This new paper in Nature gives a rare picture of human sacrifice among ancient Mayans from the Yucatán peninsula in Mexico. Paleoanthropologists had found remains before, mostly children, preserved by being tossed in sacred cenotes (wells), but this group of 64 ancient individuals was not only collected, but their DNA was analyzed from the ear bones, giving surprising results about genetic relatedness.
As with the Aztecs, human sacrifice was a fixture of ancient Mayan society, though the people killed (in this case, children) were probably captives rather than residents of the place where the killers lived. Sacrifice could have occurred via either decapitation, extraction of the heart from living individuals, or killing with arrows.
Click below to read the piece, or find the pdf here.
The figure below shows where the remains were found: in a chultún (an underground cistern) next to an airport runway near the ancient Mayan city of Chichén Itzá (now a World Heritage Site), which flourished between about 600 and 1200 A.D. This map gives the location:

They found the bones of 64 individuals, carbon-dated as being from the 7th to the 12 centuries AD. How did they know how many individuals were represented in their sample? Because they recovered 64 left petrous parts, the bit of the skull’s temporal bone that surrounds the inner ear (this bone, sequestered away from the outside of the skull, is often used to extract ancient DNA). 64 left petrous bones means 64 individuals.
First, every one of the individuals was a male between 3 and 6 years old, showing that the Mayans preferred to sacrifice young boys. Why? It’s not clear, but there’s speculation that sacrifices helped local maize crops flourish (the method of sacrifice wasn’t specified in the paper). However, other sacrificed individuals recovered, as in the famous sacred cenote, have been mixtures of males and females, but also overrepresented with children. The authors don’t speculate why, in this location, only boys were killed.
The ancestry of the sacrificed individuals was compared among each other, as well as to 68 individuals of Mayan descent living the nearby town of Tixcacaltuyub. One surprising finding was that those sacrificed included two pairs of identical (monozygotic) twins (easily seen in DNA, which is identical among two different earbones). The authors note that twins held a special position in Mayan mythology. But, as the plot of “pairwise mismatch rates” shows below), 11 pair of individuals were “close relatives”, represented by the hollow diamonds (the twins, with a mismatch rate of zero, are the two pairs of twins. The authors speculate (see below) that the individuals came from a single big event of mass killing.
The paper doesn’t say how “close” the “close relatives were”, or whether they were contemporaneous, like brothers, but given the age of the individuals, it seems likely that the related pair members came from the same family.

The comparison of the DNA of the sacrificed children with that of living people in Tixcacaltuyub, as in the principal-component cluster graph below, showed that the sacrificed individuals )”YCH”, dark purple stars) fell into a cluster of Native Americans, other Mayan individuals, people from Belize, and individuals from the nearby town (“TIX”, light blue stars), and were considerably different from individuals in Africa, Asia, and Oceania, as expected. (This shows diagnostic genetic differences between geographic groups, demonstrating that the idea of “races”—defined as “diagnostically genetically differentiated populations”—is not purely a social construct, but contains biological information.) However, the ancient sacrificed individuals, which also had a dollop of genes from the Caribbean, didn’t particularly cluster with the present day Mayans living nearby, who had their own admixture of genes from Africa and Europe, perhaps reflecting turnover of populations over time. In the sixteenth century there was a big poulation bottleneck, perhaps due to diseases introduced by Europeans. In fact, this bottleneck reduced the population of what is now Mexico by 90%!)

One other bit of information. We are able, looking at contemporary DNA sequences of a population, to judge whether natural selection is acting on genes or groups of genes. If variable genes such as the HLA (“human leukocyte antigen”) genes involved in immune response show coordinated variation (that is, variant “A” of one gene tends to co-occur with variant “B” of another gene in individuals), this gives evidence that selection is acting on groups of genes—in this case genes affecting immunity. The authors identified several HLA variants that look like they were subject to selection, and also tested some by making copies of sequences of some HLA variants and seeing how strongly they bound to proteins derived from Salmonella bacteria (strong binding means that the HLA proteins were reacting and presumably neutralizing the bacterial proteins). The authors suggest that the selection acting to promote the rise in frequency of some HLA variants was due to typhoid or paratyphoid-like infections.
The upshot: Although the data from HLA genes does indicate that there was selection for immunity in both ancient and historic times, what I find most interesting is that the sacrifice involved children, all male children, and many were close relatives. This, at least, gives us a pretty strong sociological picture of one aspect of ancient Mayan culture. To quote the authors,
In comparing the subadults in the chultún to other ancient and present-day populations in the Maya region, we find evidence of long-term genetic continuity, which also suggests that the sacrificed children and sibling pairs at Chichén Itzá were obtained from nearby ancient Maya communities. Among present-day individuals at TIX, we detect evidence of European and African admixture since the Contact period.
and
Overall, 25% of the children had a close relative within the assemblage, suggesting that the sacrificed children may have been specifically selected for their close biological kinship. Moreover, this may underestimate the true number of relatives present in chultún as only 64 of the estimated 106 individuals in the chultún had a preserved petrous portion of the left temporal bone available for analysis. The further finding that the closely related children in each set seem to have consumed a similar diet and died at a similar age suggests that they have been sacrificed during the same ritual event as a pair or twin sacrifice.
and, finally,
The discovery of two sets of identical twins, as well as other close relatives, in a ritual mass burial of male children suggests that young boys may have been selected for sacrifice because of their biological kinship and the importance of twins in Maya mythology. We show that, at a genome-wide level, the present-day Maya of Tixcacaltuyub exhibit genetic continuity with the ancient Maya who once inhabited Chichén Itzá and we demonstrate through several lines of evidence the involvement of the HLA region in a pathogen-driven selection event(s) probably caused by infectious diseases brought into the Americas by Europeans during the colonial period.

One question that comes to mind is whether there are historical, or written, records of this practice. 600-1200 AD is not all that long ago. I (obviously) know nothing of Mayan culture or record keeping practices. It would be interesting to know more about what they were trying to accomplish with these sacrifices—perhaps more than can be gleaned archaeologically.
I don’t think so, as those who could write about it–Europeans–came after the empire was over. But there are pictographs and carvings, as well as word of mouth.
There was a Mayan script, with both ideographic and phonetic characters. I’ve seen pictures of carvings in this script, but I don’t know if they used another medium like clay or paper for writing, or if any such writings survived after the Spanish conquest. The most famous Mayan text, the Popul Vuh, was written down phonetically in the Latin alphabet; I’m not sure if it was ever written out in the Mayan script prior to its transcription.
(ADDED: I see Dom beat me to this point!)
GCM
If I had to make a guess (an uninformed guess) it would be that the sons of powerful families who belonged to enemy tribes in the region were specifically murdered for safety reasons. Why allow the noble scions of the House of X to continue its tradition of murdering, threatening, inconveniencing, or just plain defying the sacred principle that only Mayans mattered by existing in the first place? Cut the source off early.
Interesting!
The Maya certainly had a script –
https://en.wikipedia.org/wiki/Maya_script
but whether they wrote anything other than inscriptions to the gods, I know not…!
I was going to make the same point. The earliest evidence of writing in the Americas is from 3,000 years ago, and is from that region. I don’t think much of it has been deciphered though.
What I meant above is that there seem to be depictions of the killing but I’m not aware of DESCRIPTIONS of the killings in words. But of course I may well be wrong.
What a horrible religion that demanded the murder of little kids. A good reminder of the value of the Enlightenment. If only there weren’t still such resistance to rational thought.
+1
But we (atheists) are dismissed for being angry.
“Excuse me! You shouldn’t be killing kids for your ‘Gods.’ (I’m sorry if my face is a little red but I feel strongly about this.)”
+2
Might as well be Moloch worship. Don’t give me any Rousseauian “noble savage” crap.
If the Mayan interest in twins could have been satisfied by fraternal twins as well as identical, perhaps the brothers in the set were fraternal twins. Of course, it would be impossible to tell if non-identical siblings were twins from their DNA, but if the non-identical siblings were closer in size than expected, that would be a clue. I scanned the paper to see if there was any mention of this possibility, but I didn’t find any.
Good point, though we’ll never know the answer. We could know whether they were siblings, though, as they’d have identical mitochondrial DNA.
I’d imagine twins were big juju.
HA!
When I saw a short article in the press on this I hoped you’d give it a closer look here. Fascinating story. Thanks.
D.A.
NYC
Say what you want, but man is this also really disturbing.
I’m surprised that such a small number of identical twins (only two pair) would get so much attention from the authors. Supposedly 3% of global births are twins. These dead kids represent 62 birth events, so the expected number of twins is 3% of 62 or 1.8 twin births, which rounds to exactly the number that was found. I think no special explanation would be required for this number of twins; it does not seem to be surprising. However, I did not read the original paper; maybe the authors addressed this.
Monozygotic or identical twins are about 4 per 1000 births or 0.4%. IDK if the two identical twin pairs in the bone pit seems like a much higher frequency than expected. Small sample size.
The higher number for all twins including identical and fraternal twins is about 12 per 1000 births (up to about 17 per 1000 in Africa and North America).
https://doi.org/10.1093%2Fhumrep%2Fdeab029
Right, I don’t know how I could miss that identical twins were such a small fraction of all twins.
The Mayan cosmology summarized in Popol Vuh (supposedly a translation from Kich’e into Spanish) involved no fewer than
three sets of twins, who are connected with the origins of the world. Interesting also that the gods created humans three times. The first models were made from mud, but they talked too much; the second out of wood, but they were too wooden; the third, successful type, were made from maize, and they pleased the gods so well that they were allowed to continue.