Figure 4. Predicting the impact of linked selection on diversity.

(A) The observed relationship between recombination map length ($L$) and census size ($N_c$) across 136 species with complete data and known phylogeny. Triangle points indicate six social taxa excluded from the model fitting since these have adaptively higher recombination map lengths (Wilfert et al., 2007). The dark gray line is the estimated relationship under a phylogenetic mixed-effects model, and the gray interval is the 95% posterior average. (B) Points indicate the observed π–$N_c$ relationship across taxa shown in Figure 2, and the blue ribbon is the range of predicted diversity were $N_e=N_c$ for $\mu ={10}^{-8}$–${10}^{-9}$, and after accounting for the expected reduction in diversity due to background selection and recurrent hitchhiking under Drosophila melanogaster parameters. In both plots, point color indicates phylum.

Figure 4—figure supplement 1. The relationship between genome size and approximate census population size.

The dashed gray line indicates the OLS fit. Tiger salamander (Ambystoma tigrinum) was excluded because of its exceptionally large genome size ( 30Gbp).

Figure 4—figure supplement 2. The relationship between genome size and recombination map length.

The dashed gray line indicates the OLS fit for all taxa, and the dashed colored dashed lines indicate the linear relationship fit by phyla. Tiger salamander (Ambystoma tigrinum) was excluded because of its exceptionally large genome size ( 30Gbp).

Figure 4—figure supplement 3. The observed π–$N_c$ relationship (points) across species compared to the predicted diversity (ribbons) under different modes of linked selection and parameters, for a range of mutation rates, 10^–9–10^–8.

In both subplots, the gray ribbon is the expected diversity if $N_e=N_c$. In (A), the predicted impact on diversity for four modes of linked selection are depicted: background selection (purple) and hitchhiking (yellow) individually under the Drosophila melanogaster parameters as in Figure 4B, and strong background selection (red) where $U_{\text{strongBGS}}=10U_{\text{Dmel}}\approx 16$, and strong recurrent hitchhiking, where ${\gamma }_{\text{strongHH}}=10{\gamma }_{\text{Dmel}}\approx 0.23$. (B) The predicted diversity under the combined effects of strong background selection and strong hitchhiking (orange) compared to the original predicted diversity as in Figure 4B (blue). Overall, under strong background selection and hitchhiking parameters, predicted diversity would be less than observed for high-$N_c$ species, indicating the poor fit to observed data is not sensitive to the choice of Drosophila melanogaster parameters.

Figure 4—figure supplement 4. The relationship between $N_c$ and diversity in the Corbett-Detig et al., 2015 data, and the relationship between estimated reduction in diversity and census size, for three different approaches.

(A) The diversity data from Corbett-Detig et al., 2015 and the census population size estimated here for metazoan taxa. (B) The reductions in diversity, ${\displaystyle R=N_e/N}$, plotted against census size across species. The red points are the reductions estimated by Corbett-Detig et al., 2015. This confirms Corbett-Detig et al., 2015 finding that the impact of selection ($I=1-R$) increases with census population size (though, in the original paper size body size and range were used as separate proxy variables for census population size). The green and red points are the predicted reduction in diversity under the recurrent hitchhiking (RHH) and background selection (BGS) model using the Drosophila melanogaster parameters as described in the main text. The reduction in the diversity due to sweeps, from Equation 1, is determined by the term $2NS$. Green points treat $N$ as the implied effective population size from diversity ${\tilde{N}}_e=\widehat{\pi }/4\mu$, assuming $\mu ={10}^{-9}$. Yellow points treat $N$ as the census size, $N=N_c$. Overall, using the census size, e.g. $2N_{c}S$, leads to reductions in diversity that far exceed the empirical estimates of Corbett-Detig et al. and reasonable model-based predictions from ${\tilde{N}}_e$.

Figure 4—figure supplement 5. Comparison of the Drosophila sweep parameters used in this study with parameters from other studies.

(A) The estimate of the number of sweeps per basepair, per genome (${\nu }_{\text{BP}}$) from Table 2 of Elyashiv et al., 2016 (the studies included are Li and Stephan, 2006; Andolfatto, 2007; Macpherson et al., 2007 and Jensen et al., 2008); the red point is my estimate used in this paper. (B) Points are the data from Shapiro et al., 2007. The blue line is the non-linear least squares fit to the data, and the green dashed line is the sweep model parameterized by the genome-wide average sweep coalescence rate $2NS\approx 0.92$ from the classic sweep and background selection model of Elyashiv et al., 2016 (r_s in Supplementary Table S6).