Living on the edge: Exploring the role of coastal refugia in the Alexander Archipelago of Alaska

Sawyer, Yadéeh E.; MacDonald, Stephen O.; Lessa, Enrique P.; Cook, Joseph A.

doi:10.1002/ece3.4861

Cited by 20 publications

(37 citation statements)

References 116 publications

(157 reference statements)

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“…The single virus recovered from a S. vagrans on Vancouver Island does not align within a defined mainland clade in the S segment and exists on a long branch in the L segment. This finding raises the question of whether there is an endemic insular clade of JMSV similar to that identified for insular S. monticola [49]. Highly negative Tajima’s D values for all three viral segments, coupled with observed patterns of sequence divergence centered in the hypothesized source population of the PC clade, strengthens the hypothesis of post-glacial expansion for JMSV (Figure 5B).…”

Section: Discussionsupporting

confidence: 64%

Complex History of Codiversification and Host Switching of a Newfound Soricid-Borne Orthohantavirus in North America

Liphardt

Kang

Dizney

et al. 2019

Viruses

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Orthohantaviruses are tightly linked to the ecology and evolutionary history of their mammalian hosts. We hypothesized that in regions with dramatic climate shifts throughout the Quaternary, orthohantavirus diversity and evolution are shaped by dynamic host responses to environmental change through processes such as host isolation, host switching, and reassortment. Jemez Springs virus (JMSV), an orthohantavirus harbored by the dusky shrew (Sorex monticola) and five close relatives distributed widely in western North America, was used to test this hypothesis. Total RNAs, extracted from liver or lung tissue from 164 shrews collected from western North America during 1983–2007, were analyzed for orthohantavirus RNA by reverse transcription polymerase chain reaction (RT-PCR). Phylogenies inferred from the L-, M-, and S-segment sequences of 30 JMSV strains were compared with host mitochondrial cytochrome b. Viral clades largely corresponded to host clades, which were primarily structured by geography and were consistent with hypothesized post-glacial expansion. Despite an overall congruence between host and viral gene phylogenies at deeper scales, phylogenetic signals were recovered that also suggested a complex pattern of host switching and at least one reassortment event in the evolutionary history of JMSV. A fundamental understanding of how orthohantaviruses respond to periods of host population expansion, contraction, and secondary host contact is the key to establishing a framework for both more comprehensive understanding of orthohantavirus evolutionary dynamics and broader insights into host–pathogen systems.

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Section: Discussionsupporting

confidence: 64%

Complex History of Codiversification and Host Switching of a Newfound Soricid-Borne Orthohantavirus in North America

Liphardt

Kang

Dizney

et al. 2019

Viruses

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“…The significant geographic break between insular and continental M. caurina is consistent with the CRH (Figure 3a, Supporting Information 5). Furthermore, the ancient split between these two lineages and distinct demographic histories (Figure 3b), with insular M. Vancouver Island, Canada (Byun et al, 1997;Heusser, 1960;Pojar, 1980;Sawyer et al, 2019;Ward et al, 2003 Lynch, 2020). Timing demographic events is sensitive to assumed mutation rates and generation times, which can expand or contract the estimated distribution of N e across evolutionary time.…”

Section: Evidence For a Cryptic Species Forested Refugia And Dynamic Contactmentioning

confidence: 99%

“…We use whole-genome resequencing data from NPC martens to test the Coastal Refugium Hypothesis (CRH; Demboski et al, 1999;Heusser, 1989;Sawyer et al, 2019;Scudder & Gessler, 1989) and refine our understanding of the dynamic biogeographic history and potential paleoenvironments of this coastal corridor. With increased F I G U R E 1 North American range map for Martes americana (green) and Martes caurina (blue), with an inset map of the North Pacific Coast.…”

Section: Introductionmentioning

confidence: 99%

Whole‐genome resequencing reveals persistence of forest‐associated mammals in Late Pleistocene refugia along North America’s North Pacific Coast

Colella

Lan

Talbot

et al. 2021

Journal of Biogeography

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Aim: Numerous glacial refugia have been hypothesized along North America's North Pacific Coast that may have increased divergence of refugial taxa, leading to elevated endemism and subsequently clustered hybrid zones following deglaciation. The locations and community composition of these ice-free areas remains controversial, but whole-genome sequences now enable detailed analysis of the demographic and evolutionary histories of refugial taxa. Here, we use genomic data to test spatial and temporal processes of diversification among martens with respect to the Coastal Refugium Hypothesis, to understand the role of climate cycling in shaping diversity across complex landscapes.Location: North America and North Pacific Coast archipelagos. Taxon: North American martens (Martes).Methods: Short-read whole-genome resequencing data were generated for 11 martens: four M. americana, four M. caurina, two hybrids, and one outgroup (Martes zibellina). Sampling was representative of known genetic clades within New World martens, including sampling within insular and continental hybrid zones and along the North Pacific Coast (five island populations). ADMIXTURE, F-statistics, and Dstatistics (ABBA-BABA) were used to identify introgression and infer directionality.Heterozygosity densities, estimated via PSMC, were used to characterize historical demography at and below the species level to infer refugial and colonization processes. Results: Forest-associated Pacific martens (M. caurina) are divided into distinct insular and continental clades consistent with the Coastal Refugium Hypothesis. There was no evidence of introgression on islands that received historical translocations of American pine martens (M. americana), but introgression was detected in two active zones of secondary contact: one insular and one continental. Only early-generational hybrids were identified across multiple hybrid zones, a pattern consistent with potential genetic swamping of M. caurina by M. americana. Main conclusions: Despite an incomplete fossil record, genomic evidence supports the persistence of forest-associated martens, likely the insular Pacific marten lineage, along the western edges of the Alexander Archipelago during the Last Glacial Maximum. This discovery informs our understanding of refugial paleoenvironments,

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“…M. caurina are among the 150 known species or species complexes that have disjunct mesic forest inland and coastal populations in Pacific Northwest (Carstens et al, 2004) due to desertification of the Columbia Plateau (Shafer et al, 2010). During last glacial maximum many species persisted in ice free Pacific Northwest refugia (e.g., Lucid and Cook, 2004) while maintaining genetic connectivity to populations persisting in coastal refugia (Sawyer et al, 2019). The fossil record indicates marten persisted disjunctly during last glacial maximum in western and eastern North America with the eastern group expanding west from the late Pleistocene to late Holocene (Graham and Graham, 1994).…”

Section: Species Fracture Zone and Taxonomic Alignmentmentioning

confidence: 99%

Carnivore Contact: A Species Fracture Zone Delineated Amongst Genetically Structured North American Marten Populations (Martes americana and Martes caurina)

et al. 2020

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North American martens are forest dependent, influenced by human activity, and climate vulnerable. They have long been managed and harvested throughout their range as the American marten (Martes americana). Recent work has expanded evidence for the original description of two species in North America-M. americana and the Pacific Coast marten, M. caurina-but the geographic boundary between these groups has not been described in detail. From 2010 to 2016 we deployed 734 multi-taxa winter bait stations across a 53,474 km 2 study area spanning seven mountain ranges within the anticipated contact zone along the border of Canada and the United States. We collected marten hair samples and developed genotypes for 15 polymorphic microsatellite loci for 235 individuals, and 493 base-pair sequences of the mtDNA gene COI for 175 of those individuals. Both nuclear and mitochondrial genetic structure identified a sharp break across the Clark Fork Valley, United States with M. americana and M. caurina occurring north and south of the break, respectively. We estimated global effective population size (N e) for each mountain range, clinal genetic neighborhood sizes (NS), calculated observed (H o) and expected (H e) heterozygosity, fixation index (F ST) , and clinal measures of allelic richness (Ar), H o , and inbreeding coefficient (F IS). Despite substantial genetic structure, we detected hybridization along the fracture zone with both contemporary (nuclear DNA) and historic (mtDNA) gene flow. Marten populations in our study area are highly structured and the break across the fracture zone being the largest documented in North America (F ST range 0.21-0.34, mean = 0.27). With the exception of the Coeur d'Alene Mountains, marten were well distributed across higher elevation portions of our sampling area. Clinal NS values were variable suggesting substantial heterogeneity in marten density and movement. For both M. americana and

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Living on the edge: Exploring the role of coastal refugia in the Alexander Archipelago of Alaska

Cited by 20 publications

References 116 publications

Complex History of Codiversification and Host Switching of a Newfound Soricid-Borne Orthohantavirus in North America

Complex History of Codiversification and Host Switching of a Newfound Soricid-Borne Orthohantavirus in North America

Whole‐genome resequencing reveals persistence of forest‐associated mammals in Late Pleistocene refugia along North America’s North Pacific Coast

Carnivore Contact: A Species Fracture Zone Delineated Amongst Genetically Structured North American Marten Populations (Martes americana and Martes caurina)

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