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miscarriage

Blue variant derived, correlated with higher anueploidy rates

A quick follow up to my previous post. To recap, a new paper in Science reports high (20-40%) derived frequencies for an allele which seems correlated with higher rates of aneuploidy. Anueploidy is bad, because often it results in nonviable offspring (individuals with Down syndrome have a viable anueploidy). The strange thing about this region of the genome is that it looks like modern humans have harbored this variant since the divergence from Neandertals. But, it has not gone to fixation. Its frequency in the intermediate range all this time, segregating in pretty much all populations from what it looks like, suggests balancing selection.

41ePHetk1dL._SY344_BO1,204,203,200_ Most of the paper is focused on medical genetics and the genome-wide association. The evolutionary aspect is interesting, but struck me as something of an afterthought. I made some chit-chat with the first author at the Bay Area Population Genomics meeting last December, and he didn’t let on that he had any good idea for why this allele was persisting. So I doubt that the group is wedded to the idea that miscarriage is a strategy for masking paternity and encouraging male investment. I’ve asked around people who work in behavioral ecology and they’re skeptical too. There’s a mystery here, and it’s kind of a big deal in my opinion, but there’s not much clarity.

On Twitter Vincent Lynch pointed out that the locus in question, PLK4, has been implicated in testes development. So one possible answer that crops up is that it is some form of sexually anatongistic selection. Meanwhile, Greg Cochran posits that we’re seeing some sort of meiotic drive, where there is selection pressure operating on the level of the genome itself (e.g., “selfish genetic elements” type dynamics). These are both plausible to me, and suggest that there needn’t be an explanation rooted in our human uniqueness to answer this particular genomic mystery.

hominids A common tendency among genomicists, who are modern humans, is to always highlight variants which have been selected in our lineage in comparison to nearby lineages. Before ancient DNA this usually meant chimpanzees, but now we’re talking Neandertals and Denisovans. Humans are a pretty big deal, and intuitively we think that our genomics are also a pretty big deal. There must be a key that unlocks our uniqueness, so searching through the 3 billion base pairs in our genome we stumble upon distinctive evolutionary histories, and think “eureka, this is It, the ultimate locus of our genius!” In pre-modern language, our souls. But the fact is that over tens of millions of polymorphisms in the genome you are naturally going to find regions where we are unique in relation to our relatives, and the broader mammalian family tree, just as a matter of chance. If we lived in the world of the Neanderthal Parallex no doubt Neandertal genomicists would be engaging in the same search for the uniqueness of their lineage, and discover regions where they are sui generis in relation to other hominins and mammals more broadly. The few times I’ve been to ASHG I stumble onto talks where the authors present evidence of genomic regions which are unique in our species, the implication being that this might be somehow responsible for the nature of who we are. Of course the researchers in question are usually not interested in that topic that much, rather, it is an interesting side element that adds to the sexiness of their results, and the glamour usually fades over time.

There is the quest for the the gene for everything. It’s a major problem with media representations of behavior genetics. But a lot of interesting traits are polygenic. We’ve long known this from classical genetics, and genomics is confirming this. There’s not a gene for anything, but a host of genes. Quantitative genetics is banal, but it is powerful. We need to be more open to the possibility that humanity as we understand it isn’t a clear and distinct thing, but the end of a distribution of possibilities long pregnant in our lineage of apes.

 
• Category: Science • Tags: Genetics, Human Evolution 
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  1. So-called humans are just low-function apes physically and high-function apes
    mentally with very few having sufficient cerebral control to become human.

    If you took an alpha-male chimp and increased its IQ by 100 you would have a politician. If you raised it by 150 points you would have a clever politician. Neither would be human because of serious shortcomings in morality.

  2. Anonymous • Disclaimer says:

    About the uniqueness issue, I am a strong advocate of comparative population genomics where the genes evolving adaptively are compared between a large number of species, in a very quantitative way and with no a priori. Imagine if FOXP2 was found in selective sweeps in 25% of primates, that would shed a very different light on why we think it has evolved adaptively in human.

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