Deep Generative Models of Evolution: SNP-level Population Adaptation by Genomic Linkage Incorporation

TL;DR

This paper introduces a deep generative neural network model that captures allele frequency trajectories and linkage disequilibrium in evolving populations using pooled sequencing data, addressing limitations of traditional models.

Contribution

The novel model integrates SNP-level and neighboring locus information to improve population genomic inference from Pool-Seq data, including LD estimation.

Findings

Model accurately captures allele frequency trajectories.

Enables estimation of pairwise linkage disequilibrium.

Outperforms existing methods in LD estimation.

Abstract

The investigation of allele frequency trajectories in populations evolving under controlled environmental pressures has become a popular approach to study evolutionary processes on the molecular level. Statistical models based on well-defined evolutionary concepts can be used to validate different hypotheses about empirical observations. Despite their popularity, classic statistical models like the Wright-Fisher model suffer from simplified assumptions such as the independence of selected loci along a chromosome and uncertainty about the parameters. Deep generative neural networks offer a powerful alternative known for the integration of multivariate dependencies and noise reduction. Due to their high data demands and challenging interpretability they have, so far, not been widely considered in the area of population genomics. To address the challenges in the area of Evolve and Resequencing experiments (E&R) based on pooled sequencing (Pool-Seq) data, we introduce a deep generative neural network that aims to model a concept of evolution based on empirical observations over time. The proposed model estimates the distribution of allele frequency trajectories by embedding the observations from single nucleotide polymorphisms (SNPs) with information from neighboring loci. Evaluation on simulated E&R experiments demonstrates the model's ability to capture the distribution of allele frequency trajectories and illustrates the representational power of deep generative models on the example of linkage disequilibrium (LD) estimation. Inspecting the internally learned representations enables estimating pairwise LD, which is typically inaccessible in Pool-Seq data. Our model provides competitive LD estimation in Pool-Seq data high degree of LD when compared to existing methods.