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!

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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

The small, big new Dmanisi skull

The 5th skull early Homo skull from the site of Dmanisi was announced last week. The skull was discovered nearly 10 years ago, but is finally (and very comprehensively) published in Science (Lordkipanidze et al. 2013). The ‘new’ D4500 cranium goes with the massive D2600 mandible, making this the earliest and most complete skull of Homo that I know of. It’s really a remarkable specimen, for a number of reasons beyond its age and completeness. I’ve been busy traveling, teaching and writing lately, so I haven’t yet gotten to pore over the details as much as I’d like. So I hope to sporadically post thoughts on this badass new skull as they come to me. In the mean time, several of what I’d consider the top biology/anthropology blogs*** have discussed the skull, so do check those out if you haven’t already.

The first thing I noted about D4500 is its small brain size, estimated at a mere 546 cubic centimeters. For perspective, D4500 is the green point in the following plot showing brain size in early human evolution:

Endocranial volume for various fossil hominin fossils. 1: Australopithecus afarensis, africanus & boisei; 2: Dmanisi specimens; 3: "habilines" 4: early African Homo erectus; 5: Indonesian and Chinese Homo erectus

Endocranial volume for various fossil hominin fossils. 1: Australopithecus afarensis, africanus & boisei; 2: Dmanisi specimens; 3: “habilines” 4: early African Homo erectus; 5: Indonesian and Chinese Homo erectus. D4500 is green with envy.

I got to see (but not study) the cranium a few years ago when I was helping with the Dmanisi Paleoanthropology field school, and I remember noting just how “robust” the specimen was – big mastoid processes, prominent and thick brow ridge, huge attachments for the neck muscles. In humans, and presumably our fossil forebears, these features are more developed in males than females, and so presumably D4500 was a male (consistent with the huge, associated D2600 mandible). In many primates, and 4 to ~1 mya hominins so far as we can tell, males are larger than females. So it is surprising that a robust probable male cranium is in fact not only the smallest in the Dmanisi sample, but also at the low end of early African Homo (i.e. habilis or rudolfensis), comparable to the largest australopiths. Of course, the only other faces known from Dmanisi are either not fully grown (D2700 and D2282) or old and decrepit (D3444), so perhaps the larger-brained specimens would have been at least as robust as D4500. An untestable hypothesis!

The new skull really highlights the overlap, or continuous variation between later australopiths and early Homo known also from eastern Africa. In association with the postcranial remains known from Dmanisi, the authors the paper posit that early Homo may have been distinguished from Australopithecus not so much in brain size as in body size. We could probably add body shape (limb proportions) and tool use to that list of distinguishing features, and to be sure there are Oldowan tools and small but human-like body size and shape indicated by postcrania at Dmanisi. But then, evidence for body proportions and for/against tool use in Australopithecus, especially later in the record, is somewhat equivocal…

More thoughts to follow.

*** https://blogs.wellesley.edu/vanarsdale/2013/10/17/uncategorized/the-new-wonderful-dmanisi-skull/; http://johnhawks.net/weblog/fossils/lower/dmanisi/d4500-lordkipanidze-2013.html; http://ecodevoevo.blogspot.com/2013/10/how-many-human-species-are-there-is-it.html

Reference: David Lordkipanidze, Marcia S. Ponce de León, Ann Margvelashvili, Yoel Rak, G. Philip Rightmire, Abesalom Vekua, and Christoph P. E. Zollikofer. 2013. A Complete Skull from Dmanisi, Georgia, and the Evolutionary Biology of Early Homo. Science: 342 (6156), 326-331.

Update: Brain growth in Homo erectus, and the age of the Mojokerto fossil

The Mojokerto calvaria. You’re looking at the left side of the
 skull: the face would be to the left. Check it out in 3D here.

A few months ago I posted an abridged version of the presentation I gave at this year’s meetings of the American Association of Physical Anthropologists, about brain growth in Homo erectus. This study, co-authored with Jeremy DeSilva, adopts a novel approach (see “Methods” in that earlier post) to analyze the Mojokerto fossil (right). The specimen is the only H. erectus non-adult complete enough to get a decent estimate of brain size (or rather, the overall volume of the brain case) – probably 630 to 660 cubic centimeters (Coqueugniot et al. 2004; Balzeau et al., 2004). So to study brain growth in the extinct species, we just have to connect a range of estimated brain sizes at birth (around 290 cubic centimeters, based on predictive equations by DeSilva and Lesnik, 2008) to that of Mojokerto. But, the speed of brain growth implied by this comparison depends on how old poor Mojokerto was when s/he died.

Most recently, Hélen Coqueugniot and colleagues (2004) used CT scans of the fossil to examine the fusion of its various bones, to suggest the poor kid died between six months to 1.5 years, if not even younger. Antoine Balzeau and team (2005) also studied scans of the fossil, and their analysis of its virtual endocast presented conflicting age estimates, but they argued the poor kid was probably no older than 4 years. Earlier studies had suggested the kid was up to 8 years. Now, for my previous post/conference presentation, we assumed the Coqueugniot estimate was correct – but what if we consider a full range of ages for Mojokerto, from 0.03-6.00 years?

Brain size, relative to newborns’ values, at different ages in humans (black circles) and chimpanzees (red triangles). Homo erectus median and mean are the thick solid and dashed blue lines, respectively, and the 90% and 95% confidence intervals are indicated by the thinner, dotted blue lines. Data are the same as in the previous post.

The plot above depicts brain size relative to newborns: each circle (humans) and triangle (chimpanzees) represents the proportional size difference between a newborn (less than 1 week) and an older individual, up to 6 years. Obviously, relative brain size gets bigger in humans and chimpanzees over time. Interestingly, even though humans and chimps have very different brain sizes, the proportional brain size changes overlap a lot between species, especially at younger ages. Ah, the joys of cross-sectional samples.

But what’s especially interesting here are the blue lines on the graph, indicating estimates of proportional size change in Homo erectus, assuming Mojokerto’s skull could hold 630 cc of delicious brain matter, and that the species’ skulls at birth could hold about 290 cc, give or take several cc. The thick solid and dashed lines just above 2 on the y-axis are the mean and median of our estimates – Mojokerto’s brain averages around 2.2 times larger than predicted newborns. Such a proportion is most likely to be found in humans between 6 months to a year of age, and in chimpanzees between around 6 months and 2 years. The confidence intervals, the highest and lowest bounds of our estimates for Homo erectus proportional size change, are the thinner dashed lines on the graph. They help us constrain our estimates, and further suggest that the proportional difference found for H. erectus is most likely to be found in either chimpanzees or humans around 1 year of age – just like Coqueugniot and colleagues predicted!!!

Thus, independent evidence – brain size of Mojokerto and estimated brain size at birth in Homo erectus – corroborates a previously estimated age at death for the Mojokerto fossil, the poor little Homo erectus baby. This further supports our estimates of brain growth rates in this species, as described in the previous post.

ResearchBlogging.orgSo to summarize, fairly scant fossil evidence compared with larger extant species samples using randomization statistics, argue for high, human-like infant brain growth rates in Homo erectus by around 1 million years ago. Our ancestors were badasses.

Remember, if you want the R code I wrote to do this study, just lemme know!

Those references
Balzeau A, Grimaud-Hervé D, & Jacob T (2005). Internal cranial features of the Mojokerto child fossil (East Java, Indonesia). Journal of human evolution, 48 (6), 535-53 PMID: 15927659

Coqueugniot H, Hublin JJ, Veillon F, Houët F, & Jacob T (2004). Early brain growth in Homo erectus and implications for cognitive ability. Nature, 431 (7006), 299-302 PMID: 15372030

DeSilva JM, & Lesnik JJ (2008). Brain size at birth throughout human evolution: a new method for estimating neonatal brain size in hominins. Journal of human evolution, 55 (6), 1064-74 PMID: 18789811

Pre-publication: Brain growth in Homo erectus (plus free code!)

The annual meetings of the American Association of Physical Anthropologists were going on all last week, and I gave my first talk before the Association (co-authored with Jeremy DeSilva). The talk focused on using resampling methods and the abysmal human fossil record to assess whether human-like brain size growth rates were present in our >1 mya ancestor Homo erectus. This is something I’ve actually been sitting on for a while, and wanted to wait til after the talk to post for all to see. I haven’t written this up yet for publication, but before then I’d like to briefly share the results here.

Background: Humans’ large brains are critical for giving us our unique capabilities such as language and culture. We achieve these large (both absolutely, and relative to our body size) brains by having really high brain growth rates across several years; most notable are exceptionally high, “fetal-like” rates during the first 1-2 years of life. Thus, rapid brain growth shortly after birth is a key aspect of human uniqueness – but how ancient is this strategy?

Materials: We can plot brain size at birth in humans and chimpanzees (our closest living relatives) to visualize what makes humans stand out (Figure 1).

Figure 1. Brain size (volume) at given ages. Humans=black, chimpanzees=red. Ranges of brain size at birth, and the chronological age of the Mojokerto fossil, in blue.

Human data come from Cogueugniot and Hublin (2012), and chimpanzees from Herndon et al. (1999) and Neubauer et al. (2012). The earliest fossil evidence able to address this question comes from Homo erectus. Because of the tight relationship between newborn and adult brain size (DeSilva and Lesnik 2008), we can use adult Homo erectus brain volumes (n=10, mean = 916.5 cm^3) to predict that of the species’ newborns: mean = 288.9 cm^3, sd = 17.1). An almost-recent analysis of the Mojokerto Homo erectus infant calvaria suggests a size of 663 cm^3 and an age of 0.5-1.25 years (Coqueugniot et al. 2004; this study actually suggests an oldest age of 1.5 years, but the chimpanzee sample here requires us to limit the study to no more than 1.25 years). Because we have a H. erectus fossil less than 2 years of age, and we can estimate brain size at birth, we can indirectly assess early brain growth in this species.

Methods: Resampling statistics allow inferences about brain growth rates in this extinct species, incorporating the uncertainty in both brain size at birth, and in the chronological age of the Mojokerto fossil. We thus ask of each species, what growth rates are necessary to grow one of the newborn brain sizes to any infant between 0.5-1.25 years? And from there, we compare these resampled growth rates (or rather, ‘pseudo-velocities’) between species – is H. erectus more similar to modern humans or chimpanzees? There are 294 unique newborn-infant comparisons for humans and 240 for the chimpanzee sample. We therefore compare these empirical newborn-infant pairs from extant species to 7500 resampled H. erectus pairs, randomly selecting a newborn H. erectus size based on the parameters above, and randomly selecting an age from 0.5-1.25 years for the Mojokerto specimen. This procedure is used to compare both absolute size change (the difference between an infant and a newborn size, in cm^3/year), and and proportional size change (infant/newborn size).

Results: Humans’ high early brain growth rates after birth are reflected in the ‘pseudovelocity curve’ (Figure 2). Chimps have a similar pattern of faster rates earlier on, but these are ultimately lower than humans’. Using the Mojokerto infant’s brain size (and it’s probable ages) and the likely range of H. erectus neonatal brain sizes (mean = 288, sd = 17), it is fairly clear that H. erectus achieved its infant brain size with high, human-like rates in brain volume increase.

Figure 2. Brain size growth rates (‘pseudo-velocity’) at given ages. Humans=black, chimpanzees=red, and Homo erectus,=blue.

However, if we look at proportional size change, the factor by which brain size increases from birth to a given age, we see a great deal of overlap both between age groups within a species, and between different species. Cross-sectional data create a great deal of overlap in implied proportional size change between ages within a species; it is easier to consider proportional size change between taxa, conflating ages, then  (Figure 3). Humans show a massive amount of variation in potential growth rates from birth to 0.5-1.25 years, and chimpanzees also show a great deal of variation, albeit generally lower than in the human sample. Relative growth rates in Homo erectus are intermediate between the two extant species.

Figure 3. Proportional brain size increase (infant/newborn size). 

Significance: Brain size growth shortly after birth is critical for humans’ adaptative strategy: growing a large brain requires a lot of energy and parental (especially maternal) investment (Leigh 2004). Plus, in humans this rapid increase may correspond with the creation of innumerable white-matter connections between regions of the brain (Sakai et al. 2012), important for cognition or intelligence. The H. erectus fossil record (1 infant and 10 adults) provides a limited view into this developmental period. However, comparative data on extant animals (e.g. brain sizes from birth to adulthood), coupled with resampling statistics, allow inferences to be made about brain growth rates in H. erectus over 1 million years ago.

Assuming the Mojokerto H. erectus infant is accurately aged (Coqueugniot et al. 2004), and that Homo erectus followed the same neonatal-adult scaling relationship as other apes and monkeys (DeSilva and Lesnik 2008), it is likely that H. erectus had human-like rates of absolute brain size growth. Thus, the energetic and parental requirements to raise such brainy babies, seen in modern humans, may have been present in Homo erectus some 1.5 million years ago or so. This may also imply rapid white-matter proliferation (i.e. neural connections) in this species, suggesting an intellectually (i.e. socially or linguistically) stimulating infancy and childhood in this species. At the same time, relative brain size growth appears to scale with overall brain size: larger brains require proportionally higher growth rates. This is in line with studies suggesting that in many ways, the human brain is a scaled-up version of other primates’ (e.g. Herculano-Houzel 2012).

ResearchBlogging.org
This study was made possible with published data, and the free statistical programming language R.

Contact me if you want the R code used for this analysis, I’m glad to share it!!!

References
Coqueugniot H, Hublin JJ, Veillon F, Houët F, & Jacob T (2004). Early brain growth in Homo erectus and implications for cognitive ability. Nature, 431 (7006), 299-302 PMID: 15372030

Coqueugniot H, & Hublin JJ (2012). Age-related changes of digital endocranial volume during human ontogeny: results from an osteological reference collection. American journal of physical anthropology, 147 (2), 312-8 PMID: 22190338

DeSilva JM, & Lesnik JJ (2008). Brain size at birth throughout human evolution: a new method for estimating neonatal brain size in hominins. Journal of human evolution, 55 (6), 1064-74 PMID: 18789811

Herculano-Houzel S (2012). The remarkable, yet not extraordinary, human brain as a scaled-up primate brain and its associated cost. Proceedings of the National Academy of Sciences of the United States of America, 109 Suppl 1, 10661-8 PMID: 22723358

Herndon JG, Tigges J, Anderson DC, Klumpp SA, & McClure HM (1999). Brain weight throughout the life span of the chimpanzee. The Journal of comparative neurology, 409 (4), 567-72 PMID: 10376740

Leigh SR (2004). Brain growth, life history, and cognition in primate and human evolution. American journal of primatology, 62 (3), 139-64 PMID: 15027089

Neubauer, S., Gunz, P., Schwarz, U., Hublin, J., & Boesch, C. (2012). Brief communication: Endocranial volumes in an ontogenetic sample of chimpanzees from the taï forest national park, ivory coast American Journal of Physical Anthropology, 147 (2), 319-325 DOI: 10.1002/ajpa.21641

Sakai T, Matsui M, Mikami A, Malkova L, Hamada Y, Tomonaga M, Suzuki J, Tanaka M, Miyabe-Nishiwaki T, Makishima H, Nakatsukasa M, & Matsuzawa T (2012). Developmental patterns of chimpanzee cerebral tissues provide important clues for understanding the remarkable enlargement of the human brain. Proceedings. Biological sciences / The Royal Society, 280 (1753) PMID: 23256194

Dmanisi Homo erectus: I’ll have what she’s having

Speaking of diet in fossil humans … Herman Pontzer and buddies just published a brief analysis of fine-scale tooth wear in the Dmanisi Homo erectus specimens.

Source: http://bit.ly/uD1LWo

Teeth are useful as hell in life. Humans’ teeth are critical not only for eating, sporting a sexy smile, and biting people (right), but also for speech and song (“f,” “th” and “v” sounds). Some parents even harvest their childrens’ exfoliated baby teeth. The things we do with teeth.

Teeth are also really useful for studying long-dead people and animals – teeth may preserve pretty well for millions of years, they can be used to estimate an individual’s age-at-death, and their shape and composition can be used to learn about diet. In a vile act of revenge, the food that sustains us also scrawls its Nom Hancock into the surfaces of our teeth. So, scientists can study the microscopic marks (= “microwear”) on tooth surfaces to see what kinds of foods were eaten shortly before death. Peter Ungar, an author of the current paper, has done a lot of work here, and his website is worth checking out if you’re interested in learning more. Microwear can’t really tell you exactly what an animal was eating, but can tell you whether the animal mostly ate grasses, leaves, hard objects like nuts, and so forth.

So Pontzer and colleagues (in press) examined the microwear on some of the lower molars of the youngest members of the nearly 1.8 million year old (Ferring et al. 2011) Homo erectus group from Dmanisi in the Republic of Georgia. To the left is a picture of the jaws, from the paper (from another paper. How meta of me). The microwear patterns of these badass early humans fit cozily within the variation exhibited by other Homo erectus specimens.

Microwear in Homo erectus is pretty variable, but still rather distinct from other fossil groups like robust Australopithecus, and a little less distinct from their putative ancestor H. habilis. This suggests that something special about Homo erectus was the species’ great dietary breadth – Homo erectus‘ key to colonial and evolutionary success might not have been the adoption of a key dietary resource, but rather the ability to utilize a wide range of food resources. Atkins diet be damned. What’s neat is that the Dmanisi hominids, though kind of primitive (Australopithecus-like) in terms of brain size and some aspects of skull shape, nevertheless demonstrated key behaviors of H. erectus, namely colonization (Dmanisi is the oldest reliably-dated hominid site outside Africa), and dietary flexibility. This really suggests the success of our ancestors was due to some behavioral innovation, aside from advances in stone tool technology.

Source: http://bit.ly/vCTfeR

Now, these Dmanisi H. erectus kids’ teeth wore like other H. erectus, and it would be reasonable to infer that this is because they ate similar foods. This makes it all the more mysterious that the other Dmanisi jaws, from older adults, have teeth completely worn to shit (sorry to swear). D3444/3900 (left) are the cranium/mandible of an individual who was missing all their teeth, except maybe a lower canine – the earliest example of edentulism in the human fossil record (Lordkipanidze et al. 2005). D2600 (below) is a very large mandible with teeth so worn that the pearly-white first-molar crowns were gone and the internal pulp cavity (and nerve) were exposed. (Interestingly, D2600 is so large that some researchers initially argued it represented a different species from the other jaws – yet Adam Van Arsdale presented evidence that this extreme tooth wear may actually be responsible for making jaws relatively taller in early humans).

Source: http://bit.ly/u6bk6h
So what’s curious is why the older Dmanisi hominids should show such an extreme amount of tooth wear compared to other H. erectus, but microwear on the young suggests their diet was the same (that is, just as diverse in texture) as others in the species. Was Dmanisi-level tooth wear (and tooth loss) comparable to other H. erectus, and we just happen not to have found them at other sites? (KNM-ER 730 from Kenya is the next-most worn early Homo that next comes to mind) Is there another aspect of diet we don’t know about, that caused the Dmanisi teeth to wear especially quickly? Or were these early Homo from Dmanisi actually living longer than other H. erectus? I suspect the second is more likely, but that’s a hypothesis that remains to be tested.
ResearchBlogging.org
Read more, dammit!
Ferring, R., Oms, O., Agusti, J., Berna, F., Nioradze, M., Shelia, T., Tappen, M., Vekua, A., Zhvania, D., & Lordkipanidze, D. (2011). From the Cover: Earliest human occupations at Dmanisi (Georgian Caucasus) dated to 1.85-1.78 Ma Proceedings of the National Academy of Sciences, 108 (26), 10432-10436 DOI: 10.1073/pnas.1106638108
Lordkipanidze, D., Vekua, A., Ferring, R., Rightmire, G., Agusti, J., Kiladze, G., Mouskhelishvili, A., Nioradze, M., de León, M., Tappen, M., & Zollikofer, C. (2005). Anthropology:  The earliest toothless hominin skull Nature, 434 (7034), 717-718 DOI: 10.1038/434717b
Pontzer H, Scott JR, Lordkipanidze D, Ungar PS. In press. Dental microwear texture analysis and diet in the Dmanisi hominins, Journal of Human Evolution (2011). DOI:10.1016/j.jhevol.2011.08.006