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.