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Taxonomic Composition of Red Knot Fecal Samples on the Virginia Coast
Taxonomic Composition of Red Knot Fecal Samples on the Virginia Coast Understanding which prey birds use and how prey selection is related to prey availability is important to understanding avian ecology and for conservation planning. Abundant prey at stopovers during migration is a key to shorebird survival and breeding success. We determined which prey were available to foraging red knots (Calidris canutus rufa) using Virginia's barrier islands during spring migration by collecting substrate core samples containing prey on sand and peat substrates in May 2017 - 2019. We also collected red knot feces during the same period and used fecal DNA metabarcoding to determine which invertebrates red knots consumed. We used compositional analysis to determine which prey red knots selected on these islands. Crustaceans (Orders Amphipoda and Calanoida) were the most abundant prey on both sand and peat. Red knots consumed bivalves (Orders Venerida and Mytiloida), crustaceans (Orders Amphipoda and Calanoida), and insect larvae (Order Diptera). Red knots selected bivalves over non-bivalve prey, though non-bivalve prey may still be an important portion of the total caloric intake on Virginia's stopover, given their abundance and use. It is important that coastal conservation practices in the Western Mid-Atlantic stopover region continue to be designed to promote natural barrier island movement which leads to the formation of the peat banks used by many prey.
Fig. 2 in Rediscovering Anhanga: redescription and considerations on its taxonomic placement (Hemiptera: Heteroptera: Pentatomidae)
Fig. 2. Lectotype of Anhanga modesta Distant, 1887.A – dorsal view; B – ventral view; C – lateral view; D – genital plates in postero-ventral view; E – labels. Scale not provided.
Fig. 4 in Rediscovering Anhanga: redescription and considerations on its taxonomic placement (Hemiptera: Heteroptera: Pentatomidae)
Fig. 4. Internal female genitalia of Anhanga modesta Distant, 1887. Abbreviations: aaf – anterior annular flange; cs – capsula seminalis; dr – ductusreceptaculi; g9 – gonapophyses IX; gc9 – gonocoxites IX; la8 – laterotergites VIII; la9 – laterotergites IX; or – orificium receptaculi; paf – posterior annular flange; pc – pars communis; pcs – finger-like process of capsula seminalis; pi – pars intermedialis; rs – ring sclerites; tvi – thickening of vaginal intima; va – vesicular area; X – tenth segment). Scale bar: 1 mm.
Fig. 1. Anhanga modesta Distant, 1887. A in Rediscovering Anhanga: redescription and considerations on its taxonomic placement (Hemiptera: Heteroptera: Pentatomidae)
Fig. 1. Anhanga modesta Distant, 1887. A – dorsal view; B – magnification of the head in ventral view, dashed line highlighting the basal segment of labium arising anteriorly to the imaginary line traversing head at anterior margin of eyes; C – ventral view; D – magnification of external scent efferent system of metathoracic scent glands; E – magnification of abdomen, highlighting the placement of the pair of trichobothria (arrows) along the imaginary line of spiracles on urosternites VI and VII. Scale bar: 5 mm.
TIPP 2.0.0 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63
<strong>Software: </strong>TIPP<br><strong>SoftwareVersion: </strong>2.0.0<br><strong>DataURL: </strong> https://data.cami-challenge.org/participate<br><strong>SoftwareURL:</strong> https://github.com/smirarab/sepp<br><strong>DockerImage:</strong> stefanjanssen/docker_profiling_tools:tipp<br><strong>IsBiobox:</strong> True<br><strong>BioboxYAMLFile:</strong> https://zenodo.org/record/3629567/files/biobox.yaml?download=1<br><strong>ReferenceDatabase:</strong> 2015<br><strong>ShortReadsUsed:</strong> True<br><strong>LongReadsUsed:</strong> False<br><strong>CommandsUsed:</strong> docker run \<br>--volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \<br>--volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \<br>--volume="/path/to/output:/bbx/mnt/output:rw" \<br>--volume="/path/to/output/metadata:/bbx/metadata:rw" \<br>--volume="/path/to/output/cache:/cache:rw" \<br>stefanjanssen/docker_profiling_tools:tipp
Bracken 2.5 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63
<strong>Software: </strong>Bracken<br><strong>SoftwareVersion: </strong>2.5<br><strong>DataURL: </strong> https://data.cami-challenge.org/participate<br><strong>SoftwareURL:</strong> https://github.com/jenniferlu717/Bracken<br><strong>DockerImage:</strong> cami/bracken:2.5<br><strong>IsBiobox:</strong> True<br><strong>BioboxYAMLFile:</strong> https://zenodo.org/record/3629567/files/biobox.yaml?download=1<br><strong>ReferenceDatabase:</strong> Kraken standard db built May 2019<br><strong>ShortReadsUsed:</strong> True<br><strong>LongReadsUsed:</strong> False<br><strong>CommandsUsed:</strong> docker run \<br>--volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \<br>--volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \<br>--volume="/path/to/output:/bbx/mnt/output:rw" \<br>--volume="/path/to/output/metadata:/bbx/metadata:rw" \<br>--volume="/path/to/output/cache:/cache:rw" \<br>cami/bracken:2.5
CAT 4.6 taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly
<p>Taxonomic binning of the gold standard pooled assembly<br> <strong>Software: </strong>CAT<br> <strong>SoftwareVersion: </strong>4.6<br> <strong>DataURL: </strong> https://data.cami-challenge.org/participate<br> <strong>SoftwareURL:</strong> https://github.com/dutilh/CAT<br> <strong>ReferenceDatabase:</strong> prebuilt 2018-12-12<br> <strong>Taxonomy:</strong> NCBI 2018-12-12<br> <strong>ShortReadsUsed:</strong> False<br> <strong>LongReadsUsed:</strong> False<br> <strong>CommandUsed:</strong> CAT contigs -c anonymous_gsa_pooled.fasta -d CAT_prepare_20181212/2018-12-12_CAT_database/ -t CAT_prepare_20181212/2018-12-12_taxonomy/ --tmpdir tmp --nproc 16</p>
PhyloPythiaS+ 1.4 taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly
<p>Taxonomic binning of the gold standard pooled assembly<br> <strong>Software: </strong>PhyloPythiaS+<br> <strong>SoftwareVersion: </strong>1.4<br> <strong>DataURL: </strong> https://data.cami-challenge.org/participate<br> <strong>SoftwareURL:</strong> https://github.com/algbioi/ppsp<br> <strong>DockerImage:</strong> cami/ppsp:1.4<br> <strong>IsBiobox:</strong> False<br> <strong>ReferenceDatabase:</strong> RefSeq 93, SILVA 132<br> <strong>Taxonomy:</strong> NCBI 2018-02-26<br> <strong>ShortReadsUsed:</strong> False<br> <strong>LongReadsUsed:</strong> False<br> <strong>CommandUsed:</strong> run_ppsp.py --pipelineDir ppsp_pipepline --inputFastaFile anonymous_gsa_pooled.fasta --databaseFile ncbi_taxonomy --refSeq refseq93 --s16Database SILVA_132 --mgDatabase reference_NCBI201502/mg5</p>
MetaPalette 1.0.0 taxonomic profiling of the CAMI 2 Mouse Gut Toy data set, samples 0-63
<strong>Software: </strong>MetaPalette<br><strong>SoftwareVersion: </strong>1.0.0<br><strong>DataURL: </strong> https://data.cami-challenge.org/participate<br><strong>SoftwareURL:</strong> https://doi.org/10.5281/zenodo.1730624<br><strong>DockerImage:</strong> stefanjanssen/docker_profiling_tools:commonkmers<br><strong>IsBiobox:</strong> True<br><strong>BioboxYAMLFile:</strong> https://zenodo.org/record/3629567/files/biobox.yaml?download=1<br><strong>ReferenceDatabase:</strong> https://zenodo.org/record/1749272<br><strong>ShortReadsUsed:</strong> True<br><strong>LongReadsUsed:</strong> False<br><strong>CommandsUsed:</strong> docker run \<br>--volume="/path/to/19122017_mousegut_scaffolds_yaml:/bbx/mnt/yaml:ro" \<br>--volume="/path/to/19122017_mousegut_scaffolds:/bbx/mnt/input:ro" \<br>--volume="/path/to/output:/bbx/mnt/output:rw" \<br>--volume="/path/to/output/metadata:/bbx/metadata:rw" \<br>--volume="/path/to/output/cache:/cache:rw" \<br>--volume="/path/to/reference_database:/exchange/db:rw" \<br>stefanjanssen/docker_profiling_tools:commonkmers
Kraken 2.0.8 beta taxonomic binning of the CAMI 2 Mouse Gut Toy data set, gold standard pooled assembly
<p>Taxonomic binning of the gold standard pooled assembly<br> <strong>Software: </strong>Kraken<br> <strong>SoftwareVersion: </strong>2.0.8 beta<br> <strong>DataURL: </strong> https://data.cami-challenge.org/participate<br> <strong>SoftwareURL:</strong> https://ccb.jhu.edu/software/kraken2/<br> <strong>ReferenceDatabase:</strong> built 2019-05-22<br> <strong>Taxonomy:</strong> NCBI 2019-05-22<br> <strong>ShortReadsUsed:</strong> False<br> <strong>LongReadsUsed:</strong> False<br> <strong>CommandUsed:</strong> kraken2-build --standard --db kraken2db_std --use-ftp<br> kraken2 --db kraken2db_std --threads 16 --output 19122017_mousegut_scaffolds.kraken --report 19122017_mousegut_scaffolds.kreport anonymous_gsa_pooled.fasta<br> cat 19122017_mousegut_scaffolds | awk '{print $2 "\t" $3}' > 19122017_mousegut_scaffolds.cami</p>
FIG. 10 in On the taxonomic position of Phaenomenella Fraussen & Hadorn, 2006 (Neogastropoda, Buccinoidea) with description of two new species
FIG. 10. — Anatomy of Siphonalia cassidariaeformis (Reeve, 1846): A, B; ventral (A) and dorsal (B) views of body of specimen no. 1, removed from the shell; C, cephalopodium of no. 2, front view; D, penis of no. 3; E, F, foregut of no. 1, with right salivary gland in original position (E) and removed (F); G, stomach of no. 2, external view; H, stomach of no. 1, opened dorsally; I, stomach of no. 2, opened dorsally. Abbreviations: see material and methods. Scale bars: A-F, 10 mm; G, I, 5 mm; H, 1 mm
FIG. 8 in On the taxonomic position of Phaenomenella Fraussen & Hadorn, 2006 (Neogastropoda, Buccinoidea) with description of two new species
FIG. 8. — Anatomy of Phaenomenella nicoi n. sp.: A-D, MNHN-IM-2013-61636, male; E-G, MNHN-IM-2013-61637, female: A, soft body removed from the shell; B, penis; C, proboscis, opened dorsally; D, foregut, right lateral view; E, foregut, right lateral view, right salivary gland displaced; F, foregut, right lateral view, right salivary gland in original position; G, stomach, outer view. Abbreviations: see material and methods. Scale bars: 5 mm.
FIG. 4 in On the taxonomic position of Phaenomenella Fraussen & Hadorn, 2006 (Neogastropoda, Buccinoidea) with description of two new species
FIG. 4. — Shells of Phaenomenella samadiae n. sp.: A-C, holotype, MNHN-IM-2013-61617, SL 58.2 mm; D, ZHONGSHA 2015, st. CP4157, non-sequenced spm, MNHN-IM-2013-59393, SL 47.2 mm; E, F, ZHONGSHA 2015, st. CP4134, sequenced spm, MNHN-IM-2013-61674, SL 51.4 mm; G, ZHONGSHA 2015, st. CP4157, non-sequenced spm, MNHN-IM-2013-59665, SL 37.1 mm. Scale bar: 5 cm.
FIG. 2 in On the taxonomic position of Phaenomenella Fraussen & Hadorn, 2006 (Neogastropoda, Buccinoidea) with description of two new species
FIG. 2. — Phylogenetic tree of a dataset of Buccinoidea Rafinesque, 1815 obtained with Bayesian analysis of 28S gene sequences. Support values shown for the supported nodes with posterior probability values between 0.70 and 1.00 only.
FIG. 1 in On the taxonomic position of Phaenomenella Fraussen & Hadorn, 2006 (Neogastropoda, Buccinoidea) with description of two new species
FIG. 1. — Phylogenetic tree of a dataset of Buccinoidea Rafinesque, 1815 obtained with Bayesian analysis of COI gene sequences. Support values shown for the supported nodes with posterior probability values between 0.70 and 1.00 only. The numbers in brackets following the species names correspond to illustrated specimens at the bottom of the figure.
FIG. 11 in On the taxonomic position of Phaenomenella Fraussen & Hadorn, 2006 (Neogastropoda, Buccinoidea) with description of two new species
FIG. 11. — Radulae of Siphonalia spp. A, S. cassidariaeformis (Reeve, 1846) no. 1; B, S. cassidariaeformis no. 2; C, S. pfefferi G. B. Sowerby III, 1900 no. 1;
Fig. 2 in Taxonomic revision of the South American subgenus Canthon (Peltecanthon) Pereira, 1953 (Coleoptera: Scarabaeidae: Scarabaeinae: Deltochilini)
Fig. 2. Canthon (Peltecanthon) staigi (Pereira, 1953), ♂, Rio de Janeiro, Restinga da Marambaia (CEMT). A. Parameres lateral view. B. Parameres dorsal view. C. Internal sac ventral view. D. Internal sac dorsal view. Abbreviations: see Material and methods.
Fig. 7 in Taxonomic revision of the South American subgenus Canthon (Peltecanthon) Pereira, 1953 (Coleoptera: Scarabaeidae: Scarabaeinae: Deltochilini)
Fig. 7. Canthon (Peltecanthon) terciae sp. nov., paratype, ♂, Rio Grande do Norte, Baia Formosa, Mata Estrela (CEMT). A. Dorsal habitus. B. Ventral surface of meso- and metafemora. C. Transverse carina in the hypomeron. D. Carina in the margin between pygidium and propygidium. E. Male protibial spur. F. Paratype, ♀, Rio Grande do Norte, Baia Formosa, Mata Estrela (CEMT), protibial spur.
Fig. 1 in Taxonomic revision of the South American subgenus Canthon (Peltecanthon) Pereira, 1953 (Coleoptera: Scarabaeidae: Scarabaeinae: Deltochilini)
Fig. 1. Canthon (Peltecanthon) staigi (Pereira, 1953), ♂, São Paulo, Bertioga (CEMT). A. Dorsal habitus. B. Ventral surface of meso- and metafemora. C. Transverse carina in the hypomeron. D. Carina in the margin between pygidium and propygidium. E. Male protibial spur. F. Female protibial spur, São Paulo, Caraguatatuba, P.E. Serra do Mar (CEMT).
Figures 1–5. Oreodera pergeri. 1–4 in A new species, new geographical records, and taxonomic notes in Oreodera Audinet-Serville, 1835 (Coleoptera: Cerambycidae: Lamiinae)
Figures 1–5. Oreodera pergeri. 1–4) Holotype male. 1) Dorsal habitus. 2) Ventral habitus. 3) Lateral habitus. 4) Head, frontal view. 5) Paratype female, dorsal habitus.
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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.