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. Each method is 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. The results 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 each large population 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.