cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7939/r3-7jk2-ph04
title: Freshwater sponge hosts and their green algae symbionts: a tractable model to understand intracellular symbiosis
title: Ephydatia muelleri Algal symbiosis transcriptomes

description: In many freshwater habitats, green algae form intracellular symbioses with a variety of heterotrophic host taxa including several species of freshwater sponge. These sponges perform important ecological roles in their habitats, and the poriferan:green algae partnerships offers unique opportunities to study the evolutionary origins and ecological persistence of endosymbioses. We examined the association between Ephydatia muelleri and its chlorophyte partner to identify features of host cellular and genetic responses to the presence of intracellular algal partners. Chlorella-like green algal symbionts were isolated from field-collected adult E. muelleri tissue harboring algae. The sponge-derived algae were successfully cultured and subsequently used to reinfect aposymbiotic E. muelleri tissue. We used confocal microscopy to follow the fate of the sponge-derived algae after inoculating algae-free E. muelleri grown from gemmules to show temporal patterns of symbiont location within host tissue. We also infected aposymbiotic E. muelleri with sponge-derived algae, and performed RNASeq to study differential expression patterns in the host relative to symbiotic states. We compare and contrast our findings with work in other systems (e.g., endosymbiotic Hydra) to explore possible conserved evolutionary pathways that may lead to stable mutualistic endosymbioses. Our work demonstrates that freshwater sponges offer many tractable qualities to study features of intracellular occupancy and thus meet criteria desired for a model system.
DOI: 10.7939/r3-wmew-4j53
title: Data associated with "Vegetative growth drives the negative effects of an invasive species on resident community diversity and is not limited by plant-soil feedbacks: a temporal assessment"

description: 1. Many pathways of invasion have been posited, but ecologists lack an experimental framework to identify which mechanisms are dominant in a given invasion scenario. Plant-soil feedbacks (PSFs) are one such mechanism that tend to initially facilitate, but over time attenuate, invasive species’ impacts on plant diversity and ecosystem function. PSFs are typically measured under greenhouse conditions and are often assumed to have significant effects under field conditions that change over time. However, direct tests of PSFs effects in natural settings and their change over time are rare. 2. Here we compare the role of PSFs to the effects of biomass in limiting the dominance of an invasive species and impacts on resident species diversity. We characterized the effects of the invader Bromus inermis (Leyss.) on native plant communities over time and measured changes its PSFs and vegetative growth to understand their integrated effects on community diversity. To do so, we combined data from a six-year field study documenting the rate and impacts of invasion with a short-term greenhouse experiment quantifying PSF as a function of time since invasion in the field. 3. We found that the nature and strength of B. inermis PSFs did not change over time and were not mediated by soil microbial communities. Though PSFs decreased B. inermis reproduction, they did not significantly limit vegetative growth nor diminish the negative impacts of B. inermis biomass on native species. 4. B. inermis experienced the full strength of its negative PSFs immediately upon invasion, but they were ineffective at reducing B. inermis vigour to facilitate the recovery of the native plant community. We recommend that conservation efforts focus on limiting B. inermis vegetative growth to facilitate community recovery.
DOI: 10.15468/dl.xn4scn
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Human Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sinomicrurus kelloggi (Pope, 1928)"
 ]
}

 The dataset includes 16 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031381-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7939/r36688w8n
title: Cost of filtration DATA for 5 demosponges - Data associated with: Ludeman, Reidenbach and Leys - JEB 2017 The energetic cost of filtration by demosponges and their behavioural response to ambient currents

description: Abstract: Sponges (Porifera) are abundant in most marine and freshwater ecosystems and as suspension feeders they play a crucial role in filtering the water column. Their active pumping enables them to filter up to 900 times their body volume of water per hour, recycling nutrients and coupling a pelagic food supply with benthic communities. Despite the ecological importance of sponge filter feeding, little is known about how sponges control the water flow through their canal system or how much energy it costs to filter the water. Sponges have long been considered textbook examples of animals that use current-induced flow. We provide evidence that suggests that some species of demosponge do not use current-induced flow, rather they respond behaviourally to increased ambient currents by reducing the volume of water filtered. Using a morphometric model of the canal system, we also show that filter feeding may be more energetically costly than previously thought. Measurements of volumetric flow rates and oxygen removal in five species of demosponge show that pumping rates are variable within and between species, with more oxygen consumed the greater the volume filtered. Together these data suggest that sponges have active control over the volume of water they process, which may be an adaptation to reduce the energetic cost of filtration in times of high stress.
DOI: 10.7939/r3ns0mb2k
title: Data from Kahn et al. (Trophic ecology of glass sponge reefs in the Strait of Georgia, British Columbia)

description: Sponges link the microbial loop with benthic communities by feeding on bacteria. Glass sponge reefs on the continental shelf of western Canada have extremely high grazing rates, consuming seven times more particulate carbon than can be supplied by vertical flux alone. Unlike many sponges, the reef building species Aphrocallistes vastus has no microbial symbionts and removes little dissolved organic carbon. To determine how reef sponges therefore get enough food to sustain such substantial grazing we measured stable carbon and nitrogen isotope signatures of water, sediment and sponge tissues. To ensure samples were temporally associated, we also studied the duration particles were retained in tissues in controlled feeding studies using microscopic beads and 13C-labeled bacteria. Although fecal pellets were expelled from sponges within 24 hours of feeding, intact bacteria were still found in tissues and sponge tissues retained elevated 13C levels for at least 14 days. These independent lines of evidence suggest that carbon in reef sponge tissues may reflect food consumed from days to weeks earlier. Stable isotope analysis suggests that heterotrophic bacteria ingested by the sponges comes from a confluence of trophic subsidies: from terrestrial and oceanic sources, and also potentially on sediment-borne bacteria resuspended by tidal currents.
DOI: 10.7939/r3-emsf-3685
title: Data associated with Grant et al (MEPS) "The Effect of Suspended Sediments on the Pumping Rates of Three Species of Glass Sponge In situ "
title: Glass Sponge Reefs and Sediment

description: The largest known glass sponge reefs in Canada are within the Hecate Strait and Queen Charlotte Sound Glass Sponge Reefs Marine Protected Area (HSQCS-MPA). However, human activities outside the core MPA boundaries, such as trawling, can create plumes of suspended sediments capable of travelling large distances. We studied the response of three glass sponge species to changes in suspended sediment concentrations (SSCs) at 170 m depth inside the HSQCS-MPA. Two species reduced excurrent flow rate in response to natural and experimentally-induced increases in suspended sediment (r = -0.8 to -0.97, p &lt; 0.05). Background suspended sediment levels were low and showed little variation (2.71 mg L-1 ± 0.09, mean ± SD). Species varied in the threshold of SSCs that triggered arrests. Sediment concentrations of 2.8 – 6.4 mg L-1 caused arrests in Rhabdocalyptus dawsoni while Heterochone calyx did not arrest until concentrations reached 5 – 10 mg L-1. Very small, but prolonged increases of suspended sediments (&lt; 1 mg L-1 for R. dawsoni and 3.2 mg L-1 for H. calyx) caused arrests of several hours in R. dawsoni and prolonged periods of reduced flow in H. calyx. No arrests were observed in Farrea occa, even after repeated exposures up to 57 mg L-1. A sediment transport model showed that sediment concentrations can remain high enough to affect sponge behavior as far as 2.39 km from the source of the plume. The results highlight the importance of understanding the biology of different species for establishment of adequate boundaries in marine protected areas.
DOI: 10.7939/r3b853k6c
title: Caribou Data Set

description: This the data associated with the manuscript: Auger-Méthé, M, AE Derocher, DA DeMars, MJ Plank, EA Codling, MA Lewis. Evaluating random search strategies in three mammals from distinct feeding guilds. Journal of Animal Ecology. In Press. The data is the step lengths and turning angles measured from caribou, grizzly bears, and polar bears.
DOI: 10.7939/r3057d48v
title: Geodia barretti - Energy budget data sheet for Limnology and Oceanography

description: Geodia barretti is a massive nearly spherical sponge that forms dense assemblages on the continental shelf of the North Altantic and the Norwegian Sea. We studied the metabolism of individual sponges collected using a remotely operated vehicle and maintained in large tanks with high volumes of unfiltered water brought from 160m depth. We used direct methods (In-Ex) to measure excurrent flow rates, oxygen removed, and carbon and nutrient flux through the sponges. G. barretti had very low specific filtration (0.26 mL min-1 mL-1sponge tissue) and low respiration (5.34± 0.98 nmol O2 min-1 mL-1 sponge tissue; 8.44 ± 1.51 µmol O2 hr-1 g C-1) rates in comparison to other sponges. A net release of nitrogen was detected as NO3-. Bacteria were removed from the water filtered with up to 99% efficiency, yet comprised only 5% of the sponges’ total carbon budget; the remainder consisted of dissolved organic carbon and detritus. High bacterial removal was aided by the presence of a tight gasket of cells that surrounds the collar of each choanocyte filter. A test for potential bypass canals showed removal of fluorescent microspheres until they were excreted 5-12 hours after feeding. Electron micrographs showed active uptake of E. coli ‘fed’ to the sponge as well as phagocytosis of symbiont microbes by sponge cells in the mesohyl. These data provide the first comprehensive study of metabolism in a deep-water high microbial abundance sponge.
DOI: 10.7939/r3s000
title: Aphrocallistes vastus Trinity transcriptome

description: Sponges (Porifera) are among the earliest evolving metazoans. Their filter-feeding body plan based on choanocyte chambers organized into a complex aquiferous system is so unique among metazoans that it either reflects an early divergence from other animals prior to the evolution of features such as muscles and nerves, or that sponges lost these characters. Analyses of the Amphimedon and Oscarella genomes support this view of uniqueness—many key metazoan genes are absent in these sponges—but whether this is generally true of other sponges remains unknown.We studied the transcriptomes of eight sponge species in four classes (Hexactinellida, Demospongiae, Homoscleromorpha, and Calcarea) specifically seeking genes and pathways considered to be involved in animal complexity. For reference, we also sought these genes in transcriptomes and genomes of three unicellular opisthokonts, two sponges (A. queenslandica and O. carmela), and two bilaterian taxa. Our analyses showed that all sponge classes share an unexpectedly large complement of genes with other metazoans. Interestingly, hexactinellid, calcareous, and homoscleromorph sponges share more genes with bilaterians than with nonbilaterian metazoans. We were surprised to find representatives ofmostmolecules involved in cell–cell communication, signaling, complex epithelia, immune recognition, and germ-lineage/sex, with only a few, but potentially key, absences. A noteworthy finding was that some important genes were absent from all demosponges (transcriptomes and the Amphimedon genome), which might reflect divergence from main-stem lineages including hexactinellids, calcareous sponges, and homoscleromorphs. Our results suggest that genetic complexity arose early in evolution as shown by the presence of these genes in most of the animal lineages, which suggests sponges either possess cryptic physiological and morphological complexity and/or have lost ancestral cell types or physiological processes.
DOI: 10.7939/r3ks6jj80
title: Data associated with Grant et al (MER) "Suspended sediment causes feeding current arrests in the glass sponge Aphrocallistes vastus"

description: Bottom-contact trawling generates large, moving clouds of suspended sediments that can alter the behaviour of organisms adjacent to trawl paths. While increased suspended sediment concentrations (SSCs) are known to cause glass sponges to arrest filtration in lab studies, the response of sponges to sediment in situ is not yet known. Here we describe arrest behaviours in response to increased SSCs recorded from the glass sponge Aphrocallistes vastus at the Fraser Ridge sponge reef in the Strait of Georgia, British Columbia, Canada. We identified 23 arrests of the sponges’ feeding current during experimental disturbances that raised SSC to between 10 and 80 mg l-1. Single arrests lasted 4.25 ± 1.3 min (± SD) and were characterized by a 2 cm s-1 reduction in feeding current lasting 0.5 - 3 min (mean 1.91 ± 0.97 min, n = 19). In comparison, coughing arrests varied in length (31 ± 22.89 min) and lasted 4 - 15 min (10.46 ± 5.26 min, n = 4). Coughing arrests showed a distinctive on/off pattern as sponge filtration returned to normal excurrent velocities, distinguishing them from single arrests. The onset of both arrest types was correlated with elevated SSCs (r = -0.83 to -0.92). Natural SSCs at the reef averaged 4.4 mg l-1 and were correlated with tidal flow (r = 0.86 and 0.89). The combined data provide evidence that suspended sediments can stop glass sponge feeding in situ even at SSCs below those known to be generated by trawling.
DOI: 10.7939/r3pc0v
title: Historical US Domestic Crude Prices

description: Coverage dates: start dates vary, earliest 1984; end date July 6, 2012.
DOI: 10.7939/r38c9r49s
title: Electronic Supplementary Material: Can reduced predation offset negative effects of sea louse parasites on chum salmon?

description: The .zip file contains R code and data that accompanies the paper \"Can reduced predation offset negative effects of sea louse parasites on chum salmon?\". The R code includes three main files: (1) code to compile chum salmon spawner-recruit data from escapement, catch and age -at-return, (2) code to fit a Ricker population model testing for an effect of sea louse abundance on farmed or wild salmon on chum salmon productivity, and (3) code to solve a host-macroparasite model that includes the effect of predation in a multi-host system. Supporting data include escapement, catch and age-at-return data made publicly available by Fisheries and Oceans Canada. Details of the files within are given in the README.txt file. <br><br>Abstract for the paper:<br> The impact of parasites on hosts is invariably negative when considered in isolation, but may be complex and unexpected in nature. For example, if parasites make hosts less desirable to predators then gains from reduced predation may offset direct costs of being parasitized. We explore these ideas in the context of sea louse infestations on salmon. In Pacific Canada, sea lice can spread from farmed salmon to migrating juvenile wild salmon. Low numbers of sea lice can cause mortality of juvenile pink and chum salmon. For pink salmon, this has resulted in reduced productivity of river populations exposed to salmon farming.However, for chum salmon, we did not find an effect of sea louse infestations on productivity, despite high statistical power. Motivated by this unexpected result, we used a mathematical model to show how a parasite-induced shift in predation pressure from chum salmon to pink salmon could offset negative direct impacts of sea lice on chum salmon. This shift in predation is proposed to occur because predators show an innate preference for pink salmon prey. This preference could be more easily expressed when sea lice compromise juvenile salmon hosts, making them easier to catch. Our results indicate how the ecological context of host-parasite interactions may dampen, or even reverse, the expected impact of parasites on host populations.
DOI: 10.7939/r3zg6gb3c
title: Grizzly Bear Data Set

description: This the data associated with the manuscript: Auger-Méthé, M, AE Derocher, DA DeMars, MJ Plank, EA Codling, MA Lewis. Evaluating random search strategies in three mammals from distinct feeding guilds. Journal of Animal Ecology. In Press. The data is the step lengths and turning angles measured from caribou, grizzly bears, and polar bears.
DOI: 10.15468/dl.d7a5e7
title: Occurrence Download

description: A dataset containing 1026 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-97.20529 15.42706,-95.0567 15.42706,-95.0567 16.13502,-97.20529 16.13502,-97.20529 15.42706))",
 "HasCoordinate is true",
 "TaxonKey is Platalea ajaja Linnaeus, 1758"
 ]
}

 The dataset includes 1026 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031383-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7939/r3g48m
title: Differentiating the Lévy walk from a composite correlated random walk - Data

description: This the data associated with the manuscript entitled: Differentiating the Lévy walk from a composite correlated random walk. It is the step lengths and turning angles of two bears collared in the Hudson Bay. The data is the step length and turning angle measured at regular time intervals (every 30 min).
DOI: 10.7939/r3-mr2c-py16
title: Pharmacology on Ephydatia muelleri primary cilia

description: Data_sheets from Ludeman et al_2014_Evolutionary origins of sensation in metazoans: functional evidence for a new sensory organ in sponges
DOI: 10.15468/dl.57hjbp
title: Occurrence Download

description: A dataset containing 125 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Dinemandra A.Juss."
 ]
}

 The dataset includes 125 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031386-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7939/r3-83m9-c987
title: Data associated with Matveev et al: Sense Induced Flow - Active use of ambient flow by a deep-sea glass sponge

description: How flow moves through porous structures like sponges is a fluid dynamic problem that has challenged physical and biological scientists. Sponges possess biological pump cells that are known to drive water flow, and yet their porous bodies have often been proposed to take advantage of ambient currents passively. Here we focus on the ‘induced-flow’ theory which proposes that pipe-shaped structures can allow flow external to the tube to drive flow through the tube. This concept has been widely applied to both living systems and biogenic structures and particularly resonates with paleontologists who often give a poriferan-affinity to fossils with holes, assuming that the canals of sponges are inert. A modern understanding of sponge morphology and physiology however, shows sponges possess a sophisticated sensory system, even in the canals. Glass sponges (Hexactinellida) are an ideal group with which to re-examine the hypothesis because individuals have large oscula and have a well-studied sensory system that can cause feeding current arrests. Here we studied filtration and metabolism from glass sponges in their natural habitat on a glass sponge reef at 190m depth. We used custom oxygen and flow sensors to record oxygen removed per liter pumped over several tidal cycles, to test the hypothesis that the glass sponge Aphrocallistes vastus expends less energy to filter more water during higher ambient flow. We found that more water was filtered during periods of higher ambient current in only one of six individuals. However, all sponges arrested pumping independently of ambient currents, indicating they have control over pumping. We compared oxygen removal between low and high ambient flow during periods when sponges were pumping (high excurrent). Surprisingly, four of six sponges removed on average 30% less oxygen when the ambient current was high. This suggests a mechanism by which the sponge senses the increase in ambient flow rates and reduces the cost of filtration. The underlying mechanism by which the sponges sense the change in ambient current and control the flow through its body remains unknown, but may involve feedback from primary cilia at the osculum that are involved in flow sensing and dilation of canals in other sponges. Our experiments show that while sponges can take advantage of current-induced flow, the flow through these animals is controlled by their complex physiology. Overall these results imply that the feedback system in nerveless sponges functions in a manner similar to other animals formed by tubes.
DOI: 10.7910/dvn/pulhtl
title: Replication Data for Undeterred: Joel Slemrod and the Evolution of Tax Evasion Research

description: This is the raw data used to generate Figure 1. Collected from Google Scholar.
DOI: 10.15468/dl.wptsmv
title: Occurrence Download

description: A dataset containing 901 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Milvago chimango (Vieillot, 1816)",
 "Country is Chile",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 901 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031387-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.srdjs3
title: Occurrence Download

description: A dataset containing 11266 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Calocedrus decurrens (Torr.) Florin"
 ]
}

 The dataset includes 11266 records from 321 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031385-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.