Gene-specific selective sweeps are pervasive across human gut microbiomes

The human gut microbiome is composed of a highly diverse consortia of species that are continually evolving within and across hosts. The ability to identify adaptations common to many human gut microbiomes would not only reveal shared selection pressures across hosts, but also key drivers of functional differentiation of the microbiome that may affect community structure and host traits. However, the extent to which adaptations have spread across human gut microbiomes is relatively unknown. Here, we develop a novel selection scan statistic named the integrated Linkage Disequilibrium Score (iLDS) that can detect sweeps of adaptive alleles spreading across host microbiomes via migration and horizontal gene transfer. Specifically, iLDS leverages signals of hitchhiking of deleterious variants with a beneficial variant. Application of the statistic to ~30 of the most prevalent commensal gut species from 24 human populations around the world revealed more than 300 selective sweeps across spec..., , # Gene-specific selective sweeps are pervasive across human gut microbiomes

Dataset DOI: [10.5061/dryad.9ghx3ffx4](https://doi.org/10.5061/dryad.9ghx3ffx4)

## Description of the data and file structure

All underlying data used in this paper is publicly available. 

### Files and variables

Note: For a complete description of iDLS output variables, see the [Output section of the associated Github repo.](https://github.com/garudlab/iLDS/tree/main/iLDS#output)

#### File: TableS4.txt

**Description:** **contains all sweeps detected in all populations analyzed (QP, UHGG, Drosophila)**

##### Variables

* Gene: the gene the variant lies in
* Contig: the contig the variant lies on (in the case of peaks for *Drosophila melanogaster,* this is the chromosome)
* SNV position (contig): the position of the central intermediate-frequency non-synonymous SNP in the analysis window with the highest iLDS value along the given contig
* Species: Name of the species
* Peak number: the unique peak to whi...,