I emailed one of the researchers and I got this response:
you are of course absolutely right. Bonobos are equally distant to
people from Africa, Europe or anywhere else in the world.
The X/A ratio measures something completely different: It compares
individuals from a certain group (bonobos, chimpanzees, or human
populations) and compares how different the X autosomes in this group are from the autosomes (the non-sex-chromosomes, i.e. everything that is not X and Y). Since each generation you have three X chromosomes per four autosomes (XX for the mother + XY from the dad = three X), you would
expect that the ratio should be 3/4 (thats why there is a dashed line at
0.75 in the plot). But there are many ways in which this measure could be nudged off this expected value. That Europeans look different in this measure could for instance be explained by later waves of primarily male migrants out of Africa that mixed with people in Europe, but there are other ideas as well.
I am really sorry to see that the plot is misconstrued as evidence for racist ideas. Hope this helped to clear up what is meant with this plot.
‘lol’ indeed. Learn how to read scientific papers
Seems to be a bit of misinformation going on because of this piece so I thought I’d clear it up.
Andrew Anglin claims that the Nature article says that blacks are genetically close to bonobos than to Europeans.
That couldn’t be more wrong.
First off, the article doesn’t talk about any type of actual genetics being closer to anything that is mentioned in the article. What the article is talking about is social and sexual behaviors.
Although they are similar in many respects, bonobos and chimpanzees differ strikingly in key social and sexual behaviours and for some of these traits they show more similarity with humans than with each other.
It also says:
We find that more than three per cent of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other.
And? Is that supposed to mean anything? Cats have 90 percent homologous genes with humans; 82% with dogs; 80% with cows; 79% with chimpanzees; 69% with rats and 67% with mice.
We share 97.5 percent of our DNA with mice.
So we see here that we share a lot of DNA with other animals, as well as animals also sharing similar amounts of DNA, which shows that it comes down to how genes are expressed and not the amount of genetic distance between the 2 animals being tested.
Looking to the image on top of the article, it shows the X/A ratio between Europeans, Africans, the Pan Ancestor and Bonobos.
The X/A ratio is the ratio between the number of X chromosomes and the number of sets of autosomes in an organism. It’s used primarily to determine sex in some species, such as the drosophila flies.
A simple reading of the text above and below this chart that was referenced to supposedly show that Africans are genetically closer to Bonobos will show you that it’s talking about the X/A ratio, not about genetics.
Differences in female and male population history, for example, with respect to reproductive success and migration rates, are of special interest in understanding the evolution of social structure. To approach this question in the Pan ancestor, we compared the inferred ancestral population sizes of the X chromosome and the autosomes. Because two-thirds of X chromosomes are found in females whereas autosomes are split equally between the two sexes, a ratio between their effective population sizes (X/A ratio) of 0.75 is expected under random mating. The X/A ratio in the Pan ancestor, corrected for the higher mutation rate in males, is 0.83.
Similarly, we estimated an X/A ratio of 0.85 (0.79–0.93) for present-day bonobos using Ulindi single nucleotide polymorphisms in 200-kb windows.
Under the assumption of random mating, this would mean that on average two females reproduce for each reproducing male. The difference in the variance of reproductive success between the sexes certainly contributes to this observation, as does the fact that whereas bonobo females often move to new groups upon maturation, males tend to stay within their natal group.
Here’s the main point:
Because both current and ancestral X/A ratios are similar to each other and also to some human groups (Fig. 4), this suggests that they may also have been typical for the ancestor shared with humans.
Talking about the X/A ratio, not genetics.
Here is the text below Fig. 4:
The X/A ratios for Ulindi (bonobo), an African human and a European human were inferred from heterozygosity, and that for the Pan ancestor was inferred from ILS. The low X/A ratio for the European has been suggested to be due to demographic effects connected to migrating out of Africa30. Errors, 95% confidence interval
I hope this clears up anything about this article.
What it’s saying is, is that the X/A ratios for the bonobo, African and European were gathered from heterozygosity, for the Pan ancestor is was gathered from incomplete lineage shortages (ILS).
Low X/A ratio for the European doesn’t mean more genetic distance from Africans or bonobos.