forensics

Carles Lalueza-Fox and colleagues [1] have a new analysis of the mitochondrial DNA from El Sidrón, Spain. The site has a minimum number of 12 Neandertal specimens, dating to 49,000 years ago. The authors recovered mtDNA from all of the skeletal individuals, and additionally tested for the presence of Y chromosome to diagnose sex.

They found that all the adult males in the sample are close maternal relatives -- that is, they all share a single mtDNA haplotype. In contrast, the adult females and juveniles have a range of different haplotypes. Using some conclusions about the archaeological context (discussed below), they interpret the 12 individuals as part (possibly all) of a kin-structured group. They note that the relationships are then consistent with a patrilocal residence pattern: The men in the group are linked by kinship, the women have come from other kin networks, possibly transferred from other groups.

In the last paragraph of the paper, the authors suggest a further conclusion about life history:

Based on the ages of the El Sidrón group members and their mtDNA lineages, we speculate that juvenile 2 is the offspring (or close matrilineal relative) of female adult 5 and that juvenile 1 and the infant are the offspring of female adult 4. If correct, the latter relationship would indicate an interbirth interval of around 3 y for Neandertals. This period fits with the average 3-4-y interbirth interval reported for several modern hunter-gatherer groups (19).

That conclusion would be based on a single birth interval. It depends on the assumption that these juveniles are in fact siblings, which further depends on the proposed site deposition scenario. So although it is consistent with the data, I think it is very weak evidence. Still, it's a lot more evidence that I expected to have anytime soon. Moreover, it seems to me that the birth interval is testable with reference to dental development. A 3-4 year birth interval implies weaning in or before the fourth year of life, which ought to be reflected in enamel formation.

Awesome! We can now test hypotheses about Neandertal social organization directly from DNA evidence. The authors' hypothesis about patrilocality is consistent with the mtDNA, and I think it is likely to be the correct one.

Still, we have many reasons to be cautious about the interpretation. For one thing, Neandertals are already known to be relatively low in mtDNA variation, with very little regional population structure in the mtDNA. In such a population, it wouldn't be surprising to find individuals sharing the same mtDNA haplotype, even if they were not close kin. It might seem surprising that the individuals sharing the mtDNA haplotype are all men, but with a sample of only 12 individuals, that coincidence isn't really all that unlikely. The limited mtDNA variation would then be a sign of inbreeding at a regional level, not necessarily the kin structure of a particular group at a particular time.

Placing those individuals together as part of the same group is a forensic challenge. For most bones at archaeological sites, we would assume that the individuals lived at different times, possibly hundreds or thousands of years apart. The interpretation that they represent a single group requires several assumptions about the deposition of the remains, which amount to a detailed and surprising scenario. Lalueza-Fox and colleagues describe the El Sidrón skeletal assemblage as a result of systematic cannibalism:

The excavations to date have yielded > 1,800 hominin skeletal fragments and ∼400 Mousterian stone tools made in situ (3), but faunal remains are very scarce. The Neandertal bones are in a secondary position, and the original deposit, worn out by erosion, is thought to have been placed either on the surface or in an upper karst level (2). The present assemblage occurred shortly after the death of the individuals by the collapse of an upper gallery into the Ossuary Gallery triggered by a natural event, probably a violent storm that also dragged down pebbles and clay (Fig. S1). Given that (i) ≈18% of the lithic industry can be refitted, and (ii) the widespread spatial distribution of these refitted artifacts, it may be surmised that they result from a single and brief cultural activity. This likelihood lends even more support to the synchrony of the whole assemblage (2, 3), dating to around 49,000 y ago (4). Some evidence, such as skeletal parts still in anatomical articulation, indicates little site disturbance since formation. Ex hypothesis, the fact that all types of skeletal remains show evidence of anthropic activities associated to cannibalism (2) could indicate that the assemblage corresponds to a Neandertal group processed by other Neandertals on the surface. Although it is impossible to be sure that the individuals represent a contemporaneous group, alternative explanations, such as recurrent accumulation over time of cannibalized individuals that were closely related through the female line, seem less plausible.

If this interpretation is correct, it would be the most stunning example of intergroup violence known from the Pleistocene. Imagine the circumstance in which a group of hunter-gatherers would kill and butcher 12 individuals in one paroxysm of aggression. Certainly it was not mere survival, it was warfare.

Is it true? The problem is the "violent storm". How do we know that the existing assemblage is a good representation of the original deposition site? The high number of refits does imply that we're not looking at a random sample of an originally much larger assemblage, but it's hard to be more definitive. If we have the remains of 12 individuals, how many may have been involved in the act?

Naturally, if the remains had actually accumulated over a longer time, the conclusions about patrilocality would be unwarranted. In that case we would be back to a more general question of regional or local inbreeding among Neandertals, interesting from the point of view of population structure, but with less concrete information about social organization.

The forensic case provides a window into behavior that is potentially much broader. Krapina is another site with hundreds of skeletal fragments representing an even larger number of individuals, which may also represent one or more instances of cannibalism. In that case, the debate about cannibalism (versus secondary reburial of defleshed bones) has flared off and on for years. It is just very difficult to attain a reasonable certainty about such behaviors from the archaeological and skeletal evidence at hand.

I will be interested to read more about the context at El Sidrón as the research continues. The issues of kinship can be easily settled with nuclear DNA sequencing, and should in fact lead to some extremely interesting science, if that can be accomplished. The authors list some of the barriers to such sequencing, given a relatively low DNA yield in many of the specimens, but the field has rapidly progressed. Meanwhile, the archaeological interpretation of the site may allow us to revisit some other Neandertal assemblages, looking for other signs of aggression, violence, and social organization.

References

I've gotten the same question a few times, and have seen it elsewhere, so I thought it would be worth a short post to explain it. And for those readers who've also been asked this question, I thought that being able to provide a simple explanation might be a great help.

How can we say that today's non-Africans derive 1-4% of their genomes from Neandertals, when we are 99.86% genetically similar to Neandertals? Or 98% similar to chimpanzees? I mean, how do we have 4% to work with to make this estimate at all?

Let me explain with another example.

You are approximately 99.9% similar to any other random human today. You're just a bit closer to your relatives, because you got some of your DNA directly from them, or you both share DNA from an immediate ancestor.

Your great-grandmother on average gave you 1/8 of her genes, making up on average 12.5% of your genome.

You are more than 99.9% similar to your grandmother, on average, yet she contributed only 12.5% of your genome.

In other words, these percentages are different things -- the fraction of your total ancestry you can trace to her, versus the fraction of base pairs you actually have identical to hers. Your genome is much more identical to hers than can be explained solely by your descent from her -- this is because you share other ancestors in common with her, and because mutations don't happen very often.

Or, think about it the opposite way. Suppose that the 12.5 percent of your genome you inherited from your great-grandmother meant that you were only 12.5 percent genetically similar to her. Where did you get the rest of your genes from? A turnip? No, you got them from other people, all of whom are roughly 99.9 percent like your great-grandmother. You're 12.5 percent more like your great-grandmother than you are like randomly chosen people in the population.

For the Neandertals, we have to separate these two kinds of similarity, sorting out the genes that we must have inherited from them, from the ones that we share because we share a more distant ancestry.

Now, suppose we don't know that this woman was your great-grandmother, that it's only a hypothesis. It's kind of thing a forensic anthropologist might want to figure out, if your great-grandmother was Anastasia. We can answer the question in this way: Test the hypothesis that she's unrelated to you, by examining whether you are equally genetically similar to her as you are to the average, randomly chosen individual from your population.

This is a statistical test. In fact some of the people in the population share more genetic similarity with you than others, and our statistic has to account for that variation. We can put whatever level of statistical confidence on it we like. If your putative great-grandmother shares substantially more with you than all but some very small fraction of people, we may conclude that she is your relative.

We might do substantially better -- if the variation in the population doesn't work against us, we might even conclude that she is in fact a third-degree relative who contributed between 10 and 14 percent of your genome. Or even better.

Our conclusion has to depend on the structure of the population. If randomly chosen people tend to look like you, for some reason of population structure, we'll have to model that population structure directly. This is, of course, what was done in the case of the Neandertal genome -- a specific population model was significantly favored by the data, and alternatives that did not include population mixture were demonstrated to be so unlikely as to be essentially impossible.

And as I pointed out the other day, if Neandertals had not donated any genes to later populations, then the most recent common ancestors of human and Neandertal genes would all be earlier than the divergence of those populations, more than 250,000 years ago. It is the observation of chromosomal segments that are identical or very near some living human chromosomes that shows that, for some genes in some living people, the Neandertals are not different enough. We have to have some of their genes.