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Ainu man from 1870 (colorized)

Well, not really. But a new paper in PLOS GENETICS has a really weird speculation nested into the discussion of what seems a relatively banal paper on the phylogeography of South Americans. It’s a Y chromosomal survey of the populations of the New World, so it’s tracing the male lineage only. Because Amerindian populations likely went through at least one (more if you accept multiple migrations) bottleneck the variation on the Y chromosome is low. Ideally you’d be looking at tens of thousands of markers on the autosome, the non-sex inherited genome. But this group had a very good population coverage. Over 1,000 men from 50 tribal populations, with a focus on South America. Additionally, non-recombining markers are more manageable in terms of reconstructing demographic histories.

Here’s the frankly bizarre inference (it may still be right, but it’s still bizarre):

In view of the above, two scenarios for the introduction of C3* into Ecuador seem credible: (i) one or more late migratory waves that quickly passed North and Central America without leaving a trace of C3*, and (ii) long-distance contact with East Asia. As regards the second scenario, there appears to be at least some…In particular, the similarity of ceramic artifacts found in both regions led to the hypothesis of a trans-Pacific connection between the middle Jōmon culture of Kyushu (Japan) and the littoral Valdivia culture in Ecuador at 4400–3300 BC. In view of the close proximity of the spotty C3* cluster to the Valdivia site, which was considered at the time to represent the earliest pottery in the New World[40], it may well be that C3* was introduced into the northwest of South America from East Asia by sea, either along the American west coast or across the Pacific (with some help by major currents). Please note that they modeled the last common ancestors of the East Asian and South American C3* lineages, and it looks to be ~6,000 years before the present. But if I’m reading the results table right the intervals could push it as far as ~10,000 years before the present.

To me this looks like the Indian-admixture-into-Australians paper. Suggestive, but so strange that we should wait until our prior expectations are obviously wrong. Unfortunately I don’t see the raw data in the links, though perhaps if someone could find them they could post that in the comments. I would be curious to replicate the results at some point.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Amerindians, Human Genetics 
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Several readers have expressed skepticism of the high mortality numbers Charles C. Mann reports in his two books in relation to the Columbian Exchange. In case you are not aware, the thesis that Mann outlines is that the primary necessary condition whereby Europeans managed to eliminate indigenous populations from much of the New World was that they brought with them diseases which the native people did not have an immunity to. This model often argues that mortality rates were on the order of 90 percent. Such a scenario has broad plausibility because the situation in the New World has an inverse counterpoint: Africa. Before quinine the European dominion on the continent was limited to outposts and fringes (e.g., the Cape region of South Africa, which was free of many of the diseases deadly to Europeans). Overall I find Mann’s argument qualitatively reasonable, even if one may qualify it on the margins quantitatively. But I stumbled upon more evidence recently: it still holds for those Amerindians which have not been exposed to Eurasian diseases. From a National Geographic story, Into the Amazon:

But violent clashes account for only a fraction of the deaths suffered by native communities at the hands of outsiders. Most died from epidemic diseases, including the common cold, for which they had no biological defenses. Ivan Arapa, one of our scouts, is from the Matis tribe, who were first contacted by the outside world about 25 years ago. Ivan still remembers the wholesale death that accompanied these very first visits of Brazilian government officials to his village.

“Everyone was coughing, everyone was dying,” he recalls. “Many, many Matis died. We didn’t know why.”

More than half of the 350 Matis living along the Ituí River inside the Javari reserve perished in the months following contact, officials say.

It’s a dismal story that’s become all too familiar to Possuelo during his 40-year career as a sertanista, a uniquely Brazilian profession that folds all the skills and passions of a frontiersman, ethnographer, adventurer, and Indian rights activist into a single, eclectic vocation. That’s why our mission is not to make contact with the Flecheiros but rather to gather information on the extent of their territory’s boundaries, information Possuelo will use to bolster his efforts to protect their lands. In other respects, the Flecheiros are to remain, in large measure, a mystery.

Over thousands of years Eurasians, and to a large extent most inhabitants of the “World Island” (Eurasia + Africa), have become habituated to a range of endemic ailments which may make us miserable, but do not kill us. Our bodies are hosts to an order of magnitude more bacteria than our own tissue cells. Most are innocuous or beneficial, but some are potentially deadly. Many of us carry pathogens which do not result in any illness over our lifetimes. There are geneticists who argue that a small minority of people exhibit genetic susceptibilities to pathogens which are normally benign. What if these people are the ancestral type?

I think about this in particular when considering the case of the Sentinel Islanders. This tribe has been left alone by the Indian government, and remains out of contact with the rest of humanity. Some of this is a function that other Andaman Island tribes which have had extensive contact with people from the mainland have not done so well due to the combined effects of Indian disease and diet. But is it right and proper that modern humans be isolated from the rest of the population for their own good? What does the reality of a whole people who are viewed as “Bubble Boys” tell us about the range of the human condition?

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Amerindians, Anthropology, Charles C. Mann, Culture 
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journal.pbio.0000027.g002

John Hawks illustrates what can be gained at the intersection of old data and analysis and new knowledge, Quote: Boyd on New World pigmentation clines:

I’m using some statistics out of William Boyd’s 1956 printing of Genetics and the Races of Man[1]. It gives a good accounting of blood group data known more than fifty years ago, which I’m using to illustrate my intro lectures. Meanwhile, there are some interesting passages, from the standpoint of today’s knowledge of the human genome and its variation.

On skin pigmentation – this is the earliest statement I’ve run across of the argument that the New World pigmentation cline is shallower than the Old World cline because of the relative recency of occupation….

Looking at what was said about pigmentation generations ago is of interest because it’s a trait which in many ways we have pegged. See Molecular genetics of human pigmentation diversity. Why humans vary in pigmentation in a deep ultimate sense is still an issue of some contention, but how they do so, and when the differences came about, are questions which are now modestly well understood. We know most of the genetic variants which produce between population variation. We also know that East and West Eurasians seem to have been subject to independent depigmentation events. We also know that some of the depigmentation was relatively recent, probably after the Last Glacial Maximum, and possibly as late as the advent of agriculture.

On the New World cline, which is clearly shallower than that of the Old World. The chart below from Signatures of positive selection in genes associated with human skin pigmentation as revealed from analyses of single nucleotide polymorphisms is useful:


skinvarianceWhat you’re seeing here are patterns of relationships by population when it comes to the select subset of genes which we know are implicated in between population variation in pigmentation. The peoples of Melanesia are arguably the darkest skinned peoples outside of Africa (and perhaps India), and interestingly they are closer to Africans than any other non-African population. But in total genome content they’re more distant from Africans than other non-African populations, excluding the peoples of the New World.

This disjunction between phylogenetic relationships when looking at broad swaths of the genome, as opposed to constraining the analysis to the half a dozen or so genes which specifically encode between population differences on a specific trait, is indicative of selection. In this case, probably functional constraint on the genetic architecture. From the reading I’ve done on skin pigmentation genetics there is an ancestral “consensus sequence” on these genes which result in dark complexions. In contrast, as has been extensively documented over the last few years there are different ways to be light skinned. In fact, the Neandertals which have been sequenced at those loci of interest also turn out to have a different genetic variant than modern humans.

How to explain this? I think here we can go back to our first course in genetics in undergrad: it is easier to lose function than gain function. The best current estimate is that on the order of one million years ago our species lost its fur, and developed dark skin. And it doesn’t look like we’ve reinvented the wheel since that time. All of the peoples termed “black” across the world, from India, to Australasia, to Africa, are dark because of that ancestral genetic innovation. In contrast, deleterious mutations which “break” the function of the genes which gave some of us an ebony complexion occur relatively frequently, and seem to have resulted in lighter skinned groups in more northerly climes. It turns out that some of the pigmentation genes which are implicated in between population variance in complexion were actually originally discovered because of their role in albinism.

So how does this relate to the New World? I think the difficulty in gaining function once it has been lost explains why the people of Peru or the Amazon are not as dark skinned as those of Africa, Melanesia, or South Asia . They haven’t had enough time to regain function which they lost as H. sapiens traversed northern Eurasia. So there you have it. A nice little illustration of how the genetics taught to 18 year olds can be leveraged by the insights of modern genomics and biological anthropology! In the end, nature is one.

Image Credit: Dennis O’Neil

(Republished from Discover/GNXP by permission of author or representative)
 
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Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"