Ghost Lineages Ride Again: the Spit Edition

Guest Blogger: Mareike Janiak


Darcy asked me to write a guest post on “the new spit paper” and it shows that she knows me well. Saliva? Salivary proteins? Functional genetic variation in those proteins? Possible interbreeding with mystery hominins? The microbiome?


The new spit paper” by Duo Xu and her colleagues is titled “Archaic hominin introgression in Africa contributes to functional salivary MUC7 genetic variation” and is going to be published in the journal Molecular Biology and Evolution.

The authors looked at genetic variation in a gene called MUC7, which codes for mucin 7, a protein that is only found in saliva. In an earlier study, they found that the number of times a specific part of the MUC7 gene is repeated varies across different primate species. In gorillas it is repeated only 4-5 times, while vervet monkeys have 11-12 repeats. Humans have 5-6 repeats, but the gene hadn’t been thoroughly investigated in our own species, which is where the current paper comes in.

One known function of mucin 7 is to bind with bacteria in the mouth, so one question the authors asked is whether genetic variation in MUC7 correlates with the type of bacteria found in a person’s mouth. Using data from the Human Microbiome Project the authors found that people that have more similarity in the MUC7 gene also have more similar bacterial profiles (microbiomes) – but only around the mouth. While this is an interesting result, it creates more questions than it answers! Do these different bacterial profiles provide an adaptive benefit? And if so, for what? In what context is it better to have one over the other? Is it dependent on pathogens in the environment or maybe on diet? Lots of great avenues for future research!

But the authors also found something else when they were looking at MUC7 variation across people, something very curious. As expected, they found a number of different patterns of MUC7. These patterns are called haplotypes and they appear as time goes by and (mostly benign) mutations accumulate along the gene. Generally these haplotypes were pretty similar to each other, but (and this is the weird part!) one of them, haplotype E, was totally different.

Most of the MUC7 haplotypes were like these poodles, small differences but all clearly poodles:


And then there’s haplotype E:


Yes, still a poodle, but also kind of…out there and unexpected.

So what’s the deal with haplotype E?

Why is this haplotype so different? The authors had some hypotheses, which they tested with different models and simulations. Based on the results of these simulations, the most plausible explanation is that haplotype E of the MUC7 gene was introduced into the modern human lineage during an interbreeding event with an extinct human species – a so-called ghost lineage.


Don’t worry, Scooby. We only call them ghost lineages because we don’t really know who they were. Now, these interbreeding events and the introduction of genetic material from extinct ancestors into our own species aren’t totally new. There are a number of examples of what we call “archaic introgression,” but so far most of them have been documented in European and Asian populations. The idea is that as humans made their way out of Africa they encountered Neanderthals and Denisovans, our now-extinct relatives, and picked up some useful tips, tricks, and genetic adaptations from them for life in the new environment.

However, the strange haplotype E that Xu and colleagues identified isn’t found in Eurasia, but only in sub-Saharan Africa! This is pretty exciting. It has been more difficult to find evidence for archaic introgression within Africa, even though we know through fossil evidence that multiple types of hominins lived there at the same time. This is partly because DNA doesn’t preserve as well in hot climates as it does in Siberia, so we have fewer ancient genomes from sub-Saharan Africa and none that are as old as those of Neanderthals and Denisovans. But techniques for extracting ancient DNA are getting better and better, and simulations can provide insight, like they did in this case.

It is fascinating to imagine how these interbreeding events actually played out. Not necessarily the breeding part (although maybe that, too), but what was life like for the hybrids? In looking at the map in Xu’s paper, it’s noteworthy that the introgressed MUC7 haplotype E is found very close to another modern haplotype. So why did haplotype E not spread further? Was there a geographical barrier that prevented further admixture? Were there “hybrid zones” like the ones we find in non-human primates, especially baboons, today?

It’s an exciting time in anthropological genetics!

References/Further Reading
Hsieh, P., Woerner, A.E., Wall, J.D., Lachance, J., Tishkoff, S.A., Gutenkunst, R.N. and Hammer, M.F. (2016). Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African PygmiesGenome research26(3), 291-300.

Racimo, F., Sankararaman, S., Nielsen, R. and Huerta-Sánchez, E. (2015). Evidence for archaic adaptive introgression in humansNature reviews. Genetics16(6), 359.

Xu, D., Pavlidis, P., Taskent, R.O., Alachiotis, N., Flanagan, C., DeGiorgio, M., Blekhman, R., Ruhl, S. and Gokcumen, O. (2017). Archaic hominin introgression in Africa contributes to functional salivary MUC7 genetic variationMolecular Biology and Evolution.

Xu, D., Pavlidis, P., Thamadilok, S., Redwood, E., Fox, S., Blekhman, R., Ruhl, S. and Gokcumen, O. (2016). Recent evolution of the salivary mucin MUC7Scientific reports6, 31791.

Mareike Janiak is a PhD candidate in the Department of Anthropology at Rutgers University. She works on functional genetic variation in the digestive enzymes of primates (and sometimes bats).

Author: bonesstonesandmonkeys

The profile of the Bones, Stones, and Monkeys blog.

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