eFfing Fossil Friday: Feces

June 27, 2014July 13, 2014 / zcofran / 1 Comment

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:

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

June 20, 2014June 20, 2014 / zcofran / 2 Comments

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!

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!

#AAPA2014

April 10, 2014April 10, 2014 / zcofran / Leave a comment

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

Ima Gona follow up on that last post

March 10, 2014March 10, 2014 / zcofran / 2 Comments

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 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

March 4, 2014March 5, 2014 / zcofran / 2 Comments

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

March 1, 2014March 4, 2014 / zcofran / 2 Comments

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).

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 ImageJ. kadabba‘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 afarensis. American Journal of Physical Anthropology 83: 13-23.

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

Paleogenomics is crushing it right now

February 14, 2014 / zcofran / 2 Comments

It’s only Valentine’s Day, and already early 2014/late 2013 have provided several fascinating, high profile studies of ancient DNA (all been published in Nature). Forecasting this deluge, last year closed with the announcement of sequenced mtDNA from a ≥400,000 year old human fossil from Sima de los Huesos, Spain (Meyer et al., 2013). This is the oldest DNA obtained for any human fossil, and among the oldest of any animal.

Shortly thereafter, Prüfer and pals (2014) published the complete genome of a Neandertal from the infamous Denisova cave. This study revealed extensive inbreeding in Siberian Neandertals; the fossil individual’s high level of homozygosity is consistent with their parents being half-siblings. Furthermore, comparison of the genome of this inbred Neandertal with modern humans’ allowed researchers to identify many mutations that have become fixed (shared by all people) by natural selection since the divergence of our and Neandertals’ ancestors. Uncovering these human-specific variants can help us understand the genetic bases for many of humans’ remarkable traits.

In January, Olalde y coautores published a genomic analysis of a 7,000 hunter-gatherer from Spain. This ancient genome contained ancestral variants for genes relating to skin pigmentation (SLC45A2, SLC45A5, MC1R, TYR, and KILTG), meaning this Mesolithic European most probably had dark skin. This individual also had a derived variant of the HERC-OCA2 locus, associated with blue eye color in present day people. This suggests that the relatively novel phenotype of non-brown eyes may have increased in frequency more quickly than light skin color in ancient Europe. This guy also had many derived loci associated with immune function, indicating that the rise of agriculture is not solely responsible for the evolution of immune function in present day Europeans.

Around the same time, Sankararamen and team published an analysis of the distribution of Neandertal genes in living people. Whereas previous studies had already shown that Neandertals contributed ≤4% on average to the genomes of living people, this study examined where in modern people’s genomes this Neandertal ancestry tends to be located. One of the most interesting findings is that Neandertal genes are not uniformly or randomly distributed across the modern human genome. Rather, some regions appear to be especially devoid of Neandertal ancestry, implying natural selection acted strongly against Neandertal genes. These Neander-nude areas are preferentially found on the the X chromosome and in genes expressed in the testes, a finding consistent with reduced fertility in hybrid males. Although the genetic contribution of Neandertals to modern humans means that the two belonged to the same species, Sankararaman et al’s findings suggest the two groups were on their way to becoming different species.

Finally, this past week Rasmussen and rascals have published an analysis of a 12,000 year old human from the Anzick site in Montana, associated with the Clovis stone tool culture. I don’t know much about this time period save for what I learned in a class on North American archaeology taught by Dr. John Speth, back when I was a young, bright-eyed graduate student. One thing I recall from this class, when we were going over Clovis, was that this tool industry was found all over the United States at the beginning of the Holocene, but I was always disappointed by the dearth of bones complementing the copious lithics. Turns out, the DNA analyzed by Rasmussen et al. comes from the only known burial from this time period. This lone burial provides compelling genetic evidence that indigenous Americans have descended largely from a single ancestral population that separated into the North and South American populations prior to the Clovis period. This ancestral population was definitely not from Europe, as a minority of researchers have argued. Check out the SEAC Underground blog for more on the archaeology and ethics of the Anzick analyses.

So, paleogenomics is really crushing it right now. There have been many of recent advances in sampling and sequencing poorly-preserved ancient DNA, and as we’re seeing now, lots of ancient bones (and teeth) are bringing awesome new, genetic insights into recent human evolution. If this is how well we’re doing so early in 2014, you can bet that the rest of the year promises many more exciting discoveries.

This human DNA is old as hell

December 5, 2013February 14, 2014 / zcofran / 6 Comments

If hell were around 400,000 years old. The people who salvaged ancient DNA from fossil Neandertals and “Denisovans” now present mitchondrial DNA (mtDNA) from a human-ish fossils from the Spanish site of Sima de los Huesos (SH; this translates as “pit of bones,” by the way, which is pretty badass). DNA-bearing Neandertal sites and Denisova cave date anywhere from around 30-100 kya, while Sima de los Huesos has been dated by various methods to 300-600 thousand years ago. So the newly announced mtDNA is the oldest human DNA ever recovered…

YET!

Now, we know what Neandertals look like, since they are perhaps the best known group of fossil humans. We don’t really know what Denisovans look like, as their unique DNA came from fossils that are anatomically ambiguous (a large molar and the end of a tiny fragment of the bone at the end of your pinky finger) – they could look like anyone. Even you! The SH fossils predate Neandertals by a few hundred thousand years, but their skulls look pretty similar; quite possibly the SH populations were ancestors of Neandertals, and you’d expect the DNA to be similar in the two groups.

So researchers were surprised to find this SH mtDNA to be more similar to Denisovan than to human or Neandertal mtDNAs. But this actually shouldn’t be that surprising, since we saw the same twist when Denisovan mt and nuclear DNA was sequenced – mtDNA first made it look like humans and Neandertals were more closely related, and the ancestors of Denisovans separated from the human+Neandertal lineage in the deep past. However, mtDNA essentially acts as a single genetic locus – a gene tree isn’t necessarily a species tree – and the more informative nuclear DNA later showed Neandertals and Denisovans to be more closely related to one another than either was to living humans (yet each of these ancient populations contributed some genes to some living people today). Denisovans held on to a very ancient mtDNA lineage, and apparently so did the people represented at Sima de los Huesos. And let’s not forget, we don’t know what Denisovans looked like – maybe they looked just like the older SH fossils.

Hopefully we’ll be able to get human nuclear DNA from Sima de los Huesos. When we do, I predict we’ll see the same kind of twist as with the Denisova DNA, with SH being more similar to Neandertals. But if I’m wrong, maybe we’ll be a step closer to knowing what the bones of the the mysterious “Denisovans” looked like…

Here’s that paper: Meyer et al. in press. A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature. doi:10.1038/nature12788

The shale revolution & lying with statistics

February 21, 2013 / zcofran / 4 Comments

Is U.S. energy independence, based in part on ‘fracking’ shale deposits to access oil and gas reservoirs, just a pipe dream? A comment by JD Hughes in this week’s Nature posits just this, pointing out that production at most of these deposits declines steeply in just a few years – the industry is simply not sustainable. But why all the hype around such an unsustainable resource?

In my view, the industry practice of fitting hyperbolic curves to data on declining productivity, and inferring lifetimes of 40 years or more, is too optimistic. Existing production histories are a few years at best, and thus are insufficient to substantiate such long lifetimes for wells. Because production declines more steeply than these models typically suggest, the method often overestimates ultimate recoveries and economic performance (see go.nature.com/kiamlk). The US Geological Survey’s recovery estimates are less than half of those sometimes touted by industry.

In short, yes you can fit a line to data points (i.e. production over time; do check out the link in Hughes’ quote) to model or predict how predict how production will change over time. But this does not necessarily make these predictions valid or accurate! These ‘hyperbolic curves’ (see bottom graph from the above link) are often calculated from only five years of data, but used to predict production some 40 years down the line. And what’s more, these predicted values (i.e. points on the fitted line) are not spot-on, but have a confidence interval, a range of uncertainty in which a predicted value could be found. This interval increases drastically the further off in time you are predicting.

The point: we shouldn’t be so confident in fracking and shale reserves to help solve the U.S.’s energy problems. In fact, we should be confident (and conservative) assuming they won’t solve anything for anyone except people making money off them (and even then, only in the short term).

I’ve commented on this blog before about the importance of understanding the statistical methods one employs. In the present case, industry ‘specialists,’ whether they understood line fitting or not, erroneously used statistics to predict optimistic outcomes for US energy production. And the US government and public were eager to swallow this up hook, line and sinker.

The comment (sorry it’s behind a paywall)

Hughes, J. (2013). Energy: A reality check on the shale revolution Nature, 494 (7437), 307-308 DOI: 10.1038/494307a

Osteology Everywhere: Zubi

November 13, 2012August 4, 2013 / zcofran / Leave a comment

We’re going over bone biology and bioarchaeology this week in my Intro to Bio class, and so I thought I’d open the unit with my patent-pending Osteology Everywhere series. I showed the students the various real-life objects from the series, and they kicked buttocks at seeing the bones in quotidian things. They even got this new one:

That yellow pepper is a ringer for a premolar crown, which hopefully was not as yellow. So I’m very proud of my students. I figure if I can make people see bones everywhere they look, well then I’ve done my job. But hopefully they don’t get as bad as me: a few months ago my friend bought one of those Kinder chocolate eggs with a prize inside. Shaking it, you could hear something rattling in there. It’s disconcerting that my mind immediately guessed, “Legos, or teeth.” At least legos came before teeth.

Also “zubi,” from the title, is the Croatian word for ‘teeth’ (and apparently also slang for ‘breasts’).

Lawn Chair Anthropology

Biological anthropology, paleontology, evolution, and development, by Dr. Zachary Cofran

Uncategorized