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Fig. 4 in Phylogenetics of the freshwater crab (Potamonautes MacLeay, 1838) fauna from 'sky islands' in Mozambique with the description of a new species (Brachyura: Potamoidea: Potamonautidae)
Fig. 4. Potamonautes licoensis sp. nov., holotype, ♂ (SAM C-A091399). A. Major right cheliped. B. Minor left cheliped. Scale bar = 10 mm.
Genbank accession numbers of sequences used in the phylogenetic analysis
<p><em>Phylogenetic analysis: </em>Sequences were assembled using Lasergene v15 (DNASTAR, Inc. Madison, USA), and combined with sequences obtained from Genebank</p>
Data from: New cranial fossils of the Jurassic turtle Neusticemys neuquina and phylogenetic relationships of the only thalassochelydian known from the Eastern Pacific
Neusticemys neuquina is a turtle from the Upper Jurassic of the Neuquén Basin, Patagonia, Argentina. Here we describe in detail a new skull, lower jaw, and a vertebra, utilizing both traditional anatomical description and computed tomography (CT). New diagnostic cranial characters of Ne. neuquina are: a round depression on the ventral surface of the basisphenoid, a relatively larger oval foramen nervi trigemini and reduced and steepened triturating surfaces on both the maxilla and dentary. The new morphological information presented in this study was included in a phylogenetic analysis, the primary result of which was recovery of Ne. neuquina within Thalassochelydia. Characters recognized as synapomorphies of this clade include (1) anterolateral recess of the anterior surface of the quadrate positioned lateral to the processus trochlearis oticum, (2) presence of a fossa on the supraoccipital-opisthotic-exoccipital contact area, (3) foramina anterius caroticus cerebralis located close together but independently perforating the basisphenoid, and (4) presence of the splenial in the mandible. Two contrasting dispersal scenarios may explain how this species of Thalassochelydia can be found outside of Europe. The presence of Ne. neuquina in the Neuquén Basin could be the consequence of an early dispersion event, for which we lack intermediate forms, or it may be the result of a later event once the clade was already established in Europe.
Fig. 1 in Molecular phylogenetics of the African horseshoe bats (Chiroptera: Rhinolophidae): expanded geographic and taxonomic sampling of the Afrotropics
Fig. 1 Type localities for recognized species of Rhinolophus (black circles), as well as subspecies and synonyms (white circles); label names represent the specific epithets of currently recognized species. Biomes of Africa and neighboring regions indicated by color shading, dark yellow: Tropical and subtropical moist broadleaf forests; orange: Flooded grasslands and savannas; gray: Tropical and subtropical grasslands, savannas, and shrublands; olive brown: Deserts and xeric shrublands; gray-green: Tropical and subtropical moist broadleaf forests; peach: Mangroves; ochre: Mediterranean forests, woodlands, and shrub; dark tan: Tropical and subtropical dry broadleaf forests [14]
Fig. 5 in Molecular phylogenetics of the African horseshoe bats (Chiroptera: Rhinolophidae): expanded geographic and taxonomic sampling of the Afrotropics
Fig. 5 Species tree estimated in StarBEAST2 using the four nuclear intron dataset. Numbers adjacent to nodes indicate posterior probabilities. Terminal tips in the tree that are statistically well-supported (PP ≥ 0.95) from BPP are indicated by "*" preceding the clade name, and terminal tips that had PP <0.95 are indicated by "?" preceding the clade name. Species groups are from [13]
Anatomical partitioning has little influence in topologies from Bayesian phylogenetic analyses of morphological data
<p>Morphological data is a fundamental source of evidence to reconstruct the Tree of Life, and Bayesian phylogenetic methods are increasingly being used for this task, along with, or instead of, traditional parsimony approaches. Bayesian phylogenetic analyses require the use of proper evolutionary models and their performance have been intensively studied in the past few years, with significant improvements to our knowledge regarding their performance. Notwithstanding, it was only recently that partitioned models for morphology received attention in studies of empirical data, but a systematic evaluation of its performances using simulations was never performed. Here we evaluate the influence of partitioned models defined by anatomical criterion in the precision and accuracy of consensus tree topologies, evaluating the possible negative effects of under and overpartitioning. For that, we analysed datasets simulated using parameters and properties of two empirical datasets, using Bayesian phylogenetic analyses in MrBayes. Additionally, we reanalysed 32 empirical datasets for diverse groups of vertebrates, applying unpartitioned and partitioned models. We found that in general, partitioning by anatomy has little to no influences in the performance of Bayesian phylogenetic methods in respect to the metrics studied here, with analyses under alternative partitioning schemes presenting very similar tree precision and accuracy. We discuss the possible reasons for the disagreement between the results obtained here and previous studies for empirical morphological data, and with empirical and simulation studies of molecular data, discussing the adequacy of anatomical partitioning relative to alternative methods to partition morphological datasets and how morphological and molecular partitioning are related.</p>
Dataset for "Phylogenetic structure of European forest vegetation" - Journal of Biogeography (DOI: 10.1111/jbi.14046)
<p>This dataset contains the list of plant occurrences and geographical and environmental attributes of the vegetation-plots analyzed in the paper titled “Phylogenetic structure of European forest vegetation” by Padullés Cubino et al. (2021; Journal of Biogeography; DOI: 10.1111/jbi.14046). </p> <p>The dataset contains 3 tables:</p> <ol> <li>“Table_taxa.csv”: It includes the list of angiosperm plant taxa in selected vegetation plots.</li> <li>“Table_sites.csv”: It includes data on the environmental variables of plots, their classification into different forest types, their location in 1<sup>o</sup> × 1<sup>o</sup> grid cells, and the reference to the original datasets archived in the European Vegetation Archive (EVA; http://euroveg.org/eva-database-participating-databases).</li> <li>“Metadata.csv”: It includes a description of the fields found in the two previous tables.</li> </ol>
Figure 13. Neoterebra guadeloupensis n in Phylogenetic classification of the family Terebridae (Neogastropoda: Conoidea)
Figure 13. Neoterebra guadeloupensis n. sp., Maculauger sudchinensis n. sp. and morphologically similar species. A. N. guadeloupensis n. sp. holotype, MNHN-2013- 61448, KARUBENTHOS 2015 Stn DW4638, 15°50'N, 61° 18'W, 305–312 m, 17.2 mm. B. MNHN-IM-2013-20531, KARUBENTHOS 2012 Stn GD55, 16° 22.48'N, 61° 35.46'W, 85 m, 9.4 mm. C. Terebra limatula syntype, USNM93971, Apalachicola Bay, FL, 17.8 mm. D, E. M. sudchinensis n. sp., holotype, MNHN-IM-2013-61887, ZhongSha 2015 Stn CP4144, 16°6'N, 114° 23'E, 160–200 m, 19.9 mm. F. Terebra helichrysum lectotype, NHMUK 1903.12.15.117, Mussandam, Persian Gulf, 47 fms (= 86 m), 24.5 mm. G. Terebra levantina holotype, MNHN-IM-2000-2812, MUSORSTOM 2 Stn CP59, 14°00'N, 120°16'E, 186–190 m, 24.2 mm.
Figure 10 in Phylogenetic classification of the family Terebridae (Neogastropoda: Conoidea)
Figure 10. Genera defined solely by shell morphology. A. Terebra bathyrhaphe lectotype, NHMUK 1873.8.6.10/1, Gulf of Yedo, 35° 35'N, 139°48'E, 6–25 fms (= 11–46 m), 24.8 mm. B. Hastulopsis melanachme lectotype, NMHUK 1873.8.6.11/1, Cape Sima, Japan, 18 fms (= 33 m), 17.8 mm. C. Terebra bifrons holotype, NHMUK 1968237, Japan, 51.0 mm. D. Gradaterebra scalariformis, SAM D-110176, Newland Head, S Australia, 20 fms (= 37 m), 12.1 mm. E. Terebra circumcincta holotype, NHMUK 1978150, Red Sea (erroneous?), 38.0 mm. F. Microtrypetes iola holotype, ANSP 155289, Mazatlan, Mexico, 20 fms (= 37 m), 14.0 mm.
Figure 11. Duplicaria herberti n in Phylogenetic classification of the family Terebridae (Neogastropoda: Conoidea)
Figure 11. Duplicaria herberti n. sp., Partecosta bozzettii n. sp. and morphologically similar species. A. D. herberti, holotype, MNHN-IM-2013-52381, INHACA 2011 Stn MR15, 26° 00.0'S, 32° 54.4'E, 0–1 m, 29.7 mm. B. D. herberti, MNHN-IM-2013-52366, INHACA 2011 Stn MM1, 26° 02.3'S, 32° 54.1'E, 0–1 m, 12.4 mm. C. D. herberti (paratype of D. mozambiquensis), NMSA 566, 27 mm. D. D. mozambiquensis, YT, Quelimane Pebane, Mozambique, 35–45 m, 19.6 mm. E. Partecosta bozzettii holotype, MNHN-IM-2009-10163, ATIMO VATAE Stn TP29, 25° 03' 43.9''S, 46°57'42.9''E, 3–4 m, 12.5 mm. F. Partecosta trilineata holotype, MNHN-IM-2000-21473, S Madagascar, Lavanono, 8.85 mm. G. P. daniae holotype, MMM, Farol das Lagostas, Luanda, Angola, 12 mm.
Figure 8. Genus Punctoterebra. A. P in Phylogenetic classification of the family Terebridae (Neogastropoda: Conoidea)
Figure 8. Genus Punctoterebra. A. P. nitida, MNHN-IM-2013-13332, PAPUA NIUGINIStn PD32, 05° 04.4'S, 145° 48.7'E, 1–8 m, 26.5 mm. B. P. teramachii, MNHN-IM-2009-9973, TERRASSES Stn DW3093, 22°06'S, 167°03'E, 190–200 m, 27.5 mm. C. P. polygyrata, MNHN-IM-2007-30424, SALOMON 2 Stn CP2282, 08° 37'S, 157°21'E, 150–160 m, 22.3 mm. D. P. succincta, MNHN-IM-2007-30385, SANTO 2006 Stn VM32, 15°26.6'S, 167°15.2'E, 0–1 m, 42.9 mm. E. P. solangeae, MNHN-IM-2009-10122, ATIMO VATAE Stn BP18, 25° 26.1–26.4'S, 44° 55.2–55.6'E, 17–20 m, 10.2 mm. F. P. sp. aff. textilis, MNHN-IM-2009-10093, MIRIKYStn CP3274, 15°30.15'S, 46°04.3'E, 29–36 m, 16.8 mm. G. P. souleyeti radula, MNHN-IM-2007-30547, SANTO 2006 Stn LD21, 15° 31.3'S, 167° 09.9'E, 1–6 m, 27 mm.
Figure 7. Genera Myurella, Maculauger n. gen. and Myurellopsis n. gen. A in Phylogenetic classification of the family Terebridae (Neogastropoda: Conoidea)
Figure 7. Genera Myurella, Maculauger n. gen. and Myurellopsis n. gen. A. Myurella affinis, MNHN-IM-2013-17860, PAPUA NIUGINIStn PR196, 05°12.3'S, 145° 48.8'E, 0 m, 39.8 mm. B. Myurella fortunei, MNHN-IM-2013-58677, KAVIENG 2014 Stn DW4468, 02°45'S, 150°37'E, 190–472 m, 25.2 mm. C. Myurella amoena, MNHN-IM-2013-46861, KAVIENG 2014 Stn KR02, 02°37.5'S, 150°46.5'E, 10–14 m, 24.9 mm. D. Myurella pygmaea, MNHN-IM-2009- 10121, off Lovanono, SMadagascar, 0–5 m, 6.1 mm. E. Maculauger pseudopertusa, MNHN-IM-2009-9954, MIRIKYStn DW3230, 13°25'S, 47°57'E, 71–158 m, 42.9 mm. F. Maculauger campbelli, MNHN-IM-2013-52252, EXBODI Stn CP3836, 22° 08'S, 167°11'E, 415–420 m, 20.5 mm. G. Myurellopsis undulata, MNHN-IM-2013-10252 PAPUA NIUGINI Stn PR07, 05°12.5'S, 145°48.5'E, 2–17 m, 31.9 mm. H. Myurellopsis kilburni, MNHN-IM-2013-12712, PAPUA NIUGINI Stn PS11, 05°04.7'S, 145° 48.9'E, 0–5 m, 24.8 mm. I. Myurellopsis joserosadoi, MNHN-IM-2013-52369, INHACA 2011 Stn MR13, 25°59.7'S, 32°54.5'E, 2–5 m, 17.9 mm.
Figure 6. Genera Hastula and Oxymeris. A. H in Phylogenetic classification of the family Terebridae (Neogastropoda: Conoidea)
Figure 6. Genera Hastula and Oxymeris. A. H. strigilata, MNHN-IM-2013-16102, PAPUA NIUGINI Stn PM41, 05° 08.1'S, 145° 49.3'E, 0–1 m, 32.4 mm. B. H. solida, MNHN-IM-2009-07098, Inhaca I., Mozambique, 25° 59.0'S, 32°54.5'E, 0 m, 25.6 mm. C. H. hectica, MNHN-IM-2009-11870, Tahiti, 17°30' 28.28''S, 149°27' 0.14''W, 0 m, 35.6 mm. D. H. cinerea, MNHN-IM-2013-9455, KARUBENTHOS 2012 Stn GM19, 16°21.3'N, 61°44.92'W, 0–1 m, 20.4 mm. E. H. lanceata radula, MNHN IM-2007-30535, PANGLAO 2004 Stn B1, 9°33.0'N, 123°46.50'E, 8–14 m, 32.5 mm (broken). F. H. hectica radula" Panglao I., Bohol" Philippines, intertidal. G. O. maculata, MNHN-IM-2013-40074, Marquesas Is, 113 mm. H. O. crenulata, MNHN-IM-2013-46877, KAVIENG 2014 Stn KR06, 02°36.3'S, 150° 46.2'E, 3–12 m, 85.9 mm. I. O. felina, MNHN-IM-2013-10283, PAPUA NIUGINI Stn PB05, 05°11.7'S, 145° 49.4'E, 0–20 m, 31 mm.
Figure 5. Genus Terebra. A. T in Phylogenetic classification of the family Terebridae (Neogastropoda: Conoidea)
Figure 5. Genus Terebra. A. T. subulata (Subclade C1), MNHN-IM-2013-47287, KAVIENG 2014 Stn KR12, 02° 36.3'S, 150°46.3'E, 0 m, 62.8 mm. B. T. guttata (Subclade C1) radula, MNHN-IM-2007-30376, SANTO 2006 Stn FR08, 15° 33,1'S, 167°12.2'E, 3–40 m, 74.6 mm. C. T. aff. fenestrata (Subclade C2), MNHN-IM-2013-46010, MADEEP Stn CP4330, 06° 07.63'S, 149°12.1'E, 315–625 m, 43.5 mm. D. T. aff. fenestrata 2 (Subclade C2) radula, MNHN- IM-2007-30418, PANGLAO 2005 Stn CP2331, 09°39'N, 123°48'E, 256–268 m, 23.1 mm. E. T. fujitai (Subclade C3-1), MNHN-IM-2007-15724, PANGLAO 2005 Stn CP2343, 09° 27'N, 123° 49'E, 273–356 m, 95.7 mm. F. T. triseriata (Subclade C4), MNHN-IM-2013-51211, KAVIENG 2014 Stn KD13, 02° 44.6'S, 150°43.1'E, 0–15 m, 25.6 mm. G. T. argus (Subclade C5), MNHN-IM-2013-46900, KAVIENG 2014 Stn KR06, 02°36.3'S, 150° 46.2'E, 3–12 m, 53.7 mm. H. T. babylonia (Subclade C6), MNHN-IM-2013-51267, KAVIENG 2014 Stn KR54, 02° 42.3'S, 150° 39.1'E, 7–10 m, 38.5 mm. I. T. sp. aff. cumingii (Subclade C7), MNHN-IM-2013-46237, MADEEP Stn CP4335, 06°05'S, 149° 18'E, 240–250 m, 62.5 mm. J. T. cingulifera (Subclade C7) radula, MNHN-IM-2007-30382, SANTO 2006 Stn VM32, 15° 26.6'S, 167° 15.2'E, 0–1 m, 49.7 mm.
Figure 9. Genera Profunditerebra n. gen. and Neoterebra n. gen. A. P. papuaprofundi n in Phylogenetic classification of the family Terebridae (Neogastropoda: Conoidea)
Figure 9. Genera Profunditerebra n. gen. and Neoterebra n. gen. A. P. papuaprofundi n. sp., MNHN-IM-2013-58123, KAVIENG 2014 Stn CP4422, 02°21'S, 150° 38'E, 496–609 m, 19.2 mm. B. P. orientalis, MNHN-IM-2009-29153, EXBODI Stn DW3930, 18° 37'S, 164°26'E, 448–464 m, 39.6 mm. C. P. brazieri, MNHN-IM-2013-55861, MORRISON AUSTRALIA Stn TA22, 43° 10.4'S, 147° 51.3'E, 1–7 m, 32.4 mm. D. Terebra specillata lectotype, NHMUK 1844.6.7.84, San Blas, Mexico, 7 fms (= 12.8 m), 39.3 mm. E. P. poppei radula, MNHN-IM-2007-30546, SANTO 2006, Stn AT44, 15°36'S, 167° 03'E, 86–118 m, broken. F. Terebra assu holotype, MNHN-IM-2000-25244, off Conceição da Barra, Espírito Santo, Brazil MD55, Stn DC75, 18°59'S, 37°50'W, 295 m, 9.8 mm. G. Terebra alagoensis holotype, MZSP 84238, continental slope off Alagoas, Brazil, 10° 05' 57''S, 35°46' 24''W, 720 m, 9.8 mm. H. Neoterebra sterigmoides, MNHN-IM-2013-20352, KARUBENTHOS 2012 Stn GD02, 16° 22.57'N, 61° 34.12'W, 0–80 m, 29.6 mm.
Figure 3. Subfamily Pervicaciinae A in Phylogenetic classification of the family Terebridae (Neogastropoda: Conoidea)
Figure 3. Subfamily Pervicaciinae A. Duplicaria duplicata, MNHN-IM-2009-29454, WESTERN AUSTRALIA 2011 Stn WB32, 33° 33'S, 115° 04'E, 5–15 m, 26.7 mm. B. Duplicaria tricincta, MNHN-IM-2013-5638, PAPUA NIUGINI Stn PD67, 05° 15.5'S, 145°46.8'E, 2–6 m, 6.9 mm. C. Duplicaria tristis lectotype, NHMUK 1979115, 'Seas of Japan', 17.7 mm. D. Duplicaria brevicula, MNHN-IM-2013-66140, off Namibe, S Angola, 40–60 m, 12.9 mm. E. Duplicaria bernardi radula, MNHN-IM-2009-10908, Australia, 26°56' 607''S; 153°23' 813''E, shell broken. F. Terebra fuscobasis lectotype, NHMUK 1873.7.5.8/1, Persian Gulf, 11.3 mm. G. Terebra nassoides lectotype, NHMUK 1968251/1, Red Sea, 13.5 mm. H. Partecosta varia, MNHN-IM-2013-52342, ATIMO VATAE Stn TM27, 24°56.4'S, 47° 06.9'E, 0–1 m, 10.4 mm. I. Partecosta sandrinae, MNHN-IM-2013-52359, INHACA 2011 Stn MM7 PL5, 26°03.7'S, 32°54.1'E, 0–1 m, 8.8 mm. J. Partecosta n. sp. aff fuscolutea radula, MNHN-IM-2009-10133, ATIMO VATAE Stn BS06, 25°26.8'S, 44° 54.9'E, 0–27 m, 6.9 mm. K. Partecosta bozzettii n. sp. paratype, MNHN-IM-2009-10162, ATIMO VATAE Stn TP29, 25° 03.7–03.8'S, 46° 57.7'E, 3–4 m, 12.4 mm. L. Partecosta trilineata, MNHN-IM-2009-10164, ATIMO VATAE Stn TP24, 25° 03.7–03.8'S, 46°57.6–57.7'E, 2–7 m, 8.2 mm. M. Partecosta macleani, MNHN-IM-2009-10115 ATIMO VATAE Stn TP19, 25°04.4–04.7'S, 46°55.3–56.3'E, 16–26 m, 8.9 mm. N, O. Partecosta macleani radula, MNHN-IM- 2009-10111, ATIMO VATAE Stn TP19, 25° 04.4–04.7'S, 46°55.3–56.3'E, 16–26 m, 12 mm.
Figure 4 in Phylogenetic classification of the family Terebridae (Neogastropoda: Conoidea)
Figure 4. Phylogenetic relationships of the subclades of the genus Terebra. Schematic of subclades C1–C7 in the genus Terebra; see Supplementary Material Fig. S1 forspecies composition (after Modica et al., 2019).
Figure 12. Profunditerebra papuaprofundi n in Phylogenetic classification of the family Terebridae (Neogastropoda: Conoidea)
Figure 12. Profunditerebra papuaprofundi n. sp., P. macclesfieldensis n. sp. and morphologically similar species. A. P. papuaprofundi holotype, MNHN-IM-2013- 58123, KAVIENG 2014 Stn CP4422, 02° 21'S, 150° 38'E, 496–609 m, 19.0 mm. B. P. papuaprofundi paratype 1, MNHN-IM-2013-45571, same locality, 29.5 mm. C. Terebra cinctella lectotype, NHMUK 197988/1, 'Mouth of the Indus', 27.8 mm. D. Terebra textilis lectotype, NHMUK 1844.6.7.80, 'Str Macassar', 25.7 mm. E. P. macclesfieldensis holotype, MNHN-IM-2013-61875, ZhongSha 2015 Stn DW4144, 16°6'N, 114° 23'E, 160–200 m, 22.4 mm. F. P. macclesfieldensis paratype 1, MNHN-IM-2013-61877, same locality, 22.2 mm. G. P. anseeuwi holotype, MNHN-IM-2000-6224, Aliguay I., Philippines, 80–150 m, 29.8 mm.
Figure 1 in Phylogenetic classification of the family Terebridae (Neogastropoda: Conoidea)
Figure 1. Phylogenetic relationships of the main lineages of Terebridae. Genera are numbered 1–13 in the tree and a shell of the type species of each genus is depicted to the left; see Supplementary Material Fig. S1 for species composition (after Modica et al., 2019).
Figure 2. Subfamily Pellifroniinae. A–C. Pellifronia jungi. A in Phylogenetic classification of the family Terebridae (Neogastropoda: Conoidea)
Figure 2. Subfamily Pellifroniinae. A–C. Pellifronia jungi. A. MNHN-IM-2013-52275, NANHAI 2014 Stn DW4102, 15°03'N, 116°31'E, 339–533 m, 25.5 mm. B. MNHN-IM-2013-52249, EXBODI Stn CP3831, 22° 02'S, 167°09'E, 523–560 m, 24 mm. C. MNHN-IM-2007-30591, SALOMON 2 Stn CP2195, 08° 26'S, 159° 26'E, 543–593 m, 29 mm (broken), D. Pellifronia brianhayesi holotype, MNHN-IM-2000-20800, S Mozambique, 22.6 mm. E–G. Bathyterebra benthalis. E. MNHN-IM-2013-60185, KARUBENTHOS 2015 Stn CP4524, 16°29'N, 61°42'W, 500–550 m, 35.5 mm. F, G. MNHN-IM- 2013-61124, KARUBENTHOS 2015 Stn DW4608, 9.3 mm. H. Bathyterebra zhongshaensis n. sp. holotype, MNHN-IM-2013-61800, ZhongSha 2015 Stn DW4138, 19° 13'N, 113°56'E, 470–494 m, 17 mm. I. Bathyterebra coriolisi, MNHN-IM-2013-52331, CONCALIS Stn DW3001 18°32'S, 163° 09'E, 390–400 m, 12.4 mm.
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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.