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764 results for “Foraminifera”
The FORCIS database: A global census of planktonic Foraminifera from ocean waters
<p>The FORCIS (Foraminifera Response to Climatic Stress) database is a synthesis grouping datasets on living planktonic foraminifera. We assembled foraminiferal diversity and distribution data in the global oceans from 1910 until 2018, curating published and unpublished datasets. This database includes data collected using plankton tows, continuous plankton recorder, sediment traps and plankton pump from the global ocean.</p> <p>The FORCIS database version 01 is composed of 5 files (“.csv” format). All data coming from different sampling devices were put into separate “.csv” files. Only the data of the CPR from the Southern Hemisphere have been separated from the Northern Hemisphere CPR data as the data structure is not the same (species counts resolved vs. binned total counts, respectively). </p> <p>Apart from the file of CPR data from the Northern Hemisphere that contains only metadata and binned total counts, all the remaining four files contain 4 blocks:</p> <ul> <li> <p>Block 1: metadata (from column 1 to 71)</p> </li> <li> <p>Block 2: original counts (from column 72 to 274)</p> </li> <li> <p>Block 3: generated counts based on the validated taxonomy (from column 275 to 331). We added “_VT” to each species name to distinguish it from other taxonomy levels. E.g. “g_bulloides” became “g_bulloides_VT”. The number of species counted per subsample is also reported in the column “number_of_species_counted_VT”</p> </li> <li> <p>Block 4: generated counts based on the lumped taxonomy (from column 332 to 379). In this case, we added “_LT” to each species name. E.g. “n_dutertrei” became “n_dutertrei_VT”. We also calculated the number of species counted per subsample and reported it in the column “number_of_species_counted_LT”</p> </li> </ul> <p>Foraminifera abundance data counts are reported in different categories in the blocks 1,2 and 3 and described in the table below:</p> <table> <tbody> <tr> <td> <p><strong>count_type</strong></p> </td> <td> <p><strong>unit</strong></p> </td> </tr> <tr> <td> <p>Absolute</p> </td> <td> <p>ind/m3</p> </td> </tr> <tr> <td> <p>Relative</p> </td> <td> <p>%</p> </td> </tr> <tr> <td> <p>Raw</p> </td> <td> <p>number of individuals</p> </td> </tr> <tr> <td> <p>Fluxes</p> </td> <td> <p>ind/m2/day</p> </td> </tr> <tr> <td> <p>Bin_Absolute</p> </td> <td> <p>ind/m3</p> </td> </tr> <tr> <td> <p>Bin_Relative</p> </td> <td> <p>%</p> </td> </tr> <tr> <td> <p>Bin_Raw</p> </td> <td> <p>number of individuals</p> </td> </tr> <tr> <td> <p>Bin_Fluxes</p> </td> <td> <p>ind/m2/day</p> </td> </tr> </tbody> </table> <p> </p> <p>For more details about the FORCIS database column description, please check the data descriptor paper <strong>Chaabane et al. (2023) (https://doi.org/10.1038/s41597-023-02264-2).</strong></p> <p>The database is kept open for any new entries and the updated version will be released in csv format. The labels of updated versions of the released “.csv” files will contain the date of their publication and versioning number.</p>
A global synthesis of high-resolution stable isotope data from benthic foraminifera of the last deglaciation
<p>In paleoceanography, carbon and oxygen stable isotope ratios from benthic foraminifera are used as tracers of physical and biogeochemical properties of the deep ocean. We present the first version of the Ocean Carbon Cycling working group database, of stable isotope ratios of oxygen and carbon from benthic foraminifera from deep ocean sediment cores from the Last Glacial Maximum (LGM, 23-20 ky before present (BP)) to the Holocene (<10 ky BP) with a particular focus on the early last deglaciation (20-15 ky BP). It includes 287 globally distributed coring sites, with metadata, isotopic and chronostratigraphic information, and age models. A quality check was performed for all data and age models. Sites with at least millennial resolution were preferred, because the main goal is to resolve ocean changes associated with the last deglaciation on at least millennial timescales. Software tools were produced to access and analyze the data, and are included with this publication. Deep water mass structure as well as differences between the early deglaciation and LGM are captured by the data in the compilation, even though its coverage is still sparse in many ocean regions. We find high correlations among time series calculated with different age models at sites that allow such analysis. The database provides a useful dynamical approach to map physical and biogeochemical changes of the ocean throughout the last deglaciation.</p>
On the validity of foraminifera-based ENSO reconstructions
<p>Video of model run. Calculated oxygen isotope values of three species of planktonic foraminifera (<span class="math-tex">\( \delta^{18}O_c\)</span>) using the Foraminifera as modeled entities (FAME) module and Ocean Reanalysis data temperature and salinity data. Upper panel represents the Oceanic Nino Index (ONI) used to determine the ocean state for each monthly time step, lower panels the <span class="math-tex">\( \delta^{18}O_c\)</span> for each individual species of planktonic foraminifera (<em>G. ruber</em>; <em>G. sacculifer</em> and <em>N. dutertrei</em>).</p>
caseysaenger/ForamMgCa_PSM: files and scripts for revised version of manuscript "Calibration and validation of environmental controls on planktic foraminifera Mg/Ca using global core-top data".
<p>files and scripts for revised version of manuscript "Calibration and validation of environmental controls on planktic foraminifera Mg/Ca using global core-top data". Saenger, C. and M. N. Evans. Resubmitted to Paleoceanography and Paleoclimatology, May 3, 2019.</p>
Gulf of Mexico planktonic foraminifera and stable isotope data from core EN-032-18PC spanning MIS 9 to MIS 5
<p><em>Database of the accepted manuscript</em>: Arellano-Torres et al., 2023. The Loop Current circulation over the MIS 9 to MIS 5 based on planktonic foraminifera assemblages from the Gulf of Mexico. Paleoceanography and Paleoclimatology, DOI: 10.1029/2022PA004568</p> <p>In the sediment Core EN-032-18PC collected below the influence of the Loop Current in the eastern Gulf of Mexico, we studied mixed layer conditions and the intensity of the surface and subsurface waters flowing from the Caribbean to the gulf. This database includes analyses of 136 samples in three Supplementary Tables. (Table S1) Bulk sediment and sand fraction (>62 μm) weight (g), the absolute abundance (tests per sample) of 33 species of planktonic foraminifera. (Table S2) Relative abundance (%) of planktonic foraminifera and factor loadings of two factors (Q-mode factor analysis). (Table S3) Stable isotopes (δ<sup>18</sup>O-PDB and δ<sup>13</sup>C-PDB) (‰) of <em>Globigerinoides ruber</em> (white) and the loess-smoothing of the series with polynomial regression.</p>
Data from: An extinction event in planktonic Foraminifera preceded by stabilizing selection
Unless they adapt, populations facing persistent stress are threatened by extinction. Theoretically, populations facing stress can react by either disruption (increasing trait variation and potentially generating new traits) or stabilization (decreasing trait variation). In the short term, stabilization is more economical, because it quickly transfers a large part of the population closer to a new ecological optimum. However, canalization is deleterious in the face of persistently increasing stress, because it reduces variability and thus decreases the ability to react to further changes. Understanding how natural populations react to intensifying stress reaching terminal levels is key to assessing their resilience to environmental change such as that caused by global warming. Because extinctions are hard to predict, observational data on the adaptation of populations facing extinction are rare. Here, we make use of the glacial salinity rise in the Red Sea as a natural experiment allowing us to analyse the reaction of planktonic Foraminifera to stress escalation in the geological past. We analyse morphological trait state and variation in two species across a salinity rise leading to their local extinction. One species reacted by stabilization in shape and size, detectable several thousand years prior to extinction. The second species reacted by trait divergence, but each of the two divergent populations remained stable or reacted by further stabilization. These observations indicate that the default reaction of the studied Foraminifera is canalization, and that stress escalation did not lead to the emergence of adapted forms. An inherent inability to breach the global adaptive threshold would explain why communities of Foraminifera and other marine protists reacted to Quaternary climate change by tracking their zonally shifting environments. It also means that populations of marine plankton species adapted to response by migration will be at risk of extinction when exposed to stress outside of the adaptive range.
Sixty-one thousand Recent planktonic foraminifera from the Atlantic Ocean
<p>Here we provide an extensive image library of Recent microfossils (primarily planktonic foraminifera) from the Atlantic Ocean, with accompanying 2D and 3D coordinate data and morphometric measurements. This data was generated using high-throughput imaging methods (<em>AutoMorph</em>) developed in P.M. Hull's lab at Yale University.</p> <p>The dataset consists of microfossils from 34 sediment samples, mounted on 155- micropaleontological slides, primarily from the North Atlantic Ocean <strong>(metadata_tables.tar.gz</strong>: Table 1). All slides are accessioned to the Yale Peabody Museum of Natural History (YPM) Division of Invertebrate Paleontology with unique YPM catalog numbers (metadata_tables.tar.gz: Table 2). Slides of microfossils were imaged at multiple focal heights (z-planes) using a light microscope with an automated stage and processed with the image processing models of <em>AutoMorph</em> as detailed in Table 2. <em>AutoMorph</em> software and tutorials can be accessed here: https://github.com/HullLab. For an example of a raw slide scan see: Hsiang, Allison Y., Nealson, Kaylea, Elder, Leanne E., Liu, Yusu, & Hull, Pincelli M. (2016). Slide scan example for Automorph. Zenodo. http://doi.org/10.5281/zenodo.167557. </p> <p>124,230 unique objects (primarily microfossils) were identified from the 155 slides of 34 sediment samples, and were classified into 16 object categories (metadata_tables.tar.gz: Table 3). Object classification is provided in Table 3 and summarized in Table 4 (metadata_tables.tar.gz). Table 5 in metadata_tables.tar.gz provides a technical validation of the automated 2D morphometric measurements; comparable data validation for the 3D morphometric measurements are provided in Hsiang et al. 2016 (http://dx.doi.org/10.1098/rstb.2015.0227).</p> <p>Images and morphometric data are provided in 12 additional datasets:</p> <p><strong>1) slide_images.tar.gz</strong> contains one image for each slide scanned in this study (155 slides), with a red box around each object extracted using the <em>AutoMorph</em> segment module. Slides are named according to their YPM catalog number and related sample and site information can be found in Tables 1 and 2 (metadata_tables.tar.gz), and in the YPM database (http://collections.peabody.yale.edu/search/) by YPM catalog number. </p> <p><strong>2) edf_images.tar.gz</strong> contains the extended depth of focus images (EDF: a 2D image composite created from multiple z-stacked photographic images) generated by the <em>AutoMorph</em> focus module for each of the 124,230 individual objects identified by segment.</p> <p><strong>3 & 4) obj_zstacks_part1.tar.gz</strong> and <strong>obj_zstacks_part2.tar.gz</strong> contain the original zstack images of each object. 2D outlines and shape measurements for each object are extracted using the<em> AutoMorph</em> module run2dmorph. </p> <p><strong>5) 2d_outline_check.tar.gz</strong> provides an overlay of the extracted 2D outline on the object EDF for quality control purposes for all extracted objects (113,847 objects) and a text file of all objects with failed 2D extractions (10,384 objects).</p> <p><strong>6) 2d_coordinates.tar.gz</strong> provides the 2D coordinates of each object in a single csv (all_coordinates.csv) and by slide (155 csv files named according to YPM catalog number), and a text file of all objects with failed 2D extractions (10,384 objects).</p> <p><strong>7) shape_measurements.csv</strong> contains the complete list of all objects in the dataset (124,230 objects) with the 2D and 3D measurements extracted by the<em> AutoMorph</em> routines run2morph and run3dmorph when available.</p> <p><strong>8 & 9) 3d_pdfs_part1.tar.gz</strong> and <strong>3d_pdfs_part2.tar.gz</strong> provide 3D pdfs of each 3D object extracted (109,207 objects) for quality control purposes and a text file of all objects with failed 3D extractions (15,023 objects). 3D pdfs, meshes and shape measurements were generated by the <em>AutoMorph</em> module run3dmorph. Note that only some pdf viewers are able to display 3d pdfs properly. </p> <p><strong>10-12) 3d_obj_files_part1.tar.gz</strong>, <strong>3d_obj_files_part2.tar.gz</strong>, and <strong>3d_obj_files_part3.tar.gz</strong> provide the 3D mesh coordinates as obj files for each extracted object and a text file of all objects with failed 3D extractions (15,023 objects).</p> <p>This dataset accompanies the manuscript "Sixty-one thousand Recent planktonic foraminifera from the Atlantic Ocean" submitted to <em>Scientific Data</em>. The manuscript describes important details related to data collection and usage and should be consulted before using the data provided here. One key note about this dataset is repeated here as a precaution. We provide image classification for only 4/5<sup>th</sup>s of the complete data set. A random subset (1/5<sup>th</sup> of the classifications) are excluded as a test set, so that this image database can be used in machine learning.</p>
FIG. 3 in First record of the new Neoplanorbulinid species (Foraminifera) from the Early Oligocene in Turkey, Malatya Basin, Eastern Taurids
FIG. 3. — Generalized stratigraphy of Cenozoic deposits in the Malatya Basin (modified from Karaman et al. 1993).
Figure 5 in A new genus of xenophyophores (Foraminifera) from Japan Trench: morphological description, molecular phylogeny and elemental analysis
Figure 5. Inductively coupled plasma mass spectrometry (ICPMS) values for the composition of the total fragment and different structural parts of Shinkaiya lindsayi gen. et sp. nov. (total fragment), and of the environmental sediment. The mass of elemental aluminium (Al), lead (Pb), magnesium (Mg), uranium (U), barium (Ba), strontium (Sr), and mercury (Hg), per gram of dry material, is shown. A semiquantitative method has been used for Pb, U, and Hg.
Figure 4 in A new genus of xenophyophores (Foraminifera) from Japan Trench: morphological description, molecular phylogeny and elemental analysis
Figure 4. Phylogenetic position of Shinkaiya lindsayi gen et sp. nov. among Foraminifera, based on complete small-subunit ribosomal DNA (SSU rDNA) gene sequences. The tree was obtained using the maximum-likelihood method with the general time-reversible (GTR + G + I) model, with four rates categories, and 1000 replicates for bootstrap analysis. Only bootstrap support values higher than 70% are indicated.
Figure 3 in A new genus of xenophyophores (Foraminifera) from Japan Trench: morphological description, molecular phylogeny and elemental analysis
Figure 3. Shinkaiya lindsayi gen. et sp. nov. A, scanning electron micrograph (SEM) of an open tube, showing its inner surface with many radiolarian tests, a granellare string (right-hand arrow), and a stercomare string (left-hand arrow). B, SEM image of an open stercomare string, containing stercomata (spherical pellets). C, SEM image of the organic sheath of the granellare. D, SEM image showing details of the external surface of the test, with agglutinated material. E, F, transmission electronic microscopy (TEM) images of a stercomare section, showing its wall (W), stercomata (S), and cytoplasm (C). Scale bars: 100 Mm (A), 10 Mm (B–D), 2 Mm (E), 1 Mm (F).
Figure 1 in A new genus of xenophyophores (Foraminifera) from Japan Trench: morphological description, molecular phylogeny and elemental analysis
Figure 1. Schematic representation of the small-subunit ribosomal DNA (SSU rDNA) sequence of Shinkaiya lindsayi gen. et sp. nov., showing the conserved regions, as well as the largest insertion and primers used for DNA amplifications.
Figure 2 in A new genus of xenophyophores (Foraminifera) from Japan Trench: morphological description, molecular phylogeny and elemental analysis
Figure 2. Shinkaiya lindsayi gen. et sp. nov. A, holotype specimen in its push core, just after collection (the authors assumed that this was a whole specimen, almost unbroken by the corer tube). B, holotype specimen out of its core. C, D, microscopic views of fragments, revealing the internal organization (G, granellare; S, stercomare). C, transversal view showing the dark stercomare strings. D, the fragment is open along a longitudinal axis, displaying the obvious whitish granellare and the stercomare. E, F, fragments of granellare stained with diaminidophenylindol (DAPI), revealing thousands of nuclei in the cytoplasm. Scale bars: 15 mm (A), 15 mm (B), 250 Mm (C), 500 Mm (D), 250 Mm (E), and 30 Mm (F).
Fig. 1 in Pseudocyclammina Sarvakensis Sp. Nov. And Pseudotextulariella Brevicamerata Sp. Nov.: Further Evidence For The Cenomanian Megadiversity Of Larger Benthic Foraminifera From The Sarvak Formation Of Sw Iran
Fig. 1 Number of agglutinated foraminiferal genera (small and large taxa) in each geological stage (modified from Kaminski et al., 2008, fig. 1).
Fig. 5 in Pseudocyclammina Sarvakensis Sp. Nov. And Pseudotextulariella Brevicamerata Sp. Nov.: Further Evidence For The Cenomanian Megadiversity Of Larger Benthic Foraminifera From The Sarvak Formation Of Sw Iran
Fig. 5 Lower and Upper Cretaceous (Cenomanian) species of Pseudotextulariella Barnard, 1953. a-i, k Pseudotextulariella brevicamerata sp. nov., middle Cenomanian Sarvak Formation of SW Iran, Tang-e Darbast section (a-i) and Arman well-1 (k), thin-sections RAP 188 and AMN 3173.49 m. a, h-i Tangential sections. b, d-e, g Subaxial section, holotype specimen in e. c, k Oblique sections. f Fragmentary transverse section. j, l Pseudotextulariella courtionensis Brönnimann, 1967, Valanginian of Switzerland (from Brönnimann, 1967, pl. 1, figs. 1 and 5). m-n Pseudotextulariella cretosa (Cushman, 1932), transverse and axial sections (from Brönnimann, 1967, pl. 3, figs. 2 and 5). Abbreviations: b = beam, cha = chamber, fo = foramen, ib = intercalary beam, r = rafter, s = septum.
Fig. 3 in Pseudocyclammina Sarvakensis Sp. Nov. And Pseudotextulariella Brevicamerata Sp. Nov.: Further Evidence For The Cenomanian Megadiversity Of Larger Benthic Foraminifera From The Sarvak Formation Of Sw Iran
Fig. 3 Lithostratigraphic log of the Tang-e Darbast section, the type locality of Pseudocyclammina sarvakensis sp. nov and Pseudotextulariella brevicamerata sp. nov., showing the distribution of some (larger) benthic foraminifera. a Neoiraqia insolita (Decrouez & Moullade), b Orbitolinopsis cenomaniensis Schlagintweit & Yazdi-Moghadam, c Conicorbitolina cf. conica (d'Archiac), d Mesorbitolina aperta (Erman), e Orbitolina ex gr. concava (Lamarck), f Rotorbinella mesogeensis (Tronchetti), g Nezzazata gr. gyra-conica (Smout), h Decastroia cf. serrakieli Vicedo & Piuz, i Myriastyla omanensis Piuz, Meister & Vicedo, j Chrysalidina gradata Orbigny, k Iraqia ultima Yazdi-Moghadam & Schlagintweit.
Fig. 3 in Upper Cretaceous Foraminifera Murgeina Apula (Luperto Sinni, 1968): A Methusalem And Cenomanian-Turonian Boundary Survivor Taxon
Fig. 3 Lithological log of the Maymand section with distribution of larger benthic foraminifera (including Murgeina apula Luperto-Sinni) (after Schlagintweit & Yazdi-Moghadam, 2020). a Nezzazata gr. gyra-conica (Smout), b Nezzazata simplex Omara, c Murgeina apula (Luperto-Sinni), d Orbitolina gr. concava Orbigny, e Rajkanella hottingerinaformis Schlagintweit & Rigaud, f Biconcava bentori Hamaoui & Saint-Marc, g Praealveolina simplex Reichel, h Chrysalidina gradata Orbigny, i Cisalveolina fraasi (Gümbel), j Persiconus sarvaki Yazdi-Moghadam & Schlagintweit.
Fig. 2 a in Upper Cretaceous Foraminifera Murgeina Apula (Luperto Sinni, 1968): A Methusalem And Cenomanian-Turonian Boundary Survivor Taxon
Fig. 2 a Simplified geological map of Iran (modified after Schlagintweit & Yazdi-Moghadam, 2021) showing the main tectonic subdivisions. b-c Position of the studied sections. d Tectono-stratigraphic units of the Zagros belt (modified after Yazdi-Moghadam & Schlagintweit, 2021) with position of the Anneh section. Abbreviations: BF Balarud Fault, CEIM Central East Iran Microplate, HZF High Zagros Fault, KZF Kazerun Fault, MFF Mountain Front Fault, MZRF Main Zagros Revers Fault, MZT Main Zagros Thrust, SSZ Sanandaj-Sirjan Zone, UDMA Uromia Dokhtar Magmatic Arc, ZFTB Zagros Fold Thrust Belt.
Fig. 1 a-b in Large Benthic Foraminifera Pfendericonus Globulus Sirel & Deceviler In Sirel Et Al., 2020 (Priabonian Of Turkey): A Junior Synonym Of Pfendericonus Mindanaoensis Matsumaru, 2017 (Thanetian? Of The Philippine Archipelago)
Fig. 1 a-b Pfendericonus mindanaoensis (from Matsumaru, 2017, pl. 4, fig. 11, figured as Chrysalidina sp. and pl. 4, fig. 8, holotype specimen) of Selandian or Thanetian age from the Island of Mindanao, Philippine Archipelago. c-d Pfendericonus globulus Sirel & Deceviler (from Sirel et al., 2020, fig. 11I and 11J) from the Priabonian of NW Turkey.
Fig. 1 in Upper Cretaceous Foraminifera Murgeina Apula (Luperto Sinni, 1968): A Methusalem And Cenomanian-Turonian Boundary Survivor Taxon
Fig. 1 Nummofallotia cretacea (Schlumberger, 1900) from the Upper Cretaceous of Austria. a Equatorial section; Wegscheidgraben, Santonian Hochmoos Formation, Gosau Group (see Wagreich, 1988). b Slightly oblique axial section, same sample as a. Note the well-preserved light brownish porcelaneous wall. c Axial section showing test dissolution affecting the porcelaneous wall dissolution, while the radial fibrous umbo remains unaffected; Uppermost Maastrichtian Kambühel Limestone, Kambühel type-locality (see Tragelehn, 1996). Scale bars = 0.2 mm.
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