The disjunct temperate rainforests of the Pacific Northwest of North America (PNW) are characterized by late-successional dominant tree species Thuja plicata (western redcedar) and Tsuga heterophylla (western hemlock). The demographic histories of these species, along with the PNW rainforest ecosystem in its entirety, have been heavily impacted by geological and climatic changes the PNW has experienced over the last 5 million years, including mountain orogeny and repeated Pleistocene glaciations. These environmental events have ultimately shaped the history of these species, with inland populations potentially being extirpated during the Pleistocene glaciations. Here, we collect genomic data for both species across their ranges to test multiple demographic models, each reflecting a different hypothesis on how the ecosystem-dominating species may have responded to dramatic climatic change. Our results indicate that inland and coastal populations in both species diverged approximately 2.5 million years ago in the early Pleistocene and experienced decreases in population size during glacial cycles, with subsequent population expansion. Importantly, we found evidence for gene flow between coastal and inland populations during the mid-Holocene. It is likely that intermittent migration in these species during this time has prevented allopatric speciation via genetic drift alone. In conclusion, our results from combining genomic data and demographic inference procedures involving machine learning establish that populations of the ecosystem dominants Thuja plicata and Tsuga heterophylla persisted in refugia located in both the coastal and inland regions of the PNW throughout the Pleistocene, with populations expanding and contracting in response to glacial cycles with occasional gene-flow.

137 Thuja plicata individuals and 48 Tsuga heterophylla individuals were sampled from throughout their geographic range in the PNW. DNA was extracted from leaf tissue and then used in double-digest restriction site associated DNA sequencing (ddRADseq). The restriction enzymes used were EcoRI and SbfI for Thuja plicata and SbfI and MspI (New England Biolabs, USA) for Tsuga heterophylla. For Thuja plicata, sequences were generated as 50 bp single end reads using an Illumina HiSeq 2500 at the Berkeley sequencing facility. For Tsuga heterophylla, sequences were generated as 150 bp paired-end reads using an Illumina HiSeq 4000 at The Ohio State University Wexner Medical Center. Raw sequences were processed using Ipyrad. All scripts associated with the anaysis of this data, including assembly, can be found at https://github.com/ruffleymr/ThujaTsugaAnalyses