cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.73n5tb2ws
title: Host controls of within-host disease dynamics: insight from an invertebrate system

description: Within-host processes (representing the entry, establishment, growth and
 development of a parasite inside its host) may play a key role in parasite
 transmission but remain challenging to observe and quantify. We develop a
 general model for measuring host defenses and within-host disease
 dynamics. Our stochastic model breaks the infection process down into the
 stages of parasite exposure, entry, and establishment and provides
 associated probabilities for a host’s ability to resist infections with
 barriers and clear internal infections. We tested our model on Daphnia
 dentifera and the parasitic fungus, Metschnikowia bicuspidata, and found
 that, when faced with identical levels of parasite exposure, Daphnia
 patent (transmitting) infections depended on the strength of internal
 clearance. Applying a Gillespie algorithm to the model-estimated
 probabilities allowed us to visualize within-host dynamics, within which
 signatures of host defense could be clearly observed. We also found that
 early within-host stages were the most vulnerable to internal clearance,
 suggesting that hosts have a limited window during which recovery can
 occur. Our study demonstrates how pairing longitudinal infection data with
 a simple model can reveal new insight into within-host dynamics and
 mechanisms of host defense. Our model and methodological approach may be a
 powerful tool for exploring these properties in understudied host-parasite
 interactions.
DOI: 10.48689/88c0d433-20a5-47ce-a710-ead5962e8e3c
title: Bird Colonies- Coastal Resource Information Management System (CRIMS)

description: The distribution of nesting areas for bird colonies in coastal British Columbia showing relative abundance (RA) by season and overall relative importance (RI). RI is based on project region and not on the province as a whole. Number counts for various species in the colony location are provided. CRIMS is a legacy dataset of BC coastal resource data that was acquired in a systematic and synoptic manner from 1979 and was intermittently updated throughout the years. Resource information was collected in nine study areas using a peer-reviewed provincial Resource Information Standards Committee consisting of DFO Fishery Officers, First Nations, and other subject matter experts. There are currently no plans to update this legacy data.
DOI: 10.7291/d1vm2b
title: Predicting the population consequences of acoustic disturbance, with application to an endangered gray whale population

description: Acoustic disturbance is a growing conservation concern for wildlife
 populations because it can elicit physiological and behavioral responses
 that can have cascading impacts on population dynamics. State-dependent
 behavioral and life history models implemented via Stochastic Dynamic
 Programming (SDP) provide a natural framework for quantifying biologically
 meaningful population changes resulting from disturbance by linking
 environment, physiology, and metrics of fitness. We developed an SDP model
 using the endangered western gray whale (Eschrichtius robustus) as a case
 study because they experience acoustic disturbance on their summer
 foraging grounds. We modeled the behavior and physiological dynamics of
 pregnant females as they arrived on the feeding grounds and predicted the
 probability of female and offspring survival, with and without acoustic
 disturbance and in the presence/absence of high prey availability. Upon
 arrival in mid-May, pregnant females initially exhibited relatively random
 behavior before they transitioned to intensive feeding that resulted in
 continual fat mass gain until departure. This shift in behavior
 co-occurred with a change in spatial distribution; early in the season,
 whales were more equally distributed among foraging areas with moderate to
 high energy availability, whereas by mid-July whales transitioned to
 predominate use of the location that had the highest energy availability.
 Exclusion from energy-rich offshore areas led to reproductive failure and
 in extreme cases, mortality of adult females that had lasting impacts on
 population dynamics. Simulated disturbances in nearshore foraging areas
 had little to no impact on female survival or reproductive success at the
 population level. At the individual level, the impact of disturbance was
 unequally distributed across females of different lengths, both with
 respect to the number of times an individual was disturbed and the impact
 of disturbance on vital rates. Our results highlight the susceptibility of
 large capital breeders to reductions in prey availability, and indicate
 that who, where, and when individuals are disturbed are likely to be
 important considerations when assessing the impacts of acoustic
 activities. This model provides a framework to inform planned acoustic
 disturbances and assess the effectiveness of mitigation strategies for
 large capital breeders.
description: These data are the output of the forward simulation model
 described in the manuscript text. Each line represents summary information
 for a single whale across the entire foraging season.
DOI: 10.48689/fde70ea1-6de4-4928-951f-1ffacded4ab4
title: Biomass of phytoplankton and microzooplankton, 2003-2006

description: Biomass of phytoplankton and microzooplankton taxa groups
DOI: 10.48689/294996e5-2c98-4235-b611-dba2b91302c3
title: Biogeoclimatic Ecosystem Classification (BEC) Map - Attribute Catalogue

description: A list of the various 'regional' (zone/subzone/variant/phase) ecological units of the current biogeoclimatic ecosystem classification.
DOI: 10.48689/f1ef52f6-bd12-4ce7-9e38-e8ada9152f03
title: Benthic Invertebrates Associated with the Islands in the Campbell River Estuary: A Preliminary Report

description: This study assessed certain factors which might have influenced the development of macrobenthic communities on the new islands. Since benthic animals provide food for fish and birds, results are pertinent to the ultimate success of the island project. Three factors were examined, namely the presence of the islands, presence of vegetation and changes through time (temporal aspects). Since the data are from the first invertebrate collections made subsequent to planting, they also represent an important baseline to measure subsequent changes against.
DOI: 10.5061/dryad.np5hqbzsp
title: The genetic architecture of temperature adaptation is shaped by population ancestry and not by selection regime

description: Understanding the genetic architecture of temperature adaptation is key
 for characterizing and predicting the effect of climate change on natural
 populations. One particularly promising approach is Evolve and Resequence
 (E&R), which combines advantages of experimental evolution such as
 time series, replicate populations and controlled environmental
 conditions, with whole genome sequencing. The recent analysis of replicate
 populations from two different Drosophila simulans founder populations,
 which were adapting to the same novel hot environment, uncovered very
 different architectures - either many selection targets with large
 heterogeneity among replicates or fewer selection targets with a
 consistent response among replicates. Here, we exposed the founder
 population from Portugal to a cold temperature regime. Although almost no
 selection targets were shared between the hot and cold selection regime,
 the adaptive architecture was similar: we identified a moderate number of
 targets under strong selection (19 selection targets, mean selection
 coefficient = 0.072) and very parallel responses in the cold evolved
 replicates. This similarity across different environments indicates that
 the adaptive architecture depends more on the ancestry of the founder
 population than the specific selection regime. These observations will
 have broad implications for the correct interpretation of the genomic
 responses to a changing climate in natural populations.
DOI: 10.48689/1bc98cd7-631f-4ec1-8105-4625344df645
title: Beach biological and environmental monitoring , 1996-2007

description: Extensive data tables: Code (identifies the name BC), descriptive location levels 1 thru 4 (only level4 contains positioning), subcode (16 weather related items), species (344) and species groups, stewards (12), substrates (10), transect events (13978 entries including est species totals, 1996-06-10 to 2011-07-29), site visits (300 details of the site sampling conditions), trips (for participants, 117), and actual participant names (67). Dataset incudes contributions from the Georgia Strait Alliance.
DOI: 10.48689/c95b932f-5e84-4e26-bfd8-b81c356315f6
title: Basking Shark Historical Abundance, 1948-1950

description: Historical abundance of Basking Sharks within the bcmca study area from 1948-1950.
DOI: 10.48689/985fef0d-204b-4e53-944b-017bcb728040
title: Barrow's Goldeneye Density

description: Spatial distribution and seasonal abundance of Barrow's Goldeneye (Bucephala islandica) in Howe Sound June 2014-May 2015 and September 2015 from a boat-based survey conducted along a transect.
DOI: 10.5061/dryad.qfttdz0gn
title: The energetic basis for smooth human arm movements

description: The central nervous system plans human reaching movements with
 stereotypically smooth kinematic trajectories and fairly consistent
 durations. Smoothness seems to be explained by accuracy as a primary
 movement objective, whereas duration seems to avoid excess energy
 expenditure. But energy does not explain smoothness, so that two aspects
 of the same movement are governed by seemingly incompatible objectives.
 Here we show that smoothness is actually economical, because humans expend
 more metabolic energy for jerkier motions. The proposed mechanism is an
 underappreciated cost proportional to the rate of muscle force production,
 for calcium transport to activate muscle. We experimentally tested that
 energy cost in humans (N=10) performing bimanual reaches cyclically. The
 empirical cost was then demonstrated to predict smooth, discrete reaches,
 previously attributed to accuracy alone. A  mechanistic,
 physiologically measurable, energy cost may therefore unify smoothness and
 duration, and help resolve motor redundancy in reaching movements.
description: Data was collected on a KINARM robot and processed using custom
 scripts in matlab.
DOI: 10.48689/ab2a6ac7-f44e-4a21-80cb-9ba2ce92e8f3
title: Barkley Sound and Alberni Inlet Juvenile Salmon/Herring, 2000-2001
title: Le saumon et le hareng juvéniles du bassin de Barkley et de la baie d'Alberni, 2000-2001

description: Biological (length, weight, origin, diet) information collected for juvenile salmon and young-of-the-year herring using purse or beach seiners in Barkley Sound and Alberni Inlet between May and July. Data used to describe residence time, distribution and feeding to evaluate the influence of food on year-class strength and salmon marine survival.
description: Des données biologiques (longueur, poids, origine, régime alimentaire) ont été recueillies sur les saumons juvéniles et les jeunes harengs de l'année à l'aide de bateaux senneurs et de sennes de plage dans le bassin de Barkley et la baie d'Alberni entre mai et juillet. Ces données permettent d'établir une description du temps de séjour, de la distribution et de l'alimentation qui serviront à évaluer l'influence de l'alimentation sur l'effectif des classes d'âge et sur la survie du saumon en mer.
DOI: 10.48689/5e10ccea-7dcf-4ba6-be53-640cf73747f7
title: Barkley Sound Zooplankton, 1991-present
title: Zooplancton dans le bassin de Barkley, de 1991 à aujourd’hui

description: Tombstone (length, weight, sex, maturity, stage, species) of zooplankton collected by Ron Tanasichuk in Barkley Sound from 1991 to the present. Dataset is used to describe variations in population biology of zooplankton.
description: Données de base (longueur, poids, sexe, maturité, âge et espèce) sur le zooplancton prélevé par Ron Tanasichuk dans le bassin de Barkley de 1991 à nos jours. On utilise cet ensemble de données pour décrire les variations dans la biologie de la population de zooplancton.
DOI: 10.5061/dryad.sn02v6x3r
title: Scent of a killer: How could killer yeast boost its dispersal?

description: Vector-borne parasites often manipulate hosts to attract uninfected
 vectors. For example, parasites causing malaria alter host odor to attract
 mosquitoes. Here we discuss the ecology and evolution of fruit-colonizing
 yeast in a tripartite symbiosis – the so-called “killer yeast” system.
 “Killer yeast” consists of Saccharomyces cerevisiae yeast hosting two
 double stranded RNA viruses (M satellite dsRNAs, L-A dsRNA helper virus).
 When both dsRNA viruses occur in a yeast cell, the yeast converts to
 lethal toxin‑producing “killer yeast” phenotype that kills uninfected
 yeasts. Yeasts on ephemeral fruits attract insect vectors to colonize new
 habitats. As the viruses have no extracellular stage, they depend on the
 same insect vectors as yeast for their dispersal. Viruses also benefit
 from yeast dispersal as this promotes yeast to reproduce sexually, which
 is how viruses can transmit to uninfected yeast strains. We tested whether
 insect vectors are more attracted to killer yeasts than to non‑killer
 yeasts. In our field experiment, we found that killer yeasts were more
 attractive to Drosophila than non-killer yeasts. This suggests that
 vectors foraging on yeast are more likely to transmit yeast with a killer
 phenotype, allowing the viruses to colonize those uninfected yeast strains
 that engage in sexual reproduction with the killer yeast. Beyond insights
 into the basic ecology of the killer yeast system, our results suggest
 that viruses could increase transmission success by manipulating the
 insect vectors of their host.
description: We tested
 the attraction of six <i>S. cerevisiae</i> strains with and
 without killer phenotype towards Drosophilidae. We used three distinct
 killer yeast strains and three different non-killer strains of <i>S.
 cerevisiae</i> (killer yeast strains: YJM4541b (K1), CLIB294_1b
 (K1), Y12_1b (K28); non-killer yeast strains: I14_1b, UC1_1b, NCYC_2743,
 Liti et al., 2009;Peter et al., 2018; Pieczynska et al., 2013, Table S1)
 each replicated six times. We inoculated 10⁴ yeast cells of each strain
 into 50 ml grape juice (homogenized and autoclaved Urpress Weiss from
 Rimuss). After 24 h of inoculation at 28°C we distributed the fermenting
 juice samples to <i>Drosophila</i> traps
 (Drosal<sup>Ⓡ</sup> Pro, Andermatt Biogarten) and randomly
 placed the 36 traps in a vineyard (Schipf: 47.291925, 8.601796; see
 supplementary Figure S1). Three traps of plain grape juice served as
 controls. After 72h we collected the 39 traps and counted the total number
 of Drosophilidae and determined the species and sex of trapped
 flies.
DOI: 10.48689/f17817c8-89c9-40f7-ba05-b5c5533b627d
title: Ballast water transport of non-indigenous zooplankton to Canadian ports

description: Ballast water is one of the primary transport vectors for the transfer and introduction of non-indigenous zooplankton (NIZ). Regulations require vessels from overseas to conduct mid-ocean exchange before discharging ballast in Canadian ports. Intracoastal vessels from nearby ports may be exempt from exchange, whereas intracoastal vessels from more distant ports are required to exchange. Zooplankton in the ballast water of transoceanic exchanged (TOE), intracoastal exchanged (ICE), and intracoastal unexchanged (ICU) vessels arriving at Canada’s west (WC) and east (EC) coasts were examined.
DOI: 10.48689/17cb09d2-5abc-4e92-9058-40a8e3cec389
title: Bald Eagles - Coastal Resource Information Management System (CRIMS)

description: Distribution of Bald Eagle habitat in coastal British Columbia showing relative abundance (RA) and overall relative importance (RI). RI is based on project region and not on the province as a whole. CRIMS is a legacy dataset of BC coastal resource data that was acquired in a systematic and synoptic manner from 1979 and was intermittently updated throughout the years. Resource information was collected in nine study areas using a peer-reviewed provincial Resource Information Standards Committee consisting of DFO Fishery Officers, First Nations, and other subject matter experts. There are currently no plans to update this legacy data.
DOI: 10.5061/dryad.b8gtht7c7
title: Data and Code for: An index for measuring functional extension and evenness in trait space

description: Most existing functional diversity indices focus on single specific facet
 of functional diversity. Although they help scrutinize the details of
 functional diversity from their own angles, they often present some
 limitations in estimating functional diversity from a broad perspective.
 Here we presented a functional extension and evenness (FEE) index that
 encloses two important aspects of functional diversity. This index is
 based on a straightforward notion that a community has high diversity when
 its species are distant from each other in trait space. We quantified the
 functional diversity by evaluating the overall extension of species traits
 and interspecific trait differences of a species assemblage in trait
 space. The concept of minimum spanning tree (MST) of points was adopted to
 obtain the essential distribution properties for a community in trait
 space. We integrated the total length of MST branches (extension) and the
 variation of branch lengths (evenness) into the FEE0 metric, and then
 translated FEE0 to a species-richness-independent FEE index using a null
 model approach. We assessed the properties of FEE and used multiple
 approaches to evaluate FEE’s performance. The results show that the FEE
 index performs well in quantifying functional diversity and presents the
 following desired properties: 1) it allows a fair comparison of functional
 diversity across different species richness; 2) it preserves the essence
 of facet-specific indices and overcomes some constraints that other
 facet-specific indices displayed; 3) it takes species pool into
 consideration; and 4) has the potential to distinguish underlying
 processes that govern species assemblies. With these attributes, we
 suggest that the FEE index is a promising metric to inform biodiversity
 conservation policy and management, especially in applications at large
 spatial or/and temporal scales.
description: The data include empirical cumulative distribution functions
 (eCDFs) used to derive the functional extension and evenness (FEE) index,
 the simulated species traits and abundances used in our analyses, and the
 FEE and other indices pre-calculated for the simulated
 communities. The R code performs all analyses in our
 paper, including generations of eCDFs using null model
 approach, calculations of the FEE and other indices for the simulated
 communities, statistical analyses, and generating figures.
description: Refer to README.txt file.
DOI: 10.48689/674db689-3039-42c5-8bf9-b6e356124ee8
title: Background sediment organic biomass and turnover database for the Strait of Georgia, 1990-present

description: Any monitoring program which aims to identify biological, geochemical and physical changes from existing conditions, and to separate natural from anthropogenic effects must start with a well-developed and understood baseline of conditions for the region of interest. This includes knowledge of inputs and cycling of organic material, particulates, contaminants, hydrographic conditions, major drivers in the natural system, and the scales of variability likely from extreme events. This was the primary goal of the first 10 years of the Strait of Georgia AMP. In addition, the 10-year AMP was designed to determine natural variability and scale of the Iona outfall footprint in terms of chemical, physical and biological indicators. Results of this basic research have been extensively published, and will be collated in Johannessen et al. (in prep.). Databases used in this work are referenced in technical reports and URL links to supplemental data for publications. The file “AMPreferences.doc” includes a hyperlinked list of publications and technical reports to date resulting from the 10-year collaborative research program between DFO and Metro Vancouver (2003-2013). Supplemental publications on related benthic ecology for the BC coast are listed in a separate folder (“Other”).
DOI: 10.5061/dryad.fqz612js7
title: Female differential allocation in response to extra-pair offspring and social mate attractiveness

description: Renewed debate over what benefits females might gain from producing
 extra-pair offspring emphasizes the possibility that apparent differences
 in quality between within-pair and extra-pair offspring are confounded by
 greater maternal investment in extra-pair offspring. Moreover, the
 attractiveness of a female’s social mate can also influence contributions
 of both partners to a reproductive attempt. Here we explore the
 complexities involved in parental investment decisions in response to
 extra-pair offspring and mate attractiveness with a focus on the female
 point of view. Adult zebra finches paired and reproduced in a colony
 setting. A male’s early-life diet quality and his extra-pair reproductive
 success were used as metrics of his mating attractiveness. Females paired
 with males that achieved extra-pair success laid heavier eggs than other
 females and spent less time attending their nests than their mates or
 other females. Extra-pair nestlings were fed more protein-rich hen’s egg
 than within-pair nestlings. Females producing extra-pair offspring had
 more surviving sons than females producing only within-pair offspring.
 Collectively, results show that females differentially allocate resources
 in response to offspring extra-pair status and their social mate’s
 attractiveness. Females may also obtain fitness benefits through the
 production of extra-pair offspring.
DOI: 10.48689/0d42f341-167e-43be-b4eb-e38700ab1910
title: BCMCA_ECO_FeatureCount, 2010

description: Number of bcmca features used in the Marxan analysis that are found in each 2 km x 2 km planning unit.
DOI: 10.5061/dryad.wh70rxwn1
title: Genetic and cellular/biochemical data for mouse Pycard gene differences altering mRNA turnover and IL-1b release

description: Quantitative trait locus mapping for interleukin-1b release after
 inflammasome priming and activation was performed on bone marrow-derived
 macrophages (BMDM) from an AKRxDBA/2 strain intercross.  The
 strongest associated locus mapped very close to the Pycard gene on
 chromosome 7, which codes for the inflammasome adaptor protein
 apoptosis-associated speck-like protein containing a CARD (ASC). 
 The DBA/2 and AKR Pycard genes only differ at single nucleotide
 polymorphism (SNP) in their 3’ untranslated region (UTR).  DBA/2
 vs. AKR BMDM had increased levels of Pycard mRNA expression and ASC
 protein, and increased inflammasome speck formation, which was associated
 with increased Pycard mRNA stability without an increased transcription
 rate.  CRIPSR/Cas9 gene editing was performed on DBA/2 embryonic
 stem cells to change the Pycard 3’UTR SNP from the DBA/2 to the AKR
 allele.  This single base change significantly reduced Pycard
 expression and inflammasome activity after cells were differentiated into
 macrophages due to reduced Pycard mRNA stability.
description: rQTL software was used for the QTL analysis, with details
 provided in the manuscript. Other data was derived from
 cell biology, biochemistry, and molecular biology studies using standard
 methods as provided in the manuscript.