancient DNA clearly warrants more work on other ancient DNA. What does that of other fossil humans look like? Will the picture of human origins become further complicated (that is, different from paradigmatic out-of-Africa replacement)? In this regard we need to analyze DNA from more late Pleistocene fossils regarded as ‘anatomically modern.’
  2. a) More about Malapa. I want to say I heard somewhere that there were more hominids than just the 2 presented in the Science paper. These additional specimens will provide further evidence, including what variation within the site was like, and how it fits with other South African specimens. From the appearance of things, these fossils may be late-persisting A. africanus, somehow contemporaneous (roughly sympatric?) with A. robustus and possibly early Homo. Perhaps more work on the geology and taphonomy of Malapa will show it to be older, contemporaneous with the nearby site of Sterkfontein known for abundant A. africanus fossils? Probably not.

    b) More hominid sites and fossils in South Africa. One thing that was neat about Malapa was that it was from slightly outside the rest of the South African ‘cradle’ sites like Sterkfontein, Kromdraai, Drimolen, and Swartkrans. When I was in the area in 2008 I went with some researchers on survey of the Sterkfontein valley, new sites are definitely being sought. Perhaps 2011 will see the discovery of more Malapa-like sites?
  3. Human fossils from East Asia. Maybe even ancient DNA recovery from the region. East Asia has long been thought to be a potential ‘center’ of human origins. Earlier in the year, fossils coming from Zhirendong suggest some of the earliest evidence of chin, arguably a ‘modern human’ feature. Recent fossil and genetic discoveries ought to usher a renewed vigor in examining human evolution in Asia.

That’s all I feel like doing for now. Happy New Year, all!

ResearchBlogging.org
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
Cann, R., Stoneking, M., & Wilson, A. (1987). Mitochondrial DNA and human evolution Nature, 325 (6099), 31-36 DOI: 10.1038/325031a0
Green, R., Krause, J., Briggs, A., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M., Hansen, N., Durand, E., Malaspinas, A., Jensen, J., Marques-Bonet, T., Alkan, C., Prufer, K., Meyer, M., Burbano, H., Good, J., Schultz, R., Aximu-Petri, A., Butthof, A., Hober, B., Hoffner, B., Siegemund, M., Weihmann, A., Nusbaum, C., Lander, E., Russ, C., Novod, N., Affourtit, J., Egholm, M., Verna, C., Rudan, P., Brajkovic, D., Kucan, Z., Gusic, I., Doronichev, V., Golovanova, L., Lalueza-Fox, C., de la Rasilla, M., Fortea, J., Rosas, A., Schmitz, R., Johnson, P., Eichler, E., Falush, D., Birney, E., Mullikin, J., Slatkin, M., Nielsen, R., Kelso, J., Lachmann, M., Reich, D., & Paabo, S. (2010). A Draft Sequence of the Neandertal Genome Science, 328 (5979), 710-722 DOI: 10.1126/science.1188021
Haile-Selassie, Y., Latimer, B., Alene, M., Deino, A., Gibert, L., Melillo, S., Saylor, B., Scott, G., & Lovejoy, C. (2010). An early Australopithecus afarensis postcranium from Woranso-Mille, Ethiopia Proceedings of the National Academy of Sciences, 107 (27), 12121-12126 DOI: 10.1073/pnas.1004527107
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
Liu W, Jin CZ, Zhang YQ, Cai YJ, Xing S, Wu XJ, Cheng H, Edwards RL, Pan WS, Qin DG, An ZS, Trinkaus E, & Wu XZ (2010). Human remains from Zhirendong, South China, and modern human emergence in East Asia. Proceedings of the National Academy of Sciences of the United States of America, 107 (45), 19201-6 PMID: 20974952
Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin JJ, Kelso J, Slatkin M, & Pääbo S (2010). Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature, 468 (7327), 1053-60 PMID: 21179161
Zalmout IS, Sanders WJ, Maclatchy LM, Gunnell GF, Al-Mufarreh YA, Ali MA, Nasser AA, Al-Masari AM, Al-Sobhi SA, Nadhra AO, Matari AH, Wilson JA, & Gingerich PD (2010). New Oligocene primate from Saudi Arabia and the divergence of apes and Old World monkeys. Nature, 466 (7304), 360-4 PMID: 20631798

Denisova the Menace II: Nuclear story

Earlier this year, I discussed the publication of a mitochondrial DNA study from a 50,000 year old pinky bone from Denisova in Siberia. The big story there was that the mtDNA of this specimen was twice as divergent (different) from modern humans as Neandertal mtDNA. This suggested to researchers that there was this rogue human group (some [not I] might say ‘species’) running around Eurasia around the time of the Upper Paleolithic.



Well now they’ve sequenced the nuclear genome of one of a Denisova denizen. The picture painted is that a Denisova-Neandertal ‘lineage’ split off from that of modern humans some time in the distant past, then the Denisovans split from Neandertals some time later. Most interesting, modern-day Melanesians seem to derive about 4% of their genes from this ‘archaic’ Denisovan lineage, whereas this archaic genetic baggage isn’t present in other modern human populations.


AMAZING! Think back to the draft of the Neandertal nuclear genome, also published earlier this year. Green and colleagues (2010) reported that the Neandertal nuclear genome revealed that Neandertals contributed up to 4% of the genomes of modern-day non-Africans. Now, the Denisova genome shows that a different and more specific group of modern humans (Melanesians) appears to uniquely share a different set of nuclear genes from an ‘extinct’ human group.


But if they contributed their genes to modern people, are they really extinct? Of course not! I’m admittedly not a geneticist, but I think what we’re seeing here are the genetic signatures of a single, ancient structured population of modern humans. That is to say, all modern humans derive different amounts of their genes from various ancient subpopulations of ‘archaic’ humans (for ‘archaic,’ think ‘people that lived a long time ago’). There was just little enough contact between these populations for them to have diverged slightly from one another, but still enough contact for them all to have contributed different parts and amounts of genes to people today.


It is weird, then, to see the ancient DNA geneticist Svante Pääbo (out of whose lab this ancient genetic work is done) say this to BBC News:

“It is fascinating to see direct evidence that these archaic species did exist (alongside us) and it’s only for the last few tens of thousands of years that is unique in our history that we are alone on this planet and we have no close relatives with us anymore.”

Why are these ‘archaic species…alongside us”? The fact that these groups were mixing means that they are a single species – the ability (and propensity) to interbreed is the standard definition of ‘species’ used in modern biology.


So contrary to Pääbo’s quote, I’d say we do have close relatives with us, it’s just that modern humans are much more closely to one another related than ancient human populations were to one another. Probably there is more contact between modern human populations, beginning a few tens of thousands of years ago, because population sizes explode to the some 7 billion people we have on earth today. This greater contact means less chance for populations to diverge from one another.


The take-home: We all have multiple ancestors, from various times and places. For more comprehensive and better-informed coverage, check out John Hawks’s post on the topic.
ResearchBlogging.org
References
Green, R., Krause, J., Briggs, A., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M., Hansen, N., Durand, E., Malaspinas, A., Jensen, J., Marques-Bonet, T., Alkan, C., Prufer, K., Meyer, M., Burbano, H., Good, J., Schultz, R., Aximu-Petri, A., Butthof, A., Hober, B., Hoffner, B., Siegemund, M., Weihmann, A., Nusbaum, C., Lander, E., Russ, C., Novod, N., Affourtit, J., Egholm, M., Verna, C., Rudan, P., Brajkovic, D., Kucan, Z., Gusic, I., Doronichev, V., Golovanova, L., Lalueza-Fox, C., de la Rasilla, M., Fortea, J., Rosas, A., Schmitz, R., Johnson, P., Eichler, E., Falush, D., Birney, E., Mullikin, J., Slatkin, M., Nielsen, R., Kelso, J., Lachmann, M., Reich, D., & Paabo, S. (2010). A Draft Sequence of the Neandertal Genome Science, 328 (5979), 710-722 DOI: 10.1126/science.1188021


Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin JJ, Kelso J, Slatkin M, & Pääbo S (2010). Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature, 468 (7327), 1053-60 PMID: 21179161

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.

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]–>