The strange days of yore

Today is not like the good ol’ days. In many ways things have changed for the better. For instance, in the good ol’ days, many paleontologists would find fossils but let nary a soul examine them; today, you can download high quality 3D models of many important fossils from both East and South Africa, completely for free!

Robert Broom’s (1938) account of the discovery of the first Paranthropus (or Australopithecus) robustus is also a reminder of the strangeness of the bygone days of yore:

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Wait for it …

In June of this year a most important discovery was made. A schoolboy, Gert Terblanche, found in an outcrop of bone breccia near the top of a hill, a couple of miles from the Sterkfontein caves, much of the skull and lower jaw of a new type of anthropoid. Not realizing the value of the find, he damaged the specimen considerably in hammering it out of the rock. The palate with one molar tooth he gave to Mr. Barlow at Sterkfontein, from whom I obtained it. Recognizing that some of the teeth had recently been broken off, and that there must be other parts of the skull where the palate was found, I had to hunt up the schoolboy. I went to his home two miles off and found that he was at the school another two miles away, and his mother told me that he had four beautiful teeth with him. I naturally went to the school, and found the boy with four of what are perhaps the most valuable teeth in the world in his trouser pocket. He told me that there were more bits of the skull on the hillside. After school he took me to the place and I gathered every scrap I could find; and when these were later examined and cleaned and joined up, I found I had not only the nearly perfect palate with most of the teeth, but also practically the whole of the left side of the lower half of the skull and the nearly complete right lower jaw.

What a wild time – Broom hunts down poor Gert, barges into the school, then makes the kid show him where he hacked the skull out of the rock. Poor, poor Gertie.

Maybe it was a different Gertie, but surely the reaction was the same.

Maybe it was a different Gertie, but surely the reaction was the same.

Of course, there was a lot at stake. I mean, brazen Gert harbored not just “beautiful teeth,” but “the most valuable teeth in the world.” IN HIS TROUSERS! And of course Gert was also the soul possessor of priceless intel – the source of the fossils. So maybe Broom was justified in this zealous abduction. And O! such prose in a Nature paper! WAS IT WORTH IT, DR. BROOM?

At Sterkfontein, a bronzed Broom considers the weight of his actions.

At Sterkfontein, a bronzed Broom considers the weight of his actions.

Of course, Gert wasn’t the last kid to discover an important human fossil. The game-changing Australopithecus sediba  was discovered when Matthew Berger, son of famed Lee Berger and only 9 years old at the time, saw a piece of a clavicle sticking out of a block of breccia. Both Gert and Matthew show that you don’t have to be a doctor to make amazing discoveries. What future fossil discoveries will be made by kids, and making my adult accomplishments pale in comparison?!

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Osteology Everywhere: Ardipithecus in Almaty?

A few weeks ago I was traipsing across Almaty, Kazakhstan’s former capital, when a stain in the road caught my eye:

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Roadside osteology. The intersection of the trunk and legs at the intersection of Abay & Seifullin?

It’s obviously iliac but it’s not just any old ilium. I think I discovered the underreported antimere of the Ardipithecus ramidus pelvis (ARA-VP 6/500; Lovejoy et al., 2009). What it’s doing in Almaty, and in the middle of a busy street, I have no idea. I’ve long thought the absence of hominin fossils in Kazakhstan was suspicious. But not this suspicious.

Roadside paleontology. The Almaty Ardi innominate (left), compared with the actual ARA-VP-1/500 innominate (center) and its reconstruction (right). Adapted from Lovejoy et al. 2009.

Roadside paleontology. The Almaty intersection innominate (left), compared with the actual ARA-VP-1/500 innominate (center) and its reconstruction (right). Adapted from Lovejoy et al. 2009.

The Ardi innominate pictured (center, above) is from the left side, and the Almaty intersection innominate is a perfect counterpart from the right. Yes, I know they found a right ilium at Aramis to go with the better preserved left half. But to that I reply:

ModernFamily-Shame-GIF

Let’s compare the “true” right ilium from Aramis (left, below) with my more likely antimere (right). Look how perfectly the Almaty Ardi fits the reconstruction:

Aramis innominate fossils (left) compared with the Almaty Ardi roadside fragment overlain on the reconstructed pelvis (right).

Aramis innominate fossils (left) compared with the Almaty Ardi roadside fragment overlain on the reconstructed pelvis (right).

The lower portion of the ilium is a bit taller than in later hominins, what’s preserved of the acetabulum is a bit small, and there’s a beautiful portion of the auricular surface for articulation with the (never recovered) sacrum. I rest my case.

Despite their strange shapes, pelvic parts seem to be the epitome of “osteology everywhere.”

ResearchBlogging.orgReference
 Lovejoy CO, Suwa G, Spurlock L, Asfaw B, & White TD (2009). The pelvis and femur of Ardipithecus ramidus: the emergence of upright walking. Science (New York, N.Y.), 326 (5949), 710-6 PMID: 19810197

You can read the media summaries (not actual articles) of the Ardipithecus ramidus reports here.

Materials from the R workshop at #AAPA2016

For last week’s AAPA conference, my friend and colleague David Pappano organized a workshop teaching about the many uses of the R programming language for biological anthropology (I’m listed as co-organizer, but really David did everything). After introducing the basics, we broke into small groups focusing on specific aspects of using R. I devised some lessons for basic statistics, writing functions, and resampling. Since each of the lessons could have easily taken up an hour and most people didn’t get to go through the activities fully, I’m posting up the R codes here for people to mess around with.

The basic stats lesson utilized Francis Galton’s height data for hundreds of families, courtesy of Dr. Ryan Raaum. To load in these data you just need to type into R: galton = read.csv(url(“http://bit.ly/galtondata“)). The code simply shows how to do basic statistics that are built into R, such as  t-test and linear regression.

Example of some summary stats for the Galton height data.

Some summary stats for the Galton  data. The code is in blue and the output in black.

Here is the Basic Stats code, download and paste it into an R file, then buckle up!

The lesson on functions and resampling was based on limb length data for apes, fossil hominins and modern humans (from Dr. Herman Pontzer). The csv file with the data can be downloaded from David’s website. R has lots of great built-in functions (see basic stats, above), and even if you’re looking to do something more than the basics, chances are you can find what you’re looking for in one of the myriad packages that researchers have developed and published over the years. But sometimes it’s necessary to write a function on your own, and with fossil samples you may find yourself needing to do resampling with a specific function or test statistic.

For example, you can ask whether a small sample of “anatomically modern” fossil humans (n=12) truly differs in femur length from a small sample of Neandertals (n=9). Traditional statistics require certain assumptions about the size and distribution of the data, which fossils fail to meet. Another way to ask the question is, “If the two groups come from the same distribution (e.g. population), would random samples of sizes n=12 and n=9 have so great an average difference as we see between the fossil samples?” A permutation test, shuffling the group membership of the fossils and then calculating the difference between the new “group” means, allows you to quickly and easily ask this question:

R code for a simple permutation test.

R code for a simple permutation test. The built-in function “sample()” is your best friend.

Although simply viewing the data suggests the two groups are different (boxplot on the left, below), the permutation test confirms that there is a very low probability of sampling so great a difference as is seen between the two fossil samples.

Left: Femur lengths of anatomically modern humans (AMH) and Neandertals. Right: distribution of resampled group differences. Dashed lines bracket 95% of the resampled distribution, and the red line is the observed difference between AMH and Neandertal femur lengths. Only about 1% of the resampled differences are as great as the observed fossil difference.

Left: Femur lengths of anatomically modern humans (AMH) and Neandertals. Right: distribution of resampled group differences. Dashed lines bracket 95% of the resampled distribution, and the red line is the observed difference between AMH and Neandertal femur lengths. Only about 1% of the resampled differences are as great as the observed fossil difference.

Here’s the code for the functions & resampling lesson. There are a bunch of examples of different resampling tests, way more than we possibly could’ve done in the brief time for the workshop. It’s posted here so you can wade through it yourself, it should keep you busy for a while if you’re new to R. Good luck!

R workshop at #AAPA2016

The 85th annual meeting of the American Association of Physical Anthropologists, in Hottlanta this year, is only a few short weeks away. The preliminary program is up, and there’s really a lot to look forward to at this year’s conference. There’s a session dedicated to Homo naledi on Saturday morning (16 April), and I’ll be presenting on dental development in Homo naledi at the very end of the last session of the day. Leading up to the conference, I’ll be tweeting teasers as I put together my talk.

My colleague David Pappano and I are also organizing a workshop on using R in biological anthropology, which will take place on Friday 15 April from 9:30-11:30 am. The goal of the workshop isn’t to make you an expert in R by the end of the two short hours, but rather to introduce you to the basic functions and potential uses of the powerful, free statistical software. So if you’Re Ready to leaRn some R basics, come to Room A601 on FRiday moRning – it’s fRee and no RegistRation is RequiRed.

Hopefully we’ll see you in Atlanta in a few weeks!

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

Sunday mornings

Usually I use my PowerPoint skills only for evil, like putting together lectures and talks. But sometimes I get distracted. Today, for instance, instead of grading and prepping next week’s lectures on Eugenics and Spine Evo-devo (don’t worry, they’re for different classes), I spent half an hour making this:

A spirited twist on Jane Austen's classic novel.

A spirited twist on Jane Austen’s classic novel. Why am I devoting my life to research and teaching when I could go to where the real money is?

This is surely the project that will land me tenure in a few years.

Osteology Everywhere: Cakes or canines?

I’ve been looking at so many teeth lately, I’m starting to feel like a sadist but with newer magazines.

Between putting together a talk about dental development in Homo naledi and teaching teeth in my human evo-devo class last week . . .

After these drawings, my students were fully trained and ready to tackle the odontological world.

After these drawings, my students are now fully trained and ready to tackle the odontological world.

. . . I’ve got dentition on the brain. WHICH IS NOT THEIR ANATOMICAL POSITION.

So last weekend some friends and I hit a local pub,  a life jacket for my dental inundation. Surely, a pint and a snack will expunge enamel, dissolve dentine, exhume zuby from my brain! We ordered some beer and baursaki, delicious fried bread made out here in Kazakhstan, the perfect snack to go with beer and chechil. Tearing into the pastry, I started to feel at peace, but then was horrified to look down and find myself hoist with my own petard:

Baursak or bite?

Baursak with a bite taken out? Our a hominin canine?

Seeing the snack, I saw the very thing I’d been fleeing – a hominin canine tooth. Inadvertently, I’d almost exactly replicated Sts 50, a lower left canine crown and broken root from the South African site of Sterkfontein.

Left: Sts 50, lower left canine. Right: bitten fried bread. Images not to scale.

Left: Sts 50, lower left canine. Right: bitten fried bread. Images not to scale. ANTIMERES?

They’re nearly identical but from opposite sides (the fancy word for which is “antimeres”). Note the tall-shouldered, sharp apex of the crown, and the little distal tubercle, the little ‘bump’ at the far left in the left picture above. The mesial, or front, crown shoulder is notably taller than the distal tubercle. At probably around 3 million years ago, Sts 50 likely belongs to Australopithecus africanus, and retains an ape-like asymmetrical crown shape compared to the more incisor-shaped canines we humans have today.

Left to right: Homo baursaki, three South African canines, and a modern human (from White et al. 2012). Images not to scale.

Hominin canines and definitely no cakes. Left to right: Homo baursaki, three canines from early Pleistocene South Africa, and a modern human (from White et al. 2011). Images not to scale. Note how much less asymmetrical the modern human canine crown (far right) is compared to the fossil hominins. Teeth 1, 2, 4, and 5 are from the right side while the center, Sts 50, is from the left.

 

Apparently all you need to go back in time is some beer and baursaki.