IntroUNET: identifying introgressed alleles via semantic segmentation

Abstract

1A growing body of evidence suggests that gene flow between closely related species is a widespread phenomenon. Alleles that introgress from one species into a close relative are typically neutral or deleterious, but sometimes confer a significant fitness advantage. Given the potential relevance to speciation and adaptation, numerous methods have therefore been devised to identify regions of the genome that have experienced introgression. Recently, supervised machine learning approaches have been shown to be highly effective for detecting introgression. One especially promising approach is to treat population genetic inference as an image classification problem, and feed an image representation of a population genetic alignment as input to a deep neural network that distinguishes among evolutionary models (i.e. introgression or no introgression). However, if we wish to investigate the full extent and fitness effects of introgression, merely identifying genomic regions in a population genetic alignment that harbor introgressed loci is insufficient--ideally we would be able to infer precisely which individuals have introgressed material and at which positions in the genome. Here we adapt a deep learning algorithm for semantic segmentation, the task of correctly identifying the type of object to which each individual pixel in an image belongs, to the task of identifying introgressed alleles. Our trained neural network is thus able to infer, for each individual in a two-population alignment, which of those individuals alleles were introgressed from the other population. We use simulated data to show that this approach is highly accurate, and that it can be readily extended to identify alleles that are introgressed from an unsampled "ghost" population, performing comparably to a supervised learning method tailored specifically to that task. Finally, we apply this method to data from Drosophila, showing that it is able to accurately recover introgressed haplotypes from real data. This analysis reveals that introgressed alleles are typically confined to lower frequencies within genic regions, suggestive of purifying selection, but are found at much higher frequencies in a region previously shown to be affected by adaptive introgression. Our methods success in recovering introgressed haplotypes in challenging real-world scenarios underscores the utility of deep learning approaches for making richer evolutionary inferences from genomic data. 2 Author SummaryIt is now known that a sizeable fraction of species occasionally hybridize with related species. Thus, many species harbor genetic material that traces its ancestry to closely related species. For example, many humans contain DNA that was "introgressed" from Neanderthals. The growing appreciation of the commonality of introgression has sparked a keen interest in determining which portions of the genome were introgressed. Several statistical approaches have been devised for identifying the population genetic signatures of introgression, but the most powerful techniques for this task take advantage of modern machine learning techniques. Here, we describe a deep learning method for identifying segments of introgressed DNA. This method is based on neural networks used to determine which pixels in an image belong to which type of object. By treating a matrix of genotypes from a sample of individuals from two closely related species, we can use this deep learning approach to accurately infer which portions of which genomes from the first population were introgressed from the second, and vice-versa. We show that our method, which we have released as an open-source software package, is highly accurate using a variety of simulated scenarios and a real test case from the genus Drosophila.