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opencc-by-4.0Apr 2024View details →

Dataset accompanying "A new species of Mesolepis from the Late Carboniferous of Scotland, with especial reference to Mesolepis wardi Young"

This dataset accompanies the manuscript "A new species of Mesolepis from the Late Carboniferous of Scotland, with especial reference to Mesolepis wardi Young" (<a href="https://doi.org/10.1017/S1755691024000094" target="_blank" rel="noopener">https://doi.org/10.1017/S1755691024000094</a>) and comprises the following items:  - Mesolepis arabellae GLAHM 163398/1 (part) raw data (TIFF stack, zipped) - Mesolepis arabellae GLAHM 163398/1 (part) .mcs file - Mesolepis arabellae GLAHM 163398/1 (part) .ply files (zipped) - Mesolepis arabellae GLAHM 163398/2 (counterpart) raw data (TIFF stack, zipped) - Mesolepis arabellae GLAHM 163398/2 (counterpart).mcs file - Mesolepis arabellae GLAHM 163398/2 (counterpart) .ply files (zipped) - Mesolepis arabellae GLAHM 163398/2 (fin region) raw data (TIFF stack, zipped) - Mesolepis arabellae GLAHM 163398/2 (fin region) .mcs file - Mesolepis arabellae GLAHM 163398/2 (fin region) .ply file

Figure 3 in A skeleton from the Middle Jurassic of Scotland illuminates an earlier origin of large pterosaurs

Figure 1 in A skeleton from the Middle Jurassic of Scotland illuminates an earlier origin of large pterosaurs

Figure 1. The new Middle Jurassic pterosaur Dearc sgiathanach (A–C) Photographs of main slab (NMS G.2021.6.1– 2), bones in dorsal view (A); wing phalanges 2–3 (NMS G.2021.6.3–4), in dorsal view (B); and main counterslab (NMS G.2021.6.3), bones in ventral view (C). (D–F) Schematic drawings of (A)–(C). (G–H) Reconstruction of skull in dorsal (G) and ventral (I) views and skeleton in lateral view (H). ar, articular region; cd, caudal vertebrae; cor, coracoid; cv, cervical vertebrae; d, digit; den, dentary; dors,dorsal vertebrae; dpc, deltopectoral crest; ep, extensor process; fm, femur; gas, gastralia; hdc, humeral distal condyle; hmt, humeral tubercle; isc, ischium; ju, jugal; max, maxilla; mc, metacarpal; mt, metatarsal; po, postorbital; r, ribs; sac, sacral plate; sca, scapula; scv, sacral (?) vertebrae; sm, sesamoid; sq, squamosal; st, sternum; symp, symphysis; uc, ulnar crest; ul, ulna; wp, wing phalanx; r/l, right/left. Blue on reconstructions are missing regions; red line in (E) is location of histological sectioning. Scale bars, 30 mm. See Figures S2 and S3.

Figure S3 in A skeleton from the Middle Jurassic of Scotland illuminates an earlier origin of large pterosaurs

Figure S3. Histology of the wing phalanx of the new Middle Jurassic pterosaur Dearc sgiathanach, Related to STAR Methods. Thin section in plane polarized light (a), crosspolarized light with a lambda filter (b), cross-polarized light (c), and illustration (d) of histological features: lines of arrested growth (red) and endosteal resorption (blue). Note position of external line of arrested growth very close to the external surface. (e) Inner cortex of wing phalanx under plane polarized light, showing densely vascularized fibrolamellar bone with a line of arrested growth (arrows). (f) Cortex of wing phalanx under cross-polarized light with a lambda filter, showing endosteal lamellae (el), lines of arrested growth (arrows), predominance of primary fibrolamellar bone (flb), and an external zone of parallel-fibered bone (pfb). Note parallel-fibered bone (appearing cyan) adjacent to the line of arrested growth. (g) External cortex of wing phalanx under plane polarized light, showing line of arrested growth (arrow) adjacent to the external bone surface (below dotted yellow line). (h) External cortex of wing phalanx under cross-polarized light, showing parallel-fibered bone (pfb) at the periosteal surface, possibly indicating a decrease in growth rate from the earlier fibrolamellar bone (flb). Arrows denote lines of arrested growth. Abbreviations: el, endosteal lamellae; flb, fibrolamellar bone; pfb, parallel-fibered bone.

Figure 3 in A skeleton from the Middle Jurassic of Scotland illuminates an earlier origin of large pterosaurs

Figure 3. Postcranial skeleton and dentition of the new Middle Jurassic pterosaur Dearc sgiathanach Photographs of the right manus (A), cervical series (B), pubic region (C), right humerus (D), left humerus (E), left metacarpal-phalanx articular region (F), right maxilla (G), and left pes (H) of NMS G.2021.6.1–4. ac, anterior caudal vertebrae; ar, articular region; c, condyle; cdv, caudal vertebrae; cor, coracoid; cv, cervical vertebrae; d, dentary; dc, distal condyle; dpc, deltopectoral crest; dvrt, dorsal vertebrae; en, enamel; exp, extensor process; fem, femur; ft, flexor tubercle; gas, gastralia; h, humerus; ic, intercondylar groove; isc, ischium; max, maxilla; mcp, metacarpal; md, maxillary dentition; mg, medial groove; mt, metatarsal; nss, neural spine scar; pa, preacetabular process; poz, postzygapophysis ppb, prepubis; prez, prezygapophysis; rad, radius; rb, rib; sac, sacrum; sm, sesamoid; uc, ulnar crest; ul, ulna; un, ungual; vert, vertebra; wp1, wing phalanx one. Scale, 10 mm per bar. See Figures S2 and S3.

Figure 2 in A skeleton from the Middle Jurassic of Scotland illuminates an earlier origin of large pterosaurs

Figure 2. Skull of the new Middle Jurassic pterosaur Dearc sgiathanach and comparisons of pterosaur brain and ear endocasts (A–L) Photographs (A–D), segmented MCT scan renderings (E–H), and schematic drawings (I–L) of the skull (NMS G.2021.6.2) in, from top to bottom, left lateral (reversed), dorsal, right lateral, and ventral views. (M–U) Brain and inner ear endocasts of Rhamphorhynchus (based on Witmer et al.7) (M, P, and Q), Dearc (N, R, and S), and Tapejara (based on Eck et al.8) (O, T, and U), shown in the skull in left lateral view and isolated in left lateral and dorsal views, respectively. asc, anterior semi-circular canal; bp, basisphenoid; cbl, cerebellum; cer, cerebrum; ch, choana; chl, channels; cv, third cervical; d, dentary; den, dentition; e, endocast; ec, ectopterygoid; et, edentulous anterior tip; f, frontal (?); hy, hyoid; ipv, interpterygoid vacuity; itf, inferior temporal fenestra; j, jugal; la, lacrimal; md, matrix infilled dent; mx, maxilla; n, nasal; olf, olfactory bulb; opl, optic lobe; p, parietal; pm, premaxilla; po, postorbital; ppd, post-palatal depression; psc, posterior semi-circular canal; ptf, pneumatic foramen; q, quadrate; qj, quadrojugal; rapr, retroarticular process; rh, probable placement of rhamphotheca; sof, suborbital fenestra; sq, squamosal; sbtf, subtemporal fenestra; stf, superior temporal fenestra. In (E)–(L), bones that cannot be distinguished in the MCT scan due to fusion or insufficient resolution are conservatively rendered together in one color. Scale bars, 30 mm. See Figure S2.

Figure S4 in A skeleton from the Middle Jurassic of Scotland illuminates an earlier origin of large pterosaurs

Figure S4. Results of phylogenetic analysis of the relationships of Dearc sgiathanach and other basal pterosaurs, Related to Figure 4 and STAR Methods. (a) Bootstrap Frequency difference (GC) tree without wildcard or problematic taxa removal from consensus (GC, 100 replicates); (b) Bootstrap absolute frequency tree with problematic taxa removed; (c) Bremer support values, (Bremer.run) with removal of problematic taxa. In each, the red box denotes the clade Angustinaripterini.

Figure S1 in A skeleton from the Middle Jurassic of Scotland illuminates an earlier origin of large pterosaurs

Figure S1. Locality information for the holotype of the new Middle Jurassic pterosaur Dearc sgiathanach, Related to STAR Methods. Map and geological context showing: Isle of Skye (a); geological map of the locality where the specimen was found, Brothers' Point (b); stratigraphic section at the discovery site (c); orthophoto of the pterosaur fossil location in relation to dinosaur trackways and evidence of desiccation (d). Figures c) & d) modified after dePolo et al. (2020).

Figure S2 in A skeleton from the Middle Jurassic of Scotland illuminates an earlier origin of large pterosaurs

Figure S2. Skull and anterior cervical vertebrae of the new Middle Jurassic pterosaur Dearc sgiathanach visualised by X-ray computed microtomography (manual & machine learning segmentation), Related to Figures 1-3. Manually segmented skull in: (a) dorsal; (b) ventral; (c) right lateral; (d) left lateral; (e) anterior; (f) posterior views. Colour code: yellow – palate & pterygoid; purple – dentary; black – teeth; green – fused dorsal cranial elements; blue – basipterygoid; light blue – dorsal unfused cranial bones. Manually segmented atlas, axis & anterior cervical complex in: (g) lateral; (h) ventral; (i) dorsal views. Cervical close up with schematic line art in: (j) dorsal and (k) ventral views. Colour code: dark yellow – 3rd cervical; cream – atlas & axis. Manually segmented brain and inner ear endocast in: (l) anterior; (m) dorsal; (n) ventral; (o) left lateral views. Colour code [annotated in the figure] channels; dark blue – optic lobes; pink – flocculus; purple – cerebrum & cerebellum; light blue – cranial nerves; WEKA trained machine learning segmentation results (p) in dorsal and ventral (left to right, respectively). Line art of select elements (q) cervical vertebral series in dorsal view, abbreviations: cv# - cervical vertebra; cr - cervical ribs; ns - neural spine; NMS G.2021.6.3 counterslab (r) in ventral orientation, abbreviations: lcv - long caudal vertebra; scv - short caudal vertebra; isc - ischium; ppb - prepubis; sv - sacral vertebra (?); gas - gastralia; sac - sacrum; dv - dorsal vertebra; rib - dorsal ribs; hum - humerus; sc - scapula coracoid; and dorsal view of right humerus (s); abbreviations: hum - humerus; ra - radius; ul - ulna. Comparative size diagram of select non-pterodactyloid humeri (t) [annotated in image]. Scales bars=20 m

Figure 4 in A skeleton from the Middle Jurassic of Scotland illuminates an earlier origin of large pterosaurs

Figure 4. Phylogenetic relationships of the Middle Jurassic pterosaur Dearc sgiathanach and wingspan estimates for Jurassic pterosaurs Strict consensus of most parsimonious trees from phylogenetic analysis, with silhouettes scaled to wingspan (Dearc = ca. 2.0 m) (1), and skull reconstructions of key taxa: (A) Scaphognathus crassirostris (based on GPIB 1304), (B) Dorygnathus banthensis (based on SMNS 55886), (C) Rhamphorhynchus muensteri (based on NHMUK R 37002), (D) Angustinaripterus longicephalus (based on ZDM T8001), and (E) Dearc sgiathanach. Wingspan plot (2): estimated wingspan range for isolated pterosaur remains from the Taynton Limestone collection. See Data S1D for complete element list. (A) NHMUK PV R 36634, (B) GSM 113726, (C) OUM J28352, (D) NHMUK PV R 38016, (E) NHMUK PV R1362, (F) LL12158, (G) NHMUK PV R 40126, (H) NMS G.2021.6.1-4 (Dearc), (I) OUM J23046, (J) OUM J28273, (K) NHM UK PV R 40126 B, (L) OUM J28319, (M) OUM J28307, (N) OUM J28271, (O) OUM J28354, (P) LL12160, (Q) OUM J23047, and (R) MJM L K1995. See Figure S4 and Data S1 and S2.

Random sample of habitat suitability for wolves in Scotland

A rule-based habitat suitability model was created for wolves (Canis lupus) in mainland Scotland. Six variations of the model were run, in order to test sensitivity to changes in input values.  In order to test for difference in the outputs of the six models, 500 random points were sampled from all six models, and then a test for statistical difference performed.  This dataset constitutes the values of the 500 random points, where 1 indicates complete suitability and 0 indicates complete unsuitability.

opencc-by-4.0Jun 2022View details →

GazetteersScotland-KG: A Knowlege Graph for representing the Gazetteers of Scotland (1803-1901)

This Knowlege Graph represents the information of the "Gazeteers of Scotland" (years: 1803 - 1901) collection in RDF (ttl format). This collection comprises twenty volumes of the most popular descriptive gazetteers of Scotland in the 19th century. Principal places in Scotland, including towns, counties, castles, glens, antiquities and parishes, are listed alphabetically. Each entry includes detailed historical and geographical information about each place.  The raw dataset is provided by the NLS in this <a href="https://data.nls.uk/data/digitised-collections/gazetteers-of-scotland/">link</a>. As  other NLS data collections, they are originally provided using two XMLs schemas: METS  for descriptive, structural, technical and administrative metadata (Title, Author, Publisher, etc); and ALTO  for encoding the OCR text of a page. In this work, we have extracted the information from METS and ALTO XMLS using <a href="https://github.com/francesNLP/defoe">defoe</a> tool and developed a <a href="https://github.com/francesNLP/defoe/blob/master/defoe/nls/queries/write_metadata_pages_yml.py">new information extraction defoe query</a> , and created a new Knowlege Graph called GazetteersScotland-KG.  The GazetteersScotland-KG uses the <a href="https://francesnlp.github.io/NLS-ontology/doc/index-en.html">NLS Ontology </a>to represent the information extracted. Furthermore, during the information extraction phase, we have employed several techniques to mitigate two common OCR errors: long-S and the line-break hyphenation. The GazetteersScotland-KG contains 354,998 RDF triples. It has information from 12 series and 20 volumes: Each serie can have several Volumes. Each serie has an Editorm Publisher, mmsid, Shelf-Locator, publication year, etc.  A Volume has several Pages,  with text in them. The data model of the GazetteersScotland-KG can be found <a href="https://francesnlp.github.io/NLS-ontology/doc/dataModel.png">here</a>. <pre>  </pre>

opencc-by-4.0Jun 2022View details →

ChapbooksScotland-KG: A Knowlege Graph for representing the "Chapbooks Printed In Scotland" (1671 - 1893)

This Knowlege Graph represents the information of the "Chapbooks Printed In Scotland" (years: 1671 - 1893) collection in RDF (ttl format). This dataset comprises more than 3,000 chapbooks printed in Scotland from the 17th to 19th century. They form part of the Lauriston Castle Collection, which was bequeathed to the Library in 1926. It includes some 500 chapbook volumes containing around 5,500 individual items, more than half of which were printed in Scotland.  The raw dataset is provided by the NLS in this <a href="https://data.nls.uk/data/digitised-collections/chapbooks-printed-in-scotland/">link</a>. As  other NLS data collections, they are originally provided using two XMLs schemas: METS  for descriptive, structural, technical and administrative metadata (Title, Author, Publisher, etc); and ALTO  for encoding the OCR text of a page. In this work, we have extracted the information from METS and ALTO XMLS using <a href="https://github.com/francesNLP/defoe">defoe</a> tool and developed a <a href="https://github.com/francesNLP/defoe/blob/master/defoe/nls/queries/write_metadata_pages_yml.py">new information extraction defoe query</a> , and created a new Knowlege Graph called ChapbooksScotland-KG.  The ChapbooksScotland-KG uses the <a href="https://francesnlp.github.io/NLS-ontology/doc/index-en.html">NLS Ontology </a>to represent the information extracted. Furthermore, during the information extraction phase, we have employed several techniques to mitigate two common OCR errors: long-S and the line-break hyphenation. The ChapbooksScotland-KG contains 352,270 RDF triples. It has information from 2728 series and 3080 volumes. Each serie can have several Volumes, Suplements, references to Books; it also has an Editor and a Publisher, which can be a Person or an Organization. A Volume has several Pages,  with text in them. The data model of the ChapbooksScotland-KG can be found <a href="https://francesnlp.github.io/NLS-ontology/doc/dataModel.png">here</a>.

opencc-by-4.0Jun 2024View details →

Costs of Peatland Restoration in Scotland: Data underpinning MACC analysis

A dataset containing anonymised records outlining the costs of a selection of peatland restoration projects in Scotland that have been granted funding by NatureScot since 2016, merged with a set of environmental/geographic variables. These data in turn are used for underpinning the marginal abatement curve (MACC) analysis as a basis of a spatial cost prediction model for potential restoration of degraded peatland in Scotland.  The observations in the database represent individual restored sites and the total costs are on a per hectare basis. The variables capture location, spatial dimensions, meteorological conditions, peat conditions, land cover, use and designation specific for each site. The information has been sourced from various publicly accessible domains, namely the Met Office, James Hutton Institute, Centre from Ecology and Hydrology, Ordnance Survey, NatureScot and Centre for Environmental Data Analysis.

opencc-by-4.0Jun 2024View details →

Water level data from the Tarland Burn, Aberdeenshire, Scotland, 1st January - 31st December 2023

Water level was recorded, in hourly intervals, at four locations on the Tarland Burn,  Aberdeenshire, Scotland from 1st January to 31st december 2023.  Measurements were made using pressure transducers and logging equipment supplied by Campbell Scientific. Station latitude and longitude are provided. Blank cells in the data sheets are due to instrument failure or temporary loss of power. This data can be used to extend the series of previously published data from 2013- 2022 (https://doi.org/10.5281/zenodo.7777653) which also included rating curves derived using a Valeport electromagnetic flow meter (801 model), or ADCP "boat" at higher water level. This work has been funded by the Scottish Government as part of the strategic research programme and provides empirical data which underpins research on natural flood management, water quality, and biodiversity.

FIGURE 31. Cheiracanthus latus scale histology. 1, NMS G.2019.9.21.5 in A redescription of the three longest-known species of the acanthodian Cheiracanthus from the Middle Devonian of Scotland

FIGURE 31. Cheiracanthus latus scale histology. 1, NMS G.2019.9.21.5, vertical transverse section, anterior half of scale. 2, NMS G.2019.9.19.2, vertical transverse section, anterior half of scale. 3, NMS G.2019.9.20.3, vertical transverse section, midscale. 4, 5, NMS G.2019.3.3.14, vertical transverse section, midscale, with closeup of central region. 6, NMS G.2019.9.21.3, vertical transverse sections of two scales, posterior half of scale. 7, NMS G.2019.3.3.12, vertical transverse section towards posterior end of scale. 8, NMS G.2019.3.7.6, subhorizontal section through anterior base and posterior crown. 9, NMS G.2019.3.7.6, vertical oblique section through posterior crown and base. 10, NMS G.2019.9.19.7, horizontal section low in crown. 11, NMS G.2019.9.22.5, horizontal section high in crown. 12, 13, NMS G.2019.9.23.7, section through fin web scales including tiny distal scales with a deep neck and flat base, closeup of distal fin web scales in 13. Scale bars equal 0.1 mm in 1-11,13, 0.5 mm in 12. Arrows indicate anterior.

FIGURE 30. Cheiracanthus latus squamation, SEM images. 1-5, NMS G. 2019.3.7.21 in A redescription of the three longest-known species of the acanthodian Cheiracanthus from the Middle Devonian of Scotland

FIGURE 30. Cheiracanthus latus squamation, SEM images. 1-5, NMS G. 2019.3.7.21 from Den of Findon: 1, NMS G. 2019.3.7.21.2, crown view; 2, NMS G. 2019.3.7.21.5, crown view; 3, NMS G. 2019.3.7.21.13, anterior view; 4, NMS G. 2019.3.7.21.7, laterocrown view; 5, NMS G. 2019.3.7.21.14, laterocrown view. 6-7: NMS G.2019.14.9.2 from Geanies Point: 6, NMS G.2019.14.9.2.8, anterocrown view; 7, NMS G.2019.14.9.2.5, crown view. 8-10: NMS G.2019.14.4.2 from Hilton or Cadboll: 8, NMS G.2019.14.4.2.15, crown view; 9, NMS G.2019.14.4.2.5, crown view; 10, NMS G.2019.14.4.2.16, laterocrown view. Scale bars equal 0.2 mm. p, pit; pr, neck protuberance.

FIGURE 28. Cheiracanthus latus pectoral spines, serial transverse section drawings. 1, NMS G.2018.28.26 in A redescription of the three longest-known species of the acanthodian Cheiracanthus from the Middle Devonian of Scotland

FIGURE 28. Cheiracanthus latus pectoral spines, serial transverse section drawings. 1, NMS G.2018.28.26 (see Figure 27): sketch map and drawings of each section. 2, NMS G.2019.3.7 (see Figure 6.7, 8): sections NMS G.2019.3.7.6-12 through pectoral spines and scapulocoracoid.

FIGURE 26 in A redescription of the three longest-known species of the acanthodian Cheiracanthus from the Middle Devonian of Scotland

FIGURE 26. Cheiracanthus latus pectoral region and spines, morphology. 1-3, QMF60004 from Tynet Burn: 1, left and right scapulocoracoids, white arrows indicate separation between scapula and coracoid; 2, close up of right coracoid shape (dotted line); 3, dorsal fin spine insertion and basal cartilage, white arrow indicates insertion/exertion boundary. 4-6, NMS G.2018.28.26 from Tarrel Bay: 4, left and right pectoral spines as collected; 5, closeup of thin ridges on lateral or medial? side of right spine; 6, insertion area of right spine. 7, NMS G.1968.19.18, anal and pelvic spines. Scale bars equal 5.0 mm in 1-3, 6, 20 mm in 4, 7, 0.5 mm in 5. a.fs, anal fin spine; bc, basal cartilage; calc, calcite infill; pelv.fs, pelvic fin spines.

FIGURE 21. Cheiracanthus grandispinus scale histology. 1, NMS G.2019.9.3.9 from Gamrie, vertical longitudinal section through posterior protuberance. 2, 9, 12, NMS G.2019.9.8 in A redescription of the three longest-known species of the acanthodian Cheiracanthus from the Middle Devonian of Scotland

FIGURE 21. Cheiracanthus grandispinus scale histology. 1, NMS G.2019.9.3.9 from Gamrie, vertical longitudinal section through posterior protuberance. 2, 9, 12, NMS G.2019.9.8 from Jessie Port, Ross and Cromarty: 2, NMS G.2019.9.8.14, anterior crown vertical transverse section; 9, NMS G.2019.9.8.10, crown vertical transverse section; 12, NMS G.2019.9.8.13, crown horizontal section. 3, NMS G.2019.9.35.6, from Achanarras, midscale vertical transverse section. 4, 5, 10, 11, from Achanarras: 4, NMS G.2019.9.2.4, posterior half of scale, vertical transverse section; 5, NMS G.2019.9.2.2, vertical longitudinal section; 10, NMS G.1893.107.9.2, horizontal section through crown base; 11, NMS G.1893.107.9.2, horizontal section through midcrown. 6-8, NMS G.2019.9.10 from Cromarty: 6, NMS G.2019.9.10.3, off-centre vertical longitudinal section; 7, NMS G.2019.9.10.5, vertical transverse section; 8, NMS G.2019.9.10.9, oblique vertical section through side of scale. Scale bars equal 0.1 mm. Arrows indicate anterior.