Cal Tech

The only time I wandered around Cal Tech, I noticed a corpse lying on the floor of an office.

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Ashkenazi Ancestry revisited

Shai Carmi has his article out on Ashkenazi Jewish ancestry.  A few comments:

First, looks like a good job, on the whole. Perhaps Carmi had special training…

Second, about dates: they assume a mutation rate of 1.44 x 10-8 per generation, and a generation length of 25 years. I think both of those are a little off.  All the directly-measured whole-genome rates are between 0.96×10−8 and 1.20×10−8: I wouldn’t go higher than 1.20 x 10-8 per generation, with what I know now.  In the course of looking at paternal age effects, I also checked out the known data on average generation lengths. In no known population is it as short as 25 years: never less than 28 for females, and almost always longer than 28 for males, usually in the 30s.  30 is a much more reasonable generation length than 25.

The date estimates are inversely related to the assumed mutation rate and directly proportional to the generation length.

In the article, they estimate an Ashkenazi bottleneck with an effective size of 250-420, 25-32 generations ago. With a mutation rate of 1.2 x 10-8 per generation, that changes to an effective size of 300-500 (not much different) 30-38.4 generations ago.

By their numbers, we’re talking 625-800 years ago.  Adjusted, 900-1150. Since we know for sure that at least some Ashkenazi Jews were in the Rhineland before the year 1000, I think that the revised estimate indicates that the original settlement was the bottleneck, which makes sense.

Third, about comparison populations: they used Flemings as a sample European population, and estimated the Ashkenazi Jews are 46-50% European. Why Flemings?  All the previous analyses have suggested that their European component is from southern Europe.  The mtDNA analysis is pretty specific: Italy and France.   I think you’d get a better estimate using Italians, and it would probably yield a slightly higher estimate of European admixture.

Posted in Ashkenazi Jews | 107 Comments

The Genghis-Khan effect

We know of several examples of a huge expansion of a paternal lineage, and several other cases seem likely to be the same thing.  It’s worth taking a close look at the first one found, the paternal lineage of Genghis Khan.

8% of the men in  Central Asia carry this y-chromosome, half a percent of all men. One of the authors of that study made an interesting mistake: Chris Tyler-Smith, in an interview, said “We don’t think that Genghis Khan was the common ancestor, because our best estimate of the time when the common ancestor lived was a few generations before he was born.”

Now that’s silly, because are big error bars in that kind of TMRCA, not least when you’re doing Y-chromosomes with STRs, the state of the art at that time. If you found a piece of trinitite at Alamagordo and came up with a date of  1943 from some kind of radioactive dating, forget it: it was July 16th, 1945, 05:29:21 MWT (plus or minus 2 seconds).  In much the same way, we know when Genghis Khan made his historical moves, and we know who the rewards flowed to – his sons, and a smaller fraction to his full brothers, not his cousins or whatever.  Genghis’s sons got countries, had harems, founded dynasties: he (or maybe his father, depending upon how successful Hasar and Hachiun were) is the TMRCA .

It seems to me that this error stems from geneticists thinking that genetic data is the only real data: sloppy genetic time estimates trump precise historical dates.  In much the same way, people (using the old too-high mutation rate) estimated that the split with Neanderthals was ~300,000  years ago, even though the fossil record clearly showed hominids in Europe shambling towards Neanderhood half a million years ago.  The new, lower estimates of the mutation rate have reconciled genetic and paleontological evidence on the split time  – but the geneticists should have realized that there was an inconsistency.

Unfortunately other disciplines have the exact same problem.

Anyhow, the existence of the Genghis effect should have us thinking more generally, about Clark’s survival of the richest, or about populations that grow from hundreds to millions in a few centuries, after chancing on a favorable ecological niche (moneylending, or being pacifist farmers in America, or perhaps a ruling class after a conquest).  A ruling class could end up replacing the original conquered population without even intending to, if it stayed fairly endogamous while having higher fertility than the serfs.

Posted in Genghis -Khan effect, Neanderthals | 119 Comments

Understanding EDAR

The east Asian EDAR mutation is screwy: it does too many things. It causes increased scalp hair thickness, shovel-shaped incisors, an increase in the number of eccrine sweat glands, and smaller breasts. Which of these seem likely to confer a few-percent advantage?  Why, none of them, of course.

Normally, an advantageous mutation does something useful and not a whole lot of anything else.  That’s because change in a trait is usually bad – it moves you away from the Darwinian optimum.  Coming up with an improved version of one trait is unlikely enough, and usually happens only in a new environment, where the selective pressures have changed.  Coming up with multiple significant changes that are all neutral is most unlikely.

Now if the side effect is in a trait that doesn’t matter anymore, you might get away with it.  For example, a mutation that has a favorable effect X while making you pale works in northern Europe.  The paleness itself may even be advantageous.

Pardis Sabeti thought that extra sweat glands might have been the advantage.  Joshua Akey suggested sexual selection – a preference for thick hair and small breasts. Kamberov thought different effects of EDAR might have been favored at different times.

They are all wrong.  Am I really supposed to believe that you needed to sweat more in ice age China than in Africa?  Breast size already varies – if for some mysterious reason human sexual fashion came to favor smaller ones,  selection on standing variation could have done the job without changing your hair and teeth and sweat glands – changes  that would almost certainly be disadvantageous..  The idea that different effects  conferred advantage at different times is also a nonstarter: any singe positive change is very unlikely, and I’m suppose to believe in several?

It’s gotta be something else, an effect that we don’t know, and it must confer a substantial advantage.

 

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We Three Kings

A recent article says that 40% of Chinese Y-chromosomes originated from 3 men in the late neolithic.  This pattern,  fantastic success for a particular paternal lineage, has been seen before, with the Golden Family (descendants of Genghis Khan) and the Qing dynasty.   Something similar may well have happened with the big R1b and R1a lineages.

Did any historian predict this pattern?  I can’t think of one, off the top of my head. Someone who went to bed with The Empire of the Steppes under his pillow, someone familiar with the continuing high status of the Golden Family in recent centuries,  might have, perhaps.

 

Posted in Genetics | 53 Comments

Degüello

There’s a new paper out on the genetic prehistory of the Canadian Arctic. Basically, it says that existing Eskimos replaced a genetically different population less than 700 years ago, and that those earlier Paleo-Eskimos (Dorset culture) represent yet another separate migration from Asia (in addition to the PaleoIndians, the Na-Dene, and the Eskimo).  They put this in such a nice way: “the genetic continuity characterizing the Paleo-Eskimo period was interrupted by the arrival of a new population.”

Which likely means that the neo-Eskimos killed off the Dorset people.  Obviously they weren’t farmers, the usual suspects in replacement, but the new guys had a more sophisticated technology ( and probably greater numbers) ,  with  bows, large skin boats, dog sleds, whale-hunting gear, etc.  The neo-Eskimos have certainly done their share of fighting in recent historical times – they went at it hammer-and-tongs with various Amerindian tribes.

This is fairly obvious, so much so that even the New York Times and the Washington Post mentioned extermination by the newcomers as a possible explanation.  There is no mention of that possibility in the original research article, but I’m sure that some of the authors were quite aware of it. What they said is probably influenced by the fear that saying anything negative, no matter how true, might cause the Eskimos to refuse cooperation in the future.

This pre-agricultural genocide makes you wonder  just how often similar wipeouts may happened in the past.  Maybe the Gravettians and Aurignacians weren’t the same people.

 

Posted in Amerindians, Eskimo | 69 Comments

The Wrong Path

Turning Pygmy hasn’t turned out to be a very good long-run strategy. All such populations have big problems.  First, they’re vastly outnumbered by peoples that adopted agriculture.  Second, they’re short – shorter than their farmer neighbors –  and generally that has been a disadvantage in disputes. Contemporary African pygmies are ‘ hereditary servants’ of their Bantu neighbors: we have another word for that.  Maybe AK-47s will turn that around some day (God made some men big and some men small, but Mikhail Kalashnikov made them all equal, like a good Communist), but it hasn’t happened yet.  And with their small numbers, I’m not optimistic.

Moreover,  it seems that they may have incurred an intellectual disadvantage as well. They have small brains, probably the smallest of any existing human population. I found a reference claiming an average endocranial volume of 1,085  cm3 for the Aka: that’s the lowest number ever reported.  Their reported IQ scores are very, very low.  Their neighbors, who don’t score high themselves, think that the Pygmies have rocks in their head, don’t plan ahead, are irresponsible, etc  And of course they have trouble with alcohol.

A recent paper by Andrea Migliano argued that high risk, mainly from infectious disease, has selected for an accelerated life-history among Pygmies. I’m not convinced, but if she’s right, they would age more rapidly as well.  I’m not sure that is actually the case.

All this should have been obvious when modern humans were wandering into the African rainforest tens of thousands of years ago. What were they thinking?

 

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