Paleo-climates and past introgression explain the spatio-temporal distribution of genetic structure in Triodanis perfoliata

The dynamic nature of intrinsic (e.g., reproductive system, hybridization) and extrinsic factors (e.g., physical barriers to gene flow) across space and time generate complex biological processes that influence contemporary patterns of genetic diversity, highlighting the need for interdisciplinary studies. Using the widespread, mixed -mating annual Triodanis perfoliata , previous work demonstrated the important roles of breeding system, isolation by distance, and isolation by resistance in shaping patterns of population genetic diversity. Here we significantly build on this first step by incorporating paleoclimatic data, historical admixture, and estimating species divergence times across 18 populations of T. perfoliata spanning the contiguous US. This current study provides novel insights into factors driving patterns of intraspecific diversification that were not explained using only contemporary climate models. Specifically, these new analyses highlight the early Holocene (11.7-8.326 ka) and the Marine Isotope Stage M2 (ca. 3.3 Ma), as important time periods for explaining patterns of contemporary population genetic diversity, the latter of which appears to be an important time period for intraspecific divergence of T. perfoliata . In addition, we explored the influence of historical intrinsic factors, via admixture to explain patterns of population isolation and connectivity. The inclusion of an admixture analysis provided clarity through evidence of historical gene flow between populations that would have experienced suitable habitat connectivity in past climates. Our study illustrates the importance of incorporating historic, as well as contemporary data, into phylogeographic studies to generate a comprehensive understanding of patterns of population diversity, and the processes important in driving these patterns.