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98 results for “planktonic 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foraminiferal diversity and distribution data in the global oceans from 1910 until 2018, curating published and unpublished datasets.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>
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>
Figure 2 in Systematic taxonomy of the Trilobatus sacculifer plexus and descendant Globigerinoidesella fistulosa (planktonic foraminifera)
Figure 2. Hypothetical visualization of morphology in a single dimension. Trait morphology is normally distributed, whereby the mean morphology (solid vertical arrow) should form the type specimen. Morphospecies with high intraspecific variation may be represented by the dot-dashed distribution curve. Conversely, morphospecies with moderate and low intraspecific variation are represented by the dashed and dotted distribution curves, respectively. Finer taxonomic splitting results in more morphospecies with a narrow (dotted line) distribution curve. SD: standard deviation.
Figure 20 in Systematic taxonomy of the Trilobatus sacculifer plexus and descendant Globigerinoidesella fistulosa (planktonic foraminifera)
Figure 20. Example of circularity and curvature values for Globigerinoidesella fistulosa specimens. More lobate values are those in blue, those less lobate are red. Specimens 1 and 2 are more elongate and possess the lowest circularity values, but have a low perimeter length compared to test area and thus also generate low curvature values. Conversely, specimens 3 and 4 have high curvature values due to the protuberances increasing the perimeter length, but also relatively high circularity values because of the large area compared to test diameter (see Material and methods). Scale bar = 200 Lm.
Figure 15 in Systematic taxonomy of the Trilobatus sacculifer plexus and descendant Globigerinoidesella fistulosa (planktonic foraminifera)
Figure 15. Protuberance development from immaturus and quadrilobatus morphotypes resulting in fistulosa morphotypes (light microscope images). A, Trilobatus quadrilobatus (d'Orbigny, 1846); B, C, Trilobatus immaturus (LeRoy, 1939); D–F, Globigerinoidesella fistulosa (Schubert, 1910). A, ODP Site 1115, Woodlark Basin, western Pacific; 11H/04/25–27 cm (umbilical view). B, C, ODP Site 1115, Woodlark Basin, western Pacific; 11H/04/25–27 cm (umbilical view). D–F, ODP Site 1115, Woodlark Basin, western Pacific; 11H/04/25–27 cm (umbilical view). Scale bar = 100 Lm.
Figure 16 in Systematic taxonomy of the Trilobatus sacculifer plexus and descendant Globigerinoidesella fistulosa (planktonic foraminifera)
Figure 16. Size and ontogeny contrasts in the Trilobatus sacculifer plexus. A–D, Trilobatus sacculifer (Brady, 1877); E, Trilobatus trilobus (Reuss, 1850); F, Globigerinoidesella fistulosa (Schubert, 1910). A–D, GLOW-3, south-west Indian Ocean (A, D, spiral view; B, C, umbilical view, B is similar to subsacculifer morphospecies, see text). E, GLOW-3, south-west Indian Ocean (spiral view; earlier whorls obscured). F, ODP Site 1115, Woodlark Basin, western Pacific; 11H/04/25–27 cm (spiral view). Scale bars = 100 Lm.
Figure 1 in Systematic taxonomy of the Trilobatus sacculifer plexus and descendant Globigerinoidesella fistulosa (planktonic foraminifera)
Figure 1. Phylogenetic interpretations of the evolution of the Trilobatus sacculifer plexus. A, phylogeny of Banner & Blow (1960); B, phylogeny of Keller (1981) based on a stratophenetic investigation (average 12,000-year resolution sampling) of Deep Sea Drilling Project (DSDP) Site 292 (north-western Pacific Ocean); C, phylogeny of Srinivasan & Kennett (1981) and Kennett & Srinivasan (1983). Note that the original nomenclatural combinations (binomial and trinomial) used in the authors' separate phylogenies are retained for this figure.
Figure 22 in Systematic taxonomy of the Trilobatus sacculifer plexus and descendant Globigerinoidesella fistulosa (planktonic foraminifera)
Figure 22. Exponential relationship between maximum test size and test surface area in morphospecies of the Trilobatus sacculifer plexus, and to a lesser extent in Globigerinoidesella fistulosa. The T. sacculifer plexus morphospecies all show comparable relationships, whereas data for G. fistulosa show more scatter.
Figure 21 in Systematic taxonomy of the Trilobatus sacculifer plexus and descendant Globigerinoidesella fistulosa (planktonic foraminifera)
Figure 21. Lobateness of Trilobatus sacculifer plexus morphospecies and Globigerinoidesella fistulosa determined through a combination of circularity and curvature values; A, demonstrates the large variability, but consistently high lobateness values for Globigerinoidesella fistulosa compared to T. sacculifer plexus morphospecies (which have comparatively high circularity and low curvature). Although the T. sacculifer plexus morphospecies appear to form a tight cluster, the lower plot, B, demonstrates the variability in lobateness values (see text for discussion).
Figure 19 in Systematic taxonomy of the Trilobatus sacculifer plexus and descendant Globigerinoidesella fistulosa (planktonic foraminifera)
Figure 19. Surface area of the final chamber compared to the remaining test is expressed in the final chamber dominance ratio, which is plotted against maximum test diameter for Trilobatus sacculifer plexus morphospecies and Globigerinoidesella fistulosa. Trilobatus trilobus values are inherently ± 1 as this forms part of its morphospecies concept (see text).
Figure 18 in Systematic taxonomy of the Trilobatus sacculifer plexus and descendant Globigerinoidesella fistulosa (planktonic foraminifera)
Figure 18. Distribution plot of test diameters (Lm) in the Trilobatus sacculifer plexus from sample GLOW-3. Black dots each represent an individual specimen, grouped at a bin width of 20 Lm per stacked row. Black diamond = mean size. White filled 'violin distributions' show variation in values.
Figure 5 in Systematic taxonomy of the Trilobatus sacculifer plexus and descendant Globigerinoidesella fistulosa (planktonic foraminifera)
Figure 5. Visual representation of image analysis software and measured morphometric and biometric parameters (see text for details of parameter equations).
Figure 4 in Systematic taxonomy of the Trilobatus sacculifer plexus and descendant Globigerinoidesella fistulosa (planktonic foraminifera)
Figure 4. Site location map. Location map showing sites from this study (black star symbols) and the type localities (black triangle symbols) for the investigated morphospecies.
Figure 3 in Systematic taxonomy of the Trilobatus sacculifer plexus and descendant Globigerinoidesella fistulosa (planktonic foraminifera)
Figure 3. Overlapping morphological clusters. As the mean morphology of a population changes gradually on a temporal scale, morphospecies are challenging to delimit, and arbitrary morphospace sectors are required for taxonomic units. SD: standard deviation.
Figure 10 in Systematic taxonomy of the Trilobatus sacculifer plexus and descendant Globigerinoidesella fistulosa (planktonic foraminifera)
Figure 10. Incipient protuberance development in Pleistocene to modern Trilobatus sacculifer. A–L, GLOW-3, south-west Indian Ocean (A, D, F, J, spiral view; B, E, G, K, umbilical view), in B note lobate sac-like chamber, in E note thin final sac-like chamber with different wall texture appearance relative to rest of test; C; detail of wall texture including spine holes; H, detail of two incipient protuberances; I, contrasting wall texture appearance in thinner final sac-like chamber with smooth topography, and penultimate chamber with well-developed sacculifer-like texture and spine holes; L, detail of wall texture showing raised spine bases); M, Barbados, Caribbean Sea, specimen cultured after plankton net collection (umbilical view; reproduced from Brummer et al. 1987, pl. 1, fig. 14); N, Barbados, Caribbean Sea, specimen cultured after SCUBA dive collection (umbilical view; reproduced from B́e et al. 1982, fig. 12); O, P, Barbados, Caribbean Sea, specimens cultured after SCUBA dive collection (umbilical view; note multiple incipient protuberances; reproduced from of Hemleben et al. 1987, pl. 2, figs 11, 12). Scale bars = 100 Lm, except close-up images (I–L) where scale bars = 20 Lm.
Figure 13 in Systematic taxonomy of the Trilobatus sacculifer plexus and descendant Globigerinoidesella fistulosa (planktonic foraminifera)
Figure 13. Globigerinoidesella fistulosa (Schubert, 1910). A–O, ODP Site 1115, Woodlark Basin, western Pacific; 11H/04/25–27 cm (A, C, E, G, I, K, M–O, spiral view, in K note infilled apertures; B, D, F, H, J, umbilical view); L, ODP Site 1115, Woodlark Basin, western Pacific; 10H/03/104–106 cm (spiral view; infilled apertures); P, ODP Site 1115, Woodlark Basin, western Pacific; 10H/04/127–129 cm (spiral view; infilled apertures). Scale bars = 200 Lm.
Figure 9 in Systematic taxonomy of the Trilobatus sacculifer plexus and descendant Globigerinoidesella fistulosa (planktonic foraminifera)
Figure 9. Morphological variation in the final sac-like chamber(s) of Trilobatus sacculifer (Brady, 1877). A–G, I, ODP Site 1115, Woodlark Basin, western Pacific; 11H/04/25–27 cm (A, B, I, spiral view, in A note elongated sac-like chamber; C–G, umbilical view, in D note kummerform sac-like chamber, in F note large, asymmetrical aperture with surrounding imperforate area); H, J–P, ODP Site 871, Limalok Guyot, Marshall Islands, equatorial Pacific 3H/03/60–62 cm (H, J–N umbilical view, in J note lobate sac-like chamber, in K note kummerform sac-like chamber, in L–N note two sac-like chambers; O, P, spiral view; note three sac-like chambers); Q, R, GLOW-3, south-west Indian Ocean (cross sectional view of wall, showing relict spines embedded within wall and chamber layers). Scale bars: A–P = 100 Lm; Q, R = 20 Lm.
Figure 7. Typical Trilobatus immaturus and intergradation with Trilobatus quadrilobatus. A–K in Systematic taxonomy of the Trilobatus sacculifer plexus and descendant Globigerinoidesella fistulosa (planktonic foraminifera)
Figure 7. Typical Trilobatus immaturus and intergradation with Trilobatus quadrilobatus. A–K, Trilobatus immaturus (LeRoy, 1939); L–N, Trilobatus quadrilobatus (d'Orbigny, 1846). A–C, I–K, ODP Site 926, Ceara Rise, western tropical Atlantic, 11H/04/ 50–52 cm (A, B, umbilical view; C, detail wall texture and infilled pores; I, spiral view; J, detail of final chamber wall texture; compare with K, detail of penultimate chamber where primary wall texture is obscured by thick gametogenic calcite); D–H, GLOW-3, south-west Indian Ocean (D, detail of wall texture and imperforate lip on first supplementary aperture; E, H, umbilical view; F, G, spiral view). L–N, GLOW-3, south-west Indian Ocean (L, spiral view; M, umbilical view; N, detail of wall texture including clear spine holes). Scale bars = 100 Lm, except for close-up images C, D, J, K, N, where scale bars = 20 Lm.
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