BalLeRMix +: mixture model approaches for robust joint identification of both positive selection and long-term balancing selection

Temporal challenges in detecting balancing selection from population genomic data

The role of balancing selection in maintaining genetic variation remains an open question in population genetics. Recent years have seen numerous studies identifying candidate loci potentially experiencing balancing selection, most predominantly in human populations. There are however numerous alternative evolutionary processes that may leave similar patterns of variation, thereby potentially confounding inference, and the expected signatures of balancing selection additionally change in a temporal fashion. Here we use forward-in-time simulations to quantify expected statistical power to detect balancing selection using both site frequency spectrum (SFS)- and linkage disequilibrium (LD)-based methods under a variety of evolutionarily realistic null models. We find that whilst SFS-based methods have little power immediately after a balanced mutation begins segregating, power increases with time since the introduction of the balanced allele. Conversely, LD-based methods have considerable power whilst the allele is young, and power dissipates rapidly as the time since introduction increases. Taken together, this suggests that SFS-based methods are most effective at detecting long-term balancing selection (>25N generations since the introduction of the balanced allele) whilst LD-based methods are effective over much shorter timescales (<1N generations), thereby leaving a large time frame over which current methods have little power to detect the action of balancing selection. Finally, we investigate the extent to which alternative evolutionary processes may mimic these patterns, and demonstrate the need for caution in attempting to distinguish the signatures of balancing selection from those of both neutral processes (e.g., population structure and admixture) as well as of alternative selective processes (e.g., partial selective sweeps).

The roles of balancing selection and recombination in the evolution of rattlesnake venom

The origin of snake venom involved duplication and recruitment of non-venom genes into venom systems. Several studies have predicted that directional positive selection has governed this process. Venom composition varies substantially across snake species and venom phenotypes are locally adapted to prey, leading to coevolutionary interactions between predator and prey. Venom origins and contemporary snake venom evolution may therefore be driven by fundamentally different selection regimes, yet investigations of population-level patterns of selection have been limited. Here, we use whole-genome data from 68 rattlesnakes to test hypotheses about the factors that drive genomic diversity and differentiation in major venom gene regions. We show that selection has resulted in long-term maintenance of genetic diversity within and between species in multiple venom gene families. Our findings are inconsistent with a dominant role of directional positive selection and instead support a role of long-term balancing selection in shaping venom evolution. We also detect rapid decay of linkage disequilibrium due to high recombination rates in venom regions, suggesting that venom genes have reduced selective interference with nearby loci, including other venom paralogues. Our results provide an example of long-term balancing selection that drives trans-species polymorphism and help to explain how snake venom keeps pace with prey resistance.