cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.48689/97b7f332-51a1-4c78-a695-a57616eb51f3
title: Dataset for manuscript "Comparison of infectious agents detected from hatchery and wild juvenile Coho salmon in British Columbia, 2008-2018"

description: High-throughput microfluidics qPCR was employed for simultaneous detection of 36 infectious agents from mixed-tissue samples (gill, brain, heart, liver, and kidney). Thirty-one agents were detected at least once, including ten with prevalence &gt;5%. Candidatus Brachiomonas cysticola, Paraneuclospora theridion, and Parvicapsula pseudobranchiocola were the most prevalent agents. Diversity and burden of infectious agents were substantially higher in marine environment than in freshwater. In Mainland BC, infectious burden and diversity were significantly lower in hatchery smolts than in wild counterparts, whereas in other regions, there were no significant differences. Observed differences in freshwater were predominantly driven by three parasites, Loma salmonae, Myxobolus arcticus, and Parvicapsula kabatai. In saltwater, there were no consistent differences in agent prevalence between hatchery and wild fish shared among the west and east coasts of Vancouver Island. Although some agents showed differential infectious patterns between regions, annual variations likely contributed to this signal. Our findings do not support the hypothesis that hatchery smolts carry higher burdens of infectious agents than conspecific wild fish, reducing the potential risk of transfer to wild smolts at this life stage. Moreover, we provide a baseline of infectious agents in juvenile Coho salmon that will be used in future research and modeling potential correlations between infectious profiles and marine survival.
DOI: 10.5061/dryad.9cnp5hqhh
title: Drivers of diversity and community structure of bees in an agroecological region of Zimbabwe

description: Worldwide bees provide an important ecosystem service of plant
 pollination. Climate change and land-use changes are among drivers
 threatening bee survival with mounting evidence of species decline and
 extinction. In developing countries, rural areas constitute a significant
 proportion of the country’s land but information is lacking on how
 different habitat types and weather patterns in these areas influence bee
 populations. This study investigated how weather variables and
 habitat-related factors influence the abundance, diversity, and
 distribution of bees across seasons in a farming rural area of Zimbabwe.
 Bees were systematically sampled in five habitat types (natural woodlots,
 pastures, homesteads, fields, and gardens) recording ground cover, grass
 height, flower abundance, and types, tree abundance and recorded
 elevation, temperature, light intensity, wind speed, wind direction, and
 humidity. Zero-inflated models, censored regression models, and PCAs were
 used to understand the influence of explanatory variables on bee community
 composition, abundance, and diversity. Bee abundance was positively
 influenced by the number of plant species in flower (P &lt; 0.0001).
 Bee abundance increased with increasing temperatures up to 28.50C but
 beyond this, the temperature was negatively associated with bee abundance.
 Increasing wind speeds marginally decreased the probability of finding
 bees. Bee diversity was highest in fields, homesteads, and natural
 woodlots compared to other habitats, and the contributions of the genus
 Apis were disproportionately high across all habitats. The genus Megachile
 was mostly associated with homesteads while Nomia was associated with
 grasslands. Synthesis and applications. Our study suggests that some bee
 species could become more proliferous in certain habitats thus
 compromising diversity and consequently ecosystem services. These results
 highlight the importance of setting aside bee-friendly habitats that can
 be refuge sites for species susceptible to land-use changes.
DOI: 10.48689/8690cbb6-47e5-4e9e-8e25-a43cf063f752
title: Systematic Literature Review of Pacific Salmon Hatchery Release Strategies in Canada and the United States

description: This literature search returned a total of 1,123 unique references. Of these, 76 met the screening criteria, covering a broad range of release strategies from California along the coast to Alaska. Research on hatchery strategies has steadily increased over the past 50 years, with significant contributions from federal, state, provincial, and academic scientists. The majority of this work has focused on systems in Washington and Oregon, although BC was a key player in much of the early research on release strategies. Chinook have been the most commonly studied species, with a dramatic increase in research on this species in the past ten years. The most well studied strategy has been the size of subyearling and yearling smolts at release, followed by the time of release and rearing conditions.
DOI: 10.48689/ce6a455b-ed5b-4cea-83d3-9fa3c5e56d73
title: Trends in size-at-age, sex ratios, and age-at-return in hatchery and wild Chinook salmon across BC

description: Annual change in mean age, age composition, mean size, size-at-age and female composition were estimated within each Chonook salmon population using linear regressions and age-specific patterns across populations and geographical regions. The clearest trends observed were in mean size and size-at-age. Both showed declines across most populations with statistical significance. Declines varied in magnitude across populations and age classes. Mean age showed variable, yet statistically significant declines across most stocks, and appeared to be driven by reductions in the relative proportion of the oldest (ocean-4) and increases in the youngest age classes (ocean-2). Low-enhancement stocks (stocks with mean pHOS &lt; 10%) showed mixed trends in mean age and age composition. The proportion of females showed variable declines across populations, of which only a small proportion were significant. There was no consistent pattern for the few wild and low-enhancement populations. Our study shows that the size and age of BC Chinook salmon have declined since the 1970s. Declines such as these may be caused by fishing, predation, competition and hatchery enhancement, however in this review we did not explore quantitative models that incorporate these factors. Simple analyses show some evidence for the effect of hatchery enhancement on declining mean size and size-at-age, with some populations showing increases in size for the youngest age class but declines for the oldest.
DOI: 10.48689/3f201316-5f3f-4f8a-ac79-3a58339c33d5
title: Application of ‘Omics’ Technologies in the Salmonid Enhancement Program

description: This document first provides a summary of the relevant regulatory components of the Salmonid Enhancement Program (SEP) management framework. After a summary of each regulatory component in the SEP management framework is an overview of the broad genomics approach that may be relevant to that management structure. Details on the genomics approach are included at the end of the document with information on the types of questions that can be addressed, considerations that must be made when sampling and storing tissues, and comments on the level of readiness of each technique for implementation.
DOI: 10.48689/3c8776d3-596a-408b-babd-e115ffe50eba
title: Hatchery, predation, and climate effects on productivity of wild Chinook, Coho, and Chum salmon

description: This paper presents a Bayesian hierarchical approach for developing and comparing performance of multipopulation spawner-recruitment models that estimate potential hatchery, predation, and/or environmental covariates effects on wild productivity for Chinook, Coho, and Chum populations in British Columbia. We investigate wild salmon productivity relationships with multiple covariates using multi-population Ricker models fit with spawner-recruit time series from 1954-2015 for 23 Coho conservations units (CUs), 1986-2013 for 24 Chinook populations (8 stocks, 16 CUs), and 1973-2013 for 28 Chum CUs.
DOI: 10.6078/d1rd88
title: Snow modulates winter energy use and cold exposure across an elevation gradient in a montane ectotherm

description: Snow insulates the soil from air temperature, decreasing winter cold
 stress and altering energy use for organisms that overwinter in the soil.
 As climate change alters snowpack and air temperatures, it is critical to
 account for the role of snow in modulating vulnerability to winter climate
 change. Along elevational gradients in snowy mountains, snow cover
 increases but air temperature decreases, and it is unknown how these
 opposing gradients impact performance and fitness of organisms
 overwintering in the soil. We developed experimentally validated
 ecophysiological models of cold and energy stress over the past decade for
 the montane leaf beetle Chrysomela aeneicollis, along five replicated
 elevational transects in the Sierra Nevada mountains in California. Cold
 stress peaks at mid-elevations, while high elevations are buffered by
 persistent snow cover, even in dry years. While protective against cold,
 snow increases energy stress for overwintering beetles, particularly at
 low elevations, potentially leading to mortality or energetic trade-offs.
 Declining snowpack will predominantly impact mid-elevation populations by
 increasing cold exposure, while high elevation habitats may provide
 refugia as  drier winters become more common.
description: <strong>Climate Data</strong> This
 is the full data set that includes all temperature measures used in cold
 exposure pricipal component analysis and energy use model output for each
 winter at each site included in study. The second tab includes metadata
 for each column. <strong>Physiology
 Data</strong> This is the data for all beetles
 used in the field snow manipulation experiment and all biochemichal assays
 performed. It includes total protein, glycerol, sorbitol, glucose, and
 triacylglycerides.
 <strong>Respirometry</strong> This
 is the data set containing all respirometry data used in making the energy
 use model.
DOI: 10.48689/a2f1a2ee-5db1-4d76-a307-a95be0aa64c1
title: Genetics and 'Omics' Technologies Review for Salmon Hatcheries

description: Given the current research focus on salmon genomics and transcriptomics technologies, there are several examples of hatchery deliverables. A broad-sense genomics tool that shows up repeatedly is parentage-based tagging (PBT), because of the amount of new information that can be provided for assessing hatchery performance and addressing knowledge gaps. This review has found that a breeding design (i.e. full factorial) with PBT can provide estimates of genetic and maternal effects explaining salmon traits important to hatcheries, e.g. fishery or escapement contributions. Large genetic effects can be examined further using an ‘omics’ technology to identify the specific targets increasing offspring quality, e.g. gene biomarkers. PBT is repeatedly identified as a useful tool because of the amount of new information that can be provided, especially for the adult life stage. In contrast, the newer proteomics and metabolomics technologies have fewer examples of hatchery deliverables so far. There are also potential hatchery deliverables that could be derived using environmental RNA, but these are theoretical and require further research to demonstrate feasibility. The review also identified four knowledge gaps: (1) group performance, (2) offspring quality, (3) health and condition biomarkers, and (4) hatchery-wild differences. Filling in the four knowledge gaps using ‘omics’ technologies can provide guidance on how to improve hatchery performance and assess effects on natural populations.
DOI: 10.48689/dc55f1a6-5318-4bfb-8f93-4d92195c4387
title: Hatchery-Wild Interactions Systematic Literature Review

description: After a search and screening process designed to be unbiased and extensive, an initial list of 4974 publications was screened down to a total of 112 relevant studies and literature reviews directly addressing interactions between wild and hatchery-origin salmon (with 85 of those suitable for analysis). The studies were categorized based on the nature of the interaction between hatchery-origin and wild fish that was explored and then assessed as to whether that interaction was positive, negative, or had no effect. The categories were: genetics, competition, population mixing, fish heath, and outcomes based studies. The majority of studies (50, including 7 literature reviews) found a negative effect of hatchery fish interactions with wild fish, whereas only two studies demonstrated a positive effect and 33 studies had no reported effects. The most studied category of interaction was genetics, the most studied species was Chinook, and the majority of studies were carried out in the United States.
DOI: 10.48689/9e319955-6d9f-4c82-afbc-d35e67a4a72f
title: Release strategy effects on survival and return ages for British Columbia Chinook and Coho hatchery releases, 1972-2017

description: This paper presents a statistical modelling approach to evaluating Fisheries and Oceans Canada (DFO) Salmon Enhancement Program (SEP) release strategies on survival rates and return ages of Chinook and Coho salmon in B.C.
DOI: 10.5061/dryad.8pk0p2nmx
title: Geographic parthenogenesis in the brown alga Scytosiphon lomentaria (Scytosiphonaceae): Sexuals in warm waters and parthenogens in cold waters

description: Geographic parthenogenesis, a phenomenon where parthenogens and their
 close sexual relatives inhabit distinct geographic areas, has been
 considered an interesting topic in evolutionary biology. Reports of
 geographic parthenogenesis from land and freshwater are numerous, however,
 this occurrence has been rarely reported from the sea. Brown algae are
 mostly marine and are thought to include numerous obligate parthenogens;
 still, little is known about the distribution, origin, and evolution of
 parthenogens in this group. Here we report a novel pattern of geographic
 parthenogenesis in the isogamous brown alga Scytosiphon lomentaria. Sex
 ratio investigation demonstrated that, in Japan, sexual populations grew
 in the coast along warm ocean currents, whereas female-dominant
 parthenogenetic populations grew mainly in the coast along a cold ocean
 current. In the two localities where sexual and parthenogenetic
 populations were parapatric, parthenogens grew in more wave-exposed areas
 than sexuals. Population genetic and phylogenetic analyses, including
 those based on genome-wide single nucleotide polymorphism data, indicated
 that parthenogens have initially evolved at least twice and subsequent
 hybridizations between the parthenogens and sexuals have generated
 multiple new parthenogenetic lineages. The origin of the initial
 parthenogens is not clear, except that it would not be inter-species
 hybridization. Interestingly, we found that the production of sex
 pheromones, which attract male gametes, has been independently lost in the
 initial two parthenogenetic lineages. This parallel loss of the sexual
 trait may represent the direct origin of parthenogens, or the regressive
 evolution of a useless trait under asexuality.
description: The diploid dataset, which were generated assuming that all
 samples are diploid, included 237 individuals from 36 populations, 818
 SNPs (loci), and the mean genotyping rate was 50.2%.
 The haploid dataset, which were generated assuming that all
 samples are haploid, included 212 individuals from 34 populations, 865
 SNPs (loci), and the mean genotyping rate was 48.8%.
 Both datasets were obtained by multiplexed inter-simple sequence
 repeat (ISSR) genotyping via sequencing (MIG-seq). SNP calling and
 filtering were performed using STACKS2 and PLINK2.
DOI: 10.48689/f88c48e6-d022-470c-9468-f8508c453619
title: Community Hatchery Interview Report

description: This review was initiated through interviews with DFO’s Community Advisors (CA) across the province and their guidance was used to create a list of CIP hatcheries to include. Information was then collected by interviewing community representatives managing 32 hatcheries with a standardized set of questions. The information was collated, summarized, and subsequently categorized to translate over 80 hours of interviews. A summary of needs was completed for each hatchery and common challenges were identified. Over 70% of hatcheries stated that their current funding was insufficient, with many others identifying issues with data feedback, water, and communication with DFO. We also included information on additional programs and experiments that the hatcheries would like to conduct in the future, underscoring the willingness of many facilities to improve and adapt.
DOI: 10.48689/3ee808d8-fb24-46d9-982d-b98e3499aff0
title: Scientific Review of Hatchery Release Strategies in BC: Final Report

description: This is the first time a comprehensive review of this scale has been conducted on hatchery release strategies in BC. Methods are developed for accessing, interpreting, analyzing, and reporting data from multiple different sources and some of the challenges in doing so are highlighted. We identify some of the main limitations in conducting the review as areas for consideration when interpreting our results, but also as areas to improve for future analyses of this kind.
DOI: 10.5061/dryad.0k6djhb0g
title: Distinct roles of the Chlamydia trachomatis effectors TarP and TmeA in the regulation of formin and Arp2/3 during entry

description: The obligate intracellular pathogen Chlamydia trachomatis manipulates the
 host actin cytoskeleton to assemble actin-rich structures that drive
 pathogen entry. The recent discovery of TmeA, which, like TarP, is an
 invasion-associated type III effector implicated in actin remodeling,
 raised questions regarding the nature of their functional interaction.
 Quantitative live-cell imaging of actin remodeling at invasion sites
 revealed differences in recruitment and turnover kinetics associated with
 the TarP and TmeA pathways, with the former accounting for most of the
 robust actin dynamics at invasion sites. TarP-mediated recruitment of
 actin nucleators, i.e. formins and the Arp2/3 complex, was crucial for
 rapid actin kinetics, generating a collaborative positive feedback loop
 that enhanced their respective actin-nucleating activities within invasion
 sites. In contrast, the formin Fmn1 was not recruited to invasion sites
 and did not collaborate with Arp2/3 within the context of Tme-aassociated
 actin recruitment. Although the TarP-Fmn1-Arp2/3 signaling axis is
 responsible for the majority of actin dynamics, its inhibition had similar
 effects as the deletion of TmeA on invasion efficiency, consistent with
 the proposed model that TarP and TmeA act on different stages of the same
 invasion pathway.
description: The mean fluorescence intensity (MFI) of individual invasion
 event was measured for each timepoint alongside the local background MFI
 of a concentric region immediately outside the recruitment event with NIH
 ImageJ. Background MFI was subtracted from recruitment MFI for each
 timepoint and converted into fold recruitment by dividing the MFI of each
 timepoint against the baseline MFI, defined as the average MFI of five
 timepoints (100 sec) prior to the start of recruitment.
 Datasets include representative time-lapse imaging videos from
 which data were acquired. In addition, results from statistical analyses,
 graphical outputs, etc are included.
DOI: 10.15468/dl.kczrua
title: Occurrence Download

description: A dataset containing 193632 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is International Barcode of Life project (iBOL)",
 "GadmLevel0Gid is NOR"
 ]
}

 The dataset includes 193632 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002825-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48689/21cf5dad-692e-42ac-98e6-e9067289814c
title: Ctd, oxygen and fluorescence-derived chlorophyll profile measurements in Strait of Georgia, 2015-2021

description: CTD cast readings in the Strait of Georgia. This dataset is unique in that it consists of near-simultaneous ctd, oxygen and electrically-sensed chlorophyll casts at typically one hundred locations on each of twenty dates from February through October, for the years 2015 to 2019. Data reprocessed in 2020 from Ocean Networks Canada archive. Note that the salinity is reported in TEOS-10 units. When relating that salinity to practical salinity, Salinity_Abs in g/kg (TEOS-10 ) = 35.16504/35 * Salinity_Practical, with an offset assumed to be zero (per R. Pawlowicz).
DOI: 10.5061/dryad.q573n5tht
title: Comparison of adult census size and effective population size support the need for continued protection of two Solomon Island endemics

description: Because a population’s ability to respond to rapid change is dictated by
 standing genetic variation, we can better predict a population’s long-term
 viability by estimating and then comparing adult census size (N) and
 effective population size (Ne). However, most studies only
 measure N or Ne, which can be misleading. Using
 a combination of field and genomic sequence data, we here
 estimate and compare N and Ne in two
 range-restricted endemics of the Solomon Islands.
 Two Zosterops White-eye species inhabit the small island
 of Kolombangara, with a high elevation species endemic to the island (Z.
 murphyi) and a low elevation species endemic to the Solomon Islands (Z.
 kulambangrae). Field observations reveal large values
 of N for both species with Z.
 kulambangrae numbering at 114,781 ± 32,233 adults,
 and Z. murphyi numbering at 64,412 ± 15,324 adults. In
 contrast, genomic analyses reveal that Ne was much lower
 than N, with Z. kulambangrae estimated at 694.5
 and Z. murphyi at 796.1 individuals. Further, positive
 Tajima’s D values for both species suggest that they have experienced a
 demographic contraction, providing a mechanism for low values
 of Ne. Comparison
 of N and Ne suggests that Z.
 kulambangrae and Z. murphyi are not at
 immediate threat of extinction but may be at genetic risk. Our results
 provide important baseline data for long-term monitoring of these island
 endemics, and argue for measuring both population size estimates to better
 gauge long-term population viability.
description: Five files are uploaded: 1) Field data (Bird
 ID, transect, sex, GPS point of capture):
 Cowles_etal_Zosterops_Dryad 2) Point count data for
 <em>Z. kulambangrae</em>: Z_kulambangrae_5-26-20.csv
 3) Point count data for <em>Z. murphyi</em>:
 Z_murphyi_5-26-20.csv 4) Processed genomics file
 containing 1508 SNPs used to measure
 <em>N<sub>e</sub></em>:
 filt_miss75_final_recode 5) ReadMe file containing
 author information, data collection information, and descriptions of the
 datasets
DOI: 10.48689/ab455d82-59c5-4d8a-9c9f-bbc9636144b5
title: Citizen Science Program

description: Collection of CTD water samples, bottom core grab, net haul, currents and bioacoustics and data from moorings around the inner lower island and lower mainland waters.
DOI: 10.48689/018ae250-8ecf-4e58-a5b0-f96cf7f354cb
title: Tagging and tracking of juvenile salmon in Vancouver Island rivers and coastal waters, 2018-present

description: Fine scale spatial and temporal patterns of habitat use by Pacific Salmon in their first year at sea. The current focus is understanding how juvenile Chinook Salmon distribution, diet and growth are influenced by the gradients of tidal mixing and water column stratification that are conspicuous characteristics of the inside waters of the Salish Sea. The study involves extensive use of pit tag technology (passive integrated transponder tags) and the pioneering microtrolling technique.