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Figure 6 in Turtle shell bone and osteoderm histology of Mesozoic and Cenozoic stem-trionychian Adocidae and Nanhsiungchelyidae (Cryptodira: Adocusia) from Central Asia, Mongolia, and North America

Figure 6. Bone histology of Trionychidae indet. (ZIN PH 11/101). Images (a), (b), (f), and (g) are in polarised light, images (c) and (e) in normal transmitted light, and image (d) in polarised light applying a lambda compensator. (a) Composite overview image assembled from several images and transferred on a black background. Note distally tapering of the internal cortex. (b) Close-up of cancellous bone and internal cortex, the latter being composed of parallel-fibred bone tissue. (c, d) Close-up of distal end of the specimen. The cancellous bone is subsequently substituted by a loose meshwork of longitudinal coarse fibre bundles. (e, f) Close-up of the proximal part of external cortex, showing a thick, more external zone of predominantly parallel trending interwoven structural fibres (mirroring parallel-fibred bone tissue arrangement), overlying a thin plywood-like system of the more internal zone. Note oblique coarser Sharpey's fibres extending over the plies. (g) Close-up of a more distally situated part the external cortex, where the individual plies of the more internal zone have increased to about twice the thickness seen in the more proximal part of the cortex. The interwoven structural fibre bundles of the more external zone show a more homogeneous distribution instead of dominance of horizontally arranged fibre bundles. Abbreviations: CB, cancellous bone; EC, erosion cavity; ECO; external cortex; EZ, more external zone; GM, growth mark; ICO, internal cortex; IZ, more internal zone, ISF, interwoven structural fibre bundles; lsFB, longitudinally sectioned fibre bundle; PC, primary vascular canal; PFB, parallel-fibred bone; ShF, Sharpey's fibres.

Figure 4 in Turtle shell bone and osteoderm histology of Mesozoic and Cenozoic stem-trionychian Adocidae and Nanhsiungchelyidae (Cryptodira: Adocusia) from Central Asia, Mongolia, and North America

Figure 4. Shell bone histology of Basilemys sp. from North America. Image (a) is in normal transmitted light, and images (b–f) are in polarised light. (a, b) Section of the external cortex of the peripheral YPM 9703 showing characteristic spindle-shaped organisation of growth marks and the "pock-mark" sculpturing pattern of the bone surface. Note "lateral" shift between successive layers causing phasedelayed "saddle and valley" ornamentation pattern. (c) Close-up of the trabecular meshwork of interior cancellous bone of YPM 9703. Note interstitial primary bone matrix in trabecular nodes. (d) Close-up of the internal cortex of the peripheral shell fragment FM P27371. Parallel-fibred bone is vascularised by scattered primary osteons and simple vascular canals. (e) Close-up of the apical external cortex of the spiked osteoderm TMP 80.08.296, showing the external "pock-mark" sculpturing pattern and the spindle-shaped arrangement of bone tissue. (f) Close-up of the internal and lateral cortex of TMP 80.08.296. Note regular arrangement of transversely and longitudinally sectioned interwoven structural fibre bundles. Abbreviations: CB, cancellous bone; ISF, interwoven structural fibre bundles; LB, lamellar bone; lsFB, longitudinally sectioned fibre bundle; PC, primary vascular canal; PO, primary osteon, PFB, parallel-fibred bone; SO, secondary osteon; trFB, transversely sectioned fibre bundle.

Figure 3 in Turtle shell bone and osteoderm histology of Mesozoic and Cenozoic stem-trionychian Adocidae and Nanhsiungchelyidae (Cryptodira: Adocusia) from Central Asia, Mongolia, and North America

Figure 3. Bone histology of Nanhsiungchelyidae from Central Asia and Mongolia. Images (a) and (e) are in normal transmitted light, images (c) and (f) in polarised light, and (b) and (d) in polarised light applying a lambda compensator. (a, b) Close-up of external cortex of ZIN PH 38/80 (Nanhsiungchelyidae indet.). The more external zone shows growth marks, representing resorption lines in the cortical tissue. The more internal zone shows interwoven structural fibre bundles, vascularised by primary osteons and simple vascular canals. Note scattered secondary osteons. (c, d) Close-up of the external cortex of PIN 3458 (Hanbogdemys orientalis). Note presence of fibres extending perpendicular to the bone surface and subparallel growth marks in the external-most layers. Isolated primary vascular canals open up to the bone surface as small foramina. Note succession of resorption lines in the cortex. (e, f) Close-up of the interior cancellous bone and internal cortex of PIN 3458 (Hanbogdemys orientalis). The cortical parallel-fibred bone tissue is increasingly invaded by erosion cavities, only in parts lined with centripetally deposited secondary lamellar bone. Abbreviations: EC, erosion cavity; GM, growth mark; ISF, interwoven structural fibre bundles; OP, ornamentation pattern; PC, primary vascular canal; PFB, parallel-fibred bone; RL, resorption line; SO, secondary osteon; TR, trabecular bone.

Figure 5 in Turtle shell bone and osteoderm histology of Mesozoic and Cenozoic stem-trionychian Adocidae and Nanhsiungchelyidae (Cryptodira: Adocusia) from Central Asia, Mongolia, and North America

Figure 5. Bone histology of Trionychidae indet. (ZIN PH 3/75). Images (a) and (e) are in normal transmitted light, images (b) and (f) in polarised light, and (c) and (d) in polarised light applying a lambda compensator. (a–c) Close-up of the external cortex showing the plywoodlike system below the external ornamentation pattern. Note internal organisation of plies into fibre bundle quadrangles (see Scheyer et al., 2007), visible as alternating light and dark bundles (b) or yellow-orange and blue-violet bundles (c). Internal to the ply system the bone is coarsely cancellous. (d) Close up of the plywood-like system showing the longitudinally trending plies separating the plies, which show the alternating longitudinally sectioned (yellow-orange) and cross-sectioned (blue-violet) fibre bundle quadrangles. (e) Interior cancellous bone showing predominantly remodelled trabeculae and horizontally oblong intertrabecular cavities. (f) Close-up of the internal cortex showing lamellar zonal bone grading into parallel-fibred bone. Abbreviations: CCB, coarse cancellous bone; FBQ, fibre bundle quadrangles; ISF, interwoven structural fibre bundles; LSO, longitudinally sectioned secondary osteon; LZB-PFB, lamellar zonal bone-parallel-fibred bone; OP, ornamentation pattern; PC, primary vascular canal; PFB, parallel-fibred bone; ShF, Sharpey's fibres; TR, trabecular bone.

Figure 2 in Turtle shell bone and osteoderm histology of Mesozoic and Cenozoic stem-trionychian Adocidae and Nanhsiungchelyidae (Cryptodira: Adocusia) from Central Asia, Mongolia, and North America

Figure 2. Bone histology of Adocidae from Central Asia and Mongolia. Images (a), (c), and (e) are in normal transmitted light, images (b), (d), and (f) in polarised light. (a) Close-up of the external cortex of ZIN PH 84/87 ("Ferganemys" itemirensis). Growth marks are visible in the more external zone, whereas the more internal zone is dominated by an extensive reticular vascularisation pattern. (b) Close-up of the external cortex of ZIN PH 2/116 (Shachemys sp., xiphiplastron: external bone surface is in lower part of image). The more external zone shows highly birefringent growth marks, whereas the more internal zone is increasingly remodelled by secondary osteons. (c) Close-up of the external cortex of ZIN PH 92 (Adocus dzhurtasensis). Note absence of the more external zone. (d) Interior coarse cancellous bone of ZIN PH 593/64 (Adocus foveatus). (e) Close-up of the interior trabecular bone of ZIN PH 2/91 (Adocus sp.). (f) Close-up of the internal cortex of ZIN PH 37/86 ("Ferganemys" itermirensis, plastron fragment) showing parallel-fibred bone grading into lamellar bone. Note the light and dark extinction pattern of the tissue. Abbreviations: EC, erosion cavities; GM, growth mark; ISF, interwoven structural fibre bundles; PFBLZB, parallel-fibred bone-lamellar zonal bone; PC, primary vascular canal; RVP, reticular vascularisation pattern; SO, secondary osteon; TR, trabecular bone.

Figure 1 in Turtle shell bone and osteoderm histology of Mesozoic and Cenozoic stem-trionychian Adocidae and Nanhsiungchelyidae (Cryptodira: Adocusia) from Central Asia, Mongolia, and North America

Figure 1. Shell bone histology of Adocus sp. from North America. Image (a) is in normal transmitted light, and images (b–d) are in polarised light. Close-up of the interwoven structural fibre bundles of external cortex of the peripheral UCMP V87101/150201. (a, b) Note presence of growth marks and perpendicular fibre bundles in the more external zone. The more internal zone shows fine-fibred homogeneous structure of the ISF. (c) Close-up of interior trabecular and coarse cancellous bone of the costal UCMP V87101/150200. (d) Close-up of parallel-fibred bone of internal cortex of the costal UCMP V87101/150200. The bone tissue is vascularised by few scattered primary vascular canals only. Abbreviations: EC, erosion cavities; GM, growth mark; ISF, interwoven structural fibre bundles; LB, lamellar bone; PC, primary vascular canal; PFB, parallel-fibred bone; SO, secondary osteon.

opencc-by-4.0May 2020View details →

Table 1 in Two unusual new species of Caleremaeus (Acari: Oribatida) from eastern North America, with redescription of C. retractus and reevaluation of the genus

Table 1 Ontogeny of leg setae and solenidia in Caleremaeus species 1, 2.<table><tbody><tr><th></th><th>Trochanter</th><th>Femur</th><th>Genu</th><th>Tibia</th><th>Tarsus</th></tr><tr><th>Leg I</th></tr></tbody><tbody><tr><th>Larva</th><td>-</td><td>d, bv"</td><td>(l), dσ</td><td>(l), v', dφ 1</td><td>(ft), (tc), (p), (u), (a), s, (pv), (pl), e, ω 1</td></tr><tr><th>Protonymph</th><td>-</td><td>-</td><td>-</td><td>-</td><td>ω 2</td></tr><tr><th>Deutonymph</th><td>-</td><td>(l)</td><td>-</td><td>φ 2</td><td>-</td></tr><tr><th>Tritonymph</th><td>v'</td><td>-</td><td>v'</td><td>v"</td><td>(it)</td></tr><tr><th>Adult</th><td>-</td><td>-</td><td>[d lost]</td><td>[d lost]</td><td>v', l"</td></tr><tr><th>Leg II</th><td></td><td></td><td></td><td></td><td></td></tr><tr><th>Larva</th><td>-</td><td>d, bv"</td><td>(l), dσ</td><td>l', v', dφ</td><td>(ft), (tc), (p), (u), (a), s, (pv), ω</td></tr><tr><th>Protonymph</th><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td></tr><tr><th>Deutonymph</th><td>-</td><td>(l)</td><td>-</td><td>l"</td><td>-</td></tr><tr><th>Tritonymph</th><td>v'</td><td>-</td><td>-</td><td>v"</td><td>-</td></tr><tr><th>Adult</th><td>-</td><td>-</td><td>[d lost]</td><td>[d lost]</td><td>l", (it)</td></tr><tr><th>Leg III</th><td></td><td></td><td></td><td></td><td></td></tr><tr><th>Larva</th><td>-</td><td>d, ev'</td><td>l’, dσ</td><td>v', dφ</td><td>(ft), (tc), (p), (u), (a), s, (pv)</td></tr><tr><th>Protonymph</th><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td></tr><tr><th>Deutonymph</th><td>v', l’</td><td>l'</td><td>-</td><td>l' 3</td><td>-</td></tr><tr><th>Tritonymph</th><td>-</td><td>-</td><td>-</td><td>l' 3, v"</td><td>-</td></tr><tr><th>Adult</th><td>-</td><td>-</td><td>[d lost]</td><td>[d lost]</td><td>it"</td></tr><tr><th>Leg IV</th><td></td><td></td><td></td><td></td><td></td></tr><tr><th>Protonymph</th><td>-</td><td>-</td><td>-</td><td>-</td><td>ft", (p), (u), (pv)</td></tr><tr><th>Deutonymph</th><td>-</td><td>d, ev'</td><td>d, l'</td><td>v', dφ</td><td>(瑣), a",⁳</td></tr><tr><th>Tritonymph</th><td>v'</td><td>-</td><td>-</td><td>l', v"</td><td>-</td></tr><tr><th>Adult</th><td>-</td><td>-</td><td>-</td><td>[d lost]</td><td>-</td></tr></tbody></table>1 Adult data are based on all studied species and populations, including C. monilipes from Sweden, Germany and Spain. Ontogenetic data are from C. arboricolus n. sp. (topotypical population), C. retractus (near-topotypical population), a species in the ‘retractus group’ (New York population; see text), and C. monilipes (Norwegian population; see Seniczak and Seniczak 2019 and corrections in R12); from each population all instars were studied, except no larva was available from the C. retractus near-topotypical population.2 Setae (Roman letters) and solenidia (σ, φ, ω) are shown where they are first added and are assumed present through the rest of ontogeny, unless noted in brackets. Setae in parentheses represent pseudosymmetrical pairs; dash indicates no addition; underline indicates solenidion is coupled to seta d, in same alveolus.3 Seta l' of tibia III is invariably deutonymphal in C. arboricolus, C. retractus and the ‘retractus group’ from New York. By contrast, in C. monilipes l' first forms along with v" in the tritonymph, according to Seniczak and Seniczak (2019); appropriately, l' is absent from both tibiae III of our single deutonymph from Sweden.

opencc-by-4.0Sep 2024View details →

The North Pacific Eukaryotic Gene Catalog: KOfam protein function annotations

KEGG functional annotation using KofamScan v1.3.0 These tables are larger alternative versions to the KOfam tables included in the North Pacific Eukaryotic Gene Catalog protein data repository here: <a href="../records/12630398">https://zenodo.org/records/12630398</a> A full description of this data is published in Scientific Data, available here: <a href="https://www.nature.com/articles/s41597-024-04005-5" target="_blank" rel="noopener">The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations</a>. Please cite this publication if your research uses this data: Groussman, R. D., Coesel, S. N., Durham, B. P., Schatz, M. J., & Armbrust, E. V. (2024). The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations. Scientific Data, 11(1), 1161. Clustered protein sequences were annotated against the KEGG collection (release 104.0) of 20,819 protein family Hidden Markov Models (HMMs) using <a href="https://github.com/takaram/kofam_scan" target="_blank" rel="noopener">KofamScan </a>and KofamKOALA. Kofam annotation code is documented in the project github repository here: <a href="https://github.com/armbrustlab/NPac_euk_gene_catalog/blob/main/scripts/aa_data/NPEGC.kofamscan_function.sh">NPEGC.kofamscan_function.sh</a> Excerpt of core NPEGC_kofam function: <code># Define input FASTA</code> <code>local INPUT_FASTA="NPac.${STUDY}.bf100.id99.aa.fasta"</code> <code># KofamScan call</code> <code>${KOFAM_DIR}/kofam_scan-1.3.0/exec_annotation -f detail-tsv -E ${EVALUE} -o ${ANNOTATION_DIR}/NPac.${STUDY}.bf100.id99.aa.tsv ${FASTA_DIR}/${INPUT_FASTA}</code> Unprocessed annotation results were filtered with a minimum score of 30 to remove low-scoring matches: <code>zcat NPac.NPacID.kofam.tsv.gz | awk -F'\t' '{ gsub(/"/, "", $5); $5 = $5 + 0; if ($5 >= 30) print }' | gzip > NPac.NPacID.UW.bf100.id99.aa.incT30.tsv.gz</code>

opencc-by-4.0Aug 2024View details →

Data from: Autumn and winter plankton composition and size structure in the North Sea

Plankton dynamics in temperate ecosystems have been mainly studied during productive seasons, with comparatively less research conducted during the winter, particularly on microplankton. Implementing plankton sampling during a regular fishery cruise, we investigated the North Sea micro- and mesozooplankton community composition, abundance and size structure (55-2000 µm) during autumn (Buchan/Banks area) and winter (Downs area) between 2013 and 2019. Samples were analyzed using image-based techniques. Community diversity (broad taxa) was relatively similar across years in both areas, with diatoms and tripos taxa sets dominating the microplankton community and gastropods and copepods the mesozooplankton one. The average micro- to mesoozooplankton ratio (in abundance) was 90:1 for Buchan/Banks, resulting in average Normalized Abundance Size Spectra (NASS) slopes of -1.45 ±0.18 SD. For Downs, the micro- to mesoozooplankton ratio was 235:1 and steeper NASS slopes of -1.67 ±0.20 SD due to a lower contribution of large organisms. Interannual changes in the planktonic community for each area and their potential environmental drivers were examined using a redundancy analysis (including taxonomy and size) and a correlation analysis using NASS slopes (size only). Both approaches highlighted the importance of water mass properties (e.g. salinity, temperature, turbidity) in shaping plankton dynamics, although the amount of explained variance differed between approaches (11 versus 46%). Our results contribute to a better understanding of standing stocks of plankton and their environmental drivers. Specifically, novel insights were gained into microplankton dynamics, which play an important role in supporting the growth and survival of winter-spawned fish larvae in the North Sea.

Figure 12 in Two new plioplatecarpine mosasaurs (Mosasauridae; Plioplatecarpinae) of the genus Ectenosaurus from the Upper Cretaceous of North America

Figure 12: Ectenosaurus shannoni sp. nov., ALMNH:Paleo:5452. A–D. Left quadrate fragment with suprastapedial-infrastapedial contact in posterior (A), anterior/interior (B), lateral (C), and medial (D) views. Arrow indicates interior flange of infrastapedial process. Scale bar=2 cm.

Figure 10 in Two new plioplatecarpine mosasaurs (Mosasauridae; Plioplatecarpinae) of the genus Ectenosaurus from the Upper Cretaceous of North America

Figure 10. Ectenosaurus tlemonectes sp. nov., YPM VP4673. Cervical vertebra in left lateral view. Arrow indicates ventral ridge connecting the hypapophyseal peduncle and cotyle. Scale bar=5 cm.

Figure 7 in Two new plioplatecarpine mosasaurs (Mosasauridae; Plioplatecarpinae) of the genus Ectenosaurus from the Upper Cretaceous of North America

Figure 7. Ectenosaurus tlemonectes sp. nov., YPM VP4673. A, B. Right coronoid in lateral (A) and medial (B) views. C, D. Left jugal in lateral (C) and medial (D) views. E, F. Right jugal in lateral (E) and medial (F) views. Scale bars for A, B=5 cm. Scale bar for C–F=2 cm.

Figure 3 in Two new plioplatecarpine mosasaurs (Mosasauridae; Plioplatecarpinae) of the genus Ectenosaurus from the Upper Cretaceous of North America

Figure 3. Ectenosaurus tlemonectes sp. nov., YPM VP4673. A–C. Left quadrate in medial (A), anterior (B), and posterior (C) views. D–F. Left squamosal in ventral (D), lateral (E), and medial (F) views. Arrow indicates suprastapedial/infrastapedial contact. Scale bars=5 cm.

Figure 14 in Two new plioplatecarpine mosasaurs (Mosasauridae; Plioplatecarpinae) of the genus Ectenosaurus from the Upper Cretaceous of North America

Figure 14: Phylogenetic trees. A. Strict consensus tree of 30 most parsimonious trees (MPTs; tree length=255, CI=0.6680; HI=0.3137; RI=0.7377; RC=0.5063). B. Tree produced using constraint option and assuming monophyly of Ectenosaurus, 30 MPTs (tree length=255, CI=06680; HI=0.3320; RI=0.7877; RC=0.5063).

Figure 6 in Two new plioplatecarpine mosasaurs (Mosasauridae; Plioplatecarpinae) of the genus Ectenosaurus from the Upper Cretaceous of North America

Figure 6. Ectenosaurus tlemonectes sp. nov., YPM VP 4673, A–D. Detail of pathologic and non-pathologic anterior terminus of left dentary in left lateral (nonpathologic) (A), right lateral (pathologic) (B), right medial (pathologic) (C), and right dorsal (pathologic) (D) views. Scale bars for A–C=5 cm. Scale bar for D=3 cm.

Figure 11 in Two new plioplatecarpine mosasaurs (Mosasauridae; Plioplatecarpinae) of the genus Ectenosaurus from the Upper Cretaceous of North America

Figure 11. Ectenosaurus shannoni sp. nov., ALMNH:Paleo:5452. A, B. Frontal in dorsal (A) and ventral (B) views. C, D. Parietal in dorsal (C) and ventral (D) views. Abbreviations: POF, excavation for postorbitofrontal; PRF, excavation for prefrontal; VSR, ventral separation ridge. Scale bars=5 cm.

Figure 2 in Two new plioplatecarpine mosasaurs (Mosasauridae; Plioplatecarpinae) of the genus Ectenosaurus from the Upper Cretaceous of North America

Figure 2. Ectenosaurus tlemonectes sp. nov., YPM VP4673. A-C. Frontal in dorsal (A) and ventral (B) views. C. Detail of olfactory canal. Abbreviations: POF, excavation for postorbitofrontal; PRF, excavation for prefrontal; VSR, ventral separation ridge. Scale bars=5 cm.

Figure 9 in Two new plioplatecarpine mosasaurs (Mosasauridae; Plioplatecarpinae) of the genus Ectenosaurus from the Upper Cretaceous of North America

Figure 9. Ectenosaurus tlemonectes sp. nov., YPM VP4673. A–E. Left angular in lateral (A), medial (B), anterior (C), dorsal (D), and ventral (E) views. F–H. Right angular in lateral (F), anterior (G), and medial (H) views. I–K. Right splenial in lateral (I), anterior (J), and dorsal (K) view. L. Articulated right splenial and angular. Arrows point to pathologic ventral rugosity on left angular. Abbreviations: SAS, surangular articulation surface. Scale bars for A–E, I–K, L=5 cm. Scale bars for F–H=3 cm.

Figure 13 in Two new plioplatecarpine mosasaurs (Mosasauridae; Plioplatecarpinae) of the genus Ectenosaurus from the Upper Cretaceous of North America

Figure 13: Ectenosaurus shannoni sp. nov., ALMNH:Paleo:5452. A–C. Right splenial in lateral (A), medial (B), and posterior (C) views. D, E. Right coronoid in lateral (D) and medial (E) views. F. Laser scan of cast of right coronoid of ALMNH:Paleo:5452 in posteromedial view. G. Cervical vertebra in ventral view. H. Caudal vertebra in ventral view. Scale bars for A–F=5 cm. Scale bar for G=4 cm.

Figure 8 in Two new plioplatecarpine mosasaurs (Mosasauridae; Plioplatecarpinae) of the genus Ectenosaurus from the Upper Cretaceous of North America

Figure 8. Ectenosaurus tlemonectes sp. nov., YPM VP4673. A, B. Left surangular-articular in lateral (A) and medial (B) views. C. Close-up of glenoid fossa in lateral view. D. Close-up of glenoid fossa in medial view. E. Close-up of glenoid fossa in dorsal view. Arrow indicates postglenoid notch. Scale bars=5 cm.