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Supplementary Material to "The Rosa genome provides new insights into the domestication of modern roses" publication.
<p>A dataset corresponding to GC-MS acquired targeted metabolite profiling in 6 rose cultivars and 3 plant parts, provided as supplementary material to the publication "The <em>Rosa</em> genome provides new insights into the domestication of modern roses" , which appeared in Nature Genetics <strong>volume 50</strong>, pages772–777 (2018) <a href="https://doi.org/10.1038/s41588-018-0110-3">(https://doi.org/10.1038/s41588-018-0110-3)</a>. The table in this upload was packaged in the following archive available from <a href="https://static-content.springer.com/esm/art%3A10.1038%2Fs41588-018-0110-3/MediaObjects/41588_2018_110_MOESM3_ESM.zip">https://static-content.springer.com/esm/art%3A10.1038%2Fs41588-018-0110-3/MediaObjects/41588_2018_110_MOESM3_ESM.zip</a></p>
MALDI-TOF spectra of archaeological (Oncorhynchus) and modern (Salmo salar) bone collagen
<p>SPECIES INFORMATION<br> csv containing information about the samples that links the information about the species and files</p> <p><br> MALDI TOF-MS</p> <p>MALDI Spectra from a Bruker Ultraflex II range m/z 800-3500<br> Three technical replicates were averaged in mMass<br> Each of these spectra a tab delimited .txt file are uploaded</p> <p><br> SEQUENCE DATA<br> An aligned FASTA file containing the bovine reference collagen sequence and both versions of S. salar and O. mykiss sequences. The sequences are concatenated with COL1A1, COL1A2, and COL1A3 for the two fish and COL1A1, COL1A2, COL1A1 for bovine.</p> <p>Three annotated gff files containing the sequence from version 1 of S. salar annotated with the locations of the published mammal markers and the biomarkers presented in this paper. Each gff file corresponds to one of the three collagen proteins COL1A1, COL1A2, and COL1A3.</p>
Pauni (पौनि Bhandārā district) Maharashtra. Stūpa site with modern temple
<p>Pauni (पौनि Bhandārā district) Maharashtra. Stūpa site with modern temple.</p>
Text-fig. 4. Dendrogram (Ward's method, squared Euclidean distance) showing the relationship between the studied fossil vegetation assemblages of Hrádek/N. (48), Wackersdorf (49), Berzdorf and Wiesa (50) and the Mydlovary Fm. (51) and the studied modern vegetation units from SE China and Japan (Teodoridis et al. 2011a, 2012, Appendix – this volume). in A Review Of The Early Miocene Mastixioid Flora Of The Kristina Mine At Hrádek Nad Nisou In North Bohemia (The Czech Republic)
Text-fig. 4. Dendrogram (Ward's method, squared Euclidean distance) showing the relationship between the studied fossil vegetation assemblages of Hrádek/N. (48), Wackersdorf (49), Berzdorf and Wiesa (50) and the Mydlovary Fm. (51) and the studied modern vegetation units from SE China and Japan (Teodoridis et al. 2011a, 2012, Appendix – this volume).
Text-fig. 2. Eospondylus primigenius (STÜRTZ) Bundenbach, Eschenbach-Bocksberg quarry, Lower Devonian, Lower Emsian (Zlichovian), Hunsrück Slate,, NM S 4764, x 3. Specimen with ventral arm coiling. The specimen is on its dorsum in slate with all five rays curled ventrally inward toward mouth area on underside of disk. Barely visible are tips of two jaws; slightly exposed are proximal parts of rays in oral view extending outward from disk. The location of abrupt ventral bending of rays is indicated by emergence from slate of five rays in aboral view that point inward toward buried disk. Based on ventral bending of rays and intimate association with crinoids Eospondylus has been interpreted as stratigraphic first occurrence of Order Euryalida, which contains epizoic gorgonocephalid and euryalid basket-stars of modern oceans. This status is rejected using new evidence from isolated vertebrae. [Photo by Alexander Glass]. in Isolated Ossicles Of The Family Eospondylidae Spencer Wright, 1966, In The Lower Devonian Of Bohemia (Czech Republic) And Correction Of The Systematic Position Of Eospondylid Brittlestars (Echinodermata: Ophiuroidea: Oegophiurida)
Text-fig. 2. Eospondylus primigenius (STÜRTZ) Bundenbach, Eschenbach-Bocksberg quarry, Lower Devonian, Lower Emsian (Zlichovian), Hunsrück Slate,, NM S 4764, x 3. Specimen with ventral arm coiling. The specimen is on its dorsum in slate with all five rays curled ventrally inward toward mouth area on underside of disk. Barely visible are tips of two jaws; slightly exposed are proximal parts of rays in oral view extending outward from disk. The location of abrupt ventral bending of rays is indicated by emergence from slate of five rays in aboral view that point inward toward buried disk. Based on ventral bending of rays and intimate association with crinoids Eospondylus has been interpreted as stratigraphic first occurrence of Order Euryalida, which contains epizoic gorgonocephalid and euryalid basket-stars of modern oceans. This status is rejected using new evidence from isolated vertebrae. [Photo by Alexander Glass].
Fig. 4 in The first identification of fossil Mesophyllum in accordance to the modern taxonomic concepts in coralline algae
Fig. 4. Coralline alga Mesophyllum crassiusculum (Foslie, 1902) Lebednik, 2004 from early Serravallian, Miocene, Modrý Majer, Slovakia. A. Carposporophyte, NHM B1858 (TS 918-7), carposporangial conceptacle with central pedestal (arrow). B. Bi/tetrasporophyte, NHM B1857/2a (counterpart of the TS 918-1). B1. Multiporate sporangial conceptacle, arrows point to the rounded epithallial cells located at the top of conceptacle roof. Rounded cell at the margin of the pore canal marks the surface of the roof. Adjacent pore canal cells are therefore considered as rosette cells. Note that rosette cells are not sunken. B2. Asexuate conceptacle with roof filaments and pore canal filaments consisting of at least 6 cells, arrows point to thinner (black arrow) and wider (white arrow) pore canal cells. C. Bi/tetrasporophyte, NHM B1857/1a (TS 918-1). C1. Asexuate multiporate conceptacle with roof filaments consisting of up to 7 cells. C2. Detail of C1 with pore lining cells (arrows), the cells are same or wider (top of the pore canal) than adjacent roof cells. C3. Embedded asexuate conceptacles (arrow). Note chambers filed with adventitious cells. The roofs are convex to flat, lacking peripheral rim.
Fig. 5 in The first identification of fossil Mesophyllum in accordance to the modern taxonomic concepts in coralline algae
Fig. 5. Coralline alga Mesophyllum crassiusculum (Foslie, 1902) Lebednik, 2004 bi/tetrasporophyte, early Langhian, Miocene, Kosihovce, Slovakia. Schaleková's collection, NHM B1859 (TS IIIb455). A1. Thallus morphology, growth form is encrusting with weak protuberances. A2. Coaxial to non-coaxial hypothallus (arrow). A3. Epithallial cells rounded or flattened (arrow). A4. Lateral cell fusions of the cells in adjacent filaments (arrow). A5. Pore canal anatomy, lining cells are same as adjacent roof cells (black arrow) or thinner near the base (white arrow). A6. Pore canal anatomy, lining cells are thinner than adjacent roof cells in some portions of the pore canal filaments. Arrows point to the center of the pore canal.
Fig. 3 in The first identification of fossil Mesophyllum in accordance to the modern taxonomic concepts in coralline algae
Fig. 3. Coralline alga Mesophyllum crassiusculum (Foslie, 1902) Lebednik, 2004 from early Serravallian, Miocene, Modrý Majer, Slovakia, male gametophyte, NHM B1857/1b (TS 918-1). A. Conceptacles of the type 1 (Johansen, 1981) were protruding above thallus surface during their maturity. Note the coaxial arrangment of the hypothallus; arrow points to the coaxial hypothallus. B. Conceptacle filled with material of unknown origin (arrow).
Fig. 2 in The first identification of fossil Mesophyllum in accordance to the modern taxonomic concepts in coralline algae
Fig. 2. Corallinae alga Mesophyllum crassiusculum (Foslie, 1902) Lebednik, 2004 from early Serravallian, Miocene, Modrý Majer, Slovakia. A. Bi/tetrasporophyte and male gametophyte, NHM B1857/1a and NHM B1857/1b (TS 918-1), respectively. An asexuate (tetra/bisporangial) plant (white arrow) overgrows a fragment of scleractinian coral colony. Growth form of coralline alga is encrusting. Male gametophyte overgrows tetrasporophyte (black arrow). B. Carposporophyte, NHM B1858 (TS 918-7). Carpogonial-carposporangial plant of M. crassiusculum (black arrow) overgrows a protuberant rhodolith of Phymatolithon calcareum (Pallas, 1766) (white arrow). Growth form of M. crassiusculum is encrusting and without protuberances. C. Bi/tetrasporophyte, NHM B1857/1a (TS 918-1). C1. Applanately branching thallus (arrows). C2. Pseudoparenchymatous thallus with coaxially to non-coaxially arranged hypothallus. Arrow points to the portion where coaxial hypothallus is best visible. C3. Magnified portion of the thallus from C2, arrows point to cell fusions in hypothallus and in the perithallus. C4. Flattened epithallial cells above meristematic cells located at the top of the embedded conceptacle.
Fig. 3 in Like phoenix from the ashes: How modern baleen whales arose from a fossil "dark age"
Fig. 3. Patterns and potential drivers of the early Miocene "dark age". A. Extinction of toothed mysticetes and eomysticetids at the beginning of the early Miocene "dark age", and subsequent reinvasion of coastal habitats by larger, toothless filter feeding mysticetes during the middle Miocene. The occurrence of eomysticetids in the earliest Miocene is based on a single, fragmentary specimen from New Zealand (Boessenecker and Fordyce 2017b). B. Global oxygen isotope curve, showing the timing of the mid-Miocene Climatic Optimum (Zachos et al. 2008). C. Global sea-level change (Miller et al. 2005). D. Global diatom abundance as derived from Deep-Sea Drilling Programme/Ocean Drilling Programme smear slides (Renaudie 2016). Highlighted events potentially relevant to the "dark age": 1, a 0.5 shift in δ18O; 2, a 40 m sea-level fall; and 3, an early Miocene decrease in global diatom abundance. Reconstructions of mysticetes by Carl Buell.
Fig. 2 in Like phoenix from the ashes: How modern baleen whales arose from a fossil "dark age"
Fig. 2. Comparison of Australasian late Oligocene baleen whale assemblages: south-eastern Australia (A1, B1) and New Zealand (A2, B2). A. Late Oligocene palaeogeographical reconstruction. B. Differences in mysticete assemblage composition. Note the widespread inundation of New Zealand. Dashed lines in A delineate the modern coastline without compensating for late Neogene Alpine Fault movement. Palaeogeographical reconstructions are based on King et al. (1999), King (2000), Holdgate and Gallagher (2003). Drawings of whales by Carl Buell.
Fig. 1 in Like phoenix from the ashes: How modern baleen whales arose from a fossil "dark age"
Fig. 1. Location of major formations that have yielded diverse odontocete assemblages, but few or no mysticetes. Sources: Clallam Formation, Nye Mudstone, and Jewett Sand (Barnes 1977; Crowley et al. 1999); Calvert Formation (Gottfried et al. 1994); Pungo River Formation (Whitmore and Kaltenbach 2008); Chilcatay Formation (Bianucci et al. 2018); Upper Marine Molasse (Pilleri 1986a, b); Libano Sandstone and "Pietra leccese" (Bianucci and Landini 2002); Central Paratethys (Grigorescu and Kazár 2006).
Fig. 2 in The oldest representative of a modern deep-sea ophiacanthid brittle-star clade from Jurassic shallow-water coral reef sediments
Fig. 2. Ophiacanthid brittle−star Ophiosternle crinitum (Quenstedt, 1876), from the Reef debris beds within the Mergelstetten Formation (Hybonoticeras beckeri Zone, Lithacoceras ulmense Subzone), latest Kimmeridgian, Late Jurassic of Buchenbrunnen near Steinenfeld, S−Germany. A. GPIT/69/96−24 (holotype). Detail of proximal arm segments in ventral view without arm spines (A1) and with arm spines (A2). B. 96/23 (paratype). Arm fragment in ventral view (B1), proximal arm segments in lateral view (B2). C. GPIT/AS/56 (paratype). Complete specimen (C1) and detail of proximal to median arm segments (C2) in dorsal view.
Fig. 1 in The oldest representative of a modern deep-sea ophiacanthid brittle-star clade from Jurassic shallow-water coral reef sediments
Fig. 1. Ophiacanthid brittle−star Ophiosternle crinitum (Quenstedt, 1876), GPIT/69/96−24 (holotype), from the Reef debris beds within the Mergelstetten Formation (Hybonoticeras beckeri Zone, Lithacoceras ulmense Subzone), latest Kimmeridgian, Late Jurassic of Buchenbrunnen near Steinenfeld, S−Germany. A. Complete specimen in ventral view. B. Detail of dorsal side showing arm base and distal tip of radial shields. C. Detail of disc in dorsal view. D, E. Detail of disc in ventral view; photograph (D) and explanatory drawing (E).
Fig. 5. Modern vesicomyids from the Hikurangi Margin. A, D in Fossil vesicomyid bivalves from Miocene hydrocarbon seep sites, North Island, New Zealand
Fig. 5. Modern vesicomyids from the Hikurangi Margin. A, D. Calyptogena sp. A. UOA L4610; right valve external (A 1) and internal (A 2) views. D. UOA L4611; external views of right (D 1) and left (D 2) valves. B, C. Archivesica sp. B. UOA L4608; left valve hinge. C. UOA L4609; left valve external (C 1) and internal (C 2) views.
Fig. 3 in In quest of the Pteraichnus trackmaker: Comparisons to modern crocodilians
Fig. 3. Plaster molds of pes and manus tracks of modern crocodilians (A–F) and Pteraichnus stokesi Lockley, Logue, Moratalla, Hunt, Schultz, and Robinson, 1995 (G). Direction of the movement is leftward for (F) and upward for the others. A, B. Tracks of Paleosuchus trigonatus Schneider, 1801. The pes track preserves imprints of all four digits, whereas the manus track shows only the imprints of digits I to III. C. Track of Tomistoma schlegelii Müller, 1838. Only claw marks are pressed for the digits III and IV of the pes. Imprints of digit IV and V of the manus show rotational movement and are hard to distinguish from each other. Claw drag marks are seen anterior to the tracks. D, E. Tracks of Crocodylus porosus Schneider, 1801. D. The pes track shows a sliding imprint and it overprinted on the manus track, although the general anatomy of the pes and manus are well preserved. Relatively deep claw and metapodial phalangeal pad imprints can be recognized as a convex part of the mold. E. Shallow imprint of pes digit IV compared to other digit imprints and the rotary motion of manus digit V can be seen. F. Track of running Paleosuchus trigonatus Schneider, 1801. The kinematics of trackmaker disrupts shape of tracks. The manus track reflects its anatomical configuration. In contrast, digit imprint number can be counted from the pes track but its general anatomical features are not preserved. G. Pes and manus sets of Pteraichnus stokesi from the Middle Jurassic Sundance Formation of Wyoming, USA. The photographs are taken from Bennett (1997) with the permission of the author. Scale bars 10 mm, except G, for which is 50 mm.
Fig. 1 in In quest of the Pteraichnus trackmaker: Comparisons to modern crocodilians
Fig. 1. Trackway measurements. Schematic diagram of pace angulation, stride length, external and internal width between opposing pes.
Fig. 2 in In quest of the Pteraichnus trackmaker: Comparisons to modern crocodilians
Fig. 2. Modern crocodilian trackways (A–E) compared to Pteraichnus saltwashensis Stokes, 1957 (F). A, B. Paleosuchus trigonatus Schneider, 1801, walking (A) and running (B). C, D. Crocodylus porosus Schneider, 1801, sprawling (C) and walking (D). E. Tomistoma schlegelii Müller, 1838, walking. F. Pteraichnus saltwashensis type specimen from the Upper Jurassic Morrison Formation of Arizona, USA (modified from Padian and Olsen 1984). Direction of the movement is from left to right.
Fig. 2 in A new brittle star from the early Carboniferous of Poland and its implications on Paleozoic modern-type ophiuroid systematics
Fig. 2. Ophiurin brittle star Aganaster jagiellonicus sp. nov. from the upper Tournaisian to lower Visean (lower Carboniferous) Mazurowe Doły Formation, Rudawa Group of Czatkowice quarry, Dębnik Massif, southern Poland; MZUJ T/0282, holotype. A. General view of the specimen, exposing the ventral side (also illustrated by O'Hara et al. 2014). B. Oral skeleton. C. Detail of the oral skeleton; photograph (C1), interpretative drawing (C2). D. Detail of basal arm segments; photograph (D1), interpretative drawing (D2).
Fig. 1 in A new brittle star from the early Carboniferous of Poland and its implications on Paleozoic modern-type ophiuroid systematics
Fig. 1. Geographical position of the investigated specimen (map after Salata 2013, with modifications).
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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
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