History of the ITR
The demographic modeling results suggest that the ITR represents expansion from pre-Pleistocene relictual inland temperate rainforests and that this forest periodically received migrants from coastal populations, presumably via wind dispersal. Genomic evidence from both western redcedar and western hemlock supports this ancient divergence between the ITR and the coastal rainforest, with the evidence apparent in the statistical model selection as well as the observed allele frequencies. The genomic signature of refugia (an anciently diverged population) is an abundance of rare alleles not shared with other populations. O’Connell et al. 2008, while they acknowledge some genetic differentiation between interior and coastal populations, suggested the divergence was shallow enough to support recent divergence with an absence of subsequent migration (e.g., model H, Fig. 2). All of the recent dispersal models were not supported by our analysis (Fig. 5). Moreover, in a recent genomic study of western redcedars (and mountain hemlock, Tsuga mertensiana , a sub-alpine congener of western hemlock examined here), Fernandez et al. (2021) found that ITR populations of western redcedar are a mix of two genomic clusters, one restricted to the southern portion of the ITR and the other more prominent in the northern portion of the ITR and shared with the central Cascades. Thus, their genomic data are the first to suggest persistence of this late successional dominant tree species in the inland region throughout the Pleistocene. Here, we have collected thousands of loci across individuals from both ITR and coastal populations for western redcedar (Thuja plicata , see also Fernandez et al. 2021), and the other late successional dominant, western hemlock (Tsuga herterophylla ). With these data, we have been able to examine the jSFS and observe the high frequency of rare alleles present in the coastal and ITR populations separately, which indicates their ancient divergence. More importantly, we have modeled coalescent processes to account for coalescent stochasticity and explicitly conducted statistical tests of multiple plausible evolutionary (phylogeographic) models. This has ultimately allowed us not only to infer the presence of ITR refugia for both species throughout the Pleistocene, but also to date the divergence times between inland and coastal populations for both species to before the Pleistocene, assess demographic histories of the two species, and estimate migration patterns between coastal and inland populations of each of the two species. These inferences illustrate the analytical power of explicit statistical phylogeographic modeling.
This has implications on how the fossil pollen record informs our understanding of the history of the PNW (Whitlock 1992). Given the difficulty of identifying cedar pollen (Faegri & Iverson 1992), the pollen classification of Thuja plicata is generally limited to being a member of the Cupressaceae family, while the identification ofTsuga heterophylla pollen is more reliable. Of thisThuja-Tsuga pollen record, the ITR is inferred to have been present at the southern and central ranges < 4-6.3 Kya (Mehringer 1996, Rosenberg et al . 2003, Chase et al. 2008, Herring & Gavin 2015), and not detected in high levels at the northern range extent until roughly 2-3 Kya (Gavin et al. 2009). Before this, the Thuja-Tsuga pollen record is not recognized in the area prior to 100 Kya, suggesting a rather recent population expansion of both species throughout the range. However, given the genomic evidence showing an abundance of rare alleles in the ITR populations and our coalescent analysis, we infer that populations of Thuja plicataand Tsuga heterophylla must have been in the ITR during the Pleistocene earlier than 6 Kya, though in such small populations that the pollen was not abundant enough for current detection.