Forecasting Genomic Change with Time Series Sequence Data

AbstractHumans drive species evolution in numerous ways, ranging from the deliberate interventions of domestication to the indirect but far-reaching impacts of climate change. Anticipating how species will adapt to these pressures assumes that evolution is, to some extent, predictable. Evidence of parallel evolution from time series studies can inform such forecasts. In this article we review time series genomic studies, which directly quantify evolution by sampling populations over time. First, we evaluate the extent to which selection drives parallel adaptation in time series studies. We give specific attention to evolution in response to anthropogenic drivers of change and within host-parasite interactions, which represent major themes in the literature. Then we analyze the patterns seen in retrospective genomic time series studies to identify how distinct drivers of change influence evolutionary processes such as population structure, gene flow, and genetic diversity. Finally, we draw from current advancements in population genomics to anticipate how time series data will be analyzed in the near future to provide recommendations for both researchers and methods developers.