Accurate inference of population history in the presence of background selection.

All published methods for learning about demographic history make the simplifying assumption that the genome evolves neutrally, and do not seek to account for the effects of natural selection on patterns of variation. This is a major concern, as ample work has demonstrated the pervasive effects of natural selection and in particular background selection (BGS) on patterns of genetic variation in diverse species. Simulations and theoretical work have shown that methods to infer changes in effective population size over time (Ne(t)) become increasingly inaccurate as the strength of linked selection increases. Here, we introduce an extension to the Pairwise Sequentially Markovian Coalescent (PSMC) algorithm, PSMC+, which explicitly co-models demographic history and natural selection. We benchmark our method using forward-in-time simulations with BGS and find that our approach improves the accuracy of effective population size inference. Leveraging a high resolution map of BGS in humans, we infer considerable changes in the magnitude of inferred effective population size relative to previous reports. Finally, we separately infer Ne(t) on the X chromosome and on the autosomes in diverse great apes without making a correction for selection, and find that the inferred ratio fluctuates substantially through time in a way that differs across species, showing that uncorrected selection may be an important driver of signals of genetic difference on the X chromosome and autosomes.

Polarization and tipping points.

Research has documented increasing partisan division and extremist positions that are more pronounced among political elites than among voters. Attention has now begun to focus on how polarization might be attenuated. We use a general model of opinion change to see if the self-reinforcing dynamics of influence and homophily may be characterized by tipping points that make reversibility problematic. The model applies to a legislative body or other small, densely connected organization, but does not assume country-specific institutional arrangements that would obscure the identification of fundamental regularities in the phase transitions. Agents in the model have initially random locations in a multidimensional issue space consisting of membership in one of two equal-sized parties and positions on 10 issues. Agents then update their issue positions by moving closer to nearby neighbors and farther from those with whom they disagree, depending on the agents' tolerance of disagreement and strength of party identification compared to their ideological commitment to the issues. We conducted computational experiments in which we manipulated agents' tolerance for disagreement and strength of party identification. Importantly, we also introduced exogenous shocks corresponding to events that create a shared interest against a common threat (e.g., a global pandemic). Phase diagrams of political polarization reveal difficult-to-predict transitions that can be irreversible due to asymmetric hysteresis trajectories. We conclude that future empirical research needs to pay much closer attention to the identification of tipping points and the effectiveness of possible countermeasures.