Did GDF6 “gene tweak” allow humans to become upright?

The short answer is, “Not really.” But as is often the case, the real story behind so many headlines last week is a bit more complicated.

smh.

smh. Links to the first, second, third, and fourth stories.

What are they talking about, Willis?

These headlines, each saying something slightly different, are referring to a study by Indjeian and colleagues published in Cell.  Researchers identified a stretch of DNA that is highly conserved across mammals, or in other words, it is very similar between very different organisms. In humans, however, this conserved region is actually missing (“hCONDEL.306”):

Fig. 4A from Indjeian et al. 2016. A stretch of DNA, "hCONDEL.306" is completely missing in humans (as is another stretch, hCONDEL.305) but otherwise very similar between chimpanzees, monkeys and mice.

Fig. 4A from Indjeian et al. 2016. A stretch of DNA on Chromosome 8, “hCONDEL.306,” is very similar between chimpanzees, macaque monkeys, and mice, but is completely missing in humans (as is another stretch, hCONDEL.305).

That a stretch of DNA should be highly conserved across diverse animal groups suggests purifying natural selection has prevented any mutations from occurring here – alterations to this stretch of DNA negatively affected fitness. But that humans should be missing such a highly conserved region suggests that this deletion came under positive natural selection at some point in human evolution. This strategy, of seeking stretches of DNA that are similar between many animals but very different in humans, has led to the identification of hundreds of genetic underpinnings of human uniqueness. Some of these, such as the case in question, involve deleted sequences and have been termed “hCONDELs,” for “regions with high sequence conservation that are surprisingly deleted in humans” (McLean et al., 2011: 216). Others involve the accumulation of mutations where other animals show few or none (e.g., HACNS1; Prabhakar et al. 2008). In many (most?) cases these are “non-coding” sequences of DNA.

How can “non-coding” DNA help make humans upright?

As was predicted 30 years ago (King and Wilson, 1975), what makes humans different from other animals isn’t so much in the protein-coding DNA (the classical understanding of the term, “genes”), but rather in the control of these protein-coding genes. “Non-coding” means that a stretch of DNA may get transcribed into RNA but is not then translated into proteins. But even though these sequences themselves don’t become anything tangible, many are nevertheless critical in regulating gene expression – when, where and how much a gene gets used. It’s wild stuff. Indeed, “Many human accelerated regions are developmental [gene] enhancers” (Capra et al., 2013).

In the present case, hCONDEL.306 refers to the human-specific deletion of a developmental enhancer located near the GDF6 gene, which is a bone morphogenetic protein. The major finding of the paper, as stated succinctly in the Highlights title page, is that “Humans have lost a conserved regulatory element [hCONDEL.306] controlling GDF6 expression…. Mouse phenotypes suggest that [this] deletion is related to digit shortening in human feet.”

How do they link this “gene tweak” to digit shortening?

Since humans have lost this gene enhancer that is highly conserved in other mammals, Indjeian and team reasoned that the chimpanzee DNA sequence associated with this deletion, retaining the enhancer sequence, is likely the ancestral condition from which the human version evolved. They inserted the chimpanzee version into mouse embryos and watched what happened as they developed. The enhancer was only active in the mice’s back legs, specifically in the cartilage that would later become the lateral toe bones and cells that would become a muscle of the big toe (abductor hallucis). These are areas where humans and chimpanzees differ: our lateral toes are shorter than chimps’, and we only have one abductor hallucis muscle whereas chimpanzees have an additional, longer abductor hallucis  (Aiello and Dean, 2002). So, we’re on our way to seeing how hCONDEL.306 might relate to our big toe or upright walking, as the headlines say.

But this still doesn’t explain how this deletion affects GDF6 gene expression, and therefore what this does for our feet. Pressing onward, the scientists compared the size of certain bones in mice with a normal Gdf6 gene, and those in which the Gdf6 gene was completely turned off (or “knocked out”).  The Gdf6 knock-out mice had shorter lateral toe bones than regular mice, but they also had shorter big toes as well – the previous experiment staining mouse embryos showed the ancestral enhancer was expressed more in the latter toes, not so much the big toe.

Figures 5-6 from Indjeian et al. (2016) sum up the findings. Figure 5 (left) shows that the ancestral version of the GDF6 enhancer (blue staining) is most strongly expressed in the lower limb, especially the fifth toe bone. Figure 6 (right) shows that a lack of GDF6 expression (black bars) results in shorter skull and toe bones. Combining these findings, humans lack a gene enhancer associated with the development of long lateral toes.

Figures 5-6 from Indjeian et al. (2016) sum up the findings. Figure 5 (left) shows that the ancestral version of the GDF6 enhancer (blue staining) is most strongly expressed in the lower half of the body, especially the fifth toe bone. Figure 6 (right) shows that a lack of Gdf6 expression (black bars) results in shorter skull and toe bones. Combining these findings, humans lack a gene enhancer associated with the development of long lateral toes.

hCONDEL.306 doesn’t completely turn off GDF6, so this second experiment doesn’t really tell us exactly what the hCONDEL does. But the results are highly suggestive. Indjeian and team showed that Gdf6 affects toe length, among other skeletal traits, in mice. The ancestral enhancer that humans are missing seems to affect GDF6 activity in the leg/foot only. This illustrates a mechanism of modularity – as the authors state, “Loss of this enhancer would thus preserve normal GDF6 functions in the skull and forelimbs, while confining any … changes to the posterior digits of the hindlimb.” In other words, developmental enhancers allow different parts of the body to evolve independently despite being made by some of the same genes (such as GDF6).

As with any good study, results are intriguing but they raise more questions for future studies. The researchers conducted two experiments to investigate the function of hCONDEL.306: first putting the chimp version in mouse embryos to see where the ancestral enhancer is expressed, and then turning off Gdf6 completely in mice to see what happens. A more direct way to see what hCONDEL.306 does might be to put a longer stretch of the human sequence surrounding GDF6 containing (or rather missing) the ancestral enhancer into mouse embryos. I’m not a molecular biologist so maybe this isn’t possible. But this is important because the ancestral (chimpanzee) enhancer appeared to be most strongly expressed in the little toe, but of course this isn’t our only toe that is short compared to chimps. Similarly, how hCONDEL.306 relates to the abductor hallucis muscle remains in question – does it reduce the size of the intrinsic muscle present in both humans and chimps, or does it prevent development of the longer muscle that chimps have but we lack? We can expect to find hCONDEL.306 in the genomes of Neandertals (and Denisovans?), since they also have short toes, but what would it mean if they retained the ancestral enhancer?

So how does this gene tweak help with upright walking?

This is a really cool paper with important implications for human evolution, but something seems to have been lost in translation between the paper and the headlines (the news pieces themselves are good, though). The upshot of the study is that humans lack a stretch of non-coding DNA, which in chimpanzees (or chimp-ified mice) promotes embryonic development of the lateral toes and a big toe muscle. This may be a genetic basis for at least some aspects of our unique feet that have evolved under natural selection for walking on two legs.

But the headlines misrepresent this result, with words like “led to,” “allowed,” and “caused,” especially when these are followed by “big toe” or “upright walking.” hCONDEL.306 doesn’t really have anything to the big toe bone itself, although it might relate to a muscle affecting our big toe. The only sense in which the “Gene tweak led to humans’ big toe” (first title above) is that hCONDEL.306 might be responsible for our short lateral toes, which make our first toe look big by comparison. The other headlines are misleading since we know from fossil evidence that hominins walked upright long before we have evidence for short toes:

These little piggies get none. Fourth toe bones of living apes and humans (left) and possible hominins from 3-5 million years ago (right).

These little piggies get none. Fourth toe bones of living apes and humans (left) and (probable) hominins from 3-5 million years ago (right). I did my best to get all images to scale.

“Epigenetic,” from the fourth article headline, is simply wrong. Modern day epigenetics is a field concerned with the chemical alterations to the structure of DNA. Even the broad concept of epigenetic as originally devised by Conrad Waddington was about how environments (cellular or outside the body) influence development.

ResearchBlogging.orgIt’s hard to fit all the important and interesting information from scientific papers into news headlines. Still, it would be good if headlines more accurately portrayed scientific findings, especially avoiding such definitive verbs as “caused.” Especially in the realm of biology, people should know that there’s a lot that we still don’t know, that there’s lots more important work left to be done.

References

Aiello and Dean, 2002. Human Evolutionary Anatomy. Academic Press.

Capra et al., 2013. Many human accelerated regions are developmental enhancers. Philosophical Transactions of the Royal Society B 368: 20130025.

Indjeian et al. 2016. Evolving new skeletal traits by cis-regulatory changes in bone morphogenetic proteins. Cell http://dx.doi.org/10.1016/j.cell.2015.12.007

King and Wilson, 1975. Evolution at two levels in humans and chimpanzees. Science 188: 107-116 DOI: 10.1126/science.1090005

McLean et al., 2011. Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature 471: 216-219.

Prabhakar et al., 2008. Human-specific gain of function in a developmental enhancer. Science 321: 1346-1350.

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Results of the toe-tally easy lab activity

Alternate title: Dorsal canting in primate PPP4s

Earlier this year I suggested a classroom activity in which students can scrutinize the evidence used to argue that the >5 million year old (mya) Ardipithecus kadabba was bipedal. To recap: Ar. kadabba is represented by some teeth, a broken lower jaw, and some fragmentary postcrania. The main piece of evidence that it is a human ancestor and not just any old ape is from a single toe bone, and the orientation of its proximal joint. In Ar. kadabba and animals that hyperdorxiflex their toes (i.e., humans and other bipeds when walking), this joint faces upward, whereas it points backward or even downward in apes. This “dorsal canting” of the proximal toe joint has also been used as evidence that the 4.4 mya Ardipithecus ramidus and 3.5 mya owner of the mystery foot from Burtele are bipedal hominins. A question remains, though – does this anatomy really distinguish locomotor groups such as bipeds from quadrupeds?

Use ImageJ to measure the canting angle between the proximal joint and plantar surface. Proximal to the right, distal to the left.

STUDENT SCIENTISTS TO THE RESCUE! Use ImageJ to measure the canting angle between the proximal joint and plantar surface, as I’ve done on this Japanese macaque monkey (they are not bipedal). Proximal to the right, distal to the left Note I changed the measured angle from the March post.

I sicked my students in Ant 364 (Human Evolutionary Developmental Biology) here at NU on this task. I had students look at only 11 modern primates from the awesome KUPRI database. Most groups are only represented by 1 (Homo sapiens, Hylobates lar and Macaca fuscata) or two (Pongo species and Gorilla gorilla) specimens, all adults. For chimpanzees (Pan troglodytes) there is one infant and four adults. The database has more individuals, and it would be better to include more specimens to get better ideas of species’ ranges of variation, but this is a good training sample for a class assignment. The fossil group includes one Ardipithecus ramidus, one Ar. kadabba, one Australopithecus afarensis, and the PPP4 of the mystery foot from Burtele. The human and all fossils except Ar. kadabba are based off of lateral photographs and not CT scans like for the living primates, meaning there may be some error in their measurements, but we’ll assume for the assignment this is not a problem. Here are their results:

Dorsal canting angle of the fourth proximal pedal phalanx in primates.

Dorsal canting angle of the fourth proximal pedal phalanx in primates. The lower the angle, the more dorsally canted the proximal joint surface. The “Fossil” group includes specimens attributed to ArdipithecusAustralopithecus and something unknown.

Great apes have fairly high angles, meaning generally not dorsally canted proximal joint surfaces. The two gorillas fall right in the adult chimpanzee (adult) range of variation, while chimp infant and orangutans have much higher angles (≥90º means they’re actually angled downward or plantarly). The gibbon (Hylobates) is slightly lower than the chimpanzee range. The macaque has an even more dorsally canted joint, and the human even more so. The fossils, except the measurement for Ar. ramidus (see note above), have lower angles than living apes, but higher than the human and the monkey. If dorsal canting really is really a bony adaptation to forces experienced during life, then the fossil angles suggest these animals’ toes were dorsiflexed more so than living great apes (but not as much as the single monkey and human).

This lab helps students become familiar with CT data, the fossil record, taking measurements (students also measure maximum length of the toe bones and look at the relationship between length and canting), analyzing data, and hypothesis testing. You can also have fun exploring inter-observer error by comparing students’ measurements.

Here’s the full lab handout if you want to use or modify it for your own class: Lab 5-Toe instructions and report

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!

Friday excitement: Panoramic data inspection

I teach Tuesdays and Thursdays this year, leaving Fridays welcomely wide open for non-teaching related productivity. Today’s task is arguably the most exhilarating aspect of doing Science – inspecting raw data to make sure there are no major errors or problems in the dataset, so I can then analyze it and change the world. The excitement is truly hard to contain.

Delectable dog food is the dataset; I’m the dog.

No, it’s not the funnest, but it’s an important part of doing Science. To make your life easier, you should inspect data daily as you collect them. This way, you can identify mistakes and make notes about outliers early on, so that you are not stupefied and stalemated by what you see when you sit down to begin analysis.

You (corgi) are getting ready to analyze and you find an anomalous observation (door stop) you didn’t notice when you were collecting data.

Today I’m looking at measurements I took from ape mandibles housed in an English museum last summer; I inspected data before I left the UK for KZ, so today should be a breeze. But no matter how meticulous you are in the field/museum, you still need to inspect your data before analyzing them, just to be safe. If you’re as disorganized as I am, there will be lots of programs each with lots of windows. Here’s a tip: plug into multiple monitors (or at least one big ass monitor), so you can easily espy all open windows and programs in prodigious panorama.

Using two monitors helps when checking data for errors and patterns

Using two monitors helps when checking data for errors and patterns. On my left screen I’m using R to visualize and examine the raw data open in Excel on the right screen. If something seems off on the left screen, I can quickly consult the original spreadsheet on the right.

Barely visible in the above screenshot, these are chimpanzee (red) and gorilla (black) mandible measurements plotted against a measure of body size, preliminarily described in this post from last August. I’m looking at whether any mandibular measurements track body size across the subadult growth period, in hopes that bodily growth can be studied in fossil species samples dominated by kid jaws. As you can (barely) see, some jaw measurements correlate with body size better than others, and sometimes the apes follow similar patterns but other times they don’t.

The data look good, so now I can go on to examine relationships between mandible and body size in more detail. Stay tuned for results!

Mandible as a measure of overall body size?

I’m currently in Kent, United Kingdom, examining African ape jaws to follow up on my dissertation research comparing jaw growth in humans and Australopithecus robustus (having a tough time writing this stuff up for journal publication, but hopefully things’ll start coming out soon). One thing I’d assumed (with evidence, of course), was that aspects of mandibular size could serve as a proxy for body size, to make inferences about body growth. Now that I’m in Kent, I’m hoping to get good evidence of this in the non-human African apes.

The Powell Cotton Museum in Kent has an awesome collection of chimpanzees and gorillas (see the Human Origins Database by Adam Gordon and Bernard Wood for more information on these samples). This collection was accumulated during a time last century when explorers would go out and collect specimens from the wild, usually by finding and killing them. Now, when Major Percy Powell-Cotton was out doing this, he or some of his assistants actually collected measurements on some of the corpses – arm span, height, head+body length, and chest girth. This means we can see which aspects of the mandible correlate with body size, which is important since the fossil record usually affords us mandibles more than any other part of the skeleton.

Length of the back of the ramus to the P4, plotted against measures of body size.

Length of the back of the ramus to the P4, plotted against measures of body size. Colors/shapes represent 1 of 5 dental eruption age groups.

There aren’t body size measurements for all individuals, and I’ve been biasing my own sampling toward subadults. So I only have body size data for up to 15 of the 70+ gorillas I’ve been able to look at. From this meager sample, though, it looks like many aspects of mandible size may well end up correlating with aspects of body size. For instance, the distance from the back of the mandibular ramus to the front of the P4 is highly correlated with all 4 of Powell-Cotton’s bodily measures (right).

Will an expanded sample size uphold these high correlations? Will we see major differences between the sexes, or between different age groups? Will chimpanzees follow the same rules as gorillas? Hopefully I’ll be able to let you know by the time I’m done working in the museum!