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Figure 16 in The Annelid Community of a Natural Deep-sea Whale Fall off Eastern Australia
Figure 16. Phylogeny of the Nereididae family based on Bayesian analysis of a combined dataset of the genes COI, 16S and 18S. Numbers adjacent to nodes indicate posterior probabilities, and taxa for which sequences have been contributed by the present study are indicated in bold.
Figure 31 in The Annelid Community of a Natural Deep-sea Whale Fall off Eastern Australia
Figure 31. Phascolosoma sp. fragments. (A) AMW.52203 anterior fragment, scalebaris 1 mm; (B) AMW.52201 anterior fragment, scale bar is 1 mm; (C) AM W.52202 fragment, scale bar is 1 mm; (D) AM W.52203 anterior fragment, scale bar is 1 mm.
Figure 13 in The Annelid Community of a Natural Deep-sea Whale Fall off Eastern Australia
Figure 13. Vrijenhoekia timoharai sp. nov. holotype AM W.53702. (A) Ethanol-preserved entire specimen (prostomium features have been outlined in grey for clarity), scale bar is 1 mm; (B) dorsal view of prostomium stained with Shirlastain, scale bar is 500 µm; (C) ventral view of partially everted pharynx stained with Shirlastain, scale bar is 1 mm; (D) parapodium, scale bar is 200 µm; (E) neurochaetae, scale bar is 30 µm; (F) dorsal view of pygidium, scale bar is 500 µm. Abbreviations: a, antennae; ft, facial tubercle; ma, median antennae; no, nuchal organ; pp, palpophore; ps, palpostyle; dc, dorsal cirri; dcp, dorsal cirriphore; nra, neuroacicula; vc, ventral cirri; chb, chaetal blade; chs, chaetal shaft.
Figure 14 in The Annelid Community of a Natural Deep-sea Whale Fall off Eastern Australia
Figure 14. Neanthes adriangloveri sp. nov., holotype AM W.53703. (A) Live specimen, scale bar is 5 mm; (B) detail of prostomium, scale bar is 500 µm; (C) anterior parapodium (number 5), scale bar is 200 µm; (D) mid-body parapodium (number 35), scale bar is 200 µm; (E) parapodium from near end of incomplete holotype specimen (number 48), scale bar is 200 µm; (F) notospinigers (parapodium number 5), scalebaris 20 µm; (G) subneurofalcigers (parapodium number 5), scalebaris 20 µm; (H) supraneurofalcigers (parapodium number 5), scale bar is 20 µm; (I) supraneurofalcigers (parapodium number 35), scale bar is 20 µm; (J) neuropodium of parapodium number 48, scalebaris 100 µm.
Figure 12 in The Annelid Community of a Natural Deep-sea Whale Fall off Eastern Australia
Figure 12. Phylogeny for the Hesionidae, Microphthalmidae and Chrysopetalidae families based on Bayesian analysis of a combined dataset of the genes COI, 16S and 18S. Numbers adjacent to nodes indicate posterior probabilities, and taxa for which sequences have been contributed by the present study are indicated in bold.
Figure 10 in The Annelid Community of a Natural Deep-sea Whale Fall off Eastern Australia
Figure 10. Ophryotrocha ravarae sp. nov. (A) Photo of holotype, dorsal and ventral side, holotype 1.6 mm long; (B) weakly sclerotized jaws, scale bar is 25 μm; (C) parapodium, scale bar is 100 μm; (D) overview of anterior end, scale bar is 250 μm; (E) supra-acicular simple chaeta, scale bar is 50 μm; (F) sub-acicular compound falcigerous chaeta, scale bar is 50 μm.
Figure 7 in The Annelid Community of a Natural Deep-sea Whale Fall off Eastern Australia
Figure 7. Ophryotrocha dahlgreni sp. nov. (A) Photo of holotype, dorsal and ventral side, holotype 1 mm long; (B) anterior end; (C) mandibles, scale bar is 50 μm; (D) everted maxillae on one side, scale bar is 50 μm; (E) parapodium, scale bar is 100 μm; (F) supraacicular simple chaeta, scale bar is 25 μm; (G) sub-acicular compound falcigerous chaeta, scale bar is 25 μm.
Figure 9 in The Annelid Community of a Natural Deep-sea Whale Fall off Eastern Australia
Figure 9. Ophryotrocha hanneloreae sp. nov. (A) Photo of holotype, dorsal side, holotype 1.3 mm long; (B) anterior end with jaws, scale bar is 25 μm; (C) details of maxillae elements with mandible shafts, scale bar is 50 μm; (D) parapodium, scale bar is 50 μm; (E) supra-acicular simple chaeta, scale bar is 50 μm; (F) sub-acicular compound falcigerous chaeta, scale bar is 50 μm.
Figure 2 in The Annelid Community of a Natural Deep-sea Whale Fall off Eastern Australia
Figure 2. Detail of the whale bones trawled during the IN2017_V03 expedition, and the dominant bivalve taxon associated with these; (A) top of whale skull; (B) underside of whale skull, covered in numerous small bivalves, hands for scale; (C) side of whale vertebra with Osedax tubes and small bivalves visible, scale bar is 30 mm; (D) cross-section view of whale vertebra with Osedax tubes, scale bar is 30 mm; (E) detail of the small bivalve associated with the whale bones, scale bar is 10 mm.
Figure 3 in The Annelid Community of a Natural Deep-sea Whale Fall off Eastern Australia
Figure 3. Paramytha cf. ossicola, specimen AM W.52208 stained with methyl blue; (A) dorsal view anterior section, scale bar is 0.5 mm; (B) prostomium, scale bar is 0.25 mm; (C) notochaetae, scale bar is 50 μm; (D) lateral view of anterior, scale bar is 50 μm; (E) thoracic uncinus, scalebaris 50 μm.
Figure 1 in The Annelid Community of a Natural Deep-sea Whale Fall off Eastern Australia
Figure 1. Location of the whale fall (white star) trawled off Byron Bay, Australia, during the IN2017_V03 expedition.
Figure 6 in The Annelid Community of a Natural Deep-sea Whale Fall off Eastern Australia
Figure 6. Phylogenyof the Amphinomidaefamily based on Bayesiananalysisof the COI, 16S and 18S gene fragments. Numbersadjacent to nodes indicate posterior probabilities, and taxa for which sequences have been contributed by the present study are indicated in bold. Specimen voucher numbers are given after taxa names.
Figure 8 in The Annelid Community of a Natural Deep-sea Whale Fall off Eastern Australia
Figure 8. Phylogeny of the Ophryotrocha genus based on Bayesian analysis of the 16S gene. Numbersadjacent to nodes indicateposterior probabilities, and taxa for which sequences have been contributed by the present study are indicated in bold. GenBank accession numbers are given after taxa names for the GenBank sequences.
Figure 11 in The Annelid Community of a Natural Deep-sea Whale Fall off Eastern Australia
Figure 11. Microphthalmus sp. (A) Photoofanethanol-preservedspecimen (NHMUKANEA 2022.412–420), scalebaris 0.25 mm; (B) light micrograph of prostomium and three anterior achaetous segments (NHMUK ANEA 2022.434), scale bar is 100 µm; (C, D) light micrographs of parapodium with the prechaetal (C) and postchaetal (D) lobes in focus (NHMUK ANEA 2022.434), scale bars are 50 µm; (E) light micrograph of heterogomph falcigers with different lengths (NHMUK ANEA 2022.434), scale bar is 20 µm; (F) light micrograph of ventral aspect of the posterior end showing anal lamellae (NHMUK ANEA 2022.412–420), scale bar is 100 µm.
Figure 4 in The Annelid Community of a Natural Deep-sea Whale Fall off Eastern Australia
Figure 4. Phylogeny of the Ampharetidae family based on Bayesian analysis of the COI, 16S and 18S gene fragments. Numbers adjacent to nodes indicate posterior probabilities, and taxa for which sequences have been contributed by the present study are indicated in bold. Specimen voucher numbers are given after taxa names.
Analyzing the Human Recommendation Community 'ifyoulikeblank' on Reddit — Auxiliary materials
<p>This repository contains auxiliary materials for the iConference 2024 paper "“If I like BLANK, what else will I like?”: Analyzing<br>a Human Recommendation Community on Reddit" by Thi Binh Minh Cao and Toine Bogers (= corresponding author)</p> <p>Published in: <em>Proceedings of the 2024 iConference</em>, April 15--26, 2024, Changchun, China.</p> <p>The paper presents the results of an analysis of /r/ifyoulikeblank, a Reddit community dedicated to requesting and providing for recommendations. This repository contains the following auxiliary materials:</p> <ul> <li>The annotated sample of threads from the /r/ifyoulikeblank subreddit (<strong>annotated-dataset.xlsx</strong>). The second sheet in the Excel file explains the contents of the file.</li> <li>The R code for performing the analysis described in the paper (<strong>annotation-analysis.R</strong>)</li> <li>CSV file containing the genres attributed to the artists as crawled from the Spotify API (<strong>artist-spotify-genres.csv</strong>)</li> <li>CSV file containing the popularity scores crawled from the Spotify API for the seed items and Spotify recommendations (<strong>recommendation-popularity.reddit-vs-spotify.csv</strong>)</li> <li>CSV file containing the popularity scores crawled from the Spotify API for the Reddit (<strong>recommendation-popularity.reddit.csv</strong>)</li> <li>The stopwords file used in the textual analysis (<strong>stopwords.csv</strong>)</li> <li>Excel file containing the activity data for the /r/ifyoulikeblank subreddit (<strong>subreddit-stats.xlsx</strong>)</li> </ul>
Mixed population trends inside a California protected area: Evidence from long-term community science monitoring
<p><span>Protected areas are one of the most widespread and accepted conservation interventions, yet their population trends are rarely compared to regional trends to gain insight into their effectiveness. Here, we leverage two long-term community science datasets to demonstrate mixed effects of protected areas on long-term bird population trends. We analyzed 31 years of bird transect data recorded by community volunteers across all major habitats of Stanford University's Jasper Ridge Biological Preserve to determine the population trends for a sample of 66 species. We found that nearly a third of species experienced long-term declines, and on average, all species declined by 12%. Further, we averaged species trends by conservation status and key life history attributes to identify correlates and possible drivers of these trends. Observed increases in some cavity-nesters and declines of scrub-associated species suggest that long-term fire suppression may be a key driver, reshaping bird communities through changes in forest and chaparral structure and composition. Additionally, we compared our results to those of the North American Breeding Bird Survey's Central California Coast region (n = 55 species) to place Jasper Ridge in a broader context. Most species experienced similar directional population trends inside vs. outside of the preserve, and only eight species (14.5%) did better inside this small, protected area. Therefore, we must identify relevant management strategies for declining populations and explicitly consider how existing protected areas target and manage each species. Further, this analysis underscores the importance of local and national community science for revealing nuanced long-term bird population trends.</span></p>
Data from: The role of fish predators and their foraging traits in shaping zooplankton community structure
<p><span>Differentiation of foraging traits among predator populations may help explain observed variation in the structure of prey communities. However, few studies have investigated the phenotypic effects of predators on their prey in natural communities. Here, we use a comparative analysis of 78 Greenlandic lakes to examine how foraging trait variation among threespine stickleback populations can help explain variation in zooplankton community composition among lakes. We find that landscape-scale variation in zooplankton composition was jointly explained by lake properties, such as size and water chemistry, and the presence and absence of both stickleback and arctic char. </span><span>Additional variation in zooplankton community structure can be explained by stickleback jaw protrusion, a trait with known utility for foraging on zooplankton, but only in lakes where stickleback co-occur with arctic char. Overall, our results illustrate how trait variation of consumers, alongside other ecosystem properties, can influence the composition of prey communities in nature.</span></p>
Drivers of plant diversity, community composition, functional traits and soil processes along an alpine gradient in the central Chilean Andes
<p>The datasets in this repository include plant community surveys, hyperspectral reflectance data at the leaf and canopy level, leaf trait data, and soil chemistry data collected at five sites along an elevation gradient of 2400m-3500m in the Chilean Andes (33°S, 70°W). The purpose of this study was to evaluate the environmental drivers of community assembly processes along the elevation gradient.</p>
COI metabarcoding data from arthropod pollinator communities in burned and unburned sites of California
<p>Novel wildfire regimes are rapidly changing global ecosystems and pose significant challenges for biodiversity conservation and ecosystem management. In this study, we used DNA metabarcoding to assess the response of arthropod pollinator communities to large-scale wildfires across diverse habitat types in California. We sampled six reserves within the University of California Natural Reserve System (UCNRS), each of which was partially burned in the 2020 Lightning Complex wildfires in California. Using yellow pan traps to target pollinators, we collected arthropods from burned and unburned sites across multiple habitat types including oak woodland, redwood, scrub, chamise, grassland, forest, and serpentine habitats. We found no significant difference in alpha diversity values between burned and unburned sites; instead, seasonal variations played a significant role in arthropod community dynamics, with the emergence of plant species in Spring promoting increased pollinator richness at all sites. When comparing all sites, we found that burn status was not a significant grouping factor. Instead, compositional differences were largely explained by geographic differences, with distinct communities within each reserve. Within a geographic area, the response of arthropods to fire was dependent on habitat type. While communities in grasslands and oak woodlands exhibited recovery following burn, scrublands experienced substantial changes in community composition. Our study highlights the importance of examining community responses to wildfires across broad spatial scales and diverse habitat types. By understanding the nuanced dynamics of arthropod communities in response to fire disturbances, we can develop effective conservation strategies that promote resilience and maintain biodiversity in the face of increasing wildfire frequency and severity driven by climate change.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.