I am always on the lookout for anomalies between human populations, especially Africans and non-Africans, because they are usually explained away by the classic Out Of Africa reasons of "lower genetic diversity", "bottlenecks", and "founder effects". Natural selection and Neanderthal admixture are also used as explanations.
But, sometimes these unusual situations point at flaws in existing theories, such as mutation rates which vary between population, and over time, or influenced by genetic diversity, non-neutral evolution, etc.
In today's post we will look into the X//A ratio.
What is the X/A Ratio?
Human beings have two sex-defining chromosomes, one is called "X", the other, "Y". Women carry two X chromosomes (they receive one from each parent). So each woman has an XX pair of sex defining chromosomes.
Men on the other hand carry the male defining chromosome Y (received from their biological father), plus an X (received from their mother). Each man, therefore carries a pair of XY chromosomes.
The remaining autosomal chromosomes add up to 22 pairs of chromosomes, a total of 44 chromosomes.
The uneven distribution of X chromosomes in each sex has some interesting consequences.
Since there is roughly one woman for every man, the 44 non-sexual chromosomes are equally distributed and represented in either sex. 44 in men, 44 in women. On average, they spend 50% of their time inside women and 50% inside men, subjected to the chance presence of random mutations, or the action of natural selection.
But, when it comes to the four sexual chromosomes, three of them are "X" and only one is "Y". Women carry two out of the three "X" chromosomes, men carry only one of them.
So X chromosomes spend more time inside women than men. This means that they could be subjected to sexually oriented processes that could modify them with a different intensity, duration and, effects, in each sex.
The expected value of X/A Ratio
In a population with N individuals, half women (N/2) and the other half men (N/2), we can calculate how many X chromosomes ther are in the population. Since women carry 2, and men carry 1, the formula is the following (X in women plus X in men):
2 x (N/2) + 1 x (N/2) = 3 x (N/2) = 1.5 N
Each individual in the population is a diploid, because he, or she, carries two copies of each autosome, having received one from each parent. So for the N individuals, there are 2 copies of each autosome, resulting in 2N autosomes in the population. These are spread 50:50 between men and women.
Now we can calculate the ratio of X chromosomes (X) to autosomes (A) in the population (X/A) can be calculated as:
X/A = 1.5N/2N = 3/4 = 0.75
The "real" value of the X/A ratio
However, when the value is measured in the field, it is not 0.75. There are higher values among Africans, and lower ones in American Latinos, Europeans, and Asians.
Let's look into the X/A ratio in different populations
Among Bonobos (Pan paniscus), our closest living relative (along with the common chimpanzee —Pan troglodytes), the X/A ratio is 0.85 (see Suplemmentary Material, p 114 in Prüfer, 2012
That same study found the X/A ratio for African Yorubas as 0.8, and for a European as 0.68 (p. 120). That is a big deviation from the expected value of 0.75.
Another study by Arbiza, 2014 found similar values; They can be seen in the chart below. The authors point out that they sampled different subpopulations and confirmed the skew in the value: "three populations from the African (AFR) continental group: all three estimates were in the range 0.76–0.77... It was 0.64–0.65 for all five populations of European (EUR) ancestry and 0.60–0.62 for the three East Asian (ASN) populations."
The authors measured but then discarded the American Latino "AMR" group, where variability was even higher, ranging from 0.71 for Puerto Rican (PUR) populations to 0.64 for Mexican Americans (MXL). The reason is that these are admixed people with African (slave trade), European (migration) and Amerindian genes, and there was a sexual bias in the introgressing groups.
This is reasonable, there were many more European males than females who came to the Americas during the first centuries after its discovery. So these men displaced local native males and married/mated with Native women. There were also more men than women in the African slave trade —roughly 1.7:1 ratio (Source). Both factors, plus the "Great Dying" that wiped out up to 90% of the Amerindians between 1492 and 1550, completely distorted the original X to A ratio in the Americas. What we see now is the outcome of admixture, extinction, and migration.
Below is a slightly modified figure 1 in Arbiza, 2014, I added the 0.75 line as a marker.
Explaining the difference. Why is the X:A ratio lower in Eurasians?
The large variation from the theoretical 0.75 ratio has led scholars to propose possible causes. Let's check them out.
To lower the X:A ratio, there are two options: increase A or reduce X. An increase in autosomal pool or a reduction in the X chromosome pool.
Polygyny
Amster et al., 2019 propose that Polygyny is an important factor. The authors attribute the high X:A ratio among Yoruba (YRI) to "substantial polygyny (i.e., that a minority of males sired offspring with multiple females)... our results suggest a few conclusions. The first is that ancestral human populations were highly polygynous, as explaining the polymorphism ratios in YRI would be difficult otherwise. Second, they indicate that non-African populations likely experienced a substantial reduction in polygyny" In other words, one man and one woman pairings.
Veeramah, 2014 agrees with this effect for polygyny (higher female-to-male breeding ratio, in other words a few men monopolize many women and breed with them). This alters the 50:50 ratio assumed further up impacting on the X:A ratio.
But there is no need to imagine a single, possessive male with a collection of wives (harem). We can imagine a scenario in monogamous societies that mimic the effects of social polygyny (societies where men have many wives) such as men remarrying after death of spouse, and having therefore more than one wife, and possibly children with both, that more men than women don't marry and that some men are more successful reproductively and have many more children than a very fertile woman (Labuda, 2010).
Polygyny increases X:A ration but reduces genetic diversity
Interestingly, polygyny reduces the genetic diversity of a population if maintained over time: a few males add their autosomes to the future generations, while most males are excluded. This reduces the contribution and diversity of the male gene pool to subsequent generations.
A society with more women reproducing than men, will maintain a high diversity in the X chromosomes, because these have a 2/3 female source. However, the impact on diversity will be noticed more on autosomal chromosomes because these are supplied on a 50:50 basis by each sex.
If African societies with a high X:A ratio are more polygynic, and this reduces autosomal genetic diversity, why are they said to be the most genetically diverse human population? There is something wrong somewhere.
Hammer et al., 2008 indeed suggest that due to polygyny, fewer unique male genes find their way into the next generation, reducing diversity.
So, can African diversity be caused by other factors, and these overcompensate the loss caused by polygyny? Admixture with superarchaic hominins is one explanation, very isolated populations admixing occasionally in a highly substructured population across Africa is another option. Perhaps, even the ratio of men to women who admixed impacted on the outcome, leading to a highly diverse population with a higher X:A ratio.
Differing mutation rates
Since autosomes and X chromosomes spend their time inside men and women, they are probably subjected to sex-specific factors that alter their random mutation rates. With X chromosomes prevalent (2/3) in women vs. men (1/3), a factor impacting on female mutation rates would have a greater impact on X chromosomes and skew the ratio. The opposite is also true, if mutation rates in males is different to that in females, half of the autosomes (shared 50:50 by each sex) would undergo more (or less) mutations, impacting on the X:A ratio.
Amster et al., 2019 mention this cause, calling it Differential mutation rates. If male-to-female mutation rates are higher, the X/A ratio would be lower. This would mean that Eurasian males have higher mutation rates than Eurasian women, or that African men have lower mutation rates than African women.
Men reproduced at an older age
Amster et al., 2019 also propose that an Increase in male-biased generation times could lead to a distorted X:A ratio. This means that men were reproducing at an older age than women, and that the age gap was growing as time passed. This effect, they suggest, took place around the time of the OOA migration.
Migration (OOA)
Arbiza et al, 2014 suggest that Male dominated Migrations can influence the X to A ratio. During the Out of Africa event there were few women and many men. This impacted on the mix of X and A chromosomes.
But, why did it impact on the initial OOA population (which would have a lower X:A ratio) and not again, as the ancestors of Europeans split from the ancestors of Asians? Wouldn't these new migrations lead to successive drops in X:A ratios? They should, but, as you can see, East Asian and North European X:A ratios are similar!
The migratory theory was first put forward by Keinan and Reich 2010 who proposed that at the OOA event, those who moved out of Africa were relatively homogeneous on a genetic level, having "relatively little genetic variability." The migrant population dispersed into the Levant and more men survived than women (or there were more men in the group than women). This would be reflected in the initial non-African population as a "pronounced reduction of chromosome X effective population size relative to the autosomes". This would reduce X:A (lower X vs. similar A).
They add a twist, suggesting that the "daughters in the founder population of non-Africans b[ore] offspring with new immigrant males more often than the converse" implying successive waves of African males migrating into the original band that left Afica. For this to happen, it had to take place within the first generation after OOA, in a spot close to Africa: "Under the hypothesis of primarily male migration, the founding population of non-Africans must have been localized to a constrained geography long enough to have received the migrants.If the population quickly dispersed throughout Eurasia, we would not see the same pattern in North Europeans and East Asians." So the added wave of Africans explains the similar values of X:A for Europeans and Asians. It took place before they split.
So, Keinan and Reich patch up this anomaly (East Asians and North Europeans, despite migrating have similar X:A ratios, while the OOA group suffered a great reduction just when they left Africa). In my layman opinion the problem is in the OOA theory. Adding Ptolemaic layers to a theory to adapt it to reality does not make sense.
In the words of Keinan and Reich: "The model involves a history in which after the founder population of non-Africans lost much of its genetic diversity, subsequent mostly male gene flow from an African source brought new diversity into the population."
Polyandry
Another option is that the Out of Africa women did not all reproduce with the same success. If very few women had most of the babies in a population where most men participated in the mating, A would be greater, and X would be smaller, leading to a lower X to A ratio. Reich and Keinan consider this "implausible". But, why should we disregard alternate pair bonding societies? A polyandric society, where several men share one wife would fit this description. There are such societies in the modern world, in India, China, Tibet, and the Amazon (Source), it is rare, but not as rare as commonly thought.
Starkweather and Hames, 2012 suggest that "polyandry likely existed during early human history and should be examined from an evolutionary perspective. Our analysis reveals that it may be a predictable response to a high operational sex ratio favoring males and may also be a response to high rates of male mortality and, possibly, male absenteeism."
It makes sense, when there are more men than women, to share wives (the sex ratio favoring males part), and also when they are gone for long periods of time, or die of more frequently, that other men are available to share the load of family responsibilities as well as the marital ones and parenting.
Introgression in Eurasia
Admixture with archaics impacts on the genetic makeup of their offspring. In Eurasia, humans admixed with Neanderthals. This event affected non-Africans. Could it have an impact on the X to A ratio?
Arbiza, 2014 report that the Neanderthal-human matings resulted in a greater effect on the autosomes than on the X chromosome, and that taking this into account led to " new estimates were ∼1% higher across all comparisons, showing that Neandertal introgression can lead to a modest underestimation of relative X/A diversity."
We know that Neanderthal males mated with human females, there was a sexual bias promoting this type of interbreeding. This was also shown by Chevy et al., 2023 who noted in their modelling that "Using simulation studies, we find that when the archaics are mostly male, modern humans end up with less archaic DNA on chromosome X than their autosomes, compared to when there is a female-bias or no sex-bias. Therefore, male sex-bias could be contributing to the difference in the amount of archaic DNA on chromosome X versus the autosomes."
But, the inverse situation could also take place, with male humans partnering with female archaics or super archaics, leading to a higher presence of human DNA in the autosomes of the offspring, and fewer human variants in the X chromosomes.
Closing comments
Sexual partner ratios, introgression, polygyny, polyandry, generation times for both sexes, different mutation rates in men and women, and migration have acted in different directions upon Africans and non-Africans. Efforts to explain the X to A ratio in the framework of an out of Africa migration requires a complex migration pattern with newly arriving men mating with the daughters of the first wave before this population split and spread into East Asia and Europe.
Using an astronomical analogy, perhaps it is time to rethink the Ptolemaic OOA theory and come up with a revolutionary Copernican one.
P.S. Spring in Buenos Aires
Spring has just begun in the Southern Hemisphere, spanning September 22 and 23, 2026 (though we always use the 21st to commemorate its arrival). Now we can expect an earlier sunrise, longer evenings, sunny days, budding trees, flowering shrubs and plants. Warmer, but with cold spells of Antarctic wind interspersed with occasional bursts of hot Amazonian air.
Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall ©
No comments:
Post a Comment