Evidence for a cryptic species, forested refugia, and dynamic contact
Significant geographic structure within Pacific martens is consistent with the Coastal Refugium Hypothesis (CRH; Fig. 3, 4) and supports the paleoendemic persistence of insular M. caurina in a North Pacific coastal refugium, potentially located along the western margins of the Alexander or Haida Gwaii archipelagos. Insular and continental M. caurina are genetically distinct despite mitochondrial nesting (Fig. 2d; Supplemental Information 5). We estimated American and Pacific pine martens diverged just over 1 Mya earlier than recent estimates based on complete mitochondrial genomes (Schwartz et al. 2020), but consistently predating the LGM. Rapid evolution of mammalian mitochondrial genomes and microsatellites and evidence of demographic bottlenecks within M. caurina (Fig. 3) suggest that previous divergence estimates may be inflated (Cox 2008; Nielsen & Beaumont 2009; Adachi et al. 1993; Goldstein & Pollock 1997; Zhivotovsky 2001). Within M. caurina , insular and continental clades are geographically discontinuous (Fig. 1) and estimated to have diverged almost 100 kya (Fig. 3b); however, PSMC date estimates are sensitive to scaling (mutation rate and generation time). IntraspecificM. caurina divergence predating the most recent interglacial suggests that insular Pacific martens may have diverged from continental populations over multiple glacial cycles, perhaps initially in a coastal refugium and then subsequently on one or more NPC islands and may represent a cryptic species previously undetected using single or multi-gene analyses.
Martens rely on deep persistent snow and complex forest structure (Proulx 1997; Pauli et al. 2013; Manlick et al. 2017; Martin et al. 2019) for predator avoidance, thermal management, and efficient locomotion, suggesting that refugial ecosystems capable of supporting martens would also support forest community assemblages. Increased consumption of marine prey items (Giannico & Nagorsen 1989), consistent with morphological shifts within M. caurina (Colellaet al. 2018b), may have enabled persistence within a relatively small geographic area. A similar dietary shift towards marine food sources is also reflected in insular NPC wolves (Darimont et al.2009; Muñoz-Fuentes et al. 2010). The insular-continental split within M. caurina is consistent with signatures from numerous other NPC paleoendemic mammals (bears, Heaton et al. 1996; wolves, Weckworth 2005; deer, Latch et al. 2009; ermine, Colellaet al. 2018c; shrews, Demboski & Cook 2001; deer mice, Sawyeret al. 2018) and also evident in the few associated parasites examined to date (Soboliphyme baturini , Koehler et al.2007, 2009; Hoberg et al. 2012). Chichagof martens harbor distinctive nematodes that are phylogenetically close to S. baturini found in other populations of M. caurina , suggestingM. caurina or a ‘ghost’ marten lineage may persist or persisted on this island until relatively recently (Koehler et al. 2007, 2009; Hoberg et al. 2012). Similarly, POW is hypothesized to have been originally occupied by endemic M. caurina (Pauli et al. 2015) and subsequently colonized by translocations of American pine martens, which included the introduction of as few as 10 (only 4 female) documented individuals (Paul 2009). Our genomic analyses, however, did not find a signature of M. caurina alleles in individuals from POW or Chichagof islands. Instead, each island was genetically aligned with M. americana (and their translocation source populations): Chichagof Island with central Alaska and POW with Revillagigedo Island (Fig. 2 and 3). These genome analyses, although based on few individuals, suggest that M. caurina were either not present on these islands prior to translocations of M. americana or that they were recently replaced or swamped by introduced M. americana .
Accidental or intentional introductions (Weber et al. 2017) motivated by economics (McNeely 2001; Fenichel et al. 2008; Powell et al. 2012), public safety (Massei et al. 2010) or conservation (Powell et al. 2012) can result in unanticipated consequences, including hybridization with native species (Todescoet al. 2016) and exchange of parasites (Prenter et al.2004) with unknown evolutionary outcomes. Genetic management strategies (Thomas et al. 2013; Whiteley et al. 2015) can be informed through investigations of existing hybrid zones or historical wildlife translocations that can provide a predictive framework for anticipating the evolutionary consequences of genetic exchange. In martens, hybridization may disproportionately impact Pacific martens through genetic dilution from outbreeding (Colella et al. 2018a). We detected two hybrid individuals, each collected from a distinct natural mixing zone: Kuiu Island Alaska and western Montana in the northern Rocky Mountains (Table 2; Fig. 2-4; Supplemental Information 9-16). Both hybrids were female, had M. americana mitochondrial haplotypes (Fig. 2d), and mixed nuclear ancestry, with the Montana hybrid containing continental M. caurina alleles and the Kuiu hybrid containing insular M. caurina alleles (Table 2; Supplemental Information 10-13, 16-17). Both admixed individuals were identified as early generational-stage hybrids (e.g., F1’s or a single generation backcrossed with M. americana , Supplemental Information 11-12) with introgression occurring recently (Supplemental Information 21). Although sample sizes are small, the absence of late-generational hybrids is surprising, especially for the Montana zone which has persisted for many generations (Wright 1953). Detection of only early-generational hybrids is consistent with the presence of hybrid incompatibilities, where F1 hybrids experience a temporary elevation in fitness (heterosis) compared to later generational-stage hybrids (e.g., F2 and beyond) that may suffer outbreeding depression as a result of disrupted co-adapted gene complexes (Todesco et al. 2016). The disruption of co-adapted gene complexes or genes involved in local adaptation via introgression, and particularly loci involved in disease and pathogen resistance (Alibert et al. 1994), may pose a particular challenge to naïve insular taxa. This hypothesis warrants further genomic investigation with expanded and fine-scale sampling from within hybrid zones and translocated islands.
Within M. americana , Chichagof Island exhibits the highest effective population size (Ne), followed by central Alaska (Fig. 3b). Although high Ne is surprising for an insular population, Chichagof Island received iterative translocations of M. americana in the mid-1900s from multiple source populations, including four other islands in southeast Alaska (Baranof, Wrangell, Mitkof [Petersburg], and Revillagigedo [Ketchikan] islands) and one distant continental locality (Polly Creek, in central AK). Those introductions likely inflate population size estimates as a consequence of outbreeding (Paul 2009) and make the historical distribution of Ne for this individual resemble that of mainland populations (e.g., MAK). In contrast, Prince of Wales Island (POW) received introductions from only two proximate sources: Revillagigedo and Mitkof islands (Burris & McKnight 1973; Paul 2009). Revillagigedo Island shows a similar demographic history to POW, suggesting those translocations resulted in successful establishment (Elkins & Nelson 1954). Absence of M. caurina alleles on POW or Chichagof suggests that interspecific competition, outbreeding, or the introduction of foreign pathogens among other variables may have impacted endemic M. caurina (Plein et al. 2016; Colellaet al. 2018b; Northover et al. 2018). Ultimately, until additional hybrids are sequenced, our results discourage further wildlife translocations into the NPC islands due to potential swamping and emphasize the importance of careful source population selection for genetic rescue, as the NPC harbors significant cryptic diversity that represents complex evolutionary histories.