Estimating recent and historical effective population size of marine and freshwater sticklebacks

Effective population size ( N e ) is a quantity of central importance in evolutionary biology and population genetics, but often notoriously challenging to estimate. Analyses of N e are further complicated by the many interpretations of the concept and the alternative approaches to quantify N e utilising different properties of the data. However, the alternative methods are also informative over different time scales, suggesting that a combination of approaches should allow piecing together the entire continuum of N e , spanning from the recent to more distant past. To test this in practice, we inferred the N e continuum for 45 populations of nine-spined sticklebacks ( Pungitius pungitius ) using whole-genome data with both LD- and coalescent-based methods. Our results show that marine populations exhibit the highest N e values in contemporary, recent, and historical times, followed by coastal and freshwater populations. They also demonstrate the impact of both recent and historical gene flow on N e estimates and show that simple summary statistics are informative in comprehending the events in the very recent past and aid in more accurate estimation of N e C , the contemporary N e , as well as in reconstruction and interpretation of recent demographic histories. Although our sample size for large populations is limited, we found that GONE can provide reasonable N e estimates. However, due to challenges in detecting subtle genetic drift in large populations, these estimates may represent the lower bound of N e . Finally, we show that combining GONE and CurrentNe2, both sensitive to population structure, with MSMC2 provides a meaningful interpretation of N e dynamics over time.