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

IMG_20160801_143520

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…

20161111_141908.jpg

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

… and 3D printing.

20161107_135616

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 …

2016-02-09 16.26.31

Anatomy terminology hidden in 3D block letters,

Picture1

Hominin canines in Kazakhstani baursaki cakes,

Picture1

The Ardipithecus ramidus ilium in Almaty,

screen-shot-2016-11-26-at-5-36-05-pm

Homo naledi juvenile femur head in nutmeg,

bangkok-erectus

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.

Did Neandertal brains grow like humans’ or not?

According to Marcia Ponce de Leon and colleagues, “Brain development is similar in Neandertals and modern humans.” They reached this conclusion after comparing how the shape of the brain case changes across the growth period of humans and Neandertals. This finding differs from earlier studies of Neandertal brain shape growth (Gunz et al. 2010, 2012).

Although Neandertals had similar adult brain sizes as humans do today, the brains are nevertheless slightly different in shape:

Screen Shot 2016-07-26 at 4.31.52 PM

Endocranial surfaces of a human (left, blue) and Neandertal (right, red), from Gunz et al. (2012). These surfaces reflect the size and shape of the brain, blood vessels, cerebrospinal fluid, and meninges.

Gunz et al. (2010, 2012) previously showed that endocranial development in humans, but not in Neandertals or chimpanzees, has a “globularization phase” shortly after birth: the endocranial surface becomes overall rounder, largely as a result of the expansion of the cerebellum:

Screen Shot 2016-07-26 at 4.38.39 PM

Endocranial (e.g., brain) shape change in humans (blue), Neandertals (red) and chimpanzees (green), Fig. 7 from Gunz et al. (2012). Age groups are indicated by numbers. The human “globularization phase” is represented by the great difference in the y-axis values of groups 1-2 (infants). The Neandertals match the chimpanzee pattern of shape change; Neandertal neonates (LeM2 and M) do not plot as predicted by a human pattern of growth.

Ponce de Leon and colleagues now challenge this result with their own similar analysis, suggesting similar patterns of shape change with Neandertals experiencing this globularization phase as well (note that endocranial shapes are always different, nevertheless):

Screen Shot 2016-07-26 at 4.47.13 PM

Endocranial shape change in humans (green) and Neandertals (red), from Ponce de Leon et al. (2016). Note that the human polygons and letters represent age groups, whereas the Neandertal polygons and labels are reconstructions of individual specimens.

The biggest reason for the difference between studies is in the fossil sample. Ponce de Leon et al. have a larger fossil sample, with more non-adults including Dederiyeh 1-2, young infants in the age group where human brains become more globular.

Screen Shot 2016-07-26 at 5.01.17 PM

Comparison of fossil samples between the two studies.

But I don’t think this alone accounts for the different findings of the two studies. Overall shape development is depicted in PC 1: in general, older individuals have higher PC1 scores. The globularization detected by Gunz et al. (2010; 2012) is manifest in PC2; the youngest groups overlap entirely on PC1. The biggest difference I see between these studies is where Mezmaiskaya, a neonate, falls on PC2. In the top plot (Gunz et al., 2012), both Mezmaiskaya and the Le Moustier 2 newborn have similar PC2 values as older Neandertals. In the bottom plot (Ponce de Leon et al., 2012), the Mezmaiskaya neonate has lower PC2 scores than the other Neandertals. Note also the great variability in Mezmaiskaya reconstructions of Ponce de Leon et al. compared with Gunz et al.; some of the reconstructions have high PC2 values which would greatly diminish the similarity between samples. It’s also a bit odd that Engis and Roc de Marsal appear “younger” (i.e., lower PC1 score) than the Dederiyeh infants that are actually a little bit older.

Ponce de Leon et al. acknowledge the probable influence of fossil reconstruction methods, and consider other reasons for their novel findings, in the supplementary material. Nevertheless, a great follow-up to this, to settle the issue of Neandertal brain development once and for all, would be for these two research teams to join forces, combining their samples and comparing their reconstructions.

REFERENCES

ResearchBlogging.org

Gunz P, Neubauer S, Maureille B, & Hublin JJ (2010). Brain development after birth differs between Neanderthals and modern humans. Current Biology : 20 (21) PMID: 21056830

Gunz P, Neubauer S, Golovanova L, Doronichev V, Maureille B, & Hublin JJ (2012). A uniquely modern human pattern of endocranial development. Insights from a new cranial reconstruction of the Neandertal newborn from Mezmaiskaya. Journal of Human Evolution, 62 (2), 300-13 PMID: 22221766

Ponce de León, M., Bienvenu, T., Akazawa, T., & Zollikofer, C. (2016). Brain development is similar in Neanderthals and modern humans Current Biology, 26 (14) DOI: 10.1016/j.cub.2016.06.022

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

eFfing #FossilFriday: Pleistocene ppl blowin up this week

This was a big week for Middle-Late Pleistocene fossil humans. Chun-Hsiang Chang and colleagues describe a mandible dredged up off the western coast of Taiwan, which they note in the title as, “The first archaic Homo” fossil known from the region. The geological context makes it difficult to date the specimen precisely, but authors argue it is probably younger than 190 thousand years old.

The Penghu mandible. Figure 3. From Chang et al.

In life, this individual was fully grown but appears never to have developed third molars (the “wisdom teeth”). Such “third molar agenesis” is relatively rare before modern times, but is also seen in the D2735 Homo erectus mandible from Dmanisi. I wouldn’t make much of this coincidence, but it does raise the question of whether the cause of agenesis, not uncommon today, was the same then as now.

Shortly after the announcement of the Penghu mandible, Israel Hershkovitz and colleagues presented a 55,000 year old brain case from Manot Cave in the Levant. The calvaria (fancy word for brain case) looks very similar to the skulls of the slightly younger “anatomically modern” humans of the Upper Paleolithic in Europe, albeit with a few Neandertal-like traits here and there (hey, just like many of the Upper Paleolithic humans).

The Manot calvaria (Figure 2 from Hershkovitz et al.) The views are (a-d) from the top with front to the left; from the left; from the front; and from the back. Extra credit: In the top view (a), can you identify the features telling that the front is to the left?

The Manot calvaria (Figure 2 from Hershkovitz et al.) The views are (a-d) from the top with front to the left; from the left; from the front; and from the back. Extra credit: In the top view (a), can you identify the features telling that the front is to the left?

John Hawks has good posts dedicated to both Penghu and Manot. The upshot of these discoveries is that Middle and Late Pleistocene human population diversity, and the interactions between these populations, are probably much more complicated and interesting than the old model of ‘modern’ humans arising singly in Africa and replacing ‘archaic’ humans in different parts of the globe. With the technological advances and fossil discoveries of the past decade, the rather simple Replacement model has given way to a better appreciation of true complexity of human evolution toward the end of the Ice Age. Both of these new papers reflect this new perspective.

Along these lines, accompanying the Manot paper in Nature is an editorial, “Human history defies easy stories.” What caught my attention reading this (anonymous?) commentary is that it puts scientific interpretations of the past into a social and historical context. The author notes that the traditional story of modern humans arising, spreading and eradicating other groups of human has “imperialist framing, in which evolution and replacement can be justified after the fact as a kind of manifest destiny.” Science doesn’t occur in a vacuum, it’s done by people whose minds and creativities are molded in specific historical, economic and cultural contexts. This editorial comment makes one wonder how the human fossil record would have been interpreted, had most of it not discovered against the social backdrop of ruthless capitalism.

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.

eFfing Fossil Friday: Feces

As we saw in last week’s FFF, Spain has some of the best human fossils. Now it also has some of the shittiest. I mean this literally, not figuratively: archaeologists working at at the ~50 thousand year old site of El Salt have found the oldest known human poop:

Neandertal coprolite

Party pooper. Left is a picture of the coprolite, right is the inset blown up. Top is regular color, bottom is under polarized light (Fig. 1D from Sistiaga et al. 2014).

Any nerd worth their el salt has surely seen/read Jurassic Park, and will recall that there’s a lot to be learned from poop. Paleontologists even have a technical term for fossilized feces – “coprolite.”  The coprolite from El Salt was excavated from a hearth (if I’m reading “combustion layer” correctly), meaning that 50,000 years ago some jerk Neandertal ruined the campfire and subsequently the whole camping trip. Analysis of the stool’s sterols and (copro-) stanols (the chemical residuals of digesting plant and animal food) adds to previous findings that Neandertals ate plants and not only meat. However, the stanol profile suggests that the majority of the diet came from meat rather than plants. Because coprostanol is created by gut microbes, this study potentially paves the way to reconstructing Neandertals’ gut microbiome. Like I said, there’s a lot to be learned from poop.

The article, by Sistiaga and colleagues and published in PLoS One, contains lots of interesting information about the digestive process that I for one didn’t know. It’s totally open access, so it’s completely free for all. Go read it now!

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.