Tree Sequences as a General-Purpose Tool for Population Genetic Inference

As population genetic data increase in size, new methods have been developed to store genetic information in efficient ways, such as tree sequences. These data structures are computationally and storage efficient but are not interchangeable with existing data structures used for many population genetic inference methodologies such as the use of convolutional neural networks applied to population genetic alignments. To better utilize these new data structures, we propose and implement a graph convolutional network to directly learn from tree sequence topology and node data, allowing for the use of neural network applications without an intermediate step of converting tree sequences to population genetic alignment format. We then compare our approach to standard convolutional neural network approaches on a set of previously defined benchmarking tasks including recombination rate estimation, positive selection detection, introgression detection, and demographic model parameter inference. We show that tree sequences can be directly learned from using a graph convolutional network approach and can be used to perform well on these common population genetic inference tasks with accuracies roughly matching or even exceeding that of a convolutional neural network-based method. As tree sequences become more widely used in population genetic research, we foresee developments and optimizations of this work to provide a foundation for population genetic inference moving forward.