Thursday 21 March 2013

Inbreeding Evident in a Chinese Fossil? Wu, Xing, and Trinkaus Have This To Say To Our Fossil Relations "Your Papa Ain't Your Papa But Your Papa Don't Know"

The title of this post contains a phrase from a classical calypso song, "Shame and Scandal [in the Family]," written and first performed by Sir Lancelot. For those not familiar with the song, it tells the story of a young man who is looking for a wife. Each time he queries his father as to the advisability of marrying a much-loved young woman, his dad confides in him that the girl is his sister, but that his mother doesn't know. The implicit message is, of course, that mating too close to the family tree-trunk is not only frowned upon, but that it also invites genetic abnormalities in the offspring of such unions. The whole tale ends happily when the boy confronts his mother with his father's infidelities. His mother reassures him in the immortal words on the marquee above, "Your daddy ain't your daddy but your daddy don't know!"

All of which brings me to the real matter of the day. The news bureaus and even the blog Surprising Science are spreading the word that the Pleistocene members of the human lineage may have suffered from inbreeding at a far higher rate than might be expected based on what we know of present-day humans. Straight from PLOS ONE: Wu X-J, Xing S, Trinkaus E (2013) "An Enlarged Parietal Foramen in the Late Archaic Xujiayao 11 Neurocranium from Northern China, and Rare Anomalies among Pleistocene Homo." PLoS ONE 8(3): e59587. doi:10.1371/journal.pone.0059587 [free access] is a rather pedestrian description of some Homo erectus parietal fragments excavated in China's Nihewan Basin in 1977. However, they conclude that this and other skeletal abnormalities in the fossil record of bipedal apes suggests the possibility that inbreeding may have been responsible, and that thus inbreeding must have been common among our fossil relations.
Xujiayao's location on the Liyi River. From Norton and Gao (2008) ScienceDirect
Palaeontological and archaeological investigations have been ongoing near Nihewan, in China, at least since the 1970s. In addition to the world famous Chinese scholars overseeing the work, a fairly large number of high-profilce North Americans have been involved. Among them are Diane Gifford-Gonzalez, Kathy Shick, Nick Toth, Desmond Clark (now deceased), and now, Erik Trinkaus.

The site of Xujiayao, the Xujiayao 11 neurocranium [from left to right, red area shows fragments' location on a complete skull in Norma superior, view of Xujiayao 11 neurocranium specimen in Norma superior, endocranial view of Xujiayao 11 neurocranium specimen]. (Photo attributed to Erik Trinkaus)
The majority of the PLOS ONE article about the Xujiayao 11 neurocranium is a straightforward description and diagnosis of a heritable condition known as an enlarged parietal foramen (EPF), in which there is bilateral, incomplete ossification of the parietal bone along the posterior sagittal suture. The authors present a creditable diagnosis, with which I have no quarrel. I am, however, disconcerted by what I think is a glaring conceptual misstep made evident in their discussion.  

Once the diagnosis is accomplished, the authors present an overview of the high number of heritable skeletal abnormalities and pathological conditions that are evident in the bipedal ape fossil record. Compared with present-day humans, the authors see a mismatch between the evidently high frequency of abnormalities among Middle Pleistocene hominininins bipedal apes and the population of present-day humans like you and I. [Admittedly the authors' is just a suggestion of what might be occurring in fossil populations. However, their saying it belies either a complete lapse of memory or a thoroughly naive understanding of the difference between a living population and a fossil one.] Let's see what the authors think it's all about.
To the extent that these abnormalities can be considered congenital or cannot be securely diagnosed, these considerations raise questions regarding the population dynamics of Pleistocene humans. To what extent could this pattern reflect small, highly inbred populations, which were also demographically unstable, resulting in both the increased appearance of congenital deleterious conditions and in their subsequent disappearance through local population extinction? Demographic instability appears to have been characteristic of most Pleistocene human populations ... . It remains unclear, and probably untestable, to what extent these populations were inbred, but close genetic relationships have been suggested for one Neandertal sample ... and some Upper Paleolithic burial groups ... .
Inbreeding! It's not impossible... However, the authors are asking us to consider the possibility that inbreeding was far more common in the Pleistocence. How else, they ask, could this phenomenon be explained. Simple, I'd say. And my explanation has nothing to do with population dynamics [yech]. Rather a sensible approach to the authors' observations has everything to do with prior probabilities.

In comparing the frequency of occurrence of skeletal abnormalities in our fossil relations, the authors use the present-day frequencies of similar occurrences in people like you and me. Knowledge of the present-day living population allows assignment of prior probability to various pathological conditions. For example, based on the occurrence of EPF in the present-day American population---i.e. 1 in 25,000---the prior probability (p) that an infant will be born with the condition is 0.00004. Roll that over in your brain for a minute, while go fill up my glass. brb.

Sorry I took so long. Had to pee, too.

Okay. What did you come up with?

Ahhhh. You note that the comparison population---a sample of present-day humans---is the entirety of those people who're alive in the present [a living assemblage, termed a 'zoocoenose']. By contrast that of the fossils is a record of the dead from several hundred individuals from across the Old World and from all times in the history of bipedal apes [a 'death' assemblage, termed a 'thanatocoenose']. Thus, the fossil population is nothing like the present-day, living human one. Mistake number one on the authors' part. Moreover, the fossil record is inherently fragmentary due to all kinds of taphonomic factors---the result is differential preservation based on the physical properties of the skeletal element in question. Thus, with only the fossil death assemblage to go on, we can have no good way of determining how truly representative the fossil sample is relative to the populations from which they're drawn. I'd call that an excellent start at rebutting the authors' claim!

What next?

Splendeedo! This article is forcing you to recall what you learned in zooarchaeology about mortality curves [or 'age profiles']. Since we can't turn the fossil record into a living, breathing population, perhaps we can pretend that the present-day living population is somehow rendered lifeless---i.e. dead. If all the members of an animal population were to be killed simultaneously---dubbed a 'catastrophic age profile'---the frequency histogram of age at death might resemble a staircase descending more or less uniformly from high numbers of young juveniles at the left, through decreasing numbers at each age stage as you go further to the right, and ending with the oldest ones at the extreme right [see below]. In fact a 'catastrophic death' age profile mirrors the living population. In such a group---present-day human populations, for example---you might expect to find 1 in 25,000 individuals with enlarged parietal foramina [according to the authors]. Next, imagine a similar histogram reflecting the ages at death for a population from which the very young and the old or infirm are culled---a so-called attritional age profile---that is often the case when the causes are disease or cursorial predation [like wolves, or big cats]. Instead of resembling a staircase this frequency histogram would look like the letter U. That is, the graph would show a spike on the left from the many killed off by disease and misfortune in their infancy or juvenile stages, very few mature animals able to look out for themselves, and a peak for the old ones too frail to endure. Excellent!

Copyright The Subversive Archaeologist [with thanks to MS EXCEL!]
Kayso, how does that knowledge feed into the circumstances of the Xujiayao 11 individual and all of the other fossil human relations?

I'll paraphrase.

Wu, Xing and Trinkaus are saying that the bipedal ape fossil record bears little similarity to a living human population, in that it contains higher frequencies of conditions than those in the present day. Yet, by comparing the two they are explicitly treating the fossil record as if it has the same age profile as present-day human populations. On the evidence I've just provided, surely this is a patently unwarranted assumption! It's one that completely ignores decades of theoretical palaeontology and palaeoanthropology. The authors should've expected life-threatening or debilitating conditions to occur at higher frequencies in the "death assemblage" (thanatocoenose) (fossil record) of any species. In fact, life history in tandem with taphonomic processes would virtually guarantee that the bipedal ape fossil record [which is, by definition a thanatocoenose] would look nothing like a living population.

Therefore, the frequency of genetic abnormalities or pathological conditions in the fossil record [whether they caused death or not] is an expectable set of circumstances and not one that requires an explanation. This article's take-home message is, therefore, completely at odds with palaeoanthropological reality.

For the authors of this latest failure from PLOS ONE, it's back to the drawing board. And this totally un-inbred archaeologist is going to vanish into the aether until next time.

'Bye fur now.

SA announces new posts on the Subversive Archaeologist's facebook page (mirrored on Rob Gargett's news feed), on Robert H. Gargett's page, Rob Gargett's twitter account, and his Google+ page. A few of you have already signed up to receive email when I post. Others have subscribed to the blog's RSS feeds. You can also become a 'member' of the blog through Google Friend Connect. Thank you for your continued patronage. You're the reason I do this.

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