In saliva, clues to a 'ghost' species of ancient human

July 21, 2017, University at Buffalo
In saliva, scientists have found hints that a "ghost" species of archaic human may have contributed genetic material to ancestors of people living in Sub-Saharan Africa today. The finding comes from a University at Buffalo-led research project that examined the evolutionary history of MUC7, a gene that codes for an important salivary protein of the same name. Credit: Bob Wilder/University at Buffalo.

In saliva, scientists have found hints that a "ghost" species of archaic humans may have contributed genetic material to ancestors of people living in Sub-Saharan Africa today.

The research adds to a growing body of evidence suggesting that sexual rendezvous between different archaic human may not have been unusual.

Past studies have concluded that the forebears of modern humans in Asia and Europe interbred with other early hominin species, including Neanderthals and Denisovans. The new research is among more recent genetic analyses indicating that ancient Africans also had trysts with other early hominins.

"It seems that interbreeding between different early hominin species is not the exception—it's the norm," says Omer Gokcumen, PhD, an assistant professor of biological sciences in the University at Buffalo College of Arts and Sciences.

"Our research traced the evolution of an important mucin protein called MUC7 that is found in saliva," he says. "When we looked at the history of the gene that codes for the protein, we see the signature of archaic admixture in modern day Sub-Saharan African populations."

The research was published on July 21 in the journal Molecular Biology and Evolution. The study was led by Gokcumen and Stefan Ruhl, DDS, PhD, a professor of oral biology in UB's School of Dental Medicine.

A tantalizing clue in saliva

The scientists came upon their findings while researching the purpose and origins of the MUC7 protein, which helps give spit its slimy consistency and binds to microbes, potentially helping to rid the body of disease-causing bacteria.

As part of this investigation, the team examined the MUC7 gene in more than 2,500 modern human genomes. The analysis yielded a surprise: A group of genomes from Sub-Saharan Africa had a version of the gene that was wildly different from versions found in other modern humans.

The Sub-Saharan variant was so distinctive that Neanderthal and Denisovan MUC7 matched more closely with those of other than the Sub-Saharan outlier did.

"Based on our analysis, the most plausible explanation for this extreme variation is archaic introgression—the introduction of from a 'ghost' species of ancient hominins," Gokcumen says. "This unknown human relative could be a species that has been discovered, such as a subspecies of Homo erectus, or an undiscovered hominin. We call it a 'ghost' species because we don't have the fossils."

Given the rate that genes mutate during the course of evolution, the team calculated that the ancestors of people who carry the Sub-Saharan MUC7 variant interbred with another ancient human species as recently as 150,000 years ago, after the two species' evolutionary path diverged from each other some 1.5 to 2 million years ago.

Why MUC7 matters

The scientists were interested in MUC7 because in a previous study they showed that the protein likely evolved to serve an important purpose in humans.

In some people, the gene that codes for MUC7 holds six copies of genetic instructions that direct the body to build parts of the corresponding protein. In other people, the gene harbors only five sets of these instructions (known as tandem repeats).

Prior studies by other researchers found that the five-copy version of the gene protected against asthma, but Gokcumen and Ruhl did not see this association when they ran a more detailed analysis.

The new study did conclude, however, that MUC7 appears to influence the makeup of the oral microbiome, the collection of bacteria within the mouth. The evidence for this came from an analysis of biological samples from 130 people, which found that different versions of the MUC7 gene were strongly associated with different oral microbiome compositions.

"From what we know of MUC7, it makes sense that people with different versions of the MUC7 gene could have different oral microbiomes," Ruhl says. "The MUC7 protein is thought to enhance the ability of saliva to bind to microbes, an important task that may help prevent disease by clearing unwanted bacteria or other pathogens from the mouth."

Explore further: Looking to saliva to gain insight on evolution

More information: Duo Xu et al, Archaic hominin introgression in Africa contributes to functional salivary MUC7 genetic variation, Molecular Biology and Evolution (2017). DOI: 10.1093/molbev/msx206

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torbjorn_b_g_larsson
5 / 5 (2) Jul 21, 2017
There has been admixture evidence of ghost lines in Africa before, as well as a recent result in Asia, but both of those have been less clear. This ghost is based on a single gene, but the most likely explanation and its preservation as a mucus mouth protection protein is strongly selected for.

However the university press release is confusing. The interbreeding age is relatively safely constrained by a population expansion, explaining why it is an African only allele. Could be a H. naledi event. But the divergence time should be even safer, and is way older in the paper. The molecular clock dates it at 4.5 Myrs, 1 Myrs after the Homo/Pan divergence and 1.5 Myrs before the rest of the alleles diverge at the time Homo appears in the fossil record [figure 4b].

If so it is extraordinary old and rather an Australopithecine [!] allele. I wonder if they have an unpublished clock model, or if it is a misprint.

Other news are that they accept the two new 0.3 Myrs human age results.
Shootist
3 / 5 (2) Jul 22, 2017
torbjorn

Based on the fossil record, Neanderthals diverged from modern humans at least 430,000 years ago1, and the analysis of a Neanderthal genome from a cave in the Altai Mountains in Siberia suggests they diverged 550,000–765,000 years ago2

1. Arsuaga JL, et al. Neandertal roots: Cranial and chronological evidence from Sima de los Huesos. Science. 2014;344:1358–1363. doi: 10.1126/science.1253958. [PubMed] [Cross Ref]
2. Prufer K, et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature. 2014;505:43–49. doi: 10.1038/nature12886. [PMC free article] [PubMed] [Cross Ref]

https://www.ncbi....3530/#R1
jonesdave
2 / 5 (4) Jul 23, 2017
@anti,
The unusually high divergence of haplogroup E from other haplogroups suggests an increased
coalescence time to the most recent common ancestor in the MUC7 locus. To investigate the
coalescent depth of the haplogroups, we used the BEAST software (Drummond and Rambaut 2007) to construct a phylogeny of two haplotypes from each haplogroup described above, including the chimpanzee and rhesus macaque reference haplotypes as outgroups (Figure 4B).
This allowed us to estimate the most likely coalescence time for haplogroup E and the other human MUC7 haplotypes to approximately 4.5 million years before present (95% confidence interval ranges from 3.2 to 6.3 million years before present). This indicates that for MUC7 both tree depth among humans and divergence between humans and chimpanzees date back further than most other parts of the genome (Schiffels and Durbin 2014).......
jonesdave
2 / 5 (4) Jul 23, 2017
Sorry, first post should have been @ Torbjorn: cont..............
The most important contribution of our study to the understanding of human evolution is the serendipitous discovery that introgression from an enigmatic African population likely contributed to the noteworthy genetic variation of the MUC7 gene at both single nucleotide and copy number variation levels. Our finding agrees with recent reports of such an introgression in sub Saharan African populations (Hammer et al. 2011; Hsieh et al. 2016), as well as the unexpectedly old human remains (Hublin et al. 2017) and lineages (Schlebusch et al. 2017).


So, evidently the whole of the haplogroup is very old, but the variation seen in the sub-saharan population comes from a recent introgression. As far as I could make out!
PoppaJ
4.2 / 5 (5) Jul 23, 2017
Humans currently have sex with various animals and items. And if they could get away with it, many people would have apes in the home for this reason. Just look at the internet. We are not a picky species about what we Romp with. It basically works like this. Hole=Romp
jonesdave
2.3 / 5 (3) Jul 23, 2017
Humans currently have sex with various animals and items. And if they could get away with it, many people would have apes in the home for this reason. Just look at the internet. We are not a picky species about what we Romp with. It basically works like this. Hole=Romp


Yep. You ever seen some of the people that get married, and have kids? Frightening. The south of the U.S. is living proof. Scary.
michael_frishberg
5 / 5 (1) Jul 24, 2017
We are not a picky species about what we Romp with. It basically works like this. Hole=Romp

As an anthro/archaeology student in the 1970's I wrote a treatise on Necrophilia, so you are correct...I could find no other animal that will mate with a corpse of their specie, so this may be one of our few unique attributes.
Urgelt
not rated yet Jul 24, 2017
Michael wrote, "...I wrote a treastise on Necrophilia... I could find no other animal that will mate with a corpse of their specie..."

You didn't look hard enough.

This behavior has been observed in 30 species of birds; in kangaroos; in lizards; in frogs; and in sea lions, to name just a few.

Even better, *homosexual* necrophilia has been observed in multiple species.

Humans aren't quite as unique (for this topic) as you supposed.

30 seconds with Google will turn up links to studies.

Too bad Google wasn't available to you when you wrote your treatise. But this offers a cautionary tale, doesn't it? Pre-search engine conclusions like 'I could find no examples of...' should not be taken to the bank today. Search was hard back then.

You're welcome.

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