PT  - JOURNAL ARTICLE
AU  - Bastian Pfeifer
AU  - Nikolaos Alachiotis
AU  - Pavlos Pavlidis
AU  - Michael G. Schimek
TI  - Genome Scans for Selection and Introgression based on <em>k</em>-nearest Neighbor Techniques
AID  - 10.1101/752758
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 752758
4099  - http://biorxiv.org/content/early/2019/09/28/752758.short
4100  - http://biorxiv.org/content/early/2019/09/28/752758.full
AB  - In recent years, genome-scan methods have been extensively used to detect local signatures of selection and introgression. Here, we introduce a series of versatile genome-scan methods that are based on non-parametric k-nearest neighbors (kNN) techniques, while incorporating pairwise Fixation Index (FST) estimates and pairwise nucleotide differences (dxy) as features. Simulations were performed for both positive directional selection and introgression, with varying parameters, such as recombination rates, population background histories, the proportion of introgression, and the time of gene flow. We find that kNN-based methods perform remarkably well while yielding stable results almost over the entire range of k. We provide a GitHub repository (pievos101/kNN-Genome-Scans) containing R source code to demonstrate how to apply the proposed methods to real-world genomic data using the population genomics R-package PopGenome.