Osteology Everywhere: Literally

Last weekend, Kazakhstan celebrated Constitution Day. Rather than stick around for the festivities in the florid Capital city, some friends and I ventured out West to Mangystau, to the deserts flanking the Caspian Sea. Although much of the area is sprawling, barren desert, it’s geologically much more interesting than my home here in the White Tomb.

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A perfect camping spot here on Mars.

The purpose of the trip was ostensibly holiday, but in landscapes such as this my field training kicks in. While I made sure to take in the scenic views, my gaze was mostly directed downward, as on survey, in search for bones, lithics and other signs of paleontological promise.

One thing about Life is that it teems. I don’t mean the obvious, ubiquitous microbes or infinitesimal infestations on all our faces. Even the big stuff can thrive, even in seemingly inhospitable places.

This little buddy wants nothing to do with everything.

This curmudgeon puts the ‘turd’ in ‘turtle.’

Some buddies on their way to work.

These buddies are on their way to an important meeting at the office.

But what goes up must come down, the only promise is The End. As a result of this shared fate, many of the landscapes we encountered were literally littered with the bony remnants previous denizens. Sun-scorched and bleached, the calling cards of Tetrapods stuck out like sore thumbs among the dirt and scrub.

Hip off the old block.

Hip off the old block.

A horse doing its best impression of SK 46.

A horse doing a good impression of SK 46.

Mangystau boasts an embarrassment of turtle bones and shells.

Mangystau boasts an embarrassment of turtle bones and shells.

A small, noble beast.

Alas, this was a noble little buddy.

I will admit I have no idea what animal this comes from, but I would guess some small mammal. If you know, please tell!

I will admit I have no idea what animal this comes from, but I would guess some small mammal. If you know, please tell me.

But this surface smorgasbord of bones will not translate into a future fossil festival. Sitting on the surface, bones like these are likely to be scattered, trampled, disturbed by anthropology nerds. Most will not get the chance to sink into the Earth, soak up leaching minerals, and lie in wait for paleontologists of the future. In desert landscapes such as in Mangystau, ‘osteology everywhere’ is an ephemeral description.

A picture is worth a thousand datapoints in #rstats

I’m finally about to push my study of brain growth in H. erectus out of the gate, and one of the finishing touches was to make pretty pretty pictures. Recall from the last post on the subject that I was resampling pairs of specimens to compute how much proportional brain size change (PSC) occurred from birth a given age in humans and chimpanzees (and now gorillas). This resulted in lots of data points, which can be a bit difficult to read and interpret when plotted. Ah, cross-sectional data. “HOW?!” I asked, “HOW CAN I MAKE THIS MORE DIGESTIBLE?” Having nice and clean plots is useful regardless of what you study, so here I’ll outline some solutions to this problem. (If you want to figure this out for yourself, here are the raw resampled data. Save it as a .csv file and load it into R)

All

Ratios of proportional size change from birth to a later age. Black/gray=humans, green=chimpanzees, red=gorillas. Left are all 2000 resampled ratios, center shows the medians (solid lines) and 95% quantiles of the ratios for each species at a given age (the small gorilla sample is still data points), and right are the loess regression lines and (shaded) 95% confidence intervals. Blue lines across all three plots are the H. erectus median (solid) and 95% quantiles (dashed).

The left-most plot above shows the raw resampled ratios: you can see a lot of overlap between humans (black), chimpanzees (green) and gorillas (red). But all those points are a bit confusing: just how extensive is the overlap? What is the central tendency of each species?

The second plot shows a less noisy way of displaying the results. We can highlight the central tendencies by plotting PSC medians for each age (I used medians and not means since the data are not normally distributed), and rather than showing the full range of variation in PSC at each age, we can simply highlight the majority (95%) of the values.

To make such a plot in R, for each species you need four pieces of information, in vector form: 1) the unique (non-repeated) ages sorted from smallest to largest, and the 2) median, 3) upper 97.5% quantile, and 4) lower 0.025% quantile for each unique age. You can quickly and easily create these vectors using R‘s built-in commands:

R codes to create the vectors of points to be plotted in the second graph. Note that vectors are not created for gorillas because the sample size is too small, or for H. erectus because the distribution is basically the same across all ages.

R codes to create the vectors of points to be plotted in the second graph. Note that vectors are not created for gorillas because the sample size is too small, or for H. erectus because the distribution is basically the same across all ages.

With these simple vectors summarizing humans and chimpanzees variation across ages, you’re ready to plot. The medians (hpm and ppm in the code above) can simply be plotted against age using the plot() and lines() functions, simple enough. But the shaded-in 95% quantiles have to be made using the polygon() function, which creates a shape (a polygon) by connecting sets of points that have to be entered confusingly: two sets of x-coordinates with the first in normal order and the second reversed, and two sets of y-coordinates with the first in normal order and the second reversed.

Plot yourself down and have a beer.

Plot yourself down and have a beer.

In our case, the first set of x coordinates is the vector of sorted, unique ages (h and p in the code), and the second set is the same vector but in reverse. The first set of y coordinates is the vector of 97.5% quantiles (hpu and ppu), and the second set is the vector of 0.025% quantiles in reverse. You can play around with ranges of colors and transparency with “col=….”

What I like about the second plot is that it clearly summarizes the ranges of variation for humans and chimps, and highlights which parts of the ranges overlap: the human and ape medians are comparable at the youngest ages, but by 6 months the human median is pretty much always above the chimpanzee upper range. The gorilla points are generally close to the chimpanzee median until around 2 years after which gorilla size increase basically stops but chimpanzees continue. Importantly, we can also see at what ages the simulated H. erectus values are most similar to the empirical species values, and when they fall out of species’ ranges. As I pointed out a bajillion years ago, the H. erectus values (based on the Mojokerto juvenile fossil) encompass most living species’ values around six months to two years.

I also like that second plot does all the above, and still honestly shows the jagged messiness that comes with cross-sectional, resampled data. Of course no individual’s proportional brain size increases and decreases so haphazardly during growth as depicted in the plot. It’s ugly but it’s honest. But if you like lying to yourself about the nature of your data, if you prefer curvy, smoothed inference to harsh, gritty reality, you can resort to the third plot above: the loess regression lines calculated from the resampled data.

Loess and lowess (not to be confused with loess) refer to locally weighted regression scatterplot smoothing, a way to model gross data like we have, but with a nice and smooth (but not straight) line. Because R is awesome, it has a loess() function built right in. The function easily does the math, and you can quickly obtain confidence intervals for the modelled line, but plotting these is another story. After scouring the internet, coding and failing (repeatedly) I finally came up with this:

Screen Shot 2014-07-26 at 6.57.01 PM

Creating vectors of points makes your lines clean and smooth.

If you simply try to plot a loess() line based on 1000s of unordered points, you’ll get a harrowing spider’s web of lines between all the points. Instead, you need to create ordered vectors of the non-repeated modelled points (hlm, plm, glm, above) and their upper and lower confidence limits. Once modelled, you can simply plot the lines and create polygons based on the confidence intervals as above.

The best way to learn to do stuff in R is to just play around with data and code until you figure out how to do whatever it is you have in mind. If you want to recreate, or alter, what I’ve described here, you can download the resampled data (link at the beginning of the post) and R code. Good luck!

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.