eFfing Fossil Friday: Feathers & Ink

I’ve been traveling here and there lately, so I’ve missed a fortnight’s FFFs. So to atone, this post is a threefer.

Last week I was visiting my family in Kansas City, and was debating whether to get a badass dinosaur tattoo. Right on cue, the cover of last week’s Nature featured this feathery friend (right): the 11th Archaeopteryx skeleton. From the previous 10 skeletons, we know that this 150 million year old dinosaur had feathers on its upper limbs and tail. But this new specimen from China, described by Foth and colleagues, also has plush pennaceous plumage bedazzling its neck, lower legs and feet. So decked in down, this new fossil suggests that Archaeopteryx and other dinos originally evolved feathers for some function besides flight, such as social displays (some living birds have taken this to ridiculous extremes). Later species of winged theropods (i.e., birds) eventually adapted feathers for flying (the concept of exaptation).

Also, this closeup, under ultraviolet light, of the specimen’s wing (impressions) and phalanges shows how badass and clawed birds used to be. They just don’t make them like they used to.

Extended Data Fig. 4a-b from Foth et al., 2014.

Taking this Nature cover as a sign, I went ahead and got a different fossil permanently etched somewhere on my person:

Fig. 1a from Rauhut et al., 2012.

This, as described in the title of the 2012 paper, is an “exceptionally preserved juvenile” of the dinosaur species Sciurumimus albersdoerferi. This little buddy is one of the most complete dinosaur skeletons in existence, and even preserves some skin and “protofeathers” (not as full and feathery as in the Archaeopteryx described above). And that little bar beneath the lower jaw is the hyoid bone. THEY HAVE ITS HYOID! If only more hominin fossil juveniles were so well preserved (and badass).

Finally, although CNN is usually insufferable, Thursday they reported that more than 18 dinosaur skeletons that had been smuggled out of Mongolia and into the U.S. have been returned to where they belong. The coverage doesn’t really get into it, but for me this highlights a major paleontological problem - private collectors (and often a black market) make scientifically important fossils unavailable to researchers (many of the Mongolian fossils were very complete skeletons). Fossils are the only direct evidence of life in the past (would you ever believe that this was a real animal if there wasn’t physical evidence?), so the theft and private trade of such important evidence is problematic. This hit home in paleoanthropology with the announcement of Darwinius masillae five years ago (the fossil was purchased for scientific study for a large sum of money). I don’t know what the Mongolian government will do with their returned fossils, but their repatriation is probably good for paleontologists.

Osteology Everywhere: Astana

I don’t usually write about the moonscaped city I’ve lived in for the past 2 years, but I stumbled upon some osteology today worth sharing. Astana is an anachronism. The capital of Kazakhstan for only 16 years, the city sports a futuristic skin, glistening with Kazakh cultural heritage and thrust upon a Soviet skeleton. This place is a palimpsest, embodying the country’s rich history and spirited aspirations.

Astana’s modern and edgy facade encroaching into the steppe and swamp on the city’s southwest outskirts

I live and work on the Left Bank of the Yesil River. Under constant development, the Left Bank often falls short of the metropolitan feel the city’s striving toward. But hop over to the other side of the river to the Right Bank, and Astana takes on a much more urban feel. This is the older part of the city (though this is still relatively young), and as such there are more people and there is more stuff.2014-06-28 13.07.46Now, to combat my summer antsiness, I recently acquired a bicycle (velosiped in Russian), not so much for exercise but to explore this colorful city. (All the pictures in this post are a result of this acquisition) This morning I rolled onto what turned out to be Eurasian National University, and was surprised to find myself besieged by bones:

BONES!

Unlike other Osteology Everywhere posts, where I think I see bones in quotidian sights, these objects are indeed bones.

In the spirit of the bone quizzes on Bone Broke Blog, I challenge you to tell me what these bones are. There are four of a kind on the red and white tiles in the foreground, and a taller one stood upright on a sphere in the background. Can you identify 1) what bone each of these is, and 2) the animal they come from? Bonus points if you can specify which side of the body. Here are some other views:

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Finally, although only mildly related but because it’s totally badass, here’s a picture of lightning I snapped during a storm last week:2014-06-20 21.57.37

 

 

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!

eFfing Fossil Friday: resurrected

It’s been a quiet month here at Lawnchair, as I’ve just returned from the Rising Star Workshop, taking part in the analysis and description of new hominin remains from South Africa. We’ll have some exciting announcements to make in the near future.

Also, I petted a ferocious, bloodthirsty lion!20140601_160436

To ease back into the Lawnchair, I thought I’d resurrect eFfing Fossil Friday, a short-lived series from when I was collecting data for my dissertation three years ago (speaking of which, a paper related to my dissertation came out in AJPA during the Workshop, as well). A lot has happened since the last installment of FFF, so whose heads will be on the chopping block today?

Crania 9, 15 and 17 (clockwise from top left). Cranium 9 is an early adolescent and the other two are adults - lookit how the facial anatomy changes with age!

Crania #s 9, 15 and 17 (clockwise from top left). Cranium 9 is an early adolescent and the other two are adults – lookit how the facial anatomy changes with age! (Fig. 1 from Arsuaga et al., 2014)

It’s new crania from Sima de los Huesos, Atapuerca! These are published today in the journal Science by Juan L. Arsuaga and colleagues. Sima de los Huesos is a pretty remarkable site in Spain dating to the Middle Pleistocene; the site is probably at least 400,000 years old, and the remains of at least 28 individuals. These specimens show many similarities with Neandertals who later inhabited the area, but don’t have all of the ‘classic’ Neandertal features.

What I like about this figure from the paper is that the comparison of the adolescent (top left) with adults (the other two) shows how the skull changes during growth. The major visible difference is that the face sticks out in front of the brain case more in the adults than the adolescent. As a result, the adolescent lacks a supraorbital torus (“brow ridge”), but this would have developed as the face grew forward and away from the brain. Ontogeny!

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.

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Hey, guy, how’s that 10th X-Men movie? What kind of shampoo is that? 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 imlposive 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.

#AAPA2014

I’ve jumped across some continents, to Calgary for the 83rd annual meeting of the American Association of Physical Anthropologists. It’s a frenetic few days to catch up with close friends and colleagues, and to discuss upcoming projects. Also hopefully there will be poutine. You can follow the conference goings-on on Twitter with the hashtag #AAPA2014.

I’ll be presenting some work I began last summer (first blogged here), as part of a symposium in honor of Alan Mann. Mann was one of the first researchers to point out the similarities in dental development between humans and australopithecines, and his book Some Paleodemographic Aspects of the South African Australopithecines (1975) was an important resource in my dissertation research. In my current project, I try to identify traits in the lower jaw that follow a similar pattern of size growth as the rest of the body, to reconstruct growth in extinct species that are represented mostly by jaw fossils.

If you’re interested in what I’ve found, come and find me at my poster Saturday afternoon. If you can’t make it, here’s the poster I’ll be presenting:

AAPA 2014 Poster

AAPA 2014 Poster