Introduction
The old-growth cedar-hemlock forests of the Pacific Northwest of North
America characterize one of the most diverse temperate rainforests in
the world (Newmaster et al. 2003). This ecosystem includes disjunct
coastal and inland temperate rainforest (ITR) elements, with the latter
located in the Northern Rocky Mountains and separated from the larger
coastal rainforest located in the Cascades and coastal ranges by
approximately 200 km of xeric habitat. The entire Pacific Northwest
region has been widely impacted by Pleistocene glacial/interglacial
cycles (Waitt & Thorson 1983), with flora and fauna being strongly
impacted by these climatic changes. The ITR has been of particular
interest because of the dramatic implications of the alternative
hypotheses that have been proposed to explain its history during and
after the Pleistocene. One, the Recent Dispersal (RD) hypothesis, posits
the recent (<5K years ago; Kya) establishment of the ITR,
invoking a post-Pleistocene colonization of the inland areas from
coastal populations, and implying that the ITR is a recent propagule of
the coastal forest with little evolutionary novelty. The second
hypothesis posits that the ITR represents an ancient disjunction between
the inland and coastal forests (Brunsfeld et al. 2001) that
occurred pre-Pleistocene (>2.5 million years ago; Mya). In
this Ancient Vicariance (AV) hypothesis, while the onset of the glaciers
caused massive contraction of the ITR, inland refugia persisted during
cold periods and subsequently expanded in-situ post-Pleistocene.
The AV hypothesis predicts that allopatry may have led to speciation of
some taxa in the ITR, and thus, that the inland region harbors a unique
endemic flora and fauna. These two hypotheses broadly encapsulate the
proposed modes of the formation of the disjunction. They are critical to
understanding general biogeographic processes associated with the
ecosystem and the region, and they also have broad implications for
conservation and management of this diversity hotspot.
The range of the PNW temperate rainforest is defined by the
distributions of the two late-successional dominant species, Tsuga
heterophylla Raf. (Sarg.) (western hemlock) and Thuja plicataDonn ex. D. Don. (western redcedar). Pollen records from the central and
southern ITR suggest these species have only been present inland for
<3 Ky (Mehringer 1996, Rosenburg et al. 2003, Chaseet al. 2008, Gavin et al. 2009), and represent the primary
data point for the RD hypothesis. Suitable inland habitat for western
hemlock is not completely occupied, suggesting the species range is
still expanding (Gavin & Hu 2006). Similarly, Rosenburg et al. (2003)
found no record of this species’ pollen in southeastern BC prior to
~ 3500 ya. Most pollen records concur that western
hemlock pre-dates evidence of western redcedar (Mehringer 1996, Whitlock
1992). This coincides with microsatellite molecular evidence for western
redcedar samples across the disjunction (O’Connell et al. 2008),
which supports one southern coastal refugium throughout the Pleistocene,
with no evidence for ancient, disjunct inland refugia, nor for northern
coastal refugia (e.g., the Haida Gwaii archipelago). O’Connell et al.
(2008) further suggested that, given the lack of hierarchical structure
in these three clusters, the divergence between them has been recent and
rapid, which is congruent with post-glacial recolonization of the
northern coast and ITR (O’Connell et al. 2008). While this
inference was based on microsatellite loci, recent advances with reduced
representation sequencing (Peterson et al. 2012, Andrews et
al. 2016) provide enhanced power to test phylogeographic hypotheses
regarding formation of disjunct populations (Carstens et al.2012, Garrick et al. 2015). Indeed, a recent study used
clustering analyses for population assignment based on a genome-wide
panel of SNPs in western redcedar to support the presence of an ITR
refugium (Fernandez et al. 2021). However, they did not attempt to
estimate population parameters, such as the timing of demographic events
through model comparisons, which would enable the demographic hypotheses
to be evaluated.
Though much of the available evidence supports the recent, post-glacial
colonization of the ITR by these dominant tree species, a number of
phylogeographic investigations have been conducted to evaluate the
impact of the disjunction on other species in the PNW temperate
rainforest (e.g., Soltis et al. 1997, Brunsfeld et al.2001). To date, eleven other species complexes with disjunct ranges in
the PNW have been investigated in a phylogeographic framework including
five amphibians (Nielson et al . 2001, Carstens et al.2004, Wilke & Duncan 2004, Steele et al. 2005, Metzger et
al. 2015), one mammal (Carstens et al. 2005), two plants
(Brunsfeld et al. 2006; Carstens et al. 2013, Ruffleyet al. 2018), three mollusks (Smith et al. 2017, Smithet al. 2019, Rankin et al. 2019), and an arthropod
(Espíndola et al. 2016). These species span the tree of life and,
based on analyses of their genetic variation, they also span the
possible phylogeographic histories for the PNW temperate rainforest.
Some species, such as the tailed frogs (Ascaphus ; Neilson et al.
2001), salamanders (Dicamptodon, Plethodon ; Carstens et
al. 2004; Steele et al. 2005), and jumping slugs (Hemphilia ;
Rankin et al., 2019) show clear evidence of an ancient divergence
between the ITR and coastal populations, indicating pre-Pleistocene
divergence. Conversely, other species, such as Salix melanopsis(Carstens et al. 2013), Microtus richardsoni (Carstenset al. 2005), and taildropper slugs (Prophysaon andersoni ;
Smith 2018) show evidence of post-glacial recolonization of the inland
from the coast. Other phylogeographic models, such as pre-Pleistocene
divergence with migration, have also been supported with genomic
evidence (Alnus rubra; Ruffley et al. 2018). These results
suggest that some ITR endemics might have been present before the
ecosystem dominant species were established if these ecosystem dominants
colonized the ITR more recently, as supported by pollen records and
early molecular studies. Inferring the phylogeographic history of the
ecosystem dominant species that establish the boundaries of the PNW
temperate rainforest will provide a critical insight for the
availability of suitable habitat for refugial populations in the ITR,
and will be a central contribution towards the understanding of the
biological history of the area.
The hypothesis that the ITR has an ancient (pre-Pleistocene) divergence
from the coastal rainforest and has persisted throughout glacial cycles
in refugia in the interior Northwest is compelling because its presence
would support the habitat requirements of other species that show
evidence of ancient vicariance. Additionally, paleontologists have
questioned the plausibility of the old-growth ITR becoming so
established in less than 3500 years (Mehringer 1996). However, the
persistence of the ITR throughout the Pleistocene has received no
support from the pollen record (e.g., Mehringer 1996, Chase et
al. 2008, Gavin et al. 2009). Whether or not the ITR persisted
throughout the Pleistocene also has other implications for how the PNW
disjunct community as a whole has adapted to the dramatic climatic
changes, either in concert or individualistically (Davis 1981, Habeck
1987, Sullivan et al. 2000, Flessa and Jackson 2005). Common
insight from paleoecology suggests that modern communities of PNW forest
have assembled over a long history of individual responses to climate
change (David 1981, Flessa and Jackson 2005), and the hypothesis of a
recently assembled, rapidly diverse ITR poses a challenge to this
insight.
This question is not novel to the PNW temperate rainforest, as the idea
of the species responding individualistically, rather than in-concert,
in response to climatic changes is an ecological notion dating back to
the early 20th century (Gleason 1926), and has been
demonstrated empirically (Burbrink et al. 2016). However,
Kirkwood (1922), one of the first to characterize the ecology of species
in the northern Rocky Mountains in general, emphasized how the
understanding of the ITR would be dramatically improved when “the
individualities of the constituent species were understood”.
Alternatively, there is evidence in other communities that species do,
in fact, respond to climatic changes in concert (Chen et al.2014, Gehera et al. 2017). For plant communities specifically,
the idea of community-wide concerted response to climatic change can be
traced back to early 20th century plant ecologist
Clements (1918), and his idea that communities are “super-organisms”
whose interactions are interwoven and dependent on one another.
Regardless of the organism or ecosystem, researchers have long been
fascinated with the question of whether or not species in the same
environment respond asynchronously or synchronously to climatic changes
(Sullivan et al. 2000, Carstens et al. 2005, Hickersonet al. 2006).
In this study, we test predictions about the phylogeographic history of
these two species, specifically with respect to whether or not they
harbor cryptic diversity across the disjunction; that is, show evidence
of pre-Pleistocene divergence and no subsequent migration. These
predictions serve as a test of the predictive framework that was
originally developed by Espíndola et al. (2016) and recently
updated with life history traits by Sullivan et al. (2019). We
then validate these predictions, and ultimately test whether the ITR
persisted throughout the Pleistocene (Brunsfeld et al . 2001) by
generating genomic data for individuals from these species throughout
their ranges. For this, we rely on coalescent simulations, the joint
site frequency spectrum, and machine learning inference procedures to
develop and test our phylogeographic hypotheses. We also validate the
power of predictive phylogeography in detecting the presence and absence
of cryptic diversity. Finally, we evaluate the potential role of genomic
data in uncovering the history of the past and explore how our
inferences can be influenced by various datatypes and perspectives in
genomics and paleontology.