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opencc-by-4.0Feb 2024View details →

Climate model and proxy input data for PaleoDA South America reconstruction

This repository contains  input data needed to run the paleoclimate reconstruction code for  "A continental reconstruction of hydroclimatic variability in South America during the past 2000 years", submitted to Climate of the Past in February 2024 [https://egusphere.copernicus.org/preprints/2024/egusphere-2024-545/].  The Github repository is located here: https://github.com/mchoblet/paleoda_sa/tree/main Structure: model_data: One File for each Model (GISS, CCSM (isoGSM), CESM, ECHAM5, iHADCM3) and variable (prec,tsurf,d18O, SPEI). Monthly resolution. proxy_data: One File for each proxy record type (Trees and corals contain a separate file for annual and djf linear regression parameters, the proxy data as such is the same). The data has yearly resolution, and thus also contains NaNs for when a year is not covered by a proxy. Note, that these time series are resampled to a regular resolution in the multi-time scale PaleoDA code. Climate Model Data: The original data can be found in https://zenodo.org/records/6610684. The data in this repository here has been slightly modified and regridded for easier processing by the reconstruction algorithm.  When using the data here, please also cite https://zenodo.org/records/6610684 and the publication  "Investigating stable oxygen and carbon isotopic variability in speleothem records over the last millennium using multiple isotope-enabled climate models", by  <div>Janica C. Bühler, Josefine Axelsson, Franziska A. Lechleitner, Jens Fohlmeister, Allegra N. LeGrande, Madhavan Midhun, Jesper Sjolte, Martin Werner, Kei Yoshimura, and Kira Rehfeld (https://cp.copernicus.org/articles/18/1625/2022/cp-18-1625-2022.html)</div> Climate Proxy Data: A regional proxy record subselection for South America. See References in Appendix A Choblet et al. (https://egusphere.copernicus.org/preprints/2024/egusphere-2024-545/). The DOI of each record is stored as Metadata. How were these files created? The steps are documented in the the Github repository https://github.com/mchoblet/paleoda_sa/tree/main (data_preprocessing). The SPEI drought index has ben computed from modeled precipitation and temperature using Thornthwaite's method (using the Climate Indices package, https://github.com/monocongo/climate_indices). Manuscript revision in July 2024: <ul> <li>Added historical documentary indices time series and the Puyehue lake record. For technical reasons in the PaleoDA algorithm, it is kept apart from the other lake records. The reconstruction code on Github has been updated for including these datasets.</li> </ul>         <div> </div>

opencc-by-4.0May 2018View details →

Calibration of test diameter and area as proxies for body size in the planktonic foraminifera Globoconella puncticulata

Here we provide an extensive image library of Globoconella puncticulata, with accompanying 2D and 3D coordinate data and morphometric measurements.  This data was generated using high-throughput imaging methods (AutoMorph) developed in P.M. Hull's lab at Yale University. This dataset accompanies the manuscript: Brombacher, J.A., Elder, L.E., Hull, P.M., Wilson, P.A. and Ezard, T.H.(In Press) Calibration of test diameter and area as proxies for body size in the planktonic foraminifera Globoconella puncticulata. Journal of Foraminiferal Research. The manuscript describes important details related to data collection and usage and should be consulted before using the data provided here.  Samples were obtained from three sites in the Atlantic Ocean: equatorial Ocean Drilling Program (ODP) Site 925, subtropical ODP Site 659, and mid-latitude Integrated Ocean Drilling Program (IODP) Site U1313. 1233 individual foraminifera of the species Globoconella puncticulata were picked from these samples to be imaged. Nine slides of microfossils were imaged at multiple focal heights (z-planes; 31.1um step distance) using a light microscope with an automated stage and processed with the image processing models of AutoMorph. AutoMorph software and tutorials can be accessed here: https://github.com/HullLab. For an example of a raw slide scan see: Hsiang, Allison Y., Nelson, Kaylea, Elder, Leanne E., Liu, Yusu, & Hull, Pincelli M. (2016). Slide scan example for Automorph. Zenodo. http://doi.org/10.5281/zenodo.167557. Slides were named with the IODP or ODP site number. Each slide was imaged with the foraminifera arranged in 2-3 orientations (i.e., umbilical, spiral, and/or edge). One of the nine slide was imaged with both light and computed tomography in order to compare the volumetric data obtained from the two approaches. This slide had 6 individual foraminifera. All individuals imaged with this combination of approaches have ‘CTscan’ included in the file name. This AutoMorph/CT scanned slide was imaged from three orientations (umbilical, spiral, and edge) and with two z-step distances (distance between imaged focal planes on the z-axis) of 11.2 um and 31.31 um. Images and morphometric data are provided in 9 datasets detailed below. Do note: our slide scanning technique often identifies background light scatter and/or other slide debris (glue, shell fragments, etc.) as ‘objects’, and these objects are numbered in sequence. We have excluded all non-foraminiferal objects from the datasets below, so the object numbers of the foraminifera will often be discontinuous (i.e.: 2,3,4,10,11,16). 1) 2d_coordinates.tar provides the 2D coordinates of each successfully extracted orientation from the 1233 individual Globoconella puncticulata (2811 total successfully extracted orientations) in a single csv (all2dcoordinates.csv). 2d_coordinates.tar also provides a csv for each slide scan at a particular orientation (26 slide scans:  4 samples imaged in 3 orientations, 4 samples imaged in 2 orientations, and 1 sample imaged from 3 orientations with two different 2 Z-step sizes per orientations (i.e., 6 scans for the one sample)). 2) 2dmorph_data_all.tar contains all Globoconella puncticulata with 2D measurements extracted by the AutoMorph routine run2morph (2811 total successfully extracted orientations), and a text file listing all objects with failed 2D extractions and non-forminiferal objects. 3) 2d_outline_check.tar provides an overlay of the extracted 2D outline on the Globoconella puncticulata EDF for quality control purposes for all extracted Globoconella puncticulata (2811 total successfully extracted orientations). 5) 3d_obj_files.tar provides directories for each slide scan with the 3D mesh coordinates as obj files for each extracted Globoconella puncticulata (2270 total successfully extracted orientations). Note: more 3D extractions failed than 2D extractions, accounting for the difference in the number of 2D extractions (2811) and 3D extractions (2270). 6) 3d_pdfs.tar provides directories of each slide scan with the 3D pdfs of each Globoconella puncticulata extracted (2270 total successfully extracted orientations) for quality control purposes. 3D pdfs, meshes and shape measurements were generated by the AutoMorph module run3dmorph. Note that only some pdf viewers are able to display 3d pdfs properly.  4) 3dmorph_data.tar contains a csv file for each slide scan with the 3d measurements generated for each Globoconella puncticulata by the AutoMorph module run3dmorph (2270 total successfully extracted objects in 26 directories representing each slide scan at a particular orientation). 7) object_ edf_images.tar contains the extended depth of focus (EDF)images in 26-directories for each slide scan at a particular orientation. The EDFs are 2D image composites created from the z-stacked photographic images by the AutoMorph focus module. Together, the 26-directories contain 2811 total images representing the successfully extracted 2D orientations. 8) sampleID.csv is a csv of all sample information. This includes the Slide name for the physical slide each sample is on, the Object number on that slide scan for each foraminifera used in the study, and the Ocean Drilling Program information for each object. Ocean Drilling Program details consist of the Leg: the Leg number for the drilling cruise, Site: the Ocean Drilling Program collection site number, the Hole:  the drilling hole ID, the Core: the Core number from that drilling site, the core Type: the type of drilling equipment used (H for all these samples which is an advanced hydraulic piston core), the Section: the section number on the core, and the Top and Bottom: the sample top and bottom interval in cm from the top of the section.  9) slide_images_boxed.tar contains one image for each slide view at a particular orientation 26 slide scans:  4 samples imaged in 3 orientations, 4 samples imaged in 2 orientations, and 1 sample imaged from 3 orientations with two different 2 Z-step sizes per orientations (i.e., 6 scans for the one sample). A red box delineates each object extracted using the AutoMorph segment module. Slides are named according to their ocean drilling sample identification (see dataset #10). 10) z-stacks.tar.gz contains the original z-stack images of each Globoconella puncticulata (2811 total representing the successfully extracted 2D orientations) in 26 directories representing each slide scan at a particular orientation).

opencc-by-4.0Oct 2018View details →

Raw data sets from Jones et al. 2018 QSR publication: A multi-proxy approach to understanding complex responses of saltlake catchments to climate variability and human pressure: A Late Quaternary case study from south-eastern, Spain

Attached are the raw data sets containing the pollen data, DXR, Grain size and C14 ages from the recent publication: Jones et al. 2018 QSR publication: A multi-proxy approach to understanding complex responses of saltlake catchments to climate variability and human pressure: A Late Quaternary case study from south-eastern, Spain. Note that these data sets do contain hiatuses and a major age-reversal due to erosian which have likely been caused by increased seasonal wetness at the onset of the Holocene. A full explanation is provided in our 2018 publication. If you do wish to use the data, it is essential that you read the publication inorder to interpret the results correctly. We also require that when using this data that you correctly cite it (Bibliographic reference and the doi number of the data set). There were some problems uploading the XRF (geochemical) data sets, so I haven't included these yet, but hopefully will do eventually.  Below I have also included the abstract from our publication, which provides an overview of the purpose of our work and a brief summary of the main findings. Abstract of Jones et al. 2018: The article focuses on a former salt lake in the upper Vinalopo Valley in south-eastern Spain. The study spans the Late Pleistocene through to the Late Holocene, although with particular focus on the period between 11 ka cal BP and 3000 ka cal BP (which spans the Mesolithic and part of the Bronze Age). High resolution multi-proxy analysis (including pollen, non pollen palynomorphs, grain size, X-ray fluorescence, and X-ray diffraction) was undertaken on the lake sediments. The results show strong sensitivity to both long term and small changes in the evaporation/precipitation ratio, affecting the surrounding vegetation composition, lake-biota and sediment geochemistry. To summarise the key findings the main general trends identified include: 1) Hyper-saline conditions and low lake levels at the end of the Late Glacial 2) Increasing wetness and temperatures which witnessed an expansion of mesophilic woodland taxa, lake infilling and the establishment of a more perennial lake system at the onset of the Holocene 3) An increase in solar insolation after 9 ka cal BP which saw the re-establishment of pine forests 4) A continued trend towards increasing dryness (climatic optimum) at 7 ka cal BP but with continued freshwater input 5) An increase in sclerophyllous open woody vegetation (anthropogenic?), and increasing wetness (climatic?) is represented in the lake record between 5.9 and 3 ka cal BP 6) The Holocene was also punctuated by several aridity pulses, the most prominent corresponding to the 8.2 ka cal BP event. These events, despite a paucity of well dated archaeological sites in the surrounding area, likely altered the carrying capacity of this area both regionally and locally, particularly during the Mesolithic-Neolithic transition, in terms of fresh water supply for human/animal consumption, wild plant food reserves and suitable land for crop growth.

opencc-by-4.0Sep 2019View details →

Proxies' response times measured by clients in an emulated community network

13 virtual nodes were deployed in Planetlab testbed (https://www.planet-lab.org) to emulate a small community network with 8 clients and 5 proxies. Each client probed all proxies every 10 seconds during two days. The same file (http://ovh.net/files/1Mb.dat) was requested in all probes. A probe was considered successful if the file was completely downloaded by the client. In this case, the response time was registered by the client, considering the time elapsed from the moment the client sent the request until the last byte of the response was received. This dataset contains the proxies' response times that were measured by clients in sucessful probes.

opencc-by-4.0Dec 2012View details →

Fig. 7 in Testate Amoebae as Proxy for Water Level Changes in a Brackish Tidal Marsh

Fig. 7. Graphs of observed versus estimated Elevation and Normalized elevation, predicted by the transfer function based on Jack-knifed WA-PLS (component 2) for the complete dataset, after the removing of outliers and for the partial dataset.

opencc-by-4.0Dec 2012View details →

Fig. 1. A in Testate Amoebae as Proxy for Water Level Changes in a Brackish Tidal Marsh

Fig. 1. A – map of the Scheldt estuary with location of Groot Buitenschoor; B – map of the brackish tidal marsh Groot Buitenschoor with indication of vegetation zones and the elevation transects that are sampled; C – photos of the two sampled transects. Photo 1 – from Salix to outer edge of Phragmites australis vegetation; Photo 2 – from Phragmites australis to outer edge of Scirpus maritimus.

opencc-by-4.0Dec 2012View details →

Fig. 6 in Testate Amoebae as Proxy for Water Level Changes in a Brackish Tidal Marsh

Fig. 6. Results of the partial RDA for both intertidal (zone B) and supratidal (zone A) bio-zones. The values in the intersection of the circle are the common variation explained by the two variables.

opencc-by-4.0Dec 2002View details →

Fig. 7. Trace element environmental proxies for the F–F in The Frasnian-Famennian events in a deep-shelf succession, Subpolar Urals: biotic, depositional, and geochemical records

Fig. 7. Trace element environmental proxies for the F–F transition in the Syv'yu River section. Bio−productivity tracers* are normalized according to Schmitzetal.(1997).DownwardarrowedtrendsarebasedonthesinglesampleCB99−222,located2.15mbelow;recognizedMo/Alenrichment,indicative of anoxic−sulfidic deposition, is shown as well. For explanations see Fig. 4.

FIGURE 2 in Big-headed marine crocodyliforms and why we must be cautious when using extant species as body length proxies for long-extinct relatives

FIGURE 2. Comparative view of three fossil thalattosuchian crocodylomorphs: (1) teleosaurid Platysuchus multiscrobiculatus SMNS 9930; (2) basal metriorhynchoid Pelagosaurus typus MTM M62 2516; and (3) metriorhynchid Cricosaurus suevicus SMNS 9808. Scale bars equal 50 cm.

FIGURE 1 in Big-headed marine crocodyliforms and why we must be cautious when using extant species as body length proxies for long-extinct relatives

FIGURE 1. Comparative view of four fossil teleosaurid crocodylomorphs used in the regression analyses: (1) Steneosaurus bollensis GPIT/RE/1193/2; (2) Steneosaurus priscus MNHN.F CNJ 78a; (3) Steneosaurus bollensis MH unnumbered A; and (4) Steneosaurus bollensis MH unnumbered B. Scale bars equal 100 cm.

FIGURE 4 in Big-headed marine crocodyliforms and why we must be cautious when using extant species as body length proxies for long-extinct relatives

FIGURE 4. Comparative least-squares regression gradient plot, of cranial length-to-total length, with the solid line representing Teleosauridae, and the dashed lines representing (1) Crocodylus, (2) Alligator, (3) Gavialis, and (4) Metriorhynchidae, respectively.

FIGURE 5 in Big-headed marine crocodyliforms and why we must be cautious when using extant species as body length proxies for long-extinct relatives

FIGURE 5. Comparative view of estimated body length of large-bodied teleosaurids (see Table 8). (1) Machimosaurus rex (holotype); (2) Machimosaurus hugii (referred specimen from Krebs, 1968); (3) Machimosaurus mosae (neotype, grey silhouette is the lost holotype); (4) Machimosaurus buffetauti (holotype, grey silhouette is the specimen from Buffetaut, 1982b); (5) Steneosaurus edwardsi (referred specimen from Johnson et al., 2015); (6) Steneosaurus obtusidens (holotype); (7) Steneosaurus bollensis (based on MH unnumbered A). The skull drawings are modified from (Fanti et al., 2016 and Young et al., 2014). Scale bar equals 1 m.

FIGURE 3 in Big-headed marine crocodyliforms and why we must be cautious when using extant species as body length proxies for long-extinct relatives

FIGURE 3. Bivariate plots of cranial (1, 3) and femoral lengths (2, 4) plotted against total lengths for complete specimens only (1, 2) and for all specimens (3, 4). In each case a line of least-squares regression is fitted along with a shaded area representing the confidence interval around the regression model.

Fig. 17 in Three-dimensional micro- and nanostructural characteristics of the scleractinian coral skeleton: A biocalcification proxy

Fig. 17. Idealized and representing two extremes, three−dimensional models of septal microstructures in corals with fibrous skeletal tissue. First extreme model (A), shows perfect continuity between organo−mineral phases of dRAF and TD regions, whereas the second extreme model (B) shows consistent discontinuity of these phases in longitudinal, perpendicular to septal plane section. Real specimens (e.g., Figs. 3E–H, 5B) usually have some regions with dRAF and TD layers continuing, and some parts where these layers discontinue. Left to A, longitudinal section through RAF plane. Septal surfaces in the RAF zone may have "microcrystalline" texture (if a snapshot were taken during formation of the mineral phase); "microcrystals" represent exposed fiber tips (fasciculi of Wise 1972) of organic−depleted zones (circle on right of A).

Fig. 16. The rugosan Endotheciumdecipiens Koker, 1924 in Three-dimensional micro- and nanostructural characteristics of the scleractinian coral skeleton: A biocalcification proxy

Fig. 16. The rugosan Endotheciumdecipiens Koker, 1924. Here re−illustrated from Schindewolf's (1942: fig. 7). Lower Upper Permian (Basleo−Schichten), Basleo, Timor. "Transverse" section of corallum (A) with septa in axial region (B) showing alternation of layers of fibers (white) and areas infilled by dark (?iron−manganese rich) minerals (see also footnote 2). TLM view.

Fig. 15. A. Pachythecalis major Cuif, 1975, ZPAL H.23 in Three-dimensional micro- and nanostructural characteristics of the scleractinian coral skeleton: A biocalcification proxy

Fig. 15. A. Pachythecalis major Cuif, 1975, ZPAL H.23/10. Triassic, Lower Norian. Alakir Çay,Turkey. Transverse polished corallite in TLM (A1); enlargement of dRAF (A2). A3. Transverse polished pachytheca in TLM; fibers show faint regular (ca. 7 µm) alternations of lighter and darker zones. B. Zardinophyllum zardini Montanaro−Gallitelli, 1975. Triassic (Middle Carnian), San Cassiano Beds, Alpe di Specie, Dolomiti (Italy). Completely smooth RAF of septum in distal view, IPUM11 (B1, SEM). B2. Transverse, polished and etched septum (ZPALH.23/11); note fissure in dRAF region (arrow), more or less regular discontinuities in arrangement of pachytheca fibers (arrows), and secondary, probably biogenic deposits filling up the calice (marked transparent dark grey). All coralla with still preserved aragonitic mineralogy.

Fig. 14. Pachysolenia cylindrica Cuif, 1975 in Three-dimensional micro- and nanostructural characteristics of the scleractinian coral skeleton: A biocalcification proxy

Fig. 14. Pachysolenia cylindrica Cuif, 1975, ZPALH. XXI/4. Triassic, Lower Norian. Alakir Çay,Turkey. A–C. Complementary regions of transversely sectioned and polished pachytheca: TLM image (A), greyscale Sr (B) and Mg (C) mapping acquired on the electron microprobe by wavelength−dispersive techniques; darker areas equal very low concentration whereas lighter areas equal slightly higher concentrations. Sr (in B) shows enrichment, at least in some regions (arrows) where Mg (in C) appears depleted. Sr mapping of diagenetically non−altered fibrous parts of coralla of extant corals (not illustrated here) invariably shows nearly homogenous distribution of this element. D. TLM view of longitudinally sectioned pachytheca and septum; part of the preserved septum encircled and enlarged in E to show "non−trabecular" nature of dRAF. F. Transverse polished section of pachytheca in TLM; fibers show faint regular 5–8 µm alternations of lighter and darker zones. G. Homogenous septal dRAF zone in SEM view of transversely polished and etched section. H. Transverse polished and etched section of pachytheca (SEM); fibrous skeleton shows negative and positive etching relief (at ca. 5–8 µm distance).

Fig. 13.Stylophyllumparadoxum Frech, 1890, NHMW 1982 in Three-dimensional micro- and nanostructural characteristics of the scleractinian coral skeleton: A biocalcification proxy

Fig. 13.Stylophyllumparadoxum Frech, 1890, NHMW 1982/57/100, corallum with aragonitic mineralogy still preserved. Triassic, Rhaetian, Fischerwiese, Northern Calcareous Alps, Austria. A, B. Transverse section of septa with concentric arrangement of fibers within septal spines (B, enlargement). C–F. Longitudinal sections crossing centers of septal spines; domed, successive layers of aragonite fibers (darker) separated by lighter "voids" infilled by spar (see D, F enlargements). Except for regular voids in spine centers, there is no difference in organization of superimposed layers of fibers within septal spine. All TLM micrographs.

Fig. 5. Flabellum chunii Marenzeller, 1904 in Three-dimensional micro- and nanostructural characteristics of the scleractinian coral skeleton: A biocalcification proxy

Fig. 5. Flabellum chunii Marenzeller, 1904. Recent, Great Meteor Seamount, SEAMOUNT2 (1993), DW 152 (January 11, 1993), 30°02.00'N, 28°22.10'W, 470 m. A. Septa and inner side of wall (A1) thickened by fibers arranged in scale−like units (A2, enlargement); ZPALH.23/2/1. B. Marginothecal wall sectioned longitudinally (large white arrow); layers of successive growth increments (dRAF) continue in wall "stereome", i.e.,TD (small white arrows); ZPAL H.23/2/2. C. Septum longitudinally sectioned in RAF plane. Dissolved or etched components of RAF form narrow "strands" (C2 enlargement); ZPALH.23/2/3. D. Transverse polished and etched section of septum; dRAF zone composed of neighboring dCRA (D1) is from both sides covered with layers of TD fibers (D2) which direction conform to that of scale−like units (i.e., semi−parallel to RAF); ZPALH.23/2/4. All SEM; growth direction within skeletal element i ndicated by black arrow in B.

Fig. 12. Undetermined conophylliid. ZPALH.23 in Three-dimensional micro- and nanostructural characteristics of the scleractinian coral skeleton: A biocalcification proxy

Fig. 12. Undetermined conophylliid. ZPALH.23/9. Triassic (Middle Carnian), San Cassiano Beds, Alpe di Specie, Dolomiti (Italy), corallum still wi th aragonitic mineralogy preserved. B. Transverse polished section of corallite in TLM (A); enlarged portions of longitudinally sectioned septa with regular growth increments of fibers (B). C. Longitudinally polished and etched section of septum with fibers regularly tapered (SEM). D. Transverse, polished and etched septum (SEM) with dCRA ("center of calcification", arrows). E. Septum longitudinally sectioned in dCRA region with domed, successive layers of fibers and occasional (arrow) larger voids between them.