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opencc-by-4.0Dec 2019View details →

Archive of JPG image files of Herbarium specimens from Columbia used in the BRAVO project.

Archive of JPG image files of Herbarium specimens used in the BRAVO project. The individual images of herbarium specimens will also be included in the Zenodo project (in time) The project will pull these files into the workbench <a href="http://bravo.rbge.info/">http://bravo.rbge.info/</a> The metadata for these images is included in the Zenodo project.

opencc-by-4.0Aug 2020View details →

In situ microcosms deployed at the coast of British Columbia (Canada) to study dilbit weathering and associated microbial communities under marine conditions. (Metagenomic data support).

This file repository contains the co-assembly of all samples from the manuscript entitled "In situ microcosms deployed at the coast of British Columbia (Canada) to study dilbit weathering and associated microbial communities under marine conditions". It also contains predicted genes sequence files in faa (fasta amino acids) and fna (fasta nucleic acids) formats.

opencc-zeroJul 2021View details →

Data from: Distribution of genetic variation underlying adult migration timing in steelhead of the Columbia River basin

Fish migrations are energetically costly, especially when moving between fresh and saltwater, but are a viable strategy for Pacific salmon and trout (Oncorhynchus spp.) due to the advantageous resources available at various life stages. Anadromous steelhead (O. mykiss) migrate vast distances and exhibit variation for migration phenotypes that have a genetic basis at candidate genes known as greb1L and rock1. We examined the distribution of genetic variation at 13 candidate markers spanning greb1L, intergenic, and rock1 regions versus 246 neutral markers for 113 populations (n = 9,471) of steelhead from inland and coastal lineages in the Columbia River. Patterns of population structure with neutral markers reflected genetic similarity by geographic region as demonstrated in previous studies, but candidate markers clustered populations by predominate genetic variation associated with migration timing. Mature alleles for late migration had the highest frequency overall in steelhead populations throughout the Columbia River, with only 9 of 113 populations that had a higher frequency of premature alleles for early migration. While a single haplotype block was evident for the coastal lineage, we identified multiple haplotype blocks for the inland lineage. The inland lineage had one haplotype block that corresponded to candidate markers within the greb1L gene and immediately upstream in the intergenic region, and the second block only contained candidate markers from the intergenic region. Haplotype frequencies had similar patterns of geographic distribution as single markers, but there were distinct differences in frequency between the two haplotype blocks for the inland lineage. Redundancy analyses were used to model environmental effects on allelic frequencies of candidate markers and significant variables were migration distance, temperature, isothermality, and annual precipitation. This study improves our understanding of the spatial distribution of genetic variation underlying migration timing in steelhead as well as associated environmental factors and has direct conservation and management implications.

opencc-zeroDec 2013View details →

Data from: Potential effects of an invasive bivalve, Nuttallia obscurata, on select sediment attributes within the intertidal region of coastal British Columbia

On the west coast of British Columbia, Canada, the varnish clam, Nuttallia obscurata, is a rapidly spreading invasive species that can reach high densities (i.e. 800 individuals m− 2). A field survey (Tier I) and an in situ mesocosm density manipulation experiment (Tier II) were applied to determine the potential effects of this invasive bivalve on select sediment attributes within the intertidal zone. In situ experiments involved seeding 1 m2 mesocosms with varnish clams at four densities; 0 (control), 200 (low), 500 (mid) and 800 (high). Sediment samples were taken 7 times over a three week period and analyzed for organic matter, ammonium and grain size (gravel, coarse silt, fine silt and silt) at three different depths, 0–3 cm (surface), 3–6 cm (intermediate) and 6–9 cm (bottom). Field surveys demonstrated that at natural densities bivalve distribution was best explained by sediment grain size. Contrary to expectations, the in situ manipulations indicated that at high densities varnish clams did not significantly increase sediment organic matter concentrations. Their ability to deposit feed and re-ingest biodeposits may have prevented accumulations. High densities of varnish clams did however result in significantly higher concentrations of sediment ammonium and percent silt, but mostly within the lower sections of the sediment core. Reworking of the surficial sediments due to intense storm activity likely obscured any differences in determined sediment attributes among the 4 treatments. Nitrogen is a limiting nutrient with ammonium preferentially used by phytoplankton and microphytobenthos. These primary producers form the basis of all marine food webs thus increases in amounts of ammonium to shallow coastal seas as a result of high densities of an invasive bivalve within intertidal zones could result in an increased risk of eutrophication within these sensitive regions.

opencc-zeroDec 2016View details →

Data from: Population structure of sea-type and lake-type sockeye salmon and kokanee in the Fraser River and Columbia River drainages

Population structure of three ecotypes of Oncorhynchus nerka (sea-type Sockeye Salmon, lake-type Sockeye Salmon, and Kokanee) in the Fraser River and Columbia River drainages was examined with microsatellite variation, with the main focus as to whether Kokanee population structure within the Fraser River drainage suggested either a monophyletic or polyphyletic origin of the ecotype within the drainage. Variation at 14 microsatellite loci was surveyed for sea-type and lake-type Sockeye Salmon and Kokanee sampled from 121 populations in the two river drainages. An index of genetic differentiation, FST, over all populations and loci was 0.087, with individual locus values ranging from 0.031 to 0.172. Standardized to an ecotype sample size of 275 individuals, the least genetically diverse ecotype was sea-type Sockeye Salmon with 203 alleles, whereas Kokanee displayed the greatest number of alleles (260 alleles), with lake-type Sockeye Salmon intermediate (241 alleles). Kokanee populations from the Columbia River drainage (Okanagan Lake, Kootenay Lake), the South Thompson River (a major Fraser River tributary) drainage populations, and the mid-Fraser River populations all clustered together in a neighbor-joining analysis, indicative of a monophyletic origin of the Kokanee ecotype in these regions, likely reflecting the origin of salmon radiating from a refuge after the last glaciation period. However, upstream of the mid-Fraser River populations, there were closer relationships between the lake-type Sockeye Salmon ecotype and the Kokanee ecotype, indicative of the Kokanee ecotype evolving independently from the lake-type Sockeye Salmon ecotype in parallel radiation. Kokanee population structure within the entire Fraser River drainage suggested a polyphyletic origin of the ecotype within the drainage. Studies employing geographically restricted population sampling may not outline accurately the phylogenetic history of salmonid ecotypes.

opencc-zeroDec 2014View details →

Data from: Paleocommunity analysis of the Burgess Shale Tulip Beds, Mount Stephen, British Columbia: comparison with the Walcott Quarry and implications for community variation in the Burgess Shale

The Tulip Beds locality on Mount Stephen (Yoho National Park, British Columbia) yields one of the most abundant and diverse (~10,000 specimens in 110 taxa) Burgess Shale fossil assemblages in the Canadian Rockies. Detailed semi quantitative and quantitative analyses of this assemblage suggest strong similarities with the Walcott Quarry on Fossil Ridge. Both assemblages are dominated by epibenthic, sessile, and suspension feeding taxa, mostly represented by arthropods and sponges and have comparable diversity patterns, despite sharing only about half the genera. However, the Tulip Beds has a higher relative abundance of suspension feeders and taxa of unknown affinity compared to the Walcott Quarry. These biotic variations are probably largely attributable to ecological and evolutionary differences between the two temporally distinct communities that adapted to similar, but not identical, environmental settings. For instance, the Tulip Beds is farther away from the Cathedral Escarpment than the Walcott Quarry. The Tulip Beds and Walcott Quarry assemblages are more similar to each other than either one is to the assemblages of the Chengjiang biota, although the relative diversity of major taxonomic groups and ecological patterns are similar in all assemblages. The conserved diversity patterns and ecological structures among sites suggest that the ecological composition of Cambrian Burgess Shale-type communities was relatively stable across wide geographic and temporal scales.

opencc-zeroSep 2019View details →

Data from: 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 non-lethally sampled and assigned back to their parents using parentage analysis, thus identifying their hatchery of origin and brood year (i.e. age). Inter- and intra-population 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 intra-population 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 non-sibs, indicating the possible presence of intra-population 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.

opencc-zeroDec 2015View details →

Data from: A new integrative framework for large-scale assessments of biodiversity and community dynamics, using littoral gastropods and crabs of British Columbia, Canada

Improving our understanding of species responses to environmental changes is an important contribution ecologists can make to facilitate effective management decisions. Novel synthetic approaches to assessing biodiversity and ecosystem integrity are needed, ideally including all species living in a community and the dynamics defining their ecological relationships. Here we present and apply an integrative approach that links high-throughput, multi-character taxonomy with community ecology. The overall purpose is to enable the coupling of biodiversity assessments with investigations into the nature of ecological interactions in a community-level data set. We collected 1,195 gastropods and crabs in British Columbia. First, the General mixed Yule-coalescent (GMYC) and the Poisson Tree Processes (PTP) methods for proposing primary species-hypotheses based on cox1 sequences were evaluated against an integrative taxonomic framework. We then used data on the geographic distribution of delineated species to test species co-occurrence patterns for non-randomness using community-wide and pairwise approaches. Results showed that PTP generally outperformed GMYC and thus constitutes a more effective option for producing species-hypotheses in community-level datasets. Non-random species co-occurrence patterns indicative of ecological relationships or habitat preferences were observed for grazer gastropods, whereas assemblages of opportunistic omnivorous gastropods and crabs appeared influenced by random processes. Species-pair associations were consistent with current ecological knowledge, thus suggesting that applying community assembly within a large taxonomical framework constitutes a valuable tool for assessing ecological interactions. Combining phylogenetic, morphological and co-occurrence data enabled an integrated view of communities, providing both a conceptual and pragmatic framework for biodiversity assessments and investigations into community dynamics.

opencc-zeroDec 2017View details →

Data from: Nest boxes increase reproductive output for Tree Swallows in a forest grassland matrix in central British Columbia

Secondary cavity-nesting birds depend on tree cavities for nesting and roosting, but many studies of these birds are conducted using nest boxes. Implementation of effective conservation strategies for cavity-nesting species such as nest-site supplementation requires careful comparisons of fecundity and other vital rates for birds using both natural and artificial nest site types. We compared breeding phenology, clutch and brood sizes, and fledging success of Tree Swallows (Tachycineta bicolor) nesting in tree cavities and nest boxes during 2001–2003 in British Columbia, Canada. Swallows using nest boxes initiated egg-laying and hatched young at approximately the same time as those in tree cavities (2 June, 23 June, respectively). Female Tree Swallows in boxes laid larger clutches (5.9 ± 0.9 eggs, N = 76) than those in tree cavities (4.2 ± 1.6 eggs, N = 67). The mean number of nestlings hatched was greater in nest boxes (5.2 ± 1.1 nestlings, N = 67) than in tree cavities (2.6 ± 2.0 nestlings, N = 58). Pairs in boxes were over twice as successful in producing fledglings (93.4%; 57 of 61 pairs fledged > 1 young) than those in tree cavities (35.8%; 19 of 53 pairs). Of those successful nests, pairs nesting in boxes fledged 5.1 ± 1.1 young (N = 57), whereas those in tree cavities fledged 3.5 ± 1.2 young (N = 18). Because cavities in nest boxes averaged 60% larger in volume and 1.8 cm wider internally than tree cavities, we suggest that increased reproductive output was correlated with boxes enabling a larger clutch size. In previous research, we found that Tree Swallows were a poor competitor with other cavity-nesting passerines for tree cavities. The addition of nest boxes may serve as an effective way to supplement local reproduction for secondary cavity-nesting bird populations by reducing competition for limited nest sites. This is especially true in regions where the availability of natural nesting sites is highly variable, and where species compete with many other cavity-nesting passerines using a similar ecological niche and nesting cavities.

opencc-zeroOct 2019View details →

Data from: Soil carbon, nitrogen and phosphorus stoichiometry (C:N:P) in relation to conifer species productivity and nutrition across British Columbia perhumid rainforests

Temperate rainforest soils of the Pacific Northwest are often carbon (C) rich and encompass a wide range in fertility reflecting varying nitrogen (N) and phosphorus (P) availability. Soil resource stoichiometry (C:N:P) may provide an effective measure of site nutrient status and help refine species-dependent patterns in forest productivity across edaphic gradients. We described the nature of soil organic matter for mineral soil and forest floor substrates across very wet (perhumid) rainforest sites of southwestern Vancouver Island (Canada), and employed soil element ratios as covariates in a long-term planting density trial to test their utility in defining basal area growth response of four conifer species. There were strong positive correlations in mineral soil C, N and organic P (Po) concentrations, and close alignment in C:N and C:Po both among and between substrates. Stand basal area after five decades was best reflected by soil C:N but included a significant species-soil interaction. The conifers with ectomycorrhizal fungi had diverging growth responses displaying either competitive (Picea sitchensis) or stress-tolerant (Tsuga heterophylla, Pseudotsuga menziesii) attributes, in contrast to a more generalist response by an arbuscular mycorrhizal tree (Thuja plicata). Despite the consistent patterns in organic matter quality we found no evidence via foliar nutrition for increased P availability with declining element ratios as we did for N. The often high C:Po ratios (as much as 3000) of these soils may reflect a stronger immobilization sink for P than N, which, along with ongoing sorption of PO4-, could limit the utility of C:Po or N:Po to adequately reflect P supply. The dynamics and availability of soil P to trees, particularly as Po, deserves greater attention as many perhumid rainforests were co-limited by N and P, or, in some stands, possibly P alone.

opencc-zeroDec 2018View details →

Data from: Variation in juvenile Chinook salmon (Oncorhynchus tshawytscha) transcription among and within eight population crosses from British Columbia, Canada

Phenotypic differences among populations within a species have been reported for a variety of traits, ranging from life history to physiology to gene transcription. Population-level phenotypic variation has been attributed to genetic differences resulting from genetic drift and/or local adaptation as well as environmental differences resulting from plasticity. We studied population- and family-level variation in gene transcription for 22 fitness-related genes, comprising immune, growth, metabolic, and stress processes in Chinook salmon (Oncorhynchus tshawytscha). We created hybrid Chinook salmon families from eight populations and treated them with an immune stimulus, a handling stress challenge, and held some as a no-treatment control group. Population effects, sire effects, and narrow-sense heritability (h2) were calculated for each candidate gene within each treatment group. We expected population to have a significant effect on gene transcription for many of our genes; however, we found a population effect for transcription at only one immune gene at rest. The limited number of significant population effects on gene transcription, combined with significant additive genetic variance within each population does not support the expectation of past strong selection pressures acting on heritable transcription profiles among populations. Instead, our results indicate that Chinook salmon likely adapt to their local environment through transcriptional plasticity rather than fixed differences. The expectation for fixed population-level differences in gene transcription at fitness-related genes, reflecting accepted models of local adaptation is high; however, comparisons among multiple populations using half-sib breeding designs are rare. Our work fills an important gap in our growing understanding of the process of among and within-population divergence.

opencc-zeroDec 2017View details →

Data from: Comparison of coded-wire tagging with parentage-based tagging and genetic stock identification in a large-scale coho salmon fisheries application in British Columbia, Canada

Wild Pacific salmon, including Coho salmon Onchorynchus kisutch, have been supplemented with hatchery propagation for over 50 years in support of increased ocean harvest and conservation of threatened populations. In Canada, the Wild Salmon Policy for Pacific salmon was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision-making. A new approach to the assessment and management of wild coho salmon, and the associated hatchery production and fishery management is needed. Implementation of parentage-based tagging (PBT) may overcome problems associated with coded-wire tag-based (CWT) assessment and management of coho salmon fisheries, providing at a minimum information equivalent to that derived from the CWT program. PBT and genetic stock identification (GSI) were used to identify coho salmon sampled in fisheries (8,006 individuals) and escapements (1,692 individuals) in British Columbia to specific conservation units (CU), populations, and broodyears. Individuals were genotyped at 304 single nucleotide polymorphisms (SNPs) via direct sequencing of amplicons. Very high accuracy of assignment to population (100%) via PBT for 543 jack (age 2) assigned to correct age and collection location and 265 coded-wire tag (CWT, age 3) coho salmon assigned to correct age and release location was observed, with a 40,774–individual, 267–population baseline available for assignment. Coho salmon from un-CWTed enhanced populations contributed 65% of the catch in southern recreational fisheries in 2017. Application of a PBT-GSI system of identification to individuals in 2017 fisheries and escapements provided high-resolution estimates of stock composition, catch, and exploitation rate by CU or population, providing an alternate and more effective method in the assessment and management of Canadian-origin coho salmon relative to CWTs, and an opportunity for a genetic-based system to replace the current CWT system for coho salmon assessment.

Figure 5 in Invertebrate communities, sediment parameters and food availability of intertidal soft-sediment ecosystems on the north coast of British Columbia, Canada

Figure 5. Non-metric multidimensional scaling (nMDS) plots showing infaunal invertebrate community at three intertidal sandy shore sites on the north coast of British Columbia, Canada during the summer of 2017. (a) the infaunal community by sandy shore site and sampling round and (b) the vector overlay indicates the direction of increased density, with correlations>0.3 shown. BO: Boulder Beach. GU: Coast Guard Beach. PI: Prescott Inlet. Round A: 23 May–1 June. Round B: 21–26 June. Round C: 19–25 July. Round D: 18–24 August.

Figure 6 in Invertebrate communities, sediment parameters and food availability of intertidal soft-sediment ecosystems on the north coast of British Columbia, Canada

Figure 6. Non-metric multidimensional scaling (nMDS) plots of (a) sediment parameters (depth to the aRPD, water content, particle size, penetrability, % macrophyte coverage, % Zostera marina cover, and % wood cover) by site and round and (b) the food availability (chlorophyll a and organic matter content) at three intertidal sandy shore sites on the north coast of British Columbia, Canada during the summer of 2017. Vector overlays for sediment and food variables show the correlation between variables and nMDS axes, with each vector showing the direction of increased value. BO: Boulder Beach. GU: Coast Guard Beach. PI: Prescott Inlet. Round A: 23 May 23–1 June. Round B: 21–26 June. Round C: 19–25 July. Round D: 18–24 August.

Figure 2 in Invertebrate communities, sediment parameters and food availability of intertidal soft-sediment ecosystems on the north coast of British Columbia, Canada

Figure 2. Flow chart demonstrating statistical analysis conducted on the biotic and abiotic variables sampled at intertidal mudflats (n = 3) and intertidal sandy shores (n = 3) on the north coast of British Columbia, Canada during the summer of 2017.

Figure 1 in Invertebrate communities, sediment parameters and food availability of intertidal soft-sediment ecosystems on the north coast of British Columbia, Canada

Figure 1. Map of intertidal mudflats and sandy shore study sties around Prince Rupert, and on Prescott Island, British Columbia, sampled during summer of 2017. Figure 1(a) shows mudflats close to the Skeena River (CC: Cassiar Cannery 54.1747, 130.1721; TB: Tyee Banks 54.2000, 129.9634; WC: Wolfe Cove 54.2424, 130.2730). Figure 1(b) shows sandy shores on Prescott Island (BO: Boulder Beach 54.0871, 130.5970; PI: Prescott Inlet 54.0709, 130.5950; GU: Coast Guard Beach 54.0659, 130.5757).

Figure 3 in Invertebrate communities, sediment parameters and food availability of intertidal soft-sediment ecosystems on the north coast of British Columbia, Canada

Figure 3. Non-metric multidimensional scaling (nMDS) graphs showing infaunal invertebrate community at three intertidal mudflats on the north coast of British Columbia, Canada during the summer of 2017. (a) the infaunal community by mudflat and sampling round and (b) the vector overlay indicates the direction of increased density, with correlations>0.3 shown. CC: Cassiar Cannery. TB: Tyee Banks. WC: Wolfe Cove. Round A: 23 May–June 1. Round B: 21–26 June. Round C: 19–25 July. Round D: 18–24 August.

Figure 4 in Invertebrate communities, sediment parameters and food availability of intertidal soft-sediment ecosystems on the north coast of British Columbia, Canada

Figure 4. Non-metric multidimensional scaling (nMDS) plots of (a) sediment parameters (depth to the aRPD [apparent redox potential discontinuity], water content, particle size, penetrability, % macrophyte coverage, and % wood cover) by site and round and (b) the food availability (chlorophyll a and organic matter content) at three intertidal mudflats on the north coast of British Columbia, Canada during the summer of 2017. Vector overlays for sediment and food variables show the correlation between variables and nMDS axes, with each vector showing the direction of increased value. CC: Cassiar Cannery. TB: Tyee Banks. WC: Wolfe Cove. Round A: 23 May–1 June. Round B: 21–26 June. Round C: 19–25 July. Round D: 18–24 August.