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

 

Ima Gona follow up on that last post

Last week, I discussed the implications of the Gona hominin pelvis for body size and body size variation in Homo erectus. One of the bajillion things I have been working on since this post is elaborating on this analysis to write up, so stay tuned for more developments!

Now, when we compared the gross size of the hip joint between fossil Homo and living apes (based on the femur head in most specimens but the acetabulum in Gona and a few other fossils), the range of variation in Homo-including-Gona was generally elevated above variation seen in all living great apes. This is impressive, since orangutans and gorillas show a great range of variation due sexual dimorphism (normal differences between females and males). However, I noted that the specimens I used were unsexed, and so the resampling strategy used to quantify variation within a species – randomly selecting two specimens and taking the ratio of the larger to smaller – probably underestimated sexual dimorphism.

Shortly after I posted this, Dr. Herman Pontzer twitterated me to point out he has made lots of skeletal data freely available on his website (a tremendous resource). The ape and human data I used for last week’s post did not have sexes (my colleague has since sent me that information), but Pontzer’s data are sexed (no, not “sext“). So, I modified and reran the original resampling analysis using the Pontzer data, and it nicely illustrates the difference between using a max/min vs. male/female ratio to compare variation:

Hip joint size variation in living African apes (left and right) compared with fossil humans (genus Homo older than 1 mya, center). Each plot is scaled to show the same y-axis range. On the left are ratios of max/min from resampled pairs from each species (sex not taken into account). On the right are ratios of male/female from resampled pairs from each species. The red dots on this plot are the medians for max/min ratios (the thick black bars in the left plot). The center plot shows ratios of Homo/Gona.

Hip joint size variation in living African apes (left and right) compared with fossil humans (genus Homo older than 1 mya, center). Each plot is scaled to show the same y-axis range. On the left are ratios of max/min from resampled pairs from each species (sex not taken into account). On the right are ratios of male/female from resampled pairs from each species. The red stars on this plot are the medians for max/min ratios (the thick black bars in the left plot). The center plot shows ratios of Homo/Gona.

The left plot shows resampled ratios of max/min in humans, chimpanzees and gorillas, while the right shows ratios of male/female in these species. If no assumption is made about a specimen’s sex (left plot), it is possible to resample a pair of the same sex, and so it is likelier to sample two individuals similar in size. Note that the ratio of max/min can never be less than 1. However, if sex is taken into account (right plot), we see two key differences. First, because of size overlap between males and females in humans and chimpanzees, ratios can fall below 1. Adult gorilla males are much larger than females, and so the ratio is never as low as 1 (minimum=1.08). Second, in more dimorphic species, the male/female ratio is elevated above the max/min ratio (red stars in the right plot). In chimpanzees, the median male/female ratio is actually just barely lower than the median max/min ratio. If you want numbers: the median max/min ratios for humans, chimpanzees and gorillas are 1.09, 1.06 and 1.16, respectively. The corresponding median male/female ratios are 1.15, 1.06 and 1.25.

Regarding the fossils, if we assume that Gona is female and all other ≥1 mya Homo hips are male, the range of hip size variation can be found within the gorilla range, and less often in the human range.

But the story doesn’t end here. One thing I’ve considered for the full analysis (and as Pontzer also pointed out on Twitter) is that the relationship between hip joint size and body weight is not the same between humans and apes. As bipeds, we humans place all our upper body weight on our hips; apes aren’t bipedal and so relatively less of their weight is transmitted through this joint. As a result, human hip joint size increases faster with increasing body mass than it does in apes.

So for next installment in this fossil saga, I’ll consider body mass variation estimated from hip joint size. Based on known hip-body size relationships in humans vs. apes, we can predict that male/female variation in humans and fossil hominins will be relatively higher than the ratios presented here – will this put fossil Homo-includng-Gona outside the gorilla range of variation? Stay tuned to find out!

Gona … Gona … not Gona work here anymore more

The Gona pelvic remains (A-D), and the reconstructed complete pelvis (E-J), Fig. 2 in Simpson et al., 2008.

A few years ago, Scott Simpson and colleagues published some of the most complete fossil human hips (right). The fossils are from the Busidima geological formation in the Gona region of Ethiopia, dated to between 0.9-1.4 million years ago. (Back when I wasn’t the only author of this blog, my friend and colleague Caroline VanSickle wrote about it here)

Researchers attributed the pelvis to Homo erectus on the basis of its late geological age and a number of derived (Homo-like) features. In addition, the pelvis’s very small size indicated it probably belonged to a female. One implication of this fossil was that male and female H. erectus differed drastically in body size.

Christopher Ruff (2010) took issue with how small this specimen was, noting that its overall size is more similar to the small-bodied Australopithecus species. Using the size of the hip joint as a proxy for body mass, Ruff argued Gona’s small size would imply a profound amount of sexual dimorphism in H. erectus: much higher than if Gona is excluded from this species, and higher than in modern humans or other fossil humans. Ruff thus proposed an alternative hypothesis to marked sexual dimorphism, that the Gona pelvis may have belonged to an australopithecine.

Fig. 3 From Ruff's (2010) reply. Australopiths (and Orrorin) are squares and Homo are circles. Busidima's estimated femur head diameter is represented by the star and bar.

Fig. 3 From Ruff’s (2010) reply. Australopiths (and Orrorin) are squares and Homo are circles. Gona’s estimated femur head diameter is represented by the star and bar.

Now, Simpson & team replied to Ruff’s comments, providing a laundry list of reasons why this pelvis is H. erectus and not Australopithecus. They cite many anatomical features of the pelvis shared with Gona and Homo fossils, but not australopithecines. They also note that there are many other bones reflective of body size, that seem to suggest a substantial amount of size variation in Homo fossils, even those from a single site such as Dmanisi (Lordkipanadze et al., 2007).

Interestingly, neither of these parties compared the implied size variation with that of living apes. So I’ll do it! Now, I do not have any acetabulum data, but a friend lent me some femur head measurements for living great apes a few years ago. Gona is a pelvis and not a femur, but there are more fossil femora than hips. Because there’s a very high correlation between femur head and acetabulum size, Ruff estimated Gona’s femur head diameter to be 32.6 mm (95% confidence interval: 30.1-35.2; Simpson et al. initially estimated 35.1 mm based on a different dataset and method). To quantify size variation, we can compare ratios of larger femur heads divided by smaller ones. Now, this ratio quantifies inter-individual variation, but it will underestimate sexual dimorphism since I’m likely sampling some same-sex pairs that aren’t so different in size. But this is just a quick and dirty look. So, here’s a box plot of these ratios for Homo fossils, larger specimens divided by Gona’s estimated femur head size in different time periods:

Ratio of a fossil Homo femur head diameter (HD) divided by Busidima's HD. E Homo = early Pleistocene, Contemporaneous = WT 15000 and OH 28, MP = Middle Pleistocene Homo. White boxes are based on Ruff's Busidima HD estimate, green boxes are based on Simpson et al.'s estimate.

Ratios of fossil Homo femur head diameter (HD) divided by Busidima’s (Gona’s) HD. E Homo = early Pleistocene, Contemporaneous = WT 15000 and OH 28, MP = Middle Pleistocene Homo. White boxes are based on Ruff’s Gona HD estimate, green boxes are based on Simpson et al.’s larger estimate. Boxes include 50% quartiles and the thick lines within are sample medians.

Clearly, Gona is much smaller than most other fossil Homo hips, since ratios are never smaller than 1.14. Average body size increases over time in the Homo lineage, reflected in increasing ratios from left to right on the plot. Early Pleistocene Homo fossils are fairly small, including Dmanisi, hence the lower ratios than later time periods. Middle Pleistocene Homo (MP), represented by the most fossils, shows a large range of variation, but even the smallest is still 1.17 times larger than the largest estimate of Gona’s femur head size. To put this into context, here are those green ratios (assuming a larger size for Gona) compared with large/small ratios from resampled pairs of living apes and humans:

*

The fossil ratios of larger/smaller HD from above, compared with resampled ratios from unsexed living apes and humans. Boxes include the 50% quartiles, and the thick lines within are sample medians. **(05/03/14: This plot has been modified from the original version post, which only included the fossil ratios based on the smaller Gona estimate)

What we see for the extant apes and humans makes sense: humans and chimpanzees show smaller differences on average, whereas average differences between gorillas and orangutans are larger. This accords with patterns of sexual dimorphism in these species. **What this larger box plot shows is that if we accept Ruff’s smaller average estimate of Gona’s femur head size (white boxes), it is relatively rare to sample two living specimens so different in size as seen between Gona and other fossils. If we use Simpson et al.’s larger Gona size estimate, variation is still elevated above most living ape ratios. Only when Gona is compared with the generally-smaller, earlier Pleistocene fossils, does the estimated range of variation show decent overlap with living species. Even then, the overlap is still above the median values.

These results based on living species agree with Ruff’s concern, that including Gona in Homo erectus results in an unusually large range of variation in this species. Such a large size range isn’t necessarily impossible, but it would be surprising to see more variation than is common in gorillas and orangutans, where sexual size dimorphism is tremendous. Ruff suggested that the australopith-sized Gona pelvis may in fact be an australopith. This was initially deemed unlikely, in part because the fossil is well-dated to relatively late, 0.9-1.4 million years ago. However, Dominguez-Rodgrigo and colleauges (2013) recently reported a 1.34 mya Australopithecus boisei skeleton from Olduvai Gorge, so it is possible that australopiths persisted longer than we’ve got fossil evidence for, and Gona is one of the latest holdouts.

So many possible explanations. More clarity may come with further study of the fossils at hand, but chances are we won’t be able to eliminate any of these possibilities until we get more fossils. (also, the post title wasn’t a jab at the fossils or researchers, but rather a reference to the movie Office Space)

References

Dominguez-Rodrigo et al. 2013. First partial skeleton of a 1.33-million-year-old Paranthropus boisei from Bed II, Olduvai Gorge, Tanzania. PLoS One 8: e80347.

Ruff C. 2010. Body size and body shape in early hominins – implications of the Gona pelvis. Journal of Human Evolution 58: 166-178.

Simpson S et al. 2008. A female Homo erectus pelvis from Gona, Ethiopia. Science 322: 1089-1092.

Simpson S et al. In press. The female Homo pelvis from Gona: Response to Ruff (2010). Journal of Human Evolution. http://dx.doi.org/10.1016/j.jhevol.2013.12.004

Toe-tally easy virtual lab activity: Ardipithecus kadabba

The focus of my human evolution class the past few weeks has been uncovering the earliest human ancestors. The main adaptation distinguishing our first forebears from other animals is walking on two legs (“bipedalism”), so researchers try to identify features reflective of bipedalism in fossils over 4 million years ago. But this isn’t so easy – not all fossils will tell us how an animal walked around, and even with the right bones, it’s not always clear what the earliest bipeds “should” look like. Take the case of Ardipithecus kadabba: there are a handful of seemingly nondescript fossils (below) from a number of Ethiopian sites dating 5.2-5.8 million years ago. Can we really tell if this species was bipedal? LET YOUR STUDENTS DO SCIENCE TO DECIDE FOR THEMSELVES!

Can you spot a biped? Ardipithecus kadabba fossils (Fig. 1 from Haile-Selassie, 2001).

Can you spot a biped? Ardipithecus kadabba fossils. Scale bar is 1 cm (Fig. 1 from Haile-Selassie, 2001).

In the jumble of fragments pictured above, the key bone possibly revealing a bipedal animal is in square b, a toe bone shown in several views. This is a fourth proximal pedal phalanx (PPP4), where a wedding ring would sit if people put rings on their feet instead of their hands. Ew. Anyway, here’s closer view, from the Ar. kadabba monograph (Haile-Selassie and WoldeGabriel, 2009):

AME-VP 1/71, the sciencey name of the toe bone in question. The proximal end, toward the foot, is to the left and the distal end, toe-tipward, is to the right. Modified from plates 7.8 and 7.21 in the monograph.

Top: AME-VP 1/71, the sciencey name of the toe bone in question. The proximal end (toward the foot) is to the left and the distal end (toward the tip of the toe), is to the right. Bottom: Lookit how tiny it is! Modified from plates 7.8 and 7.21 in the monograph.

Although absolutely small, the kadabba PPP4 is relatively long, narrow and curved, like an ape’s and unlike a human’s. Haile-Selassie and colleagues (monograph chapter) compared this fossil with chimpanzee and the bipedal Australopithecus afarensis‘s PPP4s (below I have scaled them to the same length). As you can see, kadabba and the chimp are fairly narrow compared to the stout afarensis toe, although they are all curved:

Comparison of 4th proximal pedal phalanges, scaled to same length. Left to right, and top to bottom: Chimp, Ar. kadabba and Au. afarensis. Modified from plates 7.24-7.25 in the kadabba monograph)

Comparison of PPP4s, scaled to same length. Left to right, and top to bottom: Chimp, Ar. kadabba and Au. afarensis. The left box is a bottom view (proximal at the bottom) and the right box from the side (proximal to the left). Modified from plates 7.24-7.25 in the kadabba monograph.

These gross shape comparisons don’t make kadabba‘s toe look that like of a bipedal animal. However, one thing we can’t see in these views – and that you can have your students examine in virtual lab – is the orientation of the proximal joint surface. In humans (Griffin and Richmond, 2010) and the later Ardipithecus ramidus and australopithecines (Latimer and Lovejoy 1990; Lovejoy et al., 2009; Haile-Selassie et al., 2012), this joint surface angles upward, a result of the great force this joint experiences as it hyper-dorsiflexes during walking. Apes and other animals are not bipedal, and they do not dorsiflex their toes to the degree that we do, so this joint does not usually angle upward as much.

Schematic of a hyper-dorseflexed proximal toe joint (indicated by red star).

Schematic of a hyper-dorseflexed proximal toe joint (indicated by red star).

Now here’s that joint in the kadabba PPP4. The kadabba monograph has a nice midsagittal CT scan revealing this joint’s orientation, the angle of which I have measured using the free image analysis software ImageJkadabba‘s angle of ‘dorsal canting’ is 102.2 degrees. A mild fever.

Measuring the dorsal canting of the AME-VP-1/71 proximal joint surface, using ImageJ.

Measuring the dorsal canting (the angle theta) of the AME-VP-1/71 proximal joint surface, using ImageJ.

This measurement is at the low end of the human range (averaging around 110 degrees for the 2nd, not 4th, digit), and above all but just a few apes analyzed by Griffin and Richmond (2010). Now, these authors looked at PPP2s, but PPP4s would be more appropriate for comparison with kadabba. LUCKY YOU - your students can collect these data, using CT scans from the KUPRI digital morphology museum. This collection has dozens of apes and monkeys (and even some other mammals), presumably none of which were habitually bipedal, and which should have relatively low angles of canting. (many of these specimens are from zoos, however, so their activity patterns and anatomies may not be the same as wild animals’; lookit the gorilla below) Your students can isolate and section proximal pedal phalanges as I have below, and measure the angle of canting with ImageJ. SCIENCE!

Easy image acquisition on the KUPRI database (this is a gorilla, with a pretty messed up fourth digit). Have your students save the sectioned image as above, which can then be analyzed as illustrated in the previous figure.

Easy image acquisition on the KUPRI database (this is a gorilla, with a pretty messed up fourth digit beyond the distal PPP). Have your students save the sectioned image as above, then measure the angle theta.

This activity is simple way for your students to set up a hypothesis, collect quality data and analyze them – essentially for free!

Some light weekend reading

Griffin and Richmond (2010). Joint orientation and function in great ape and human proximal pedal phalanges. American Journal of Physical Anthropology 141: 116-123.

Haile-Selassie (2001). Late Miocene hominids from the Middle Awash, Ethiopia. Nature 412: 178-181.

Haile-Selassie and WoldeGabriel, eds. (2009) Ardipithecus kadabba: Late Miocene Evidence from the Middle Awash, Ethiopia. Chapter 7.

Haile-Selassie et al. (2012). A new hominin foot from Ethiopia shows multiple Pliocene bipedal adaptations. Nature 483: 565-570.

Latimer and Lovejoy (1990). Metatarsophalangeal joints of Australopithecus afarensisAmerican Journal of Physical Anthropology 83: 13-23.

Lovejoy et al. (2009). Combining prehension and propulsion: The foot of Ardipithecus ramidusScience 326: 72e1-72e8