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Research compendium for 'Refitting the Context: A Reconsideration of Cultural Change among Early Homo sapiens at Fumane Cave through Blade Break Connections, Spatial Taphonomy, and Lithic Technology'
<div> <h3>Compendium DOI:</h3> <p><a href="../doi/10.5281/zenodo.10965413">https://zenodo.org/doi/10.5281/zenodo.10965413</a> </p> </div> <p>The content available at the above provided URL will reproduce the results as documented in the publication. Instead, the files hosted at <a href="https://github.com/ArmandoFalcucci/Refitting-The-Context">https://github.com/ArmandoFalcucci/Refitting-The-Context</a> represent the developmental versions and might have undergone modifications since the paper's publication.</p> <div> <h3>Maintainer of this repository:</h3> </div> <p>Armando Falcucci (<a href="mailto:armando.falcucci@uni-tuebingen.de">armando.falcucci@uni-tuebingen.de</a>)</p> <div> <h3>Published paper:</h3> </div> <p>Armando Falcucci, Domenico Giusti, Filippo Zangrossi, Matteo De Lorenzi, Letizia Ceregatti, Marco Peresani. Refitting the Context: Revisiting the Aurignacian sequence at Fumane Cave through blade fragment connections, spatial taphonomy, and lithic technology. <em>Journal of Paleolithic Archaeology</em> (2024). DOI: <a href="https://doi.org/10.1007/s41982-024-00203-0" rel="nofollow">10.1007/s41982-024-00203-0</a></p> <div> <h3>Abstract:</h3> </div> <p>High-resolution stratigraphic frameworks are crucial for unraveling the biocultural processes behind the dispersals of Homo sapiens across Europe. Detailed technological studies of lithic assemblages retrieved from multi-stratified sequences allow archaeologists to precisely model the chrono-cultural dynamics of the early Upper Paleolithic. However, it is of paramount importance to verify the integrity of these assemblages before building explanatory models of cultural change. In this study, multiple lines of evidence suggest that the stratigraphic sequence of Fumane Cave in northeastern Italy experienced minor post-depositional reworking, establishing it as a pivotal site for exploring the earliest stages of the Aurignacian. By conducting a systematic search for break connections between blade fragments and applying spatial analysis techniques, we identified three well-preserved areas of the excavation containing assemblages suitable for renewed archaeological investigations. Subsequent technological analyses, incorporating attribute analysis, reduction intensity, and multivariate statistics, have allowed us to discern the spatial organization of the site during the formation of the Protoaurignacian palimpsest A2–A1. Moreover, diachronic comparisons between three successive stratigraphic units prompted us to reject the hypothesis of techno-cultural continuity of the Protoaurignacian in northeastern Italy after the onset of the Heinrich Event 4. Based on the variability of the lithic and osseous artifacts, the most recent assemblage analyzed, D3b alpha, is now ascribed to the Early Aurignacian, aligning the evidence from Fumane with the current understanding of the development of the Aurignacian across Europe. Overall, this study demonstrates the high effectiveness of the break connection method when combined with detailed spatial analysis and lithic technology, providing a methodological tool particularly amenable to be applied to sites excavated in the past with varying degrees of recording accuracy.</p> <div> <h3>Keywords:</h3> </div> <p>Protoaurignacian; Early Aurignacian; Lithics; Refittings; Assemblage integrity; Spatial analysis; Italy</p> <div> <h3>Overview of contents and how to reproduce:</h3> </div> <p>Within this repository, various folders house data (<code>data</code>), code (<code>script</code>), and output files (<code>output</code>) pertinent to the paper. The data folder encompasses the blank and core datasets from the Aurignacian of Fumane Cave and the dataset of the blade fragment connection study. To replicate the results, download the entire repository and employ <code>Refitting-The-Context.Rproj</code> and open the folder <code>script</code>. For ensuring reproducibility, the <code>renv</code> package (v. 1.0.3) was utilized, following the procedures detailed in its vignette. All analyses and visualizations in the paper were conducted using R 4.3.1 on Microsoft Windows 10.0.19045 (64-bit). As the necessary packages are available in the <code>renv</code> folder, they are not explicitly listed here.</p> <div> <h3>Licenses:</h3> </div> <p>Code: <strong>MIT</strong> <a href="http://opensource.org/licenses/MIT" rel="nofollow">http://opensource.org/licenses/MIT</a>, copyright holder: Armando Falcucci (2024).</p> <p>Data and intellectual work: <strong>Creative Commons Attribution 4.0 International License</strong> (<a href="http://creativecommons.org/licenses/by/4.0/" rel="nofollow">http://creativecommons.org/licenses/by/4.0/</a>), copyright holder: the authors (2024).</p>
Evidence for Early Mesozoic diversification of Hypsimetopidae Nicholls, 1943 (Isopoda), with the description of a new genus from Andhra Pradesh and notes on threats to Indian cave environments
<p>Datafiles and scripts for https://doi.org/10.1093/jcbiol/ruac052</p> <p>Evidence for Early Mesozoic diversification of Hypsimetopidae Nicholls, 1943 (Isopoda), with the description of a new genus from Andhra Pradesh and notes on threats to Indian cave environments</p> <p>George D. F. Wilson1,2 and Shabuddin Shaik 3</p> <p>1 Saugatuck Natural History Laboratory, Saugatuck, MI, USA; gdfw@snhlab.com</p> <p>3 Department of Life Science, Central University of Karnataka, Kadaganchi, 585 367, India; shabu.biologist@gmail.com</p> <p>2 Corresponding author: George D. F. Wilson, P. O. Box 714, Saugatuck, Michigan 49453, USA. e-mail: gdfw@snhlab.com </p> <p>File List:</p> <p>Phreatoi20220525.nex <br> Mesquite data file that contains all data from the DELTA taxonomic database that were used for data presentation, organization, analysis, as well as trees resulting from all analyses. For Mesquite version 3.70; Maddison WP, Maddison DR. 2021. Mesquite: a modular system for evolutionary analysis. Version 3.6 University of British Columbia & Oregon State University., http://www.mesquiteproject.org/ <br> <br> The DELTA database is still being edited and changed so it is not included here<br> For DELTA, see website https://www.delta-intkey.com/<br> publications:<br> Dallwitz MJ. 1980. A general system for coding taxonomic descriptions. TAXON 29: 41-46.<br> Dallwitz MJ, Paine TA, Zurcher EJ. 2000. User's guide to the DELTA system: a general system for processing taxonomic descriptions. CSIRO: Canberra.</p> <p> <br> Phreatoi20220525.tnt - the TNT data file generated by Mesquite<br> Analyses were performed using TNT-64bit, version 1.5, Goloboff PA, Catalano SA. 2016. TNT version 1.5, including a full implementation of phylogenetic morphometrics. Cladistics 32: 221-238.<br> Note: TNT counts zero as a number so the first tree, taxon or k paramter is 0, the second is 1, the third is 2 and so on </p> <p>TNT Scripts were written or modified for this project by George D. F. Wilson. They were run using the console in Ubuntu 20.04 but should work using the console version of TNT in other operating systems available from http://www.lillo.org.ar/phylogeny/tnt/. I recommend using the console because it allows you do to multiple analysis with one script. </p> <p>Each script has a banner that explains what is being done. If this fails to appear the first time, enter n and restart the script</p> <p>These are easily modified in a text editor to change the analysis<br> -- tnt.run : standard run of tnt. <br> -- tnt-jacK.run : symmetric jackknife analysis with concavity parameter, select file, concavity and prob parameter <br> -- piwe_rangeK.run : A range of concavity parameters are selected at the beginning and run sequentially<br> -- setk_trans.run : Modified from setk.run by Salvador Arias, Instituto Miguel Lillo, San Miguel de Tucuman, Argentina<br> -- aquickie_bt1000.run : Modified from the standard script distributed with TNT with more iterations of jackknifing<br> <br> If you are new to using TNT, see the information available on http://www.lillo.org.ar/phylogeny/tnt/ as well as these articles:<br> Goloboff PA. 1993. Estimating character weights during tree search. Cladistics 9: 83-91.<br> Goloboff PA. 1997. Self-Weighted Optimization: Tree Searches and Character State Reconstructions under Implied Transformation Costs. Cladistics 13: 225-245.<br> Goloboff PA, Carpenter JM, Arias JS, Esquivel DRM. 2008. Weighting against homoplasy improves phylogenetic analysis of morphological data sets. Cladistics 24: 758-773.<br> Goloboff PA, Catalano SA. 2016. TNT version 1.5, including a full implementation of phylogenetic morphometrics. Cladistics 32: 221-238.<br> Goloboff PA, Farris JS. 2001. Methods for Quick Consensus Estimation. Cladistics 17: S26-S34.<br> Goloboff PA, Farris JS, Källersjö M, Oxelman B, Ramírez MJ, Szumik CA. 2003. Improvements to resampling measures of group support. Cladistics 19: 324-332.<br> Goloboff PA, Farris JS, Nixon KC. 2008. TNT, a free program for phylogenetic analysis. Cladistics 24: 774-786.</p>
Bhiwkund, Maharashtra, India. Lower cave, from south
<p>Bhiwkund, Maharashtra, India (21.052010, 79.45922). Lower cave from the south, as documented 2/2015.</p>
Bhiwkund, Maharashtra, India. Main cave, veranda roof with brahmī inscription
<p>Bhiwkund, Maharashtra, India (21.052010, 79.45922). Main cave, veranda roof of the iron age, with brahmī inscription, as documented 2.2015.</p>
Bhiwkund, Maharashtra, India. Lower cave, from above
<p>Bhiwkund, Maharashtra, India. Lower cave, from above, showing re-used megalith from an iron-age stone circle, and rock-cut channel on eastern side, as documented in 2/2015.</p>
Bhiwkund, Maharashtra, India. Lower cave, shell inscription
<p>Bhiwkund, Maharashtra, India (21.052010, 79.45922). Lower cave, shell inscription, as documented 2/2015.</p>
Bhiwkund, Maharashtra, India. Main cave, veranda roof
<p>Bhiwkund, Maharashtra, India (21.052010, 79.45922). Main cave, veranda roof made of an iron-age megalith, showing circular markings, as documented 2/2015.</p>
Udayagiri, Madhya Pradesh. Cave 5, detail of devotee.
<p>Udayagiri, Madhya Pradesh. Cave 5, detail of devotee, probably Candragupta II attended by his minister Vīrasena.</p>
Udayagiri, Madhya Pradesh. Cave 6, relief sculpture of Mahīṣāsuramardinī.
<p>Udayagiri, Madhya Pradesh. Cave 6, relief sculpture of Mahīṣāsuramardinī, Durgā slaying the buffalo demon, probably early 5th century CE.</p>
Kanheri (Bombay, Maharashtra, India). Plan of Kanheri caves complex
<p>Kanheri (Bombay, Maharashtra, India). Plan of Kanheri caves complex, dated 1881 and published in Campbell, James M. <em>Gazetteer of the Bombay Presidency</em>. Bombay: Government Central Press, 1896.</p>
Multi-year temperature and humidity time series from ice caves on Mauna Loa, Hawaii
<p>Air temperature and humidity time series from data loggers in two lava tube caves on Mauna Loa, Hawaii 2011-2017.</p> <p> </p>
Kreuzloch cave stream pressures
<p>Cave stream data collected in the Kreuzloch cave (Unteriberg, Switzerland).</p> <p>Water pressure and temperature were measured every 2 seconds during 8 months with RBR data loggers.</p>
Rakhterā (रखतेरा or Rakhetrā, Ashoknagar). Location of the Bhiyāṃdāṃt caves with inscriptions and images of Ādinātha and other deities.
<p>Rakhterā (रखतेरा or Rakhetrā, Ashoknagar). Location of the Bhiyāṃdāṃt caves with inscriptions and images of Ādinātha and other deities.</p>
Rakhterā (रखतेरा or Rakhetrā, Ashoknagar). Site of the Bhiyāṃdāṃt caves and images of Ādinātha and other deities.
<p>Rakhterā (रखतेरा or Rakhetrā, Ashoknagar). Site of the Bhiyāṃdāṃt caves and images of Ādinātha and other deities.</p>
Pathari पठारी (Madhya Pradesh). Cave inscription
<p><a href="https://de.wikipedia.org/wiki/Pathari">Pathari</a> पठारी (Madhya Pradesh). Cave inscription of Kumāragupta.</p> <p>Selected Bibliography:</p> <ul> <li><a>GAR (VS 1981/AD 1924-25)</a> 12</li> <li><a>Casile (2014)</a> 245-68</li> <li><a>Balogh (2019)</a> 191-226</li> </ul>
The immature Homo naledi ilium from the Lesedi Chamber, Rising Star Cave, South Africa
<p>To use any of these data, please cite: Cofran Z, VanSickle C, Valenzuela R, García-Martínez D, Walker CS, Hawks J, Zipfel B, Williams SA, & Berger LR. 2022. The immature <em>Homo naledi</em> ilium from the Lesedi Chamber, Rising Star Cave, South Africa. American Journal of Biological Anthropology 179:3–17. (https://onlinelibrary.wiley.com/doi/full/10.1002/ajpa.24522)</p> <p>Lesedi Ilium Landmark Dataset_R1.csv = A comma separated values (.csv) format file containing 148 3D landmarks describing shape of the right ilium, for 23 immature humans, <em>Australopithecus</em> fossils MLD 7 and MLD 25, and two reconstructions of the <em>Homo naledi</em> fossil U.W. 102a-138. The first naledi reconstruction utilizes a reference template based on MLD 7 and MLD 25, and the second reconstruction is based on the average of the human ilia. The .csv file contains columns for individual ID, landmark name, and the x-, y-, and z-coordinates of the landmark, and each row is a unique landmark coordinate.</p> <p>Lesedi_Ilium_Height_Data.csv = A comma separated values (.csv) format file containing developmental stage and iliac height (in mm) for 43 humans, U.W. 102a-138, and three <em>Australopithecus</em> fossils (MLD 7, MLD 25, and the left and right sides of Sts 14).</p> <p>A 3D mesh of the U.W. 102a-138 ilium is available on Morphosource: https://www.morphosource.org/concern/media/000383216?locale=en</p>
Evolution of left-right asymmetry in the sensory system and foraging behavior during adaptation to food-sparse cave environments
<p>Laterality in relation to behavior and sensory systems is found commonly in a variety of animal taxa. Despite the advantages conferred by laterality (e.g., the startle response and complex motor activities), little is known about the evolution of laterality and its plasticity in response to ecological demands. In the present study, a comparative study model, the Mexican tetra (<em>Astyanax mexicanus</em>), composed of two morphotypes, i.e., riverine surface fish and cave-dwelling cavefish, was used to address the relationship between environment and laterality. The use of a machine learning-based fish posture detection system and sensory ablation revealed that the left cranial lateral line significantly supports one type of foraging behavior, i.e., vibration attraction behavior, in one cave population. Additionally, left-right asymmetric approaches toward a vibrating rod became symmetrical after fasting in one cave population but not in the other populations. Based on these findings, we propose a model explaining how the observed sensory laterality and behavioral shift could help adaptation in terms of the tradeoff in energy gain and loss during foraging according to differences in food availability among caves.</p> <p>This repository contains all of raw videos used in this study.</p> <p>Please let us know if you have any question on these videos</p>
FIG. 15. — A, B in The high complexity of Micronetinae Hull, 1920 (Araneae, Linyphiidae) evidenced through ten new cave-dweller species from the Morocco
FIG. 15. — A, B, epigyne of Palliduphantes banderolatus Barrientos n. sp. in lateral (A) and ventral (B) views; C, male copulatory bulb of P. banderolatus Barrientos n. sp. retrolateral view; D-F, epigyne of Palliduphantes megascapus Barrientos n. sp. in lateral (D) and ventral (E and F) views.
FIG. 14. — A, B in The high complexity of Micronetinae Hull, 1920 (Araneae, Linyphiidae) evidenced through ten new cave-dweller species from the Morocco
FIG. 14. — A, B, Epigyne of Lepthyphantes imazigheni Barrientos n. sp. in lateral (A) and ventral (B) views; C, epigyne of Lepthyphantes leknizii Barrientos n. sp. in dorsal view; D, E, epigyne of Lepthyphantes lamellatus Barrientos n. sp. in lateral (D) and ventral (E) views; F, male copulatory bulb of Lepthyphantes lamellatus Barrientos n. sp. in retrolateral view; G, H, epigyne of Lepthyphantes sasi Barrientos n. sp. in lateral (G) and ventral (H) views; I, male copulatory bulb of Lepthyphantes sasi n. sp. in retrolateral view.
FIG. 4. — Lepthyphantes ensiferus Barrientos n in The high complexity of Micronetinae Hull, 1920 (Araneae, Linyphiidae) evidenced through ten new cave-dweller species from the Morocco
FIG. 4. — Lepthyphantes ensiferus Barrientos n. sp., genital organs: A, B, male copulatory bulb, retrolateral view (A), ventral view (B); C, schema of the embolic division; D, E, epigyne, ventral view (D), lateral view (E). Abbreviations: see Material and methods. Scale bar: 0.5 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)
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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.