Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data

Author summary With the rapid advancement of sequencing technologies it has become feasible to use genome sequence data from several individuals per population/species to learn about the past history of populations, such as changes in population size, timing of colonization of a given habitat/continent or past migration events. However, all statistical methods to date rely on a mathematical model built upon characteristics of hominid species. Namely, this model ignores specific ecological traits common to many plant, invertebrate, or fungal species such as self-fertilization and dormancy. The latter is defined as the ability of plant seeds or invertebrates to remain dormant for long periods of time in the soil or sediments. Here we develop a new statistical method which uses several whole genome sequence data per population/species to simultaneously infer 1) the rates of dormancy and of self-fertilization, and 2) past demographic history. We demonstrate the accuracy of our method using extensive simulations. We also apply our method to Arabidopsis thaliana confirming a high rate of selfing and the absence of long term seed dormancy, and to Daphnia Pulex demonstrating a long lived egg bank. We discuss the wide applicability of our method to draw accurate inference of past evolution for non-hominid species. Several methods based on the Sequential Markovian coalescence (SMC) have been developed that make use of genome sequence data to uncover population demographic history, which is of interest in its own right and is a key requirement to generate a null model for selection tests. While these methods can be applied to all possible kind of species, the underlying assumptions are sexual reproduction in each generation and non-overlapping generations. However, in many plants, invertebrates, fungi and other taxa, those assumptions are often violated due to different ecological and life history traits, such as self-fertilization or long term dormant structures (seed or egg-banking). We develop a novel SMC-based method to infer 1) the rates/parameters of dormancy and of self-fertilization, and 2) the populations' past demographic history. Using simulated data sets, we demonstrate the accuracy of our method for a wide range of demographic scenarios and for sequence lengths from one to 30 Mb using four sampled genomes. Finally, we apply our method to a Swedish and a German population of Arabidopsis thaliana demonstrating a selfing rate of ca. 0.87 and the absence of any detectable seed-bank. In contrast, we show that the water flea Daphnia pulex exhibits a long lived egg-bank of three to 18 generations. In conclusion, we here present a novel method to infer accurate demographies and life-history traits for species with selfing and/or seed/egg-banks. Finally, we provide recommendations for the use of SMC-based methods for non-model organisms, highlighting the importance of the per site and the effective ratios of recombination over mutation.