disperseNN2: a neural network for estimating dispersal distance from georeferenced polymorphism data

Abstract

AbstractSpatial genetic variation is shaped in part by an organism’s dispersal ability. We present a deep learning tool,disperseNN2, for estimating the mean per-generation dispersal distance from georeferenced polymorphism data. Our neural network performs feature extraction on pairs of genotypes, and uses the geographic information that comes with each sample. These attributes leddisperseNN2to outperform a state-of-the-art deep learning method that does not use explicit spatial information: the mean relative absolute error was reduced by 33% and 48% using sample sizes of 10 and 100 individuals, respectively.disperseNN2is particularly useful for non-model organisms or systems with sparse genomic resources, as it uses unphased, single nucleotide polymorphisms as its input. The software is open source and available fromhttps://github.com/kr-colab/disperseNN2, with documentation located athttps://dispersenn2.readthedocs.io/en/latest/.