January 26, 2014

Human Y chromosome undergoes purifying selection

A somewhat technical yet interesting study on Y chromosome evolution in humans:

Melissa A. Wilson Sayres et al., Natural Selection Reduced Diversity on Human Y Chromosomes. PLoS ONE 2014. Open accessLINK [doi:10.1371/journal.pgen.1004064]

Abstract

The human Y chromosome exhibits surprisingly low levels of genetic diversity. This could result from neutral processes if the effective population size of males is reduced relative to females due to a higher variance in the number of offspring from males than from females. Alternatively, selection acting on new mutations, and affecting linked neutral sites, could reduce variability on the Y chromosome. Here, using genome-wide analyses of X, Y, autosomal and mitochondrial DNA, in combination with extensive population genetic simulations, we show that low observed Y chromosome variability is not consistent with a purely neutral model. Instead, we show that models of purifying selection are consistent with observed Y diversity. Further, the number of sites estimated to be under purifying selection greatly exceeds the number of Y-linked coding sites, suggesting the importance of the highly repetitive ampliconic regions. While we show that purifying selection removing deleterious mutations can explain the low diversity on the Y chromosome, we cannot exclude the possibility that positive selection acting on beneficial mutations could have also reduced diversity in linked neutral regions, and may have contributed to lowering human Y chromosome diversity. Because the functional significance of the ampliconic regions is poorly understood, our findings should motivate future research in this area.


Positive selection (or directional selection) happens when a variant gets so good that everything else becomes bad by comparison. This may be just because an environmental change, possibly caused by migration (or whatever other reason) substantially alters the rules of the game. Much more rarely a novel mutation (or accumulation of several of them) may happen to generate a phenotype that is much more fit even for pre-existent conditions. As I understand it, positive selection does happen only rarely (but spectacularly). An example in humans is the selection of whiter skin shades in latitudes far away from the tropics (because of the "photosynthesis" of vitamin D in the skin, crucial for early brain development), another more generalized one is the selection for improved brains (not necessarily just bigger), able to face changing conditions more dynamically and develop more efficient tools and weapons.

Purifying selection (or negative selection) is quite different and surely much more common. As novel mutations arise randomly, in at least many cases, the vast majority I dare say, they happen to be harmful for a previously well-tuned genotype (and its derived phenotype). As result, the carriers have decreased opportunities for reproduction, when they don't just die right away. Natural selection acts mostly this way and in many cases the types can become very stable for this reason, as happens with genera that have been successful on this planet since long before humankind arose, such as sharks or crocodiles.

This last is what seems to be happening to the human Y chromosome: novel mutations are at least quite often harmful (maybe they cause sterility or whatever other traits in the male that cause decreased reproductive efficiency) and they are regularly pruned off the tree by natural selection. 


Purifying selection slows down the effective mutation rate

Interestingly the authors mention that:
... if purifying selection is the dominant force on the Y chromosome, the topology of the tree should remain intact, but the coalescent times are expected to be reduced.

That would be, I understand, because the observed mutation rate has little relation with the actual accumulated (effective) mutation rate, which is much slower because of the continuous pruning of the negative selection.

Purifying selection has also been observed in the mitochondrial DNA, having the same kind of slowing impact on the "molecular clock".

6 comments:

  1. kaixo, I wonder if you are considering that the Andalusian population, overwhelmingly, is relatively recent in the territory. Do not forget that most of the Andalusian (I come from Málaga) come from the repopulation which carried out the Christian conquerors in the XIII century (Western Andalusia and Jaén) and XV (old Nazari kingdom of Granada), in fact Huelva was one the first territories to be repopulated and eastern Andalusia, the last, mostly with people from the north and center of the Iberian Peninsula but also from present France, in the case of Eastern Andalusia, as far as I know the majority came from neighboring territories. The Muslim population (mostly native, as far as I know was expulsed to the kingdoms of León, Galicia and Valencia). Is my perception correct or should I change the chip?.
    Ezkerrik asko, me encanta tu blog y estoy aprendiendo mucho contigo

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  2. Aupa, Jandro. I wonder if you wanted to comment in some other thread, maybe this one on W-E Andalusian genetics, which I bet you'd find interesting.

    The big question is: is actually "the Andalusian population, overwhelmingly, is relatively recent in the territory" as you (and many others) seem to believe? And my answer would be: probably not, at least not to any great extent. There were localized repopulations no doubt but it seems clear that they overall impact was limited: after all Castile is a rather arid steppary land and instead Andalusia a fertile country densely inhabited since very old. In addition to that, many Andalusians were Christians and those who adopted Islam were forced to convert.

    But my main argument is that there is no obvious N-S genetic cline in Iberia, as would be expected if there would have been important demographic changes with the Muslim and Christian sequential invasions. The main cline in Iberia seems to be a W-E one, in which North African influence is concentrated in the Western third, including such unlikely places as Galicia, Asturias, León and even Cantabria. This cline also divides Andalusia in two areas. Ironically there's almost no remnant of North African influence in the last Moorish stronghold of Granada and that is extremely hard to explain if we assume that important demographic movements were at play and that the so-called Moriscos were still clearly important in the region long after the conquest.

    The situation reminds a bit of Bosnia, where Muslims were converted from the locals with nearly no external genetic input (Bogomils massively embraced Islam) only that here they were also re-converted to Christianity, even if by force in many cases, instead of just being ethnically cleansed.

    "Huelva was one the first territories to be repopulated and eastern Andalusia, the last, mostly with people from the north and center of the Iberian Peninsula but also from present France".

    Actually the Onubense genetic pool is most similar to the Portuguese one, although I strongly doubt it has anything to do with the Christian conquest, being most likely something older, which was only slightly modified by it. Some details are unusual in any case: the frequency of mtDNA K is higher in Huelva than in any other part of West Iberia and probably all Iberia. It is this kind of traits what point to a local deeply rooted population, even if its origins may well be in the Bronze Age, when it was affected by the southern Portuguese "horizons" phenomenon (or whatever else). Unless you want to posit a strong recent founder effect of most unclear origin, which seems to me most unlikely.

    In the Y-DNA side, Huelva again does not look like the bulk of Iberia but rather Portuguese-like, although with some differences again.

    ...

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  3. "The Muslim population (mostly native, as far as I know was expulsed to the kingdoms of León, Galicia and Valencia)".

    What's your source for this claim? I never heard this story. I know that the Muslims were in 1492 given the painful choice of exile or conversion and that many remained as clandestine Muslims for long, while the elites of Valencia and Aragón particularly (but probably also in other places) tried to dribble the edict because these were too valuable workers to force them out.

    I think that there are many myths regarding colonization, not just of Andalusia but even of America. Recently I was surprised to discover (needs confirmation but seems very solid so far) that most "Spanish" ancestry in Caribbean America is in fact Guanche (→ read especially the update at this entry, also comments).

    Similarly, I suspect that a number of localized episodes of colonization in former Al Andalus, have served as basis for the creation of a chauvinist myth, something that certain Spanish nationalist historiography is very inclined to do. Just like deciding that ancient Cantabri and Astures were "Celts", no matter that they fought with the Aquitani (Basque speakers) because they were "relatives" and quite a bit of other evidence against the Celtic hypothesis. After all for certain people history is a tool for a nationalist and often imperialist ideology and not the unveiling of truth by means of impartial research.

    "Is my perception correct or should I change the chip?."

    That's up to you to decide. I can only offer my opinion and some information in any case. But I do think that, judging on Portuguese and Basque ancient DNA, as well as other info from around Europe, the population structure was in many consolidated in either the Neolithic (few cases, Basques may be one) or the Metal Ages (probably most but over a Neolithic substrate of importance, which in turn also had important Paleolithic elements incorporated). Later changes have happened locally (most importantly in Poland after WWII) but they seem less important and more localized.

    A good example of quasi-mythological migration is that of the Slavs to the Balcans. The reality is that Balcanic Slavs are, with the only exception of Slovenes, very much indistinct from the non-Slavic peoples of the Balcans and quite different from Northern Slavs instead. I wouldn't say that there was zero immigration in the 7th century over there but mostly they are descendants of assimilated locals. That's almost certainly also the case in Andalusia.

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  4. Another thing that came to my mind. Maybe better researched is the similar colonization movement in East Germany, Austria parts of Czechia and much of historical Poland known as Drang Nach Östen. In those areas there were new German settlers, yes, but the original Slavic population did not disappear: both merged as time passed and became Germans. Actually a Slavic population still survives with such identity in East Germany: the Sorbs. It's very likely that East Germans and Austrians are at least largely of Slavic ascent.

    However, unlike the Castilian repoblaciones, this was a sustained movement of colonization through many centuries, what is much more likely to make an impact, both cultural and genetic. The Castilian colonization happened at most just once, not being a sustained movement, so the influence in both aspects must have been much weaker. Incidentally, how can you imagine such a distinct dialect as Andalusian (whose pronunciation can be so extremely different from the original Castilian that I compare with the differences between this romance and French) could have coalesced without a most strong substrate influence? If Andalusia would have been colonized as you think, you should speak with a Burgos accent or almost. Even American Spanish is much more similar to original Castilian than hardcore Andalusian is.

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  5. And also: how many small farms do you know in your area? The colonization of agricultural areas was always done by giving people land (otherwise why would they go?) but Andalusia is the epitome of latifundism, what means that the original inhabitants were kept as serfs. And in the Middle Ages farm workers were more than 90% of the population everywhere. This actually happened in all Al Andalus, including Zaragoza (incorporated to Aragon), Valencia, Extremadura, Southern Portugal, etc.: the Muslim or later convert peasants were kept because they were very valuable.

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  6. "But my main argument is that there is no obvious N-S genetic cline in Iberia, as would be expected if there would have been important demographic changes with the Muslim and Christian sequential invasions."

    I think strategic locations may explain this. Any conqueror and their demographic impact is likely to be concentrated in the most militarily strategic locations - which are also the places most likely to be massacred by the next conqueror. So a region with an important town/fortress controlling a ford might be conquered and the original population completely replaced while the surrounding region remains demographically the same. If another conqueror comes along soon enough before that demographic center has spread and massacres the town again and repopulates it it could be like nothing ever happened.

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