Researchers in Carlos Bustamante's lab at Stanford have recently compared the Y chromosomes of humans and Neandertals. They exome'd an exhumed 49k-year-old Neandertal male from El Sidron, Spain and found that his Y chromosome was not one that has been observed in modern humans. That is, his Y is likely extinct, gone from among the living.
About a month ago, I wrote about how the offspring of human and Neandertal matings couldn't have all been "mules" (couldn't have all been sterile), as some of us have Neandertal DNA in us. But what Bustamante's research reveals is that there were some male Neandertals who may not have mated successfully with humans (the success here being a fertile child), and they provide intriguing speculations about why.
Some of the genes on the Y chromosome can cause immune ruckus for the pregnant, whose male fetuses begin to express their male-specific histocompatibility genes. This can lead to miscarriages. Furthermore, (and equally fascinating) is that there are Neandertal and human-unique mutations on the Y chromosome in genes that are, in fact, histocompatibility genes. It's possible that these lineage-bound differences were incompatible with life when present in the fetuses of male human-Neandertals, perhaps explaining the absence of Neandertal Y in modern humans. As the authors muse, this is consistent with Haldane's rule: if one sex is absent, rare, or sterile among the the first generation matings of different groups, that sex is the heterogametic sex (the sex with the differing sex chromosomes; e.g. X/Y for males).
Mendez, F. L., Poznik, G. D., Castellano, S., & Bustamante, C. D. (2016). The Divergence of Neandertal and Modern Human Y Chromosomes. The American Journal of Human Genetics, 98(4), 728–734. doi:10.1016/j.ajhg.2016.02.023
Vernot and colleagues recently mined the genomes of Europeans and East Asians scouting for sequences from Neandertals and Denisovans (two archaic hominin lineages with whom ancient humans interbred) . They found an absence of archaic hominin sequence in some regions of the genome. These 'deserts', as they call them, may reflect loci where Neandertal and Densiovan DNA were deleterious and purged. Remarkably, one of the deserts contains FOXP2, a gene involved in speech and language (I refer readers to Geoffrey Pullum's Language Log write-up for how people have thought about FOXP2 and language , as well as to Steven Pinker's elegant discussion of the topic ).
The suggestion that FOXP2 is not under neutral selection is not new [3,4]. In 2002, Enard and colleagues in Svante Paabo's lab compared FOXP2 in humans and chimps, speculating that the human-specific signatures in FOXP2 occurred relatively recently, about 200,000 years ago, Later, these human-specific variants were thought to have arisen somewhat earlier, around 300,000 to 400,000 years ago, before the most recent common ancestor of humans and Neandertals. Why? Because, while humans and chimps have different FOXP2 sequences, it was discovered that humans and Neandertals share the same evolutionary changes in FOXP2 .
Since humans and Neandertals have comparable FOXP2 sequences, it is interesting that FOXP2 falls in a large desert where no archaic hominin introgression was observed. Why is that? The authors state that their findings are inconsistent with neutral selection (implying some kind of regional target for selection?) but that the mechanism explaining the deserts is uncertain. Structural variation, alteration involving segments longer than 1 kb, are one possibility, as large regions of the genome can be substrates for natural selection .
Update (and parenthetical)
A reader let me know that the above synopsis was too technical. He attributed this to him not having the background to understand. But I believe the issue is mine (not his). At the risk of introducing (or exposing) errors in my own thinking, here's my attempt to say what I wrote above but in plain English.
Ancient humans had sex with their now-extinct cousins (Neandertals and Denisovans). By comparing our DNA with theirs, we can get clues about what makes us unique. There are some long stretches in our DNA that don’t have much of our extinct cousins’ DNA mixed in with them. One of these regions contains a gene called FOXP2, which was the first gene discovered (years ago) to have an influence on speech development. Language is a feature that is unique to humans. So interestingly, humans and Neandertals have the same DNA for FOXP2, which implies that Neandertals may have been equipped, like us, to make fine movements with their mouths. This is in contrast with chimpanzees. Chimps have a different DNA signature at FOXP2 than we do, and they don’t speak. But what’s super interesting about recent research is that these long regions of DNA without Neandertal DNA mixed in may give us clues to our evolution. For some reason, FOXP2 occurs in a region that may have been protective for our ancestors’ survival.
An international team led by researchers at the University of Washington made splashes when their newest article , revealing the sexual escapades of our hominin ancestors, made it into the popular press. See their figure below displaying how ancestral humans interbred.
This led to a flurry of activity on Twitter with speculations about the frequency of matings and how often mating resulted in viable offspring. I found the tweets by Matthew Herper and Carl Zimmer, two science journalists, to be especially interesting.
In thinking about Carl Zimmer's comment about the offspring of human-Neanderthal matings not being mules, several thoughts come to mind. To start, what's a mule? Answer: a mule is the product of interbreeding of two distinct species, horses and donkeys, which have a different number of chromosomes. As a result, mules are sterile. So to say that the offspring of human-Neanderthal (or human-Denisovan) matings weren't mules might imply that they weren't sterile. Indeed, humans and Neanderthals (and Denisovans) have the same number of chromosomes, making our ancestors less like mules. But more than this, Neanderthal and Denisovan DNA survives in us. For this reason, we can infer that, minimally, some of the offspring of the ancient interbreeders were fertile.
Second (and more tangential) thought: what is our closest relative who has a different number of chromosomes? (Perhaps this is something you learned in junior high and high school biology, but I missed this piece of not-so trivial trivia.) Well, if you already know that humans and chimps share most of their DNA, then chimps are a good guess. As it turns out, chimps have 48 chromosomes. We have 46. So how is it that we can have a different number of chromosomes but share so much DNA? Part of the answer is that our chromosome 2 is actually a hybrid of the two more ancient chromosomes existing among members of the Hominidae family (humans, Neanderthals, and Denisovans being the exception). The evidence for this is that human chromosome 2 actually contains a vestigial centromere, the remains of two telomeres joining that resulted in the singular human chromosome 2 [2,3]. The genes on our chromosome 2 and the corresponding ones in chimps match up.
I'm a Public Health Genetics PhD student at the University of Washington and a molecular epidemiology research fellow at the Fred Hutchinson Cancer Research Center. I post (mostly) about topics in epidemiology and genetics.