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

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eFfing Fossil Friday: Frozen Femur

A 45,000 year old human femur from Siberia provides new information about genetic mutation rates and modern human origins. As Quiaomei Fu and colleagues report in this week’s issue of Nature, this seemingly simple leg bone carries so much information, not because of its gross anatomy, but because of the ancient DNA it preserves.

The femur wasn’t discovered by paleontologists, but by an artist/historian looking for fossils around the Irtysh River. The bone came from from a site called Ust’-Ishim, only some 650 km north of the snowy capital where I work in Kazakhstan:

Ust'-Ishim

The site in question, Ust’-Ishim is marked by the yellow star. The red and blue sites to the southeast are other Upper Paleolithic sites. Okladnikov (3) and Denisova (4) have also yielded fossils preserving ancient DNA. Modified from Fu et al. figure 1.

The bone was directly radiocarbon dated to around 45,000 years ago. With a fairly precise age of the bone, Fu et al. could estimate the rate at which genetic mutations arise, by counting the number of new mutations in recent humans that aren’t shared by the Ust’-Ishim femur. This led to an estimate of around 0.43×10−9  new mutations per site per year. This is a relatively low rate compared to estimates based on geologically older fossils, but consistent with more recent estimates that directly compare parents and offspring.

The Ust’-Ishim individual had levels of Neandertal ancestry comparable to living Eurasians (~2.3% of the genome), but there is no evidence of any Denisovan ancestry. Because this individual lived closer to the date of modern-Neandertal admixture, the Neandertal segments of its genome are longer than in modern people (recombination over generations breaks these regions apart into shorter segments). Knowing about recombination rates, Fu et al. could infer that admixture between Neandertal and modern human populations occurred between 50-60,000 years ago.

This eFfing Friday fossil provides more tantalizing evidence for DNA-bearing human fossils just across the Kazakhstan border. With Ust’-Ishim to the north, Denisova and Okladnikov caves to the east, and Teshik Tash to the south, my colleagues and I are very keen to find similar sites here on the KZ side.

Reference: Fu et al. 2014. Genome sequence of a 45,000-year-old modern human from Siberia. Nature 514: 445–449. doi:10.1038/nature13810.

Dawn of Paleoepigenomics

It was only a matter of time. In the 1990s scientists started extracting, sequencing and analyzing mitochondrial DNA from Neandertal fossils. In the 2000s they made major advances in obtaining and analyzing ancient nuclear DNA, which is much trickier than mtDNA. In just the past year, paleogeneticists pushed the envelope in sequencing truly ancient DNA, announcing hominin and horse genomes from 400 and 700 thousand years ago, respectively. As I mentioned a few months ago, the burgeoning field of paleogenomics is revealing things about human evolution that could hardly be dreamt of only a few decades ago.

But world of DNA is so much more than just ceaseless sequences of four letters, and the field of ‘epigenetics’ has emerged to investigate the complex way that chemical alterations to DNA structure (not sequence) affect gene expression. Melding epigenetics & paleogenomics, David Gokhmen and colleagues report in Science, “Reconstructing the DNA methylation maps of the Neandertal and the Denisovan.” For a review of what DNA methylation is and does, check out this Scitable overview. In short, DNA methylation is part of the reason why not all of your genes in your genome are expressed at all times throughout your body, even though all of your genes are physically present in all of the cells of your body. Methylation plays an important role in turning genes on or off during development. It’s nuts. Now, the structure of DNA breaks down over time after an animal dies, obscuring original methylation patterns. But the decompositoin process is becoming better understood, including patterns at methylated vs. unmethylated sites. As Gokhmen et al. write, these patterns “may serve as a proxy for the levels of methylation in ancient DNA.”

This brilliant insight allowed Gokhmen and colleagues to identify some 2000 genomic regions in bone cells that differed in methylation between a living human, a Neandertal and a Denisovan (2000 less than 1% of all regions). One such region was the HOXD cluster, which is known to be involved in embryonic limb development. Neandertals and Denisovans were more methylated than humans at the HOXD9 and HOXD10 loci. Whether and how these epigenetic differences might be responsible for anatomical differences between these populations is not at all clear yet. But Neandertals are known to differ from humans in some aspects of arm and leg anatomy – authors point out that Neandertals generally have larger and more robust joints but shorter limbs. They state, “together, these findings suggest that the HOXD cluster might have played a key role in the recent evolution of human limbs.”

Importantly, “Denisovans” are only known from 2 teeth and part of a finger bone, no other limb fossils are known (or at least published) for this ancient population. This leads us to a prediction – if the similarly hypermethylated HOXD sites in Denisova and Neandertals are functionally important, then Denisovan limb fossils, if ever found, should be more like Neandertals than like humans. If this prediction is borne out, this would provide evidence of specifically how HOXD9-10 affect limb development, and how HOXD epigenetic regulation has changed in human evolution. This hypothesis can be tested, but only with the discovery of the right fossils (i.e., genetically attributable to Denisovans). Well, the functional importance of hyper/hypomethylation at these sites could probably also be assessed with transgenic mouse experiments…

There is truly remarkable work being done in paleogenomics – and now paleoepigenomics – which will probably begin to form the basis of some exciting new human evo-devo research.

Kryptonians’ DNA in the Sts 71 fossil

I don’t love flying. In fact I’m writing this post in a traffic jam on the tarmac of Frankfurt International between a 9 hour and a 5 hour flight. On a related note, reclining your seatback all the way for most of a long flight does in fact make you the worst person on earth.

wp-1397479298557

Hey, guy, how’s that 10th X-Men movie? What kind of shampoo is that I smell? Why yes, I do work best when I can’t open my computer fully. What a joyous way for us to learn all about each other, new best friend!

A plus of all this airtime, though, is that I can get caught up on recent movies I’ve missed living under the proverbial rock of research and teaching. On the ~7500 mile trip from Kazakhstan to Kanada I got to watch Man of Steel, a new take on an ancient comic. It was tacky and entertaining and there are some interesting takes on biology, but it had a boss paleo surprise.

The best part of the movie is at the beginning when The Gladiator steals a mysterious “codex” as his planet Krypton plunges catastrophically into implosive oblivion. Amid the chaos, Russel Crowe swims through some chamber, and what does he encounter?

The codex? No, it’s…

Sts 71_R lateral1

Sts seventy f*ing one

Sts 71 is my favorite fossil I’ve seen because it looks totally badass (not a scientific reason, but it’s the truth). It comes from Sterkfontein cave in South Africa, dates to probably around 2.5 million years ago, and is attributed to the species Australopithecus africanus.

I realize I’m behind the times here, but in case you haven’t seen the movie but are planning to, then read no further (SPOILER ALERT). In the film, this codex/fossil apparently contains the genetic code for the entire species of Kryptonians (whose resemblance to living humans is so remarkable it requires a statistically impossible amount of parallel evolution). Now, the oldest DNA recovered from a fossil is from a horse that lived about 700 thousand years ago (Orlando et al., 2013). Sts 71 is some 3-4 times older than that, and illusorily contains the genomes of a billion human-like aliens with super powers.

What a badass fossil.

Paleogenomics is crushing it right now

It’s only Valentine’s Day, and already early 2014/late 2013 have provided several fascinating, high profile studies of ancient DNA (all been published in Nature). Forecasting this deluge, last year closed with the announcement of sequenced mtDNA from a ≥400,000 year old human fossil from Sima de los Huesos, Spain (Meyer et al., 2013). This is the oldest DNA obtained for any human fossil, and among the oldest of any animal.Meyer title copy 2

Shortly thereafter, Prüfer and pals (2014) published the complete genome of a Neandertal from the infamous Denisova cave. This study revealed extensive inbreeding in Siberian Neandertals; the fossil individual’s high level of homozygosity is consistent with their parents being half-siblings.  Furthermore, comparison of the genome of this inbred Neandertal with modern humans’ allowed researchers to identify many mutations that have become fixed (shared by all people) by natural selection since the divergence of our and Neandertals’ ancestors. Uncovering these human-specific variants can help us understand the genetic bases for many of humans’ remarkable traits.Prufer title

In January, Olalde y coautores published a genomic analysis of a 7,000 hunter-gatherer from Spain. This ancient genome contained ancestral variants for genes relating to skin pigmentation (SLC45A2, SLC45A5MC1R, TYR, and KILTG), meaning this Mesolithic European most probably had dark skin. This individual also had a derived variant of the HERC-OCA2 locus, associated with blue eye color in present day people. This suggests that the relatively novel phenotype of non-brown eyes may have increased in frequency more quickly than light skin color in ancient Europe. This guy also had many derived loci associated with immune function, indicating that the rise of agriculture is not solely responsible for the evolution of immune function in present day Europeans.

Olalde title

Around the same time, Sankararamen and team published an analysis of the distribution of Neandertal genes in living people. Whereas previous studies had already shown that Neandertals contributed ≤4% on average to the genomes of living people, this study examined where in modern people’s genomes this Neandertal ancestry tends to be located. One of the most interesting findings is that Neandertal genes are not uniformly or randomly distributed across the modern human genome. Rather, some regions appear to be especially devoid of Neandertal ancestry, implying natural selection acted strongly against Neandertal genes. These Neander-nude areas are preferentially found on the the X chromosome and in genes expressed in the testes, a finding consistent with reduced fertility in hybrid males. Although the genetic contribution of Neandertals to modern humans means that the two belonged to the same species, Sankararaman et al’s findings suggest the two groups were on their way to becoming different species.sanakararaman

Finally, this past week Rasmussen and rascals have published an analysis of a 12,000 year old human from the Anzick site in Montana, associated with the Clovis stone tool culture. I don’t know much about this time period save for what I learned in a class on North American archaeology taught by Dr. John Speth, back when I was a young, bright-eyed graduate student. One thing I recall from this class, when we were going over Clovis, was that this tool industry was found all over the United States at the beginning of the Holocene, but I was always disappointed by the dearth of bones complementing the copious lithics. Turns out, the DNA analyzed by Rasmussen et al. comes from the only known burial from this time period. This lone burial provides compelling genetic evidence that indigenous Americans have descended largely from a single ancestral population that separated into the North and South American populations prior to the Clovis period. This ancestral population was definitely not from Europe, as a minority of researchers have argued. Check out the SEAC Underground blog for more on the archaeology and ethics of the Anzick analyses.rasmussen

So, paleogenomics is really crushing it right now. There have been many of recent advances in sampling and sequencing poorly-preserved ancient DNA, and as we’re seeing now, lots of ancient bones (and teeth) are bringing awesome new, genetic insights into recent human evolution. If this is how well we’re doing so early in 2014, you can bet that the rest of the year promises many more exciting discoveries.

This human DNA is old as hell

If hell were around 400,000 years old. The people who salvaged ancient DNA from fossil Neandertals and “Denisovans” now present mitchondrial DNA (mtDNA) from a human-ish fossils from the Spanish site of Sima de los Huesos (SH; this translates as “pit of bones,” by the way, which is pretty badass). DNA-bearing Neandertal sites and Denisova cave date anywhere from around 30-100 kya, while Sima de los Huesos has been dated by various methods to 300-600 thousand years ago. So the newly announced mtDNA is the oldest human DNA ever recovered…

YET!

Now, we know what Neandertals look like, since they are perhaps the best known group of fossil humans. We don’t really know what Denisovans look like, as their unique DNA came from fossils that are anatomically ambiguous (a large molar and the end of a tiny fragment of the bone at the end of your pinky finger) – they could look like anyone. Even you! The SH fossils predate Neandertals by a few hundred thousand years, but their skulls look pretty similar; quite possibly the SH populations were ancestors of Neandertals, and you’d expect the DNA to be similar in the two groups.

So researchers were surprised to find this SH mtDNA to be more similar to Denisovan than to human or Neandertal mtDNAs. But this actually shouldn’t be that surprising, since we saw the same twist when Denisovan mt and nuclear DNA was sequenced – mtDNA first made it look like humans and Neandertals were more closely related, and the ancestors of Denisovans separated from the human+Neandertal lineage in the deep past. However, mtDNA essentially acts as a single genetic locus – a gene tree isn’t necessarily a species tree – and the more informative nuclear DNA later showed Neandertals and Denisovans to be more closely related to one another than either was to living humans (yet each of these ancient populations contributed some genes to some living people today). Denisovans held on to a very ancient mtDNA lineage, and apparently so did the people represented at Sima de los Huesos. And let’s not forget, we don’t know what Denisovans looked like – maybe they looked just like the older SH fossils.

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. But if I’m wrong, maybe we’ll be a step closer to knowing what the bones of the the mysterious “Denisovans” looked like…

Here’s that paper: Meyer et al. in press. A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature. doi:10.1038/nature12788

Ancient DNA & admixture: One of Science’s breakthrough in 2011

The high-profile journal Science has compiled a list of the top breakthroughs of 2011, some of the most major discoveries and and advances across scientific fields. The top breakthrough was research finding that antiretroviral drugs can act not only to treat patients infected with HIV, but also these antiretrovirals significantly reduce the likelihood of transmission of the disease. This is a pretty effing big deal, as HIVand AIDS are tragically rampant in many parts of the world.

One of the runners-up to this breakthrough: “Archaic Humans’ DNA lives on.” The brief exposé highlights the studies from this year that corroborated the 2010 evidence for Neandertal and “Denisovan” DNA in living people. The exposé concludes with a short and rather out-of-the-blue paragraph about the Australopithecus sediba fossils from Malapa. How about that – anthropological research as a major scientific breakthrough; FL governor Rick Scott certainly didn’t see that one coming.

ResearchBlogging.org
See for yourself:
Anonymous (2011). The Runners-Up Science, 334 (6063), 1629-1635 DOI: 10.1126/science.334.6063.1629