The signal crayfish is not a single species: cryptic diversity and invasions in the Pacific Northwest range of Pacifastacus leniusculus

1. We used historical sources, morphology‐based taxonomy and mtDNA sequence data to address questions about the signal crayfish Pacifastacus leniusculus. These included evaluating unrecognised cryptic diversity and investigating the extent to which P. leniusculus may have been introduced within its presumed native range in the Pacific Northwest region of North America. Our study builds and expands on Pacific Northwest phylogeographic knowledge, particularly related to patterns of glacial refugia for freshwater species. 2. Extensive collections (824 specimens) from British Columbia (Canada), Idaho, Nevada, Oregon and Washington (United States) were used to characterise P. leniusculus at the mitochondrial 16S rRNA gene. Genetic groups within the species were elucidated by phylogenetics and amova ; evolutionary relationships within the most common and diverse group were investigated using a statistical parsimony haplotype network, a nested amova , and tests of isolation by distance. Morphological measurements were used to relate findings of molecular analyses to three historically recognised P. leniusculus subspecies and characterise cryptic diversity by morphology. 3. We found substantial cryptic diversity, with three groups highly distinct from P. leniusculus in discrete geographic regions: the Chehalis River glacial refugium, Central Oregon and the Okanagan Plateau. Disjunct distributions of P. leniusculus relative to these cryptic groups and known patterns of Pleistocene glaciation and landscape evolution cast doubt on whether P. leniusculus is native to some areas such as coastal drainages of northern Washington and southern British Columbia. Morphological traits previously used to characterise P. leniusculus subspecies still persist but may be incapable of distinguishing P. leniusculus from newly discovered cryptic groups. 4. Cryptic diversity found within P. leniusculus highlights the pressing need for a thorough investigation of the genus Pacifastacus using data based on more extensive gene and taxon sampling. It also warrants conservation attention, as introductions of P. leniusculus within the Pacific Northwest may carry risks of hybridisation and introgression for cryptic groups. Owing to high genetic diversity and limited dispersal capacity relative to more vagile organisms like freshwater fish, crayfish of the genus Pacifastacus offer powerful potential insights into the geological history and phylogeography of the Pacific Northwest region. Finally, by shedding light on the long‐neglected native range of P. leniusculus, our results should also better inform our understanding of potential source populations for, and the ecology of, this important invasive species in regions including Europe, Japan and elsewhere in North America.     

American marten (Martes americana) in the Pacific Northwest: population differentiation across a landscape fragmented in time and space

American marten (Martes americana) have a close association with mature temperate forests, a habitat that expanded throughout the Pacific Northwest as glaciers receded at the end of the Pleistocene. Similar to several other forest-associated mammals in North America (e.g. black bear), genetic analysis of the marten shows a deep phylogeographical subdivision that reflects populations with distinctive evolutionary histories. Using a suite of 14 microsatellite markers, we explored the genetic structure of marten populations in two reciprocally monophyletic clades in the Pacific Northwest identified previously as M. caurina and M. americana by mitochondrial haplotypes and morphology. Microsatellite phylogeographical patterns were congruent with mitochondrial analyses. These independent data sets shed light upon hybridization patterns, population structure and evolutionary histories. Hybridization between M. caurina and M. americana individuals was documented in two regions of sympatry (Kuiu Island in southeastern Alaska and southern Montana). Northern insular populations of M. caurina exhibited higher differentiation and lower variability relative to northern populations of M. americana. Greater divergence among M. caurina populations may reflect longer isolation and persistence in coastal forest habitat that was fragmented by rising sea level in the early Holocene. Lower differentiation among northern M. americana populations and close relationship to other continental M. americana populations may reflect more recent expansion into the Pacific Northwest and/or continued gene flow among populations. Differentiation among M. caurina populations was attributed to habitat fragmentation (i.e. rising sea level), as opposed to isolation-by-distance; oceanic straits pose significant barriers to gene flow among M. caurina populations and between populations of M. caurina and M. americana.     

Post-glacial colonization of northwestern North America by the forest-associated American marten (Martes americana,Mammalia: Carnivora: Mustelidae)

Phylogeographic patterns were used to assess intraspecific diversification of American martens (Martes americana). Within martens, two morphological groups (americana and caurina) have been recognized, though the level of distinction between them has been debated. We examined mitochondrial cytochrome b gene haplotypes from 680 martens to explore the colonization history of the Pacific Northwest and found two clades that correspond to the morphological groups. The widespread americana clade extends from interior Alaska south to Montana and eastward to Newfoundland and New England (i.e. northwestern, north-central and northeastern North America). The caurina clade occurs in western North America, minimally extending from Admiralty Island (southeastern Alaska) south to Oregon and Wyoming. Our data indicated two colonization events for the Pacific Northwest (one by members of each clade) and were consistent with the persistence of populations throughout past glacial periods in eastern and western refugia. Due to vegetational and geological history following the past deglaciation, we hypothesize that martens of the caurina clade spread along the North Pacific Coast, and into southeastern Alaska, earlier than martens of the americana clade. Mismatch distributions for the americana clade were indicative of populations that recently experienced demographic expansion, while mismatch distributions for the caurina clade suggested that populations were at equilibrium. These clades are reciprocally monophyletic and distinctive (interclade divergence ranged from 2.5 to 3.0% (uncorrected p), whereas, intraclade divergence was < 0.7%), and two regions of sympatry have been identified. Genetic signatures of past admixture in hybrid zones may have been extinguished during subsequent glacial periods when ranges contracted. This recurrent pattern of relatively restricted western, or Pacific coastal, lineages and more widespread eastern, or interior continental, lineages exists across broad taxonomic groups and suggests a shared biogeographical history.     

Stream Restoration in the Pacific Northwest: Analysis of Interviews with Project Managers

Hundreds of millions of dollars per year are spent on river restoration in the Pacific Northwest (PNW), but little is known about the effectiveness of this effort. To help address this gap, we analyzed a database containing 23,000 projects at 35,000 locations in the region. We selected a subset of these projects for interviews using a survey instrument developed by a national team of scientists. In total, 47 project contacts in the PNW were interviewed to learn from the individuals directly involved in restoration. At least one‐third of the projects surveyed (34%) did not conduct sufficient monitoring to evaluate effectiveness. More than two‐thirds (70%) of all respondents reported their projects were successful, but 43% either have no success criteria or are unaware of any criteria for their project. Although almost two‐thirds (66%) of respondents anticipate a need for ongoing project maintenance, less than half (43%) have maintenance funds available. These findings suggest that establishing a connection between effectiveness monitoring and project implementation is not a usual component of project design. Consequently, we can only assess the benefits in a few isolated projects and cannot quantify the cumulative benefits of restoration on a larger scale. These findings highlight the need for (1) planning prior to implementation of restoration projects that accounts for monitoring design; (2) coordinated effectiveness monitoring to assess cumulative effects of restoration; and (3) management and maintenance of projects based on real measures of project performance.     

Glacial vicariance in the Pacific Northwest: evidence from a lodgepole pine mitochondrial DNA minisatellite for multiple genetically distinct and widely separated refugia

The Canadian side of the Pacific Northwest was almost entirely covered by ice during the last glacial maximum, which has induced vicariance and genetic population structure for several plant and animal taxa. Lodgepole pine ( Pinus contorta Dougl. ex. Loud.) has a wide latitudinal and longitudinal distribution in the Pacific Northwest. Our main objective was to identify relictual signatures of glacial vicariance in the population structure of the species and search for evidence of distinct glacial refugia in the Pacific Northwest. A maternally inherited mitochondrial DNA minisatellite-like marker was used to decipher haplotype diversity in 91 populations of lodgepole pine located across the natural range. Overall population differentiation was sizeable ( G _ST = 0.365 and R _ST = 0.568). Four relatively homogeneous groups of populations, possibly representative of as many genetically distinct glacial populations, were identified for the two main subspecies, ssp. latifolia and ssp. contorta . For ssp. contorta , one glacial lineage is suggested to have been located at high latitudes and possibly off the coast of mainland British Columbia (BC), while the other is considered to have been located south of the ice sheet along the Pacific coast. For ssp. latifolia , two genetically distinct glacial populations probably occurred south of the ice sheet: in the area bounded by the Cascades and Rocky Mountains ranges, and on the eastern side of the Rockies. A possible fifth refugium located in the Yukon may have also been present for ssp. latifolia . Zones of contact between these ancestral lineages were also apparent in interior and northern BC. These results indicate the role of the Queen Charlotte Islands and the Alexander Archipelago as a refugial zone for some Pacific Northwest species and the vicariant role played by the Cascades and the American Rocky Mountains during glaciation.     

Phylogeographic structure and deep lineage diversification of the red alga Chondrus ocellatus Holmes in the Northwest Pacific

A major goal of phylogeographic analysis using molecular markers is to understand the ecological and historical variables that influence genetic diversity within a species. Here, we used sequences of the mitochondrial Cox1 gene and nuclear internal transcribed spacer to reconstruct its phylogeography and demographic history of the intertidal red seaweed Chondrus ocellatus over most of its geographical range in the Northwest Pacific. We found three deeply separated lineages A, B and C, which diverged from one another in the early Pliocene–late Miocene (c. 4.5–7.7 Ma). The remarkably deep divergences, both within and between lineages, appear to have resulted from ancient isolations, accelerated by random drift and limited genetic exchange between regions. The disjunct distributions of lineages A and C along the coasts of Japan may reflect divergence during isolation in scattered refugia. The distribution of lineage B, from the South China Sea to the Korean Peninsula, appears to reflect postglacial recolonizations of coastal habitats. These three lineages do not coincide with the three documented morphological formae in C. ocellatus, suggesting that additional cryptic species may exist in this taxon. Our study illustrates the interaction of environmental variability and demographic processes in producing lineage diversification in an intertidal seaweed and highlights the importance of phylogeographic approaches for discovering cryptic marine biodiversity.     

Molecular systematics and phylogeography of the Plethodon elongatus species group: combining phylogenetic and population genetic methods to investigate species history

Plethodon elongatus and P. stormi (Caudata: Plethodontidae) are Pacific Northwest endemic species which occur in northwestern California and southwestern Oregon. Studies on these salamanders have resulted in differing taxonomic conclusions, but the underlying historical hypotheses, at both inter- and intraspecific levels, have never been examined in a molecular framework. Here, representatives of 81 populations from throughout the range of both taxa are sequenced. Portions of three mitochondrial protein-coding genes (cytochrome b, NADH dehydrogenase subunit 4, and ATPase 6) were sequenced. Four haplotype groups with nonoverlapping geographical ranges were recovered in separate and combined analyses of the data. One clade corresponds to the distribution of P. stormi, while the remaining three comprise P. elongatus. Phylogenetic relationships among haplotype groups differ in separate analyses of the genes but converge on a well-supported topology, with P. elongatus and P. stormi as monophyletic sister taxa, in combined Maximum Parsimony and Maximum Likelihood analyses. Population genetic analyses of mismatch distributions and Tajima's D-statistic are consistent with range expansion for the largest clade within P. elongatus, covering the northern two-thirds of the species range. In contrast, the P. stormi haplotype clade and the P. elongatus clade from the southern third of the species range may have been relatively stable. Morphological boundaries between P. elongatus and P. stormi are largely congruent with mitochondrial DNA breaks and continued treatment as sister taxa is supported. Although mitochondrial DNA haplotype groups may reflect historical separation within P. elongatus, genetic barriers are incongruent with intraspecific patterns of morphological variation.     

Restoring Wild Salmon to the Pacific Northwest: Framing the Risk Question

In the Pacific Northwest of the United States, it is urgent to assess accurately the various options proposed to restore wild salmon. For the past 150 years, a variety of analytic approaches have been employed to assess the ecological consequences of salmon management options. Each approach provided useful information to decision makers, but each also suffered from limitations, some relatively minor, others sufficient to undermine any potential utility. Risk assessment has become the most widely used analytic approach to evaluate environmental policy options. To date its use in ecological policy has been largely constrained to evaluating relatively simple technical questions (e.g., regulatory actions associated with specific chemicals or hazardous waste sites). Recently, however, there has been interest in applying risk assessment to more complex ecological policy problems (e.g., the decline of wild salmon in the Pacific Northwest). Although its use has become commonplace and widely accepted, especially among regulatory and land management agencies, risk assessment remains contentious. The most heated debates revolve around delineating the specific meaning of risk; that is, framing the risk “question” to be answered.     

Forest Management Policy, Amenity Migration, and Community Well-Being in the American West: Reflections from the Northwest Forest Plan

This paper examines the relation between public land management policy, amenity migration, and socioeconomic well-being using the case of the Northwest Forest Plan—a forest management policy that caused 11.6 million acres of federal land in the US Pacific Northwest to be reallocated from commodity production to biodiversity services. Our analysis focuses on three propositions implicit in much of the amenity migration literature in the USA: land management policies that reduce commodity production and/or increase environmental protection (1) improve the natural amenity values of public lands; (2) increase amenity migration to communities near public lands; and (3) stimulate economic development and increase socioeconomic well-being in these communities. Our findings indicate that all three propositions are problematic and demonstrate the importance of community-scale analysis for understanding the relation between land management policies, amenity migration, and community well-being. We discuss the implications of our findings for public land management and rural community development.

Social Identity and Culture Change on the Southern Northwest Coast

Driven by the participation of Native American people in the contemporary political, cultural, and academic landscape of North America, public and academic discussions have considered the nature of contemporary American Indian identity and the persistence, survival, and (to some) reinvention of Native American cultures and traditions. I use a case study—the historical anthropology of the Native American people of the Oregon coast—to examine the persistence of many American Indian people through the colonial period and the subsequent revitalization of "traditional" cultural practices. Drawing on archaeological data, ethnohistorical accounts, and oral traditions, I offer a reading of how, set against and through an ancestral landscape, traditional social identities and relationships of gender and authority were constructed and contested. I then consider how American Indian people negotiated the new sets of social relationships dictated by the dominant society.     

Phylogeography of the flathead mullet Mugil cephalus in the north-west Pacific as inferred from the mtDNA control region

The population genetic structure and historical demography of the flathead mullet Mugil cephalus were investigated using the mtDNA control region (CR) sequences (909–1015 bp) of 126 individuals collected from seven locations in the north-west Pacific between 2005 and 2007. Haplotype diversity ( h = 0·9333–1·000) and nucleotide diversity (π = 0·0046–0·1467) varied greatly among the sampling locations. Phylogenetic analysis of the CR sequences indicated that M. cephalus in the north-west Pacific belongs to two highly divergent lineages (lineages 1 and 2), with the inferred population structure being closely associated with the distribution of both lineages. Two populations were identified, one from the East China Sea and the other from the South China Sea. The former samples were obtained from Taiwan and Qingdao of north China and associated with lineage 1 haplotypes. The latter samples were collected from the Philippines, Pearl River of South China and two samples from Japan, all of which were associated with lineage 2. Japanese samples from Okinawa and Yokosuka had different degrees of mixing between lineages 1 and 2. Historical demographic variables in both populations indicated that Pleistocene glaciations had a strong impact on M. cephalus in the north-west Pacific, resulting in a recent demographic decline of the East China Sea population but in demographic equilibrium for the South China Sea population. Japan appears to be a contact zone between lineages 1 and 2, but it may also be indicative of coexistence between resident and migratory populations. Further global studies are required to clarify the taxonomic status of this cosmopolitan species.     

Ecological assessment criteria for restoring anadromous salmonid habitat in Pacific Northwest estuaries

Restoration of estuarine habitats is essential for the conservation and recovery of depressed Pacific salmon populations. However, assessing the functions of recently restored habitat poses a number of problems because of the transitory occurrence of salmonids in any one location. We propose assessment criteria and metrics that are based on the habitat’s capacity, opportunity, and realized function to enhance survivability of juvenile salmon. Because of the paucity of data relating capacity and opportunity attributes to realized function (e.g. growth, consumption rate, survival), there continues to be a need for manipulative experiments to assess the developmental status of restoration sites. Such a self-monitoring approach of letting the fish diagnose the ecological state of restoration would effectively address the small-scale, site-specific assessment goals and criteria, but ignores the larger-scale issues relating to the ability of diverse salmon species and life histories to occupy estuarine habitat landscapes. If coastal restoration is going to contribute the recovery of anadromous salmonid populations, a landscape perspective is fundamental to restoration planning, implementation, and particularly assessment.     

Optimal PAR intensity for spring bloom in the Northwest Pacific marginal seas

Using ten years (2003–2012) of satellite Chlorophyll-a data, we report that annual phytoplankton bloom climax in the Northwest Pacific marginal seas (17°–58°N) delays northward at a rate of 22.98 ± 2.86 km day⁻¹. The spring bloom is a dominant feature of the phytoplankton seasonal cycle in this region, except for the northern South China Sea, which features a winter bloom. The sea surface hourly Photosynthetically Available Radiation (PAR) intensity averaged over the bloom peak duration is nearly uniform (1.04 ± 0.10 W m⁻² h⁻¹) among the four sub-regions (i.e. the northern South China Sea, the Kuroshio waters, the Sea of Japan and the Sea of Okhotsk), although different algal species in these four distinct ecological provinces could adapt to a much larger change in other environmental parameters (including total daily PAR, day length, sea surface temperature, net surface heat flux, mixed layer depth, wind speed and euphotic depth). The differences of the hourly PAR intensity between the four provinces during their bloom periods are smaller than those during non-bloom seasons. In contrast, an increasing total daily PAR (W m⁻² day⁻¹), due to the longer day length at higher latitudes, may balance decreasing sea surface temperature and induce algal flowering. Our results point to an optimal hourly light intensity for the annual phytoplankton bloom peak timing in this entire region, which could potentially become an indicator for the requirement of these annual bloom peaks.     

Phylogeography of the tailed frog (Ascaphus truei): implications for the biogeography of the Pacific Northwest

Tailed frogs are distributed in high-gradient streams within the disjunct mesic forests of the Pacific Northwest and represent the basal lineage of the anurans. We sequenced 1,530 nucleotides of the mitochondrial cytochrome b and NADH dehydrogenase subunit two genes from 23 populations and used parsimony, maximum-likelihood, and nested-clade analyses to estimate relationships among populations and infer evolutionary processes. We found two divergent haplotype clades corresponding with inland Rocky Mountain populations and coastal populations and separated by up to 0.133 substitutions per site. Within the coastal assemblage, haplotypes formed clades by mountain range with 0.010-0.024 substitutions per site divergence among populations. Inland haplotypes exhibited minimal genetic structure, with the exception of 0.021 substitutions per site distance between populations from the East Fork of the South Fork of the Salmon River and all other inland haplotypes. The magnitude of divergence between inland and coastal populations, as well as the paleobotanical record, suggest isolation of these lineages occurred during the late Miocene to early Pliocene, probably in response to the rise of the Cascade Mountains. Genetic structure within coastal and inland populations is consistent with isolation in refugia during the late Pliocene and early Pleistocene. Closely related inland haplotypes reflect range expansion following glaciation. The depth of divergence between inland and coastal populations supports the persistence of mesic forests within the inland Pacific Northwest throughout the Pleistocene and is congruent with patterns found in several other mesic forest species. Based on mitochondrial divergence and previous allozyme and morphological data, we recommend recognition of inland populations as a distinct species, Ascaphus montanus.     

Geographic Variation in Roost-Site Selection of Long-Legged Myotis in the Pacific Northwest

Abstract: Several species of bats in the Pacific Northwest of the United States, including long-legged myotis (Myotis volans), are dependent on snags in coniferous forests during summer for roosting and rearing young. Thus, data on roosting preferences of this species are needed to integrate their habitat requirements into shifting plans for management of forests in this region. Therefore, from 2001 to 2006, we radiotracked adult female long-legged myotis (n = 153) to day roosts (n = 395) across 6 watersheds in Washington, Oregon, and Idaho, USA, and compared characteristics associated with roosting sites to those of random snags (n = 260) sampled in the same watersheds using use-availability logistic regression and an information-theoretic approach. Model rankings varied among geographic locations, with quantity of stem surface for roosting the best model for explaining roost-site selection of long-legged myotis in both Washington and Oregon. Model rankings for populations of bats in Idaho found stand- and landscape-scale features to be important in roost-site selection, with a habitat fragmentation model and a foraging habitat quality model both demonstrating strong support as best model. Choice of day roosts by long-legged myotis was associated with snags that were taller, intact at the top of the stem, possessing a greater amount of exfoliating bark, in stands with a larger basal area of dead stems, and in landscapes that were unfragmented (i.e., supporting lesser amounts of edge). Results indicate that roost-site selection of bats in western coniferous forests, particularly long-legged myotis, is likely to be region-specific. We encourage land managers to consider importance of geographic variation in intraspecific habitat use in forest-dwelling bats when implementing silvicultural systems to promote biological diversity in actively managed forests of the Pacific Northwest region.     

Phylogeographical lineages of Arctic grayling (Thymallus arcticus) in North America: divergence, origins and affinities with Eurasian Thymallus

The number and location of Arctic glacial refugia utilized by taxa during the Pleistocene are continuing uncertainties in Holarctic phylogeography. Arctic grayling (Thymallus arcticus) are widely distributed in freshwaters from the eastern side of Hudson Bay (Canada) west to central Asia. We studied mitochondrial DNA (mtDNA) and microsatellite DNA variation in North American T. arcticus to test for genetic signatures of survival in, and postglacial dispersal from, multiple glacial refugia, and to assess their evolutionary affinities with Eurasian Thymallus. In samples from 32 localities, we resolved 12 mtDNA haplotypes belonging to three assemblages that differed from each other in sequence by between 0.75 and 2.13%: a 'South Beringia' lineage found from western Alaska to northern British Columbia, Canada; a 'North Beringia' lineage found on the north slope of Alaska, the lower Mackenzie River, and to eastern Saskatchewan; and a 'Nahanni' lineage confined to the Nahanni River area of the upper Mackenzie River drainage. Sequence analysis of a portion of the control region indicated monophyly of all North American T. arcticus and their probable origin from eastern Siberian T. arcticus at least 3 Mya. Arctic grayling sampled from 25 localities displayed low allelic diversity and expected heterozygosity (H(E)) across five microsatellite loci (means of 2.1 alleles and 0.27 H(E), respectively) and there were declines in these measures of genetic diversity with distance eastward from the lower Yukon River Valley. Assemblages defined by mtDNA divergences were less apparent at microsatellite loci, but again the Nahanni lineage was the most distinctive. Analysis of molecular variance indicated that between 24% (microsatellite DNA) and 81% (mtDNA) of the variance was attributable to differences among South Beringia, North Beringia and Nahanni lineages. Our data suggest that extant North American Arctic grayling are more diverse phylogeographically than previously suspected and that they consist of at least three major lineages that originated in distinct Pleistocene glacial refugia. T. arcticus probably originated and dispersed from Eurasia to North America in the late to mid-Pliocene, but our data also suggest more recent (mid-late Pleistocene) interactions between lineages across Beringia.     

Possible female philopatry of the smooth hammerhead shark Sphyrna zygaena revealed by genetic structure patterns

We assessed the spatial pattern of genetic structure of smooth hammerhead shark Sphyrna zygaena in 10 localities from the Northern Mexican Pacific. A total of 35 haplotypes were identified in 129 sequences of the mtDNA control region. The results showed slight but significant genetic structure among localities (Φ_ST = 0.044, P < 0.001). In addition, the localities with highest number of juveniles were genetically different (Φ_ST = 0.058, P < 0.024), which may be representative of nursery areas. The genetic differentiation pattern can be associated to female philopatry and preference for particular birthing sites. Finally, historical demography shows that S. zygaena populations present a recent demographic expansion that occurred during glacial events in the late Pleistocene to early Holocene.     

Phylogeographical analysis of an estuarine fish, Salanx ariakensis (Osmeridae: Salanginae) in the north-western Pacific

This study extended the geographic coverage of a previous study to explore population genetic structure and demographic history in the Ariake icefish Salanx ariakensis from three populations of continental coastlines and one island population in the north-western Pacific based on a partial sequence of the mitochondrial cytochrome b gene. The S. ariakensis showed high genetic diversity and strong genetic structure. Phylogenetic analysis showed a shallow gene tree with no clear phylogeographical structure. Contiguous range expansion and restricted gene flow were inferred to be main population events by nested-clade analysis. Significant genetic differentiations between populations could be attributable to negligible gene flow by coalescent analysis. High nucleotide diversity of each population was due to geographic mixing of heterogenous haplotypes during lowering sea levels of the Pleistocene. These findings indicate that cycles of geographic isolation and secondary contact happened in the Pleistocene glacial–interglacial cycles shaping genetic structure and population demography of S. ariakensis .