The post‐Pleistocene population genetic structure of a western North American passerine: the chestnut‐backed chickadee Poecile rufescens

The population genetic structure of many high‐latitude species in North America was affected by the last glaciation, and current structure reflects isolation in refugia and colonisation patterns. Large ice‐free areas, both south of the ice sheets and in the north‐west, supported numerous flora and fauna throughout this period. Fossil evidence suggests additional western glacial refugia existed both on Haida Gwaii (the Queen Charlotte Islands) and in northern Idaho. The chestnut‐backed chickadee Poecile rufescens is a songbird found along the western edge of Canada and the United States, with a linear distribution along the coast, and an isolated interior population. Mitochondrial DNA sequence data (control region and ATPase 6–8) from 10 populations (n = 122) were used to test for population genetic structure. The data supported a general north/south separation. Haida Gwaii was found to be genetically distinct from the rest of the populations, and the two northern British Columbia populations separated from all but Alaska. The interior population showed evidence of both historical isolation and secondary colonisation by birds from coastal populations. Neutrality tests suggested a past population expansion in all populations from previously glaciated areas, and a stable population in areas believed to be unglaciated. This pattern supports the use of multiple glacial refugia by the chestnut‐backed chickadee. We could not reject the use of Haida Gwaii or the interior (i.e. Clearwater Basin) as glacial refugia.     

Cover

Rhodymenia cf. rhizoides in the low intertidal of Gwaii Haanas; a species with a predominantly disjunct distribution between California and northern British Columbia. [Vol. 50, No. 6, pp. 968–974]     

NORTH AMERICAN BLACK BEAR mtDNA PHYLOGEOGRAPHY: IMPLICATIONS FOR MORPHOLOGY AND THE HAIDA GWAII GLACIAL REFUGIUM CONTROVERSY

The controversial role of Haida Gwaii (Queen Charlotte Islands) as a biological refugium on the northwestern coast of North America has been widely discussed for more than fifty years. The presence of morphologically divergent subspecies on Haida Gwaii is one of the major lines of evidence suggesting this archipelago's role as a refugium during the Wisconsin. However, since morphological distinction can be derived postglacially as well as in extended isolation, such evidence is ambiguous. To examine this question, we did a phylogenetic analysis of cytochrome b sequences (719 bp) of black bear (Ursus americanus), one of the distinctive endemics of Haida Gwaii, and compared these with conspecifics from across North America, focusing primarily on the northwestern coast. We found that the Haida Gwaii bear are indistinguishable from coastal bear of British Columbia and Vancouver Island, but are highly distinct from continental bear. Coastal and continental bears differ by 24 synapomorphies and an average sequence divergence of 3.6%. The coastal mitochondrial lineage occurs in each of the three recognized coastal subspecies suggesting that the morphological characteristics differentiating these taxa may be postglacially derived. The data are consistent with recent suggestions that a glacial refugium existed on the now submerged continental shelf connecting Haida Gwaii, Vancouver Island, and the coastal fringe of mainland British Columbia. This refugium would have been an additional source for postglacial recolonization of northwestern North America.     

First evidence of east–west migration across the North Pacific in a marine bird

Many marine birds undertake long migrations between breeding and wintering areas, including some species that undertake long‐distance east–west or west–east movements across many degrees of longitude. To date, however, no east–west migrations have been described across the North Pacific. Geolocators were deployed on Ancient Murrelets Synthliboramphus antiquus breeding in Haida Gwaii, British Columbia, in 2013 and four were retrieved the following year. Longitude positions showed that all four moved rapidly westwards after breeding, three of them reaching waters between Japan and China by November and this location was also supported by ringing data. Return migration was rapid, beginning in February and reaching Haida Gwaii in March, providing the first evidence for bird migration spanning the entire width of the North Pacific. This is the longest migration recorded in any of the Alcidae.     

DISCORDANT DISTRIBUTION OF POPULATIONS AND GENETIC VARIATION IN A SEA STAR WITH HIGH DISPERSAL POTENTIAL

Patiria miniata, a broadcast‐spawning sea star species with high dispersal potential, has a geographic range in the intertidal zone of the northeast Pacific Ocean from Alaska to California that is characterized by a large range gap in Washington and Oregon. We analyzed spatial genetic variation across the P. miniata range using multilocus sequence data (mtDNA, nuclear introns) and multilocus genotype data (microsatellites). We found a strong phylogeographic break at Queen Charlotte Sound in British Columbia that was not in the location predicted by the geographical distribution of the populations. However, this population genetic discontinuity does correspond to previously described phylogeographic breaks in other species. Northern populations from Alaska and Haida Gwaii were strongly differentiated from all southern populations from Vancouver Island and California. Populations from Vancouver Island and California were undifferentiated with evidence of high gene flow or very recent separation across the range disjunction between them. The surprising and discordant spatial distribution of populations and alleles suggests that historical vicariance (possibly caused by glaciations) and contemporary dispersal barriers (possibly caused by oceanographic conditions) both shape population genetic structure in this species.     

First Report of the Asian kelp Undaria pinnatifida in the Northeastern Pacific Ocean

The Asian kelp Undaria pinnatifida was discovered in southern California in the spring of 2000, and by the summer of 2001 had been collected at several California sites from Los Angeles to Long Beach Harbors and Catalina Island as far north as Monterey Harbor. From its native range in the northwestern Pacific, Undaria has now been introduced to the northeastern and southwestern Atlantic and the southwestern and northeastern Pacific, through a combination of intentional transport for cultivation, accidental transport with oysters, as fouling on vessel hulls, and possibly other means. In the northeastern Pacific, water temperatures are suitable for its establishment from at least Baja California to British Columbia, where it is likely to grow well in sheltered and partially sheltered waters.     

Salmon species, density and watershed size predict magnitude of marine enrichment in riparian food webs

Resource subsidies across habitat boundaries can structure recipient communities and food webs. In the northern Pacific region, bears Ursus spp. foraging on anadromous salmon Oncorhynchus spp. provide a key link between marine and terrestrial ecosystems, with salmon density, fish size and watershed size as potential predictors of the magnitude of marine subsidy to terrestrial habitats. We use nitrogen and carbon stable isotopes to provide an assessment of the patterns of marine‐enrichment in riparian plants (11 species, 4 guilds) and litter invertebrates (4 guilds) sampled from 27 watersheds in coastal British Columbia, Canada. Watersheds occurred in three geographical regions (Vancouver Island, mainland midcoast and Haida Gwaii) and varied in size, and in biomass (kg m^?1 of spawning length) and species of salmon (chum O. keta, pink O. gorbuscha and coho O. kisutch). δ¹⁵N values in all plant species and invertebrate guilds were positively predicted by total salmon biomass (kg m^?1) and negatively predicted by watershed size. We observed replicated parallel slopes among plant species and invertebrate guilds across the gradient in salmon biomass, with differences in means hypothesized to be due to plant fractionation and animal trophic position. As such, we derived a watershed δ¹⁵N‐index averaged across guilds, and using an information theoretic approach we find that the biomass of chum salmon is a much stronger predictor of the δ¹⁵N‐index than either pink or coho salmon, or the sum biomass of all species. The top linear model contained chum biomass and watershed size. Chum salmon biomass independently predicted δ¹⁵N‐index variation in all three regions of British Columbia. Chum salmon are larger than pink or coho and provide an energetic reward for bears that facilitates carcass transfer, tissue selective foraging, and nutrient distribution by insect scavengers. Analyses of biodiversity and habitat data across many watersheds moves towards a long‐term goal in fisheries ecology to better integrate ecosystem values in salmon conservation.     

Thermal regime,predation danger and the early marine exit of sockeye salmon Oncorhynchus nerka

Marine exit timing of sockeye salmon Oncorhynchus nerka populations on the Haida Gwaii Archipelago, British Columbia, Canada, is described, with specific focus on Copper Creek. Marine exit in Copper Creek occurs > 130 days prior to spawning, one of the longest adult freshwater residence periods recorded for any O. nerka population. Copper Creek presents an easy upstream migration, with mild water temperatures (7 to 14° C), short distance (13·1 km) and low elevation gain (41 m) to the lake where fish hold prior to spawning. An energetic model estimates that <1% of the initial energy reserve is required for upstream migration, compared with 62% for lake holding and 38% for reproductive development. Historical records suggest that it is unlikely that water temperature in any of the O.nerka streams in Haida Gwaii has ever exceeded the presumed temperature threshold (19° C) for early marine exit. Although it is not impossible that the thermal tolerance of Copper Creek O.nerka is very low, the data presented here appear inconsistent with thermal avoidance as an explanation for the early marine exit timing in Copper Creek and in three other populations on the archipelago with early marine exit.     

Glacial biogeography of North American coho salmon (Oncorhynchus kisutch)

To study the glacial biogeography of coho we examined 20 microsatellite loci and mitochondrial DNA D-loop sequence in samples from Alaska to California. Microsatellite data divided our samples among five biogeographic regions: (1) Alaska and northern coastal British Columbia; (2) the Queen Charlotte Islands; (3) the mainland coast of British Columbia and northern Washington State; (4) the Thompson River; and (5) Oregon and California. The D-loop sequence data suggested three geographical regions: (1) Oregon and California; (2) the Thompson River; and (3) all the other sites north of the southern ice margin. Microsatellite data revealed no difference in the number of alleles in different regions, but mitochondrial DNA data revealed a cline of decreasing diversity from south to north. We suggest that the two signals presented by these different marker types illuminate two time frames in the history of this species. Endemic microsatellite diversity in Alaska and on the Queen Charlotte Islands provides evidence in favour of Fraser Glaciation refugia in these regions. The loss of mitochondrial variation from south to north suggests that one of the earlier, more extensive, Pleistocene glaciations eliminated coho from its northern range.     

Molecular phylogeography of common garter snakes (Thamnophis sirtalis) in western North America: implications for regional historical forces

Complete ND2 and partial ND4 and cytochrome b mitochondrial DNA (mtDNA) sequences were analysed to evaluate the phylogeographic patterns of common garter snakes (Thamnophis sirtalis) in western North America. This species is widely distributed throughout North America, and exhibits extensive phenotypic variation in the westernmost part of its range. The overall phylogeographic pattern based on mtDNA sequences is concordant with results from studies of other species in this region, implicating historical vicariant processes during the Pleistocene and indicating bottleneck effects of recent dispersal into postglacial habitat. Indeed, the topology is statistically consistent with the hypothesis of both southern (Great Basin and California) and northern (Haida Gwaii) refugia. Specifically, we identified genetic breaks among three major clades: Northwest Coastal populations, Intermountain populations, and all California populations. The California clade contained the only other well-supported branching patterns detected; relationships among populations within the two northern clades were indistinguishable. These molecular splits contrast sharply with all prior geographical analyses of phenotypic variation in T. sirtalis in this region. Our results suggest that the extensive phenotypic variation in western T. sirtalis has been shaped more by local evolutionary forces than by shared common ancestry. Consequently, we consider all morphologically based subspecies designations of T. sirtalis in this region invalid because they do not reflect reciprocal monophyly of the mtDNA sequences.     

Variation in migration pattern,broodstock origin,and family productivity of coho salmon hatchery populations in British Columbia,Canada, derived from parentage‐based tagging

In salmonid parentage‐based tagging (PBT) applications, entire hatchery broodstocks are genotyped, and subsequently, progeny can be nonlethally sampled and assigned back to their parents using parentage analysis, thus identifying their hatchery of origin and brood year (i.e., age). Inter‐ and intrapopulation variability in migration patterns, life history traits, and fishery contributions can be determined from PBT analysis of samples derived from both fisheries and escapements (portion of a salmon population that does not get caught in fisheries and returns to its natal river to spawn). In the current study of southern British Columbia coho salmon (Oncorhynchus kisutch) populations, PBT analysis provided novel information on intrapopulation heterogeneity among males in the total number of progeny identified in fisheries and escapements, the proportion of progeny sampled from fisheries versus escapement, the proportion of two‐year‐old progeny (jacks) produced, and the within‐season return time of progeny. Fishery recoveries of coho salmon revealed heterogeneity in migration patterns among and within populations, with recoveries from north and central coast fisheries distinguishing “northern migrating” from “resident” populations. In northern migrating populations, the mean distance between fishery captures of sibs (brothers and sisters) was significantly less than the mean distance between nonsibs, indicating the possible presence of intrapopulation genetic heterogeneity for migration pattern. Variation among populations in productivity and within populations in fish catchability indicated that population selection and broodstock management can be implemented to optimize harvest benefits from hatcheries. Application of PBT provided valuable information for assessment and management of hatchery‐origin coho salmon in British Columbia.     

Disentangling the causes of damage variation by deer browsing on young Thuja plicata

Long‐lived trees experience different levels of damage due to mammalian herbivores. To untangle the mechanisms that underlie this variation, we combined chemical with dendrochronological analyses to study variation in browsing on Western redcedars (Thuja plicata) on Haida Gwaii (British Columbia, Canada). Since the last glaciation, Haida Gwaii forests had lacked large herbivore browser until Sitka black‐tailed deer (Odocoileus hemionus sitkensis) were introduced at the beginning of the 20th century. Dendrochronology yielded information on radial growth and plant annual responses to environmental stresses including herbivory. Secondary metabolite content and plant nutritional quality provided insights into proximate causes of food choices made by herbivores. We sampled lightly‐ and heavily‐browsed young trees at four sites: three clear‐cut sites with high browsing pressure and one old‐growth forest site where browsing pressure had, until recently, been lower. Heavily‐browsed young trees had lower concentrations of secondary metabolites and were of lower nutritive value than lightly‐browsed trees at all sites. Under high browsing pressure, tree growth patterns suggested that all young trees were initially severely browsed until some trees, currently scored as lightly‐browsed, started to escape deer. At the old‐growth site, both lightly‐ and heavily‐browsed trees tended to have lower overall average secondary metabolite concentrations than those of all other sites, a trend possibly related to greater canopy closure. Lightly‐browsed trees were older than heavily‐browsed ones which resulted, during the period of lower browsing pressure, in higher growth rate and a same pattern of change in growth from one year to the next year. This suggests that, under low browsing pressure, selection of young trees related to chemical defense was weak and that growth differences due to other factors than browsing could be expressed. Under strong browsing pressure, however, all young trees had equally low growth rates until trees with better genetic potential to produce effective defenses were able to escape deer. This suggests that selection by deer could occur on a long‐lived tree.     

Seascape genetics of the stalked kelp Pterygophora californica and comparative population genetics in the Santa Barbara Channel

We conducted a population genetic analysis of the stalked kelp, Pterygophora californica, in the Santa Barbara Channel, California, USA. The results were compared with previous work on the genetic differentiation of giant kelp, Macrocystis pyrifera, in the same region. These two sympatric kelps not only share many life history and dispersal characteristics but also differ in that dislodged P. californica does not produce floating rafts with buoyant fertile sporophytes, commonly observed for M. pyrifera. We used a comparative population genetic approach with these two species to test the hypothesis that the ability to produce floating rafts increases the genetic connectivity among kelp patches in the Santa Barbara Channel. We quantified the association of habitat continuity and oceanographic distance with the genetic differentiation observed in stalked kelp, like previously conducted for giant kelp. We compared both overall (across all patches) and pairwise (between patches) genetic differentiation. We found that oceanographic transit time, habitat continuity, and geographic distance were all associated with genetic connectivity in P. californica, supporting similar previous findings for M. pyrifera. Controlling for differences in heterozygosity between kelp species using Jost's D_EST, we showed that global differentiation and pairwise differentiation were similar among patches between the two kelp species, indicating that they have similar dispersal capabilities despite their differences in rafting ability. These results suggest that rafting sporophytes do not play a significant role in effective dispersal of M. pyrifera at ecologically relevant spatial and temporal scales.     

Loss of a chloroplast encoded function could influence species range in kelp

Kelps are important providers and constituents of marine ecological niches, the coastal kelp forests. Kelp species have differing distribution ranges, but mainly thrive in temperate and arctic regions. Although the principal factors determining biogeographic distribution ranges are known, genomics could provide additional answers to this question. We sequenced DNA from two Laminaria species with contrasting distribution ranges, Laminaria digitata and Laminaria solidungula. Laminaria digitata is found in the Northern Atlantic with a southern boundary in Brittany (France) or Massachusetts (USA) and a northern boundary in the Arctic, whereas L. solidungula is endemic to the Arctic only. From the raw reads of DNA, we reconstructed both chloroplast genomes and annotated them. A concatenated data set of all available brown algae chloroplast sequences was used for the calculation of a robust phylogeny, and sequence variations were analyzed. The two Laminaria chloroplast genomes are collinear to previously analyzed kelp chloroplast genomes with important exceptions. Rearrangements at the inverted repeat regions led to the pseudogenization of ycf37 in L. solidungula, a gene possibly required under high light conditions. This defunct gene might be one of the reasons why the habitat range of L. solidungula is restricted to lowlight sublittoral sites in the Arctic. The inheritance pattern of single nucleotide polymorphisms suggests incomplete lineage sorting of chloroplast genomes in kelp species. Our analysis of kelp chloroplast genomes shows that not only evolutionary information could be gleaned from sequence data. Concomitantly, those sequences can also tell us something about the ecological conditions which are required for species well‐being.     

Prevailing sea surface temperatures inhibit summer reproduction of the kelp Laminaria digitata at Helgoland (North Sea)

The impact of abiotic factors on kelp sporophyte reproduction has rarely been investigated. Laminaria digitata (Hudson) J.V. Lamouroux is one of the few summer fertile Laminaria species worldwide and reproduction is subjected to relatively high water temperatures. We investigated the impact of prevailing summer temperatures (~18°C in August) on the induction of sporangia, meiospore release, and germination at the island of Helgoland (North Sea). At Helgoland, fertile sporophytes are found between April and December with a maximum in late summer. While released meiospore numbers were constant between June and October, germination rates decreased significantly in summer. Short‐term exposure of mature sori to 17°C–22°C induced a significantly higher meiospore release indicating enhancement of sporulation by elevated temperatures. Induction of sporangia on vegetative blade disks was not possible at 20°C, and fertility was only 20% at 18°C–19°C, but it was 100% in cool temperatures of 1°C–10°C. It was shown for the first time in a kelp species that “sporogenesis” is the life‐cycle process with the narrowest temperature window compared to growth or survival of the sporophyte or reproduction, growth, and survival of the gametophyte. We incorporated several parameters (induction time, fertile area, and relative fertility) into a “Reproductive efficiency index.” This indicates that sporogenesis of L. digitata is a cold‐adapted process with an optimum at (5)–10°C. The results show that the population at Helgoland is at its reproduction limit despite the existence of other geographically more southerly located populations.     

Is escaping deer browse just a matter of time in Picea sitchensis? A chemical and dendroecological approach

We combined chemical and dendroecological analyses to understand the mechanisms that are involved in escaping deer browse by young Sitka spruce (Picea sitchensis) exposed to browsing by Sitka black-tailed deer (Odocoileus hemionus sitchensis) on Haida Gwaii (British Columbia, Canada). We compared chemical defences (terpenes), nutritive compounds (nitrogen, non-structural constituents, cellulose, and lignin), as well as age and radial growth of two young spruce categories growing side by side: (1) stunted spruces that were heavily browsed, shorter than the browse line, and (2) escaped spruces that were taller than the browse line but still browsed below the browse line. Escaped and stunted spruces did not differ in terpene concentrations, or in nutritive compound contents, suggesting that they had similar palatability. Escaped spruces were older that stunted spruces. Stunted and escaped trees had similar slow growth when young, suggesting no difference in initial browsing between the two spruce categories. For escaped spruce, there was a dramatic increase in radial growth at about 12-13 years old, suggesting that the apex of the trees had escaped deer browse. Because the two categories of spruces were equally accessible and did not differ in chemical defences or in nutritive compounds, and because escaped spruces were older than stunted trees and had a similar slow radial growth in their first 12-13 years, we conclude that morphological differences between stunted and escaped browsed trees are due to age and that it is only a matter of time before spruce escape deer on Haida Gwaii.     

Plant DNA‐barcode library and community phylogeny for a semi‐arid East African savanna

Applications of DNA barcoding include identifying species, inferring ecological and evolutionary relationships between species, and DNA metabarcoding. These applications require reference libraries that are not yet available for many taxa and geographic regions. We collected, identified, and vouchered plant specimens from Mpala Research Center in Laikipia, Kenya, to develop an extensive DNA‐barcode library for a savanna ecosystem in equatorial East Africa. We amassed up to five DNA barcode markers (rbcL, matK, trnL‐F, trnH–psbA, and ITS) for 1,781 specimens representing up to 460 species (~92% of the known flora), increasing the number of plant DNA barcode records for Africa by ~9%. We evaluated the ability of these markers, singly and in combination, to delimit species by calculating intra‐ and interspecific genetic distances. We further estimated a plant community phylogeny and demonstrated its utility by testing if evolutionary relatedness could predict the tendency of members of the Mpala plant community to have or lack “barcode gaps”, defined as disparities between the maximum intra‐ and minimum interspecific genetic distances. We found barcode gaps for 72%–89% of taxa depending on the marker or markers used. With the exception of the markers rbcL and ITS, we found that evolutionary relatedness was an important predictor of barcode‐gap presence or absence for all of the markers in combination and for matK, trnL‐F, and trnH–psbA individually. This plant DNA barcode library and community phylogeny will be a valuable resource for future investigations.     

Cobble community DNA as a tool to monitor patterns of biodiversity within kelp forest ecosystems

Kelp forest ecosystems dominate 150,000 km of global temperate coastline, rivalling the coastal occurrence of coral reefs. Despite the astounding biological diversity and productive ecological communities associated with kelp forests, patterns of species richness and composition are difficult to monitor and compare. Crustose coralline algae are a critically important substrate for propagule settlement for a range of kelp forest species. Coralline‐covered cobbles are home to hundreds of species of benthic animals and algae and form a replicable unit for ecological assays. Here, we use DNA metabarcoding of bulk DNA extracts sampled from cobbles to explore patterns of species diversity in kelp forests of the central California coast. The data from 97 cobbles within kelp forest ecosystems at three sites in Central California show the presence of 752 molecular operational taxonomic units (MOTUs) and 53 MOTUs assigned up to the species level with >95% similarity to current databases. We are able to detect spatial patterns of important management targets such as abalone recruits, and localized abundance of sea stars in 2012. Comparison of classic ecological surveys of these sites reveals large differences in species targets for these two approaches. In order to make such comparisons more quantitative, we use Presence/Absence Metabarcoding, using the fraction of replicate cobbles showing a species as a measure of its local abundance. This approach provides a fast and repeatable survey method that can be applied for biodiversity assessments across systems to shed light on the impact of different ecological disturbances and the role played by marine protected areas.     

Evaluation of remote sensing techniques for monitoring giant kelp populations

Photographs and maps of the floating canopy of the giant kelp, Macrocystis pyrifera, provide an important data source to monitor nearshore water quality in southern California. Declines in water quality related to turbidity from coastal development, ocean discharges, and non-point source runoff have caused reductions in the areal extent of these kelp beds. Historically the kelp beds have been monitored by a variety of methods including small format infrared and color photography. New digital remote sensing instruments combined with geographical information system (GIS) databases offer an efficient method for collecting and analyzing data on changes in kelp bed size and location. SPOT satellite imagery has been found to provide adequate resolution for mapping the larger beds of giant kelp along the California coast. Beds smaller than 10 ha are not resolved well with SPOT imagery and need to be mapped with a resolution greater than the 20 m pixel size provided by the SPOT multispectral imagery. Imagery from a prototype of the Positive Systems ADAR system, an airplane mounted multispectral video sensor, provided a spatial resolution of 2.3 m in 4 spectral bands. ADAR imagery taken on 2 October 1991 of the San Onofre Kelp Bed in northern San Diego County showed 39% more kelp than small format color infrared photography made during the same time period.