The MUC19 Gene: An Evolutionary History of Recurrent Introgression and Natural Selection

We study the gene MUC19, for which some modern humans carry a Denisovan-like haplotype. MUC19 is a mucin, a glycoprotein that forms gels with various biological functions. We find diagnostic variants for the Denisovan-like MUC19 haplotype at high frequencies in admixed Latin American individuals, and at highest frequency in 23 ancient Indigenous American individuals, all predating population admixture with Europeans and Africans. We find that the Denisovan-like MUC19 haplotype is under positive selection and carries a higher copy number of a 30 base-pair variable number tandem repeat, and that copy numbers of this repeat are exceedingly high in American populations. Finally, some Neanderthals carry the Denisovan-like MUC19 haplotype, and that it was likely introgressed into human populations through Neanderthal introgression rather than Denisovan introgression., All code, meta information, and final results can be viewed on GitHub. These data are the intermediary files used to produce our final set of results., # Dryad Data

**Citation:** Please cite [Villanea and Peede et al. 2025](https://doi.org/10.1126/science.adl0882) ([https://doi.org/10.1126/science.adl0882](https://doi.org/10.1126/science.adl0882)) when using this data.

To use the data, you will first need to extract the individual data archives (`.tar.gz`). For example, run `tar -xf {data_archive}.tar.gz`. After extraction, you may need to edit the code on [GitHub](https://github.com/David-Peede/MUC19) so that the paths are appropriate for the computer on which the code is run. The paths provided in this README reflect my original project directory structure.

Below is a quick reference of the naming conventions I used throughout the project.

**Naming Conventions**

* Archaic Individuals
* `den`: Altai Denisovan
* `alt`: Altai Neanderthal
* `cha`: Chagyrskaya Neanderthal
* This individual is considered a late Neanderthal.
* `vin`: Vindija Neanderthal
* This individual is considered a late Neanderthal.
* Modern Human ...,