Friday, October 24, 2014

Native American DNA in Easter Islanders

An article has come out in Current Biology in which the authors report the sequencing of  over 650,000 SNPs (single nucleotide polymorphisms) from 27 Rapa Nui individuals. I don't have access to the full article, but I've read the abstract and a discussion of it from today's issue of Science (Lawler, Andrew, 2014, Epic pre-Columbian Voyage Suggested by Genes, Science Vol. 346, No. 6208, p. 406). Native American DNA composed about 8% of the Rapanui genome. They explain this by invoking pre-Columbian trans-Pacific journeys from Easter Island to the Americas and back. They argue that the introgression took place in pre-Columbian times, rather than in recent or historical times, because the Native American DNA segments are fragmented and scattered. The degree of fragmentation and dislocation allow the authors to infer a date of AD 1280–1495 for the contact.

Of course, these issues--Easter Island and trans-Pacific contact--are popular and therefore controversial questions. So, naturally some Norwegians have to defend Thor Heyerdahl by saying that this means that the South Americans sailed to Easter Island. Right. And just happened to get there at the same time as the Polynesians. Sure. That's more likely than the Polynesians, who'd been sailing around the Pacific for thousands of years and who had developed unique maritime technology and navigational knowledge, sailing to South America. Nothing against the South Americans, but dude, this was the Polynesians' thing. In fact, it's hard to imagine that the Polynesians, who, over a period of two or three thousand years, had found and settled virtually all the tiny Polynesian islands, would suddenly stop at Hawaii and Easter Island. Right. You sail all over the Pacific for millennia and find all the little islands, but miss the giant continent in front of you. Yeah, that's really likely.

Of course, the South Americans did have boats and sailed around some, but there's little evidence that they crossed the open ocean to Polynesia. Sure, a boat might have drifted there, as they occasionally do today, but that's not really in the same league.

Added to the pre-Columbian chicken bones from Chile with (possibly) Polynesian chicken DNA in them and the evidence that the yam diffused to Polynesia from South America, and the evidence for pre-Columbian trans-Pacific contact is getting stronger.

The citation for the article is:

Moreno-Mayar, J. Víctor, Simon Rasmussen, Andaine Seguin-Orlando, Morten Rasmussen, Mason Liang, Siri Tennebø Flåm, Benedicte Alexandra Lie, Gregor Duncan Gilfillan, Rasmus Nielsen, Erik Thorsby, Eske Willerslev, and Anna-Sapfo Malaspinas. (2014). Genome-wide Ancestry Patterns in Rapanui Suggest Pre-European Admixture with Native Americans. Current Biology In press. DOI:

Beware the words in your Custom Dictionary file!

I accidentally added a misspelled word to my word processor's custom dictionary, so I had to edit it, which required a long, convoluted, painful web search for instructions. But once I had it open, I reviewed it and found all kinds of weird stuff in it. Here are the interesting ones:

alluviation, bioarchaeology, bioarchaeological, calendrically, ceiba, cenote, Chaak, chert, Chichigalpa, Chontal, Chorotega, Chorrera, chroma, conchoidal, Cosigüina, Cosmapa, Cusirisna, debitage, eastings, ecofacts, econophysics, ethnoarchaeological, Ethnoarchaeology, ethnohistoric, ethnohistorical, ethnohistorically, ethnohistory, extrajudicially, fechamiento, flintknapper, flintknapping, fractality, francosa, francoso, geoarchaeological, georeference, georeferenced, georeferencing, hammerstone, hammerstones, handaxes, Ixtepeque, Izamal, Jōmon, knapper, knappers, lacunarity, lithics, Manteño, Maribio, Maribios, matings, Mayapán, Mazatega, megafauna, micaceous, midden, middens, Middens, Nahua, Ocós, osteological, paleobotánicos, Paleodemography, perimortem, Physiographically, Postclassic, Preclassic, Puuc, replicability, Research, schadenfreude, sedentism, seriation, sherds, Somotillo, Speleothem, Springer, Stela, stelae, suprayacente, swidden, symphysis, tafonomía, tafonómica, tafonómicos, taphonomy, Tecoh, Telchaquillo, Términos, toponyms, uncountably, Undergraduate, undiagnostic, unslipped, vigesimal, Yucatec

Why should you care?

It's very revealing, practically a list of keywords for your life.

If someone steals your custom dictionary file, perhaps with malware, they can figure out a lot about you!

Beware! What's in your file?

45,000-Year-Old Modern Human Genome from Western Siberia is the Earliest Yet

Svante Pääbo's team has produced the earliest Homo sapiens genome so far, extracted from a directly radiocarbon-dated femur found in western Siberia. Two AMS dates on the collagen combined to produce a calibrated date of 46,880-43,210 cal BP. Stable C and N isotope analyses indicate a diet based on C3 plants and animals that ate them. The bone is from a male whose mtDNA falls near the root of the R haplogroup, which is widespread in modern Europe and Asia. The Y chromosome is similarly ancestral a widespread Eurasian haplogroup. They called the specimen  "Ust'-Ishim" after the location in which it was recovered.

The authors find that the individual was probably related to or derived from an early population involved in the dispersal of modern humans out of Africa. Principal components analyses (PCAs) of the autosomal DNA suggest this guy was more closely related to non-Africans than Africans. In fact, when comparing the autosomal DNA only to modern non-Africans the authors observe that the specimen falls near the origin of the graph (of the first two components) and interpret that to indicate that he was equally-closely related to all modern non-Africans.

There may, however, be a better interpretation. In both PCA plots the Ust'-Ishim genome fell closest to modern Central and South Asians, which would make sense too, given the location of the find. I haven't read the Supplementary materials yet (they're 115 pages long), but I did review Section 10, which addresses this issue. To my mind, the results of the admixture analysis shown in Supplementary Figure S10.3 do indeed suggest that the Ust'-Ishim genome is closest to Central Asians, such as the Pathan, Sindhi, Burusho, Hazara, and Uygur. (The ethnic labels come from the article.) These are all central Asian peoples from Pakistan, Afghanistan, and western China. The match between the bars representing those peoples and the Ust'-Ishim genome is not perfect (the former are missing a purple patch and a bit of dark blue that appear in the ancient genome), but to me that match it does seem markedly more similar than the others. Unfortunately, the subsequent phylogenetic analyses do not address this question as they do not include central Asian genomes. So, I'm not sure I agree with the authors' interpretation that this new specimen is equally related to all Eurasians. If the Ust'-Ishim individual is more closely related to central Asians than to others, it implies a remarkable degree of geographic stability. This is an obvious hypothesis that probably should have been addressed. I hope it is investigated in the future.

They also found a 2.3 +/- 0.3% Neanderthal admixture, showing that their inter-species cuddling had already taken place by 45,000 BP. Curiously, given the date and location, there was no Denisovan admixture. The percentage of Neanderthal admixture is a bit higher than in modern humans, but not by much. As one would expect, the characteristic length of the Neanderthal DNA segments is substantially greater (~1.8-4.2 x) in the Ust'-Ishim genome than in modern ones, because the fragments were subsequently broken up further by recombination. Actually, this fragmentation process can provide an estimate of the length of time since the admixture took place, which the authors estimate as 232-430 generations earlier, or 50,000-60,000 BP, using a 29-year generation length. This corresponds approximately to some estimates of the time of expansion of modern humans out of Africa, but post-dates the putatively early modern humans from Skhul and Qafzeh. Some longer Neanderthal segments in the Ust'-Ishim genome imply that later admixture events also occurred. Interestingly, Figure 5 in the article illustrates homozygous versus heterozygous Neanderthal-derived alleles in the Ust'-Ishim genome compared to several modern ones. The Neanderthal alleles in the ancient genome are all heterozygous whereas some of the modern ones are homozygous. This makes sense, as one would expect by chance alone (panmixia) that heterozygous derived alleles would be more common earlier in the gene flow process. Probabilistically, it would take time for homozygosity to develop. Figure 5 only shows Chromosome 12, but it is suggestive.

Because the specimen is directly dated, it could be used (along with other specimens) to help calibrate the "genetic clock" that calculates age of genetic divergence from mutation rates, and the authors did so. The new estimates of mutation rates in autosomal DNA from this study are lower (slower) than some, possibly implying a longer time interval since the split from archaic human relatives.They also provided new Y Chromosome and mtDNA mutation rate estimates.

Finally, it is noteworthy that the authors find that the Ust'Ishim individual was not more closely related to the Andaman Islanders than he was to modern East Asians or Native Americans. I say this is noteworthy because some documentaries have made, in my opinion, far too much of the Andaman Islanders' genes as evidence for a coastal, southern migration route for early modern humans.

Quite the interesting article. Here's the reference:

Fu, Qiaomei, Heng Li, Priya Moorjani, Flora Jay, Sergey M. Slepchenko, Aleksei A. Bondarev, Philip L. F. Johnson, Ayinuer Aximu-Petri, Kay Prüfer, Cesare de Filippo, Matthias Meyer, Nicolas Zwyns, Domingo C. Salazar-García, Yaroslav V. Kuzmin, Susan G. Keates, Pavel A. Kosintsev, Dmitry I. Razhev, Michael P. Richards, Nikolai V. Peristov, Michael Lachmann, Katerina Douka, Thomas F. G. Higham, Montgomery Slatkin, Jean-Jacques Hublin, David Reich, Janet Kelso, T. Bence Viola & Svante Pääbo (2014). Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514: 445-450. doi:10.1038/nature13810.

Tuesday, October 14, 2014

Icebergs in Florida

In today's weird science news, icebergs in Florida. Yup:

Hill, Jenna C. and Alan Condron (2014). Subtropical icebergs scours and meltwater routing in the deglacial western North Atlantic. Nature Geoscience PUBLISHED ONLINE: 12 OCTOBER 2014 | DOI: 10.1038/NGEO2267.

Okay, so they recorded high resolution bathymetry of the continental shelf along the Carolinas and Florida coast. They noticed these big furrows that they apparently can attribute to the keels of icebergs dragging through the sediments. Then they ran ocean circulation simulations that showed that big meltwater discharges from Hudson Bay or the St. Lawrence during the last deglaciation could have pushed icebergs as far south as the tip of Florida, although they would have been more common further north, along the Carolina coast. These kinds of events ought to have provided bursts of cold fresh water. I wonder if signals from those events could have been recorded in coral or shellfish.

Pretty cool work! (No pun intended.)

Wednesday, October 8, 2014

The Archaeologist Was a Spy by Charles H. Harris III and Louis R. Sadler

I recently read The Archaeologist Was a Spy by Charles H. Harris III and Louis R. Sadler (Albuquerque: University of New Mexico Press, 2003). It's a detailed exposition and discussion of Sylvanus Morley's espionage work during World War I. I think I knew previously that he was one of those denounced for spying by Franz Boas in his famous letter to The Nation after the war. But I did not know how central the role that he played was in not only in the spying itself but also in setting up the entire network of spies. I also knew nothing about the object of the espionage or its significance. As it turns out, the historians who wrote the book showed that Morley played a pivotal role in identifying and recruiting others, particularly archaeologists, into the network, which was run out the Office of Naval Intelligence. In those years, German U-boats threatened not only United States shipping and even our ports and coastal towns, but also the vital military links between the US and its European allies. The possibility that German U-boats could refuel and re-arm in nearby waters was a grave concern because it would have multiplied their effectiveness. Morley's primary task was to survey the Atlantic coast of Mexico and Central America to determine where it was physically--bathymetrically--possible for the U-boats to put in to ports, bays or inlets (preferably undetected) and resupply themselves. He was also on the lookout for German activities ashore that might indicate the willingness or ability to assist such a mission. I was surprised to learn that he was one of the dominant actors in such a key drama.

A couple of warnings. First, there is exceedingly little archaeology in the book. It's not a biography of Morley as much as it is a history of American espionage. Second, toward the end, the authors celebrate Boas's censure, and by implication the vindication of their protagonists, by the American Anthropological Association. But it's not clear to me what they are really saying. That American scientists ought to spy using their profession as a cover? That it's patriotic to do so? That we can do so with a clear conscience because we can assume that foreign scientists (or perhaps American ones) are spying on us? What about the argument that spying by some puts us all under suspicion? This not just theoretical for me. I have worked in countries that are not America's best friends, and who therefore would reasonably be on the lookout for American spies. Not only am I an archaeologist, but I worked for the Navy for a time. Worst of all I went to Yale, the great hothouse in which American has long propagated her budding spies. None of that means that I'm a spy, and in fact I'm not, but I don't want to have convince an interrogator of that.

Lunar eclipse

Sorry for not posting...blah, blah, blah...

Got up this morning at 4:00 am to see lunar eclipse, which was slated to begin at 4:17 here. By 4:30, I still couldn't see anything, but by about 5:30 it was well underway.

Here's a picture.
I could probably take a better photo if I knew how to use all the functions on my fancy camera.

It's a pretty night, partly cloudy, with the bright full moon being eaten by the dragon.

Friday, June 27, 2014

Mexican DNA patterns reveal indigenous history and migrations

A major article in Science last week reveals the potential for modern DNA studies to reveal historic patterns of interaction and migration. It has implications for archaeology and especially for the use of ancient human DNA.

Moreno-Estrada, Andrées, et al. (2014). The Genetics of Mexico Recapitulates Native American Substructure and Affects Biomedical Traits. Science 344(6189): 1280-1285.

The authors sequenced large numbers (hundred of thousands) of SNPs (single nucleotide polymorphisms) from about 1000 individuals in Mexico, split between natives and mestizos (although I couldn't find in the article or the supplementary material how they determined who was which). In the data, you can see strong evidence for the genetic substructure of the population. That is, cultural, ethnic, and linguistic groups do have distinctive genetic signatures. For example, the Maya form a distinct group with additional internal structure. Within the Maya "clade" the Lacandon and Tojolobal form especially homogeneous subgroups that display little outside admixture. There's also a widespread "Central or Southern Mexican" clade (medium blue in Figure 2B and C) that impinges on the Maya. This clade is purest in southern Mexico (Oaxaca and environs), where it shows relatively little admixture. Maya genes also flowed into central Mexico (Figure 2B, bottom). In many cases, geography is a better predictor of genetics than language. Note, for example, how Nahua-speaking groups fall into more than one genetic group that is better defined spatially, which makes some sense when you think about actual mechanisms of gene flow. On the other hand, the data does contain genetic evidence of at least a couple of migrations. The most prominent one appears to go from the Yucatan Peninsula to what the authors call the Totonac region. If you plot the latitude and longitude of the sampling location given in the supplementary materials, it seems that it also close to the Huasteca. Whether this genetic contribution comes from the quite ancient Huastec migration or from a more recent Maya incursion, such as the Olmeca-Xicalanca conquest of Cacaxtla, is not addressed. I suspect, however, that the data could in theory be used as a molecular clock to date the migration, at least very roughly. Since the Huastec and Olmeca-Xicalanca migration are far apart in time, even a crude estimate would be sufficient to distinguish between them.

So, for archaeologists, there are a couple of significant facts. These kinds of studies can be used to understand prehistoric population dynamics. This is not news, perhaps. Genetic studies in Europe have been used for years to investigate the spread of agriculture and determine whether it was migration, diffusion, or both, and what the spatial dynamics were. It is interesting, however, to see it working in Mexico, which seems to me to be even more complex. Another important issue this study raises is the potential for ancient DNA to be matched to modern patterns. Presumably now we could take DNA from an archaeological individual and potentially match it preferentially to a "clade" defined by modern genetic distributions. That's an exciting possibility. It would provide far more information than the strontium isotope methods currently in use. Little ancient DNA has been sequenced in Mesoamerica, but now we have even more reason to do it.

Puerto Rican origins and Maize

Nice letter in yesterday's edition of Nature in which the authors point out that maize DNA in human coprolites from Vieques Island off Puerto Rico does not imply an origin in the Bolivian Andes, for the obvious reason that maize was widespread, not to mention that it had already arrived in the area at an earlier date.

Pagán-Jiménez, Jaime R., Reniel Rodriguez-Ramos, and José R. Oliver (2014). Ancient Cultures: Maize is not a clue to Puerto Rican Origins. Nature 510:473.

Friday, June 13, 2014

George Stuart, distinguished Maya archaeologist, has passed away

National Geographic, where he worked for many years, has posted a gracious obituary. He was a truly nice and unpretentious gentleman. Condolences to his friends and family.

Friday, May 30, 2014

Nicaragua trip

Last week, I returned from my first trip this summer to Nicaragua. I was fortunate to be able to spend some time with colleagues, friends, and family.

First, we went to Cusirisna Cave in the Department of Boaco. Kendra Philmon wrote her thesis on the materials in the cave, which are curated at the Harvard Peabody. We are hoping to publish a revision of her thesis as a monograph. At the SAA meetings, she asked me if it were possible that some of the teeth remained on the floor of the cave. Most of the crania in the collection have lost their front teeth. So, I stopped by with my wife to take a look. I also wanted to take more photos because those from my first trip were not great. It was a terrible mistake. Getting to the cave requires a bit of a scramble. It's in a gorge with very steep walls that are paved with loose rock. Moreover, I'm in terrible condition. My wife is in better condition, but she took a serious fall while I got overheated. I managed to get some pictures and take a quick look in the cave.I didn't see any teeth, but I noticed that there is a layer of earth that might conceal additional remains and could be excavated.
Cusirisna Cave. Right hand chamber. Machete points approximately north

Cusirisna Cave. Left-hand chambers

Lahar deposit underlying Cusirisna Cave.
From Cusirisna, we went to the town of Boaco to visit our friend Edgar Espinoza, a semi-retired archaeologist. He has a lovely home there, and he kindly invited us to spend the night.

The next day he took us to see some petroglyphs in the surrounding hills.

Petroglyphs near the base of the hill, Boaco

Petroglyph of a fawn near Las Lagunas, Boaco

Anthropomorphic petroglyph (shaman?) near Las Lagunas, Boaco
A couple of days later, we had the opportunity to visit a couple of sites near Somotillo, in the Department of Chinandega, that had been previously found by Jorge Zambrana and reported by Rigoberto Navarro. We first went to see a couple of sites named Don Noe, after the landowner. We found a historic wall, but we're not sure if it is part of one of the previously reported sites. We chatted with Don Noe, but he did not know where the previously reported prehistoric mound site was located. After I came back and mapped our points, I saw that we were a couple of hundred meters too far north.

Historic wall remnant on the property of Don Noe, southwest of Somotillo, Chinandega

Then we drove back to Somotillo and looped around to cross the Rio Gallo and then came back southwest to its junction with the Rio Negro.  Heading south from El Tejar, we found the site of Los Andinos, which turned out to be impressive. According to the original report, it has over 30 mounds, densely packed. We saw lots of material on the surface, including chert (perhaps heat-treated--see photo below), obsidian, and fine-paste ceramics. The fields with the mounds are being plowed, but fortunately with oxen. Tractors will destroy the mounds in no time. This site has more architecture than any other we have seen to date in the Department of Chinandega.

Artifacts in the road at Los Andinos. Note the dark red chert that may have been heat-treated. The fine paste ceramics are typical of the region, including the red slip and the light grey cores. The compass/clinometer has a centimeter scale on the side.

The largest mound that we saw at Los Andinos, which apparently lies in the northern part of the site.
My wife threw me a surprise birthday party in Somotillo in the Restaurante Katin in Somotillo. I can't remember the last time I had a birthday party, but it must have been when I was a small child. It was also the first time I had a piñata. If you watch shows like America's Funniest Home Videos, you know that gringos are incompetent at whacking a piñata, which is, frankly, embarrassing. I didn't hit anyone or break anything, and I didn't have to dance!

Birthday party at Rancho Katin, Somotillo

Birthday party at Rancho Katin, Somotillo

Whacking the piñata
Adios for now.