Genomic and ecological signatures of landscape change: a geologically-constrained, simulation-based case study in the Baja California Peninsula

Abstract:

Earth’s surface dynamics shape biological evolution as landscape changes can influence organismal dispersal and adaptation. The extent to which we can measure the effects of landscape change on biological evolution is in part determined by the methodological approaches used to assess these relationships. Here we use genetic simulations and climatic niche characterization to determine whether different types of genetic data can record a signature of landscape change under different geological scenarios. We use the Baja California peninsula as a study system, where patterns of north-south genetic divergence are observed in multiple organisms, suggesting an isolation mechanism in the mid-peninsular region that has been hypothesized to be related to geological processes such as a seaway barrier. The lack of existing geological evidence to generate and constrain biological hypotheses and the absence of available biological data to differentiate between vicariant and natural selection processes, have hindered the ability to interpret what geologic processes have forced biodiversity in this region. In this study we assess the genomic signature produced by a hypothetical geological barrier of different starting times (5, 3 and 1 Ma) and with different durations (0.05, 0.5 and 2 Myr), based on preliminary results from our new geologic and tectonic mapping. Recent discovery of Pliocene-age tidal deposits up to 60–90 km inboard from the Pacific coast, at elevations up to 320 m near the regional drainage divide, provide a new constraint on model boundary conditions. To assess the predicted signal of a barrier on the landscape, we (1) simulate genetic data using the “CDPOP” software to determine which geological barrier scenarios are detectable in different types of genetic data and (2) analyze the climatic divergence signature by analyzing the ecological niches of the lizard Sceloporus zosteromus and the rodent Dipodomys merriami to parameterize a second set of genetic simulations that are shaped by both physical barrier and climatic forces. These results will help to define a ‘detectability baseline’ to understand what geological hypotheses are testable with genetic data, which is vital to developing a framework to describe the interaction and sensitivity of biological evolution to geological change.