Ancient humans who interbred with a closely related but now extinct species called Denisovans may have polluted their own gene pool with certain genetic traits responsible for male infertility. According to a new study in the journal Current Biology, the same defects were probably also picked up as a result of humans mating with Neanderthals, although interestingly the researchers discovered that some modern human populations actually inherit more of their DNA from Denisovans than from Neanderthals.

As hominids, Denisovans belonged to the same family as Homo sapiens, with both species being descended from a common ancestor. Neanderthals also belong to this family, and while a genetic trace of their interbreeding with humans can be found in the majority of people living today, Denisovan ancestry had been thought to be much less prominent in modern humans.

However, by analyzing the complete genomes of 257 individuals from 120 non-African populations, researchers discovered that some present-day humans actually derive a higher proportion of their ancestry from Denisovans than from Neanderthals. This is particularly true of certain groups living in Oceania, where fragments of Denisovan DNA account for 5 percent of the genetic constitution of modern individuals, while Neanderthal genes make up just 2 percent of this.

It is generally considered that the introduction of both types of archaic genes into the human gene pool had a deleterious effect on survival chances, resulting in this ancestry becoming increasingly diluted over time as a result of natural selection. Therefore, the fact that such high proportions of Denisovan genetic material still persist led the researchers to conclude that it must have been introduced to the human genome much later than Neanderthal DNA. Based on this, they calculate that humans may have mated with Denisovans around 100 generations after they did with Neanderthals.

^{Map shows proportion of genome inherited from Denisovans in different global populations. Red signifies the highest proportion of Denisovan ancestry. Sankararaman et al./Current Biology 2016}

Some of the alleles – or gene variants – derived from Denisovans are considered to be at least partially responsible for certain modern human traits. For instance, natives of Papua New Guinea are thought to have inherited certain genes that contribute to an enhanced sense of smell, while other Denisovan genes may contribute to the high-altitude adaptations of modern Tibetans.

However, breeding with Denisovans may also have led to an increase in human male infertility. To determine this, the researchers searched for Denisovan genes that are expressed predominantly on the X chromosome, and found that these tended to be more diluted in modern humans than Denisovan genes occurring on other chromosomes.

Other hybrid species have been found to carry genes for male infertility on the X chromosome, and the depletion of these Denisovan genes suggests that they probably also produced this phenotype and therefore have not been passed on as successfully as other archaic genes.

This theory would appear to be confirmed by the fact that Denisovan genes that are mainly expressed in the testes were also found to have been phased out to a much greater extent than those expressed elsewhere on the genome. The depletion of genes expressed in the testes is another known characteristic of hybrid male infertility.

Based on these findings, study co-author David Reich explained that “males who happened to carry Denisovan or Neanderthal DNA in these sections were not as successful in terms of producing offspring as others, and because of that those sections were removed in that first handful of generations after the mixture occurred.”

Consequently, these genetic traits have been phased out to such an extent that they are not thought to produce male infertility in modern humans, even in populations with high proportions of Denisovan ancestry.