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Figure 6 in Spatiotemporal distribution of planktonic copepod communities in Tokyo Bay where Oithona davisae Ferrari and Orsi dominated in mid-1980s

Figure 6. Horizontal distributions of the identified community groups in Tokyo Bay (the letters in parentheses in legends show the indicator species).

Figure 3 in Seasonal changes in the population structure of dominant planktonic copepods collected using a sediment trap moored in the western Arctic Ocean

Figure 3. Seasonal changes in sea ice concentration, surface chl. a (from satellite) and total mass flux (a), and daylight hours (b) at St. NAPt from October 2010 to September 2012.

Figure 8 in Seasonal changes in the population structure of dominant planktonic copepods collected using a sediment trap moored in the western Arctic Ocean

Figure 8. Seasonal changes in sea ice concentration, daylight hours, chl. a, and total mass flux from January to December (upper panel). The ecological characteristics of the five dominant copepods (lower panel). The open and solid bars indicate the high abundance and reproductive periods for each species, respectively.

Figure 4 in Inter-oceanic comparison of planktonic copepod ecology (vertical distribution, abundance, community structure, population structure and body size) between the Okhotsk Sea and Oyashio region in autumn

Figure 4. Copepod species composition (centre) and copepodid stage structures of the dominant species (left: Oyashio region, right: Okhotsk Sea). All data are integrated means of a 0– 500 m water column based on the IONESS samples in the Oyashio region (St. 19) and Okhotsk Sea (St. OK24) from October to November 1996. Error bars for the copepodid stage indicate standard deviations of each daily duplicate.

Figure 3 in Inter-oceanic comparison of planktonic copepod ecology (vertical distribution, abundance, community structure, population structure and body size) between the Okhotsk Sea and Oyashio region in autumn

Figure 3. Vertical distribution of zooplankton biovolume in the Oyashio region (upper panels) and Okhotsk Sea (lower panels) from September to December in 1996–1998. Note that the biovolume axes are not the same between panels. Tc: thermocline.

opencc-by-4.0Oct 2020View details →

Illuminating the planktonic stages of salmon lice: a unique fluorescence signal for rapid identification of a rare copepod in zooplankton assemblages.

The Excitation Emission Matrix (EEM) measurements were taken with Shimadzu's proprietary software ‘LabSolutions RF’. All files are in the exported csv format with columns representing the excitation wavelengths and rows the emission wavelengths. Wavelengths range from 200-600 nm with a 2 nm increment. Fluorescence intensity was influenced by the fluctuating number of animals in the path of the excitation beam during the 5 minute measurement. We compensated for this artefact by repeating measurements of each sample five times, calculating the mean, and applying a smoothing function which found the median value within 10 nm. The fluorescence intensity was further normalized on a 0 to 1 scale by dividing intensity by the maximum fluorescence within each EEM measurement. Supplemental Table 1. The metadata of EEM measurements. The measurements were used for the spectrum section analysis and correspond to those depicted in Figures 2, 3, 4, & 5. See sections 3.1, 3.1.1, & 3.1.2. The Sample column indicates which lab culture cohort the sea lice came from (BGO*), which wild caught fish sample they came from (WC*), or the sampling date of non-target copepods (DDMMYY). The filename of each mean measurement is listed and indicates the first of 5 repeated measurements. Corresponding files can be found in the deposited.csv files at Zendo. In those files, data columns represent the excitation wavelengths, 200nm to 600nm increasing in 2 nm increments. Likewise, the rows represent the emission wavelengths. NaN’s are present where scattering layers were removed. All fluorescence intensity values are normalized to the maximum within each EEM.

opencc-by-4.0Jan 2021View details →

Automatic plankton image classification - can capsules and filters help coping with data set shift?

This data set is related to the article 'Automatic plankton image classification - can capsules and filters help coping with data set shift?' published in 'Limnology and Oceanography: Methods' by Plonus et al. (2021). The images belong to the trainings set used to train the models in the aforementioned paper (training_) and three different additional data sets which were used to evaluate the performance of the trained models in application mode (fs446_; fs466_; fs534_). The Python-Script 'separate_files.py' can be used to move all the images in different folders for each data set and class respectively.

dryad40/100

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.

opencc-zeroOct 2019View details →

opencc-zeroDec 2016View details →

FIGURE 1 in On the occurrence of caligids (Copepoda: Siphonostomatoida) in the marine plankton: a review and checklist

FIGURE 1. Map showing geographical distribution (38 localities) of caligid species collected in plankton samples. Details of species with known hosts are summarized in Table 1; those known exclusively from planktonic records are listed in Table 2. Localities marked are: 1. Black Sea, 2. San Francisco, 3. Newport Beach, 4. Sonora, 5. Off Laguna de Tamiahua, 6. Texas, 7. Miami, 8. Chelem, 9. Costa Rica, 10. Venezuela, 11. Easter Islands, 12. Falkland Islands, 13. Rio Grande do Sul, 14. Gulf of Guinea, 15. off Trivandrum, 16. off Kayankulam, 17. Gulf of Thailand, 18. east of New Zealand, 19. Mindanao, 20. Amoy, 21. Qingdao (= Tsingtao), 22. Yantai (= Chefoo), 23. Yellow River estuary, 24. Mankyong River, 25. Seomjin River, 26. Iheyashima, 27. Amami Island, 28. Akuseki-shima, 29. Ariake Sea, 30. Hirado Island, 31. Suo-nada (Seto Inland Sea), 32. Ube, 33. Mukaijima, 34. Takamatsu, 35. Nagasu, 36. Osaka Port, 37. Tokushima, and 38. Uwajima.

opencc-zeroDec 2016View details →

FIGURE 2 in A new species of Caligus Müller, 1785 (Copepoda: Siphonostomatoida: Caligidae) from coral reef plankton in the Mexican Caribbean

FIGURE 2. Caligus ilhoikimi sp. nov. (adult female holotype). A, maxilliped; B, first leg; C, detail of distal elements of first leg; D, second leg; E, detail of third exopodal segment of second leg; F, genital complex showing fifth legs and abdomen, ventral view. Scale bars: A, D = 0.2 mm; B = 0.1 mm; E, C = 0.05 mm; F = 0.5 mm.

opencc-by-4.0May 2017View details →

Sixty-one thousand Recent planktonic foraminifera from the Atlantic Ocean

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 (AutoMorph) developed in P.M. Hull's lab at Yale University. The dataset consists of microfossils from 34 sediment samples, mounted on 155- micropaleontological slides, primarily from the North Atlantic Ocean (metadata_tables.tar.gz: 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 AutoMorph as detailed in Table 2. AutoMorph 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.  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). Images and morphometric data are provided in 12 additional datasets: 1) slide_images.tar.gz contains one image for each slide scanned in this study (155 slides), with a red box around each object extracted using the AutoMorph 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.  2) edf_images.tar.gz contains the extended depth of focus images (EDF: a 2D image composite created from multiple z-stacked photographic images) generated by the AutoMorph focus module for each of the 124,230 individual objects identified by segment. 3 & 4) obj_zstacks_part1.tar.gz and obj_zstacks_part2.tar.gz contain the original zstack images of each object.  2D outlines and shape measurements for each object are extracted using the AutoMorph module run2dmorph.  5) 2d_outline_check.tar.gz 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). 6) 2d_coordinates.tar.gz 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). 7) shape_measurements.csv contains the complete list of all objects in the dataset (124,230 objects) with the 2D and 3D measurements extracted by the AutoMorph routines run2morph and run3dmorph when available. 8 & 9) 3d_pdfs_part1.tar.gz and 3d_pdfs_part2.tar.gz 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 AutoMorph module run3dmorph. Note that only some pdf viewers are able to display 3d pdfs properly.  10-12) 3d_obj_files_part1.tar.gz, 3d_obj_files_part2.tar.gz, and 3d_obj_files_part3.tar.gz 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). This dataset accompanies the manuscript "Sixty-one thousand Recent planktonic foraminifera from the Atlantic Ocean" submitted to Scientific Data. 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 4/5ths of the complete data set. A random subset (1/5th of the classifications) are excluded as a test set, so that this image database can be used in machine learning.

opencc-by-4.0Jul 2024View details →

Europe-wide public preferences for plankton-based ecosystem services and marine biodiversity from a series of Deliberative Monetary Valuation workshops

The data were collected as part of the Horizon Europe project BIOcean5D – Marine Biodiversity Assessment and Prediction Across Spatial, Temporal and Human Scales. The aim of the study was to elicit public preferences for marine biodiversity and ecosystem services, with a particular focus on plankton. This dataset comprises responses from a series of Deliberative Monetary Valuation workshops held across Europe, along with the corresponding supplementary material. The responses encompass a range of data, including socio-demographic information, personal characteristics, beliefs, prior knowledge, preferences derived from a Discrete Choice Experiment, and the associated motivations of each respondent. In total, 15 workshops were conducted between October 2023 and February 2024 in the following locations: Poland (Poznan and Sopot), Italy (Padova and Chioggia), the Basque Country (Vitoria-Gasteiz and Bilbao), Germany (Bremerhaven and Hannover), and France (Rennes and Brest).

Fig.ç4.C aligus longiramus sp. nov., holotype, female (KMNH IvR 500,511). A, leg 2, dorsal view; B, leg 3, dorsal view; C, leg 4, dorsal view; D, leg 5, ventral view. Scale bars: 0.1 mm. in Occurrence of Caligid Copepods (Crustacea) in Plankton Samples Collected from Japan and Ŋailand, with the Description of a New Species

Fig.ç4.C aligus longiramus sp. nov., holotype, female (KMNH IvR 500,511). A, leg 2, dorsal view; B, leg 3, dorsal view; C, leg 4, dorsal view; D, leg 5, ventral view. Scale bars: 0.1 mm.

Fig.ç3.C aligus longiramus sp. nov., holotype, female (KMNH IvR 500,511). A, maxilla, dorsal view; B, maxilliped, dorsal view; C, sternal furca, dorsal view; D, leg 1, ventral view; E, exopod of leg 1 enlarged, ventral view. Scale bars: 0.1 mm. in Occurrence of Caligid Copepods (Crustacea) in Plankton Samples Collected from Japan and Ŋailand, with the Description of a New Species

Fig.ç3.C aligus longiramus sp. nov., holotype, female (KMNH IvR 500,511). A, maxilla, dorsal view; B, maxilliped, dorsal view; C, sternal furca, dorsal view; D, leg 1, ventral view; E, exopod of leg 1 enlarged, ventral view. Scale bars: 0.1 mm.

Fig.ç2.A, Caligus latigenitalis Shiino, 1954, male (KMNH IvR 500, 510), habitus, dorsal view; B–F. Caligus longiramus sp. nov., holotype, female (KMNH IvR 500, 511): B, habitus, dorsal view; C, caudal rami, dorsal view; D, antennule, ventral view; E, antenna, postantennal process, and maxillule, ventral view; F, mandible. Scale bars: 1 mm (A, B); 0.1 mm (C–F). in Occurrence of Caligid Copepods (Crustacea) in Plankton Samples Collected from Japan and Ŋailand, with the Description of a New Species

Fig.ç2.A, Caligus latigenitalis Shiino, 1954, male (KMNH IvR 500, 510), habitus, dorsal view; B–F. Caligus longiramus sp. nov., holotype, female (KMNH IvR 500, 511): B, habitus, dorsal view; C, caudal rami, dorsal view; D, antennule, ventral view; E, antenna, postantennal process, and maxillule, ventral view; F, mandible. Scale bars: 1 mm (A, B); 0.1 mm (C–F).

Fig.ç1.C ollection sites of pelagic caligids including 3 stations in Japanese waters (St. 2–4, 2010) and 1 station in the Gulf of ffiailand (St. 1, 2006). in Occurrence of Caligid Copepods (Crustacea) in Plankton Samples Collected from Japan and Ŋailand, with the Description of a New Species

Fig.ç1.C ollection sites of pelagic caligids including 3 stations in Japanese waters (St. 2–4, 2010) and 1 station in the Gulf of ffiailand (St. 1, 2006).

opencc-by-4.0Dec 2014View details →

Fig. 2A–H in Dirty Tricks in the Plankton: Diversity and Role of Marine Parasitic Protists

Fig. 2A–H. Protistan parasites of marine zooplankton. A – the dinoflagellate Haplozoon inerme (bottom left) parasitizing Appendicularia sicula (after Cachon 1964); B, C – hyperparasitic Amobophrya grassi in Oodinium poucheti, an ectoparasites on Oikopleura (after Cachon 1964); B – several early-stage parasites inside the host; C – macrospore (left) and dividing microspores (right) of A. grassi; D, E – the syndinean dinoflagellate Syndinium bogerti in the acantharian Amphilonche sp. (after Hollande and Enjumet 1955); D – multinuclear parasites inside the host; E – relased parasite macrospore (left) and microspore (right); F–H – Syndinium- like parasite in the copepod Clausocalanus sp. from the NW Mediterranean Sea; F, G – dinospores originating from the infected host in H. Scale bars: 10 µm; H – recently diseased host filled with live dinospores. Scale bar: 100 µm.

opencc-by-4.0Dec 2014View details →

Fig. 1A in Dirty Tricks in the Plankton: Diversity and Role of Marine Parasitic Protists

Fig. 1A–-E. Protistan parasites of marine phytoplankton. A – Amoeba biddulphiae in the diatom Odontella sinensis. Left: recently attached parasite cell. Center: parasitic amoeba inside the host. Rigth: almost empty diatom frustule with protoplasm transformed into 10 amoebae (after Zuelzer 1927); B, C – the stramenopile fungi Lagenisma coscinodisci in the diatom Coscinodiscus sp.; B – host cell protoplasm transformed into parasite hyphae; C – expulsion of parasite swarmer cells. Courtesy of Gerhard Drebes, Plankton*Net Data Provider at the Alfred Wegener Institute for Polar and Marine, http://planktonnet. awi.de; D – Parvilucifera sp. sporangium in a deceased dinoflagellate, Tripos macroceros, from the North Sea; E – Amoebophrya sp. in the dinoflagellate Tripos fusus from the North Sea. Arrows show extreme points of parasite. All scale bars: 50 µm.