Sensitive Detection of gene flow

One problem with arguing with ignorant people is that they don’t usually have indicator lights that tell you exactly how ignorant they are.  This matters when you’re trying to explain something: it’s not always clear  how much goes without saying.

About the imaginary high levels of gene flow between distant populations in the past: if that had happened, Fst between those populations would be close to zero.  It’s not. And when an inevitable consequence of a certain proposition is false, the proposition is false.

But here’s another example: falciparum malaria probably originated in Africa ( it’s closely related to a kind of malaria that infects gorillas). At some point it spread to humans, and it’s a bear – in terms of evolutionary pressures, probably the worst disease in the world.

Many different expensive genetic defenses have arisen in populations exposed to malaria. But those seen in southeast Asia/PNG are, at the molecular level, entirely different from the ones seen in  Africa. As far as I know, there is no overlap at all. You see mutations of the same gene showing up in those far-separated populations ( convergence) , but the SNPs are never the same.

The sickle-cell allele would have been advantageous in, say, PNG lowlands, and if even a few copies had ever arrived there, it would have become common rather rapidly. A smidgen of gene flow from sub-Saharan africa , even 20 individuals total, would have left a genetic signature in PNG. [ just as a few copies of Denisovan altitude-tolerance alleles were enough to transform Tibetans]  That smidgen would have grown geometrically with time: it would function as a very sensitive detector of African gene flow.  But it never happened. Contrariwise, some of the malaria defenses in PNG ( like Melanesian ovalcytosis)  would have spread widely in Africa with even a little gene flow.  But that never happened either.



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Ashkenazi PRS

There are now a couple of surveys with Ashkenazi EA polygenic scores.  We don’t know that the populations were representative, but probably they weren’t far off. Scores correspond to an IQ of about 110. Personally, I’m still pulling for 112.

A fair number of people publicly disagreed with our Ashkenazi hypothesis.

They were wrong.



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Herbert West

Just ran into an interesting question from a biology problem set:

” Using the laws of thermodynamics, explain why it’s impossible to re-animate organisms that have died ( making Frankenstein’s monster and zombies impossible so we don’t have to worry about a zombie apocalypse.) “

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Homo Japonicus

Near glacial maxima, archaic humans could have walked to Japan, so they surely did. Elephants made it.

Most of the time, even in the ice ages,  Japan was fairly isolated. Maybe the northern path through Sakhalin was open  (although glaciated) , but most of the time water separated Korea and Japan.

There must have been versions of homo erectus and  Denisovans in Japan. They haven’t  been found, but I think people haven’t looked much.. It used to be assumed nobody lived in Japan before the  Jōmon, so people didn’t dig before the Jōmon  stratum (14,000 BC).

But there must have been archaics there, back in the Paleolithic.

Seek and ye shall find.




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LINEs, SINEs, and Sundaland

Maybe ten years ago,  Henry was analyzing some retrotransposons, sequences that randomly make and insert more copies of themselves. These mutations are statistically simpler in some ways that nucleotide substitutions:  insertions are unique.

Henry had gotten some sign reversed while I was distracting him, so for a moment it looked as if modern humans had originated in Southeast Asia, instead of  Africa or nearby.  So the new task  was to come up with a scenario that might explain that.  I was in a silly mood, which helped: took me about a minute to suggest that some of  the Indonesian islands and their neighbors went back and forth between between being accessible during deep glacial maxima ( low sea levels, Indonesian archipelago turns into Sundaland)  and separated most of the rest of the time:  allowing  for occasional colonization by archaic sapiens, isolation and local adaptation, maybe even speciation.

Since then we’ve found signs of Denisovan admixture in people in Melanesians ( PNG, Australia, the Solomons), hobbits on Flores, other little guys in the Philippines, and old tools in Sulawesi.  Very likely we’re going to find Sulawesi man.  I wouldn’t be surprised to see five or more separate archaic pops in those islands. Maybe derived erectus, maybe something earlier, maybe highly differentiated Denisovans, maybe all of the above and a few dark elves. I still don’t think they made to Australia, but I wouldn’t bet my life on it.

While it looks as if Neanderthals made it to Crete.

Since there were land bridges to Japan in  glacial maxima, you’d have to to suspect that they had their own local archaic populations as well.  To a decent approximation, if elephants could colonize a place, so could archaic humans.



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No, No, Not Rogov!

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If  Amerindians had a lot fewer serious infectious diseases than Old Worlders, something else had to limit population – and it wasn’t the Pill.

Surely there was more death by violence. In principle they could have sat down and quietly starved to death, but I doubt it. Better to burn out than fade away.


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