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Data and Analysis for Kaplanis, Denny, and Raimondi 2024, "Vertical distribution of rocky intertidal organisms shifts with sea-level variability on the Northeast Pacific Coast".
<p>This repository contains all the data and R scripts used to produce all analyses and figures for Kaplanis, Denny, and Raimondi 2024, as well as all intermediate outputs and final figures. To access this content, download and unzip the intertidalvertdist folder (for intertidal vertical distribution). The R Project is titled "intertidalvertdist". All pertinent information needed to access data, replicate the analyses, and produce figures is contained within the README file, but a brief desciption is below.</p> <p><br>Directory Architecture:</p> <p>Data:<br>Contains all data. Within this folder are two subdirectories - Raw Data, and Processed Data. Raw Data are unmanipulated, straight from the data source. Processed Data are outputs from scripted data wrangling and transformations. </p> <p>Within each of these folders are two more subdirectories: Tide Gauge Data, and MARINe Data. These are the two data sources used in this manuscript - monthly sea-level data from The National Oceanic and Atmospheric Administration Center for Operational Oceanographic Products and Services (NOAA CO-OPS) tide gauge stations, and long-term rocky intertidal biological monitoring data from Multi-Agency Rocky Intertidal Network (MARINe) survey sites.</p> <p>Scripts:<br>All R scripts are contained within the Scripts folder. The scripts have the prefix IVD (for intertidal vertical distribution), then a name that indicates the major function of the code. The scripts either downloads data, manipulates data, conducts analyses, and/or produces a figure.</p> <p>Outputs:<br>Any figures and tables from preliminary analyses, but that are not used in the final manuscript, are saved in Outputs.</p> <p>Figures:<br>All final figures and tables are contained in the Figures folder. All figures are produced by scripts, except Figs. 1 and 2, which are schematics produced manually in a graphics editor. This folder contains two other folders: Supplemenatary Figures, and Partial Regression Plots. Partial Regression plots are the same as the final Figures 8-12, except they are grouped by taxa rather than by explanatory variable.</p> <p>Data Processing Workflow - Overview: <br>Tide Gauge Data (Data/Raw Data/Tide Gauge Data/individual stations) were downloaded using the NOAA Co-Ops API URL Builder (https://tidesandcurrents.noaa.gov/api-helper/url-generator.html), merged, then analyzed. Three MARINe data sets from the Coastal Biodiversity Survey (CBS) were accessed via data requests (https://marine.ucsc.edu/explore-the-data/contact/data-request-form.html). The first MARINe dataset (Data/Raw Data/MARINe Data/CBS_Percent Cover Data, both First Sample and Full Sample) was used to determine the top ten most abundant taxa (hereafter termed “dominant taxa”) across CBS survey sites during the monitoring period of 2001-01-01 to 2021-09-30. The second MARINe dataset (Data/Raw Data/MARINe Data/CBS_Elevation Data) was used to describe the upper limits of vertical distribution of dominant taxa through time. The third MARINe dataset (Data/Raw Data/MARINe Data/CBS_Presence Data) was used to visualize latitudinal distribution of taxa.</p> <p>Location information for Tide Gauge Stations and CBS Survey Sites were assembled into a table (Data/Raw Data/CBS_Tide Gauge_Data.csv)</p> <p>Tide Gauge Data were processed first, then MARINe Data. To replicate this workflow follow the steps described in the README file, in order.</p>
Figs 24–29 in Macrobiotus polypiformis sp. nov., a new tardigrade (Macrobiotidae; hufelandi group) from the Ecuadorian Pacific coast, with remarks on the claw abnormalities in eutardigrades
Figs 24–29. Macrobiotus polypiformis sp. nov. 24. Chorion. 25. Long, hair-like flexible filaments on terminal discs. 26. Egg processes with faint annular undulations. 27. Surface between egg processes with reticular design. 28. Terminal discs with small, randomly arranged granules. 29. Small granules on filaments. All in SEM. Scale bars in μm.
Figs 20–23 in Macrobiotus polypiformis sp. nov., a new tardigrade (Macrobiotidae; hufelandi group) from the Ecuadorian Pacific coast, with remarks on the claw abnormalities in eutardigrades
Figs 20–23. Macrobiotus polypiformis sp. nov. 20. Chorion. 21. Long, hair-like flexible filaments on terminal discs. 22. Egg processes and the surface between egg processes with reticular design. 23. Egg processes with filaments. All in PCM. Scale bars in μm.
Figs 16–19 in Macrobiotus polypiformis sp. nov., a new tardigrade (Macrobiotidae; hufelandi group) from the Ecuadorian Pacific coast, with remarks on the claw abnormalities in eutardigrades
Figs 16–19. Macrobiotus polypiformis sp. nov., paratypes. 16. Granulation on the II pair of legs, arrow (PCM). 17. Granulation on IV pair of legs, arrow (PCM). 18. Granulation on II pair of legs (SEM). 19. Modified claw IV (arrowheads) and granulation on IV pair of legs, arrow (SEM). Scale bars in μm.
Figs 3–6 in Macrobiotus polypiformis sp. nov., a new tardigrade (Macrobiotidae; hufelandi group) from the Ecuadorian Pacific coast, with remarks on the claw abnormalities in eutardigrades
Figs 3–6. Macrobiotus polypiformis sp. nov. 3. Cuticular pores visible in PCM (paratype). 4. Cuticular pores visible in SEM (paratype). 5–6. Bucco-pharyngeal apparatus (dorso–ventral projection), the filled arrowhead indicates the first macroplacoid with central constriction (Fig. 5 = paratype in PCM; Fig. 6 = holotype in DIC). Scale bars in μm.
Figs 7–9 in Macrobiotus polypiformis sp. nov., a new tardigrade (Macrobiotidae; hufelandi group) from the Ecuadorian Pacific coast, with remarks on the claw abnormalities in eutardigrades
Figs 7–9. Macrobiotus polypiformis sp. nov., paratypes. 7. Third band of teeth visible under PCM (empty arrowhead). 8–9. Oral cavity armature (SEM), the filled arrowheads indicate teeth of the first band, arrows indicate teeth of the second band, the empty arrowheads indicate teeth of the third band, M = median teeth, L = lateral teeth, a = accessory teeth, rhombi = ring folds, asterisks = ventral side.
Figs 10–15. Claws. 10. Claw II in Macrobiotus polypiformis sp. nov., a new tardigrade (Macrobiotidae; hufelandi group) from the Ecuadorian Pacific coast, with remarks on the claw abnormalities in eutardigrades
Figs 10–15. Claws. 10. Claw II with smooth lunules (PCM, paratype). 11. Claw IV (PCM, holotype). 12. Indented lunules on claw IV (PCM, paratype). 13. Claw I with smooth lunules (SEM, paratype). 14. Claw IV with indented lunules (SEM, paratype). 15. Aberrant claw IV (SEM, paratype). Numbers 1–2 indicate normally developed claw branches/spurs, whereas 3–4 indicate aberrant claw branches/ spurs. Scale bars in μm.
Figs 1–2 in Macrobiotus polypiformis sp. nov., a new tardigrade (Macrobiotidae; hufelandi group) from the Ecuadorian Pacific coast, with remarks on the claw abnormalities in eutardigrades
Figs 1–2. Macrobiotus polypiformis sp. nov., holotype, habitus, dorso-ventral projection. 1. Seen in PCM. 2. Seen in DIC. Scale bars in μm.
Figure 25 in Littoral caprellids (Crustacea: Amphipoda) from the Mexican Central Pacific coast, with the description of four new species
Figure 25. Paracaprella isabelae sp. nov. Holotype male antennae, gnathopod 1 and 2. Allotype female gnathopod 2. Scale bar x (A1, A2) and y (Gn1-2): 0.2 mm.
Figure 24 in Littoral caprellids (Crustacea: Amphipoda) from the Mexican Central Pacific coast, with the description of four new species
Figure 24. Paracaprella isabelae sp. nov. Holotype male mouthparts. Scale bar x (Mx1, Mx2, LMd, RMd, LL, UL) and y (Mxp): 0.05 mm.
Figure 18 in Littoral caprellids (Crustacea: Amphipoda) from the Mexican Central Pacific coast, with the description of four new species
Figure 18. Liropus isabelensis sp. nov. Holotype male pereopods 3–7 and abdomen. Allotype female abdomen. Scale bar x (P3-7) and y (Ad): 0.1 mm.
Figure 26 in Littoral caprellids (Crustacea: Amphipoda) from the Mexican Central Pacific coast, with the description of four new species
Figure 26. Paracaprella isabelae sp. nov. Holotype male pereopods 3–7 and abdomen. Allotype female abdomen. Scale bar: x (P5-7): 0.3 mm; y (Ad): 0.1; z (P3-4): 0.05 mm.
Fig. 2 in Taxonomy of Eudistoma okai (Urochordata: Ascidiacea) Inhabiting the Pacific Coast of Japan, with a Revised Description of Larvae
Fig. 2. In situ photos of Eudistoma okai Sanamyan. A, Taken in the rocky intertidal zone at Jyogashima Island, Miura Peninsula, Sagami Bay, 17 April 2014, representative of colonies of NSMT-Pc 3323; B, taken in a very shallow tide pool, Yoshio, Boso Peninsula, 24 March 2011, representative of colonies of NSMT-Pc 5051–5053.
Fig. 1 in Taxonomy of Eudistoma okai (Urochordata: Ascidiacea) Inhabiting the Pacific Coast of Japan, with a Revised Description of Larvae
Fig. 1. Eudistoma okai Sanamyan from Misaki, Sagami Bay, 5 June 1928, registered as NSMT-Pc 7485. A, Fragment of colony; B, larva incubated in thorax (tail omitted), two lateral ampullae behind, which were concealed by the frontal lateral ampullae, are not shown. Abbreviations: AP, attachment process; LA, lateral ampulla; MA, median ampulla. Scales: A, 5 mm; B, 250 µm.
Fig. 4. Leocratides filamentosus Ehlers, 1908 in Leocratides (Annelida: Hesionidae) from the Pacific Coast of Middle Honshu, Japan, with a Description of Leocratides kimuraorum sp. nov.
Fig. 4. Leocratides filamentosus Ehlers, 1908. Right parapodium of chaetiger 10, NSMT-Pol 113219. A, General appearance of parapodium, posterior view; B, cirrophore; C, ventral cirrus; D, acicular lobe; E, bundle of neurochaetae; F, blade of neurochaeta. Scale bars: A, 1 mm; B–E, 300 µm; F, 100 µm.
Fig. 1 in Leocratides (Annelida: Hesionidae) from the Pacific Coast of Middle Honshu, Japan, with a Description of Leocratides kimuraorum sp. nov.
Fig. 1. Leocratides kimuraorum sp. nov., holotype, NSMT-Pol H-622. A, Live specimen, dorsal view; B, same, ventral view; C, integument and lateral cushions in chaetigers 4–5, dorsal view; D, prostomium, dorsal view; E, pharynx and peristomium, ventral view, showing facial tubercle (white arrow), cushion-shaped appendages (black arrows), and dorsal jaw plates (arrowheads); F, pharynx with terminal papillae, ventral view. Scale of the ruler: A, B, 1 mm. Scale bars: C–F, 1 mm.
Fig. 2 in Leocratides (Annelida: Hesionidae) from the Pacific Coast of Middle Honshu, Japan, with a Description of Leocratides kimuraorum sp. nov.
Fig. 2. Leocratides kimuraorum sp. nov., right parapodium of chaetiger 5, holotype, NSMT-Pol H-622. A, General appearance of parapodium, anterior view; B, cirrophore; C, ventral cirrus; D, acicular lobe, arrow indicating its tip, the base side of photo is the parapodial tip; E, bundle of neurochaetae; F, blade of neurochaeta. Scale bars: A, 2 mm; B–E, 300 µm; F, 50 µm.
Fig. 3. Leocratides filamentosus Ehlers, 1908. A, B, F in Leocratides (Annelida: Hesionidae) from the Pacific Coast of Middle Honshu, Japan, with a Description of Leocratides kimuraorum sp. nov.
Fig. 3. Leocratides filamentosus Ehlers, 1908. A, B, F; NSMT-Pol 113220, C–E; NSMT-Pol 113219. A, Live specimen inside a fragment of an Aphrocallistes sp. hexactinellid sponge, dorsal view; B, same specimen, ventral view; C, integument and lateral cushions in chaetigers 2–4, dorsal view; D, prostomium, dorsal view; E, pharynx and peristomium, ventral view, showing facial tubercle (white arrow) and papillose peristomial membrane (black arrows); F, pharynx with terminal papillae, ventral view. Scale bars: A, B, 10 mm; C–F, 1 mm.
FIGURE 10 in A New Species of Gorgonian Octocoral from the Mesophotic Zone off the Central Coast of California, Eastern Pacific with a Key to Related Regional Taxa (Anthozoa, Octocorallia, Alcyonacea)
FIGURE 10. Scanning electron micrographs of coenenchymal sclerites. A. Chromoplexaura cordellbankensis sp. nov. (CASIZ 228194). B. Chromoplexaura marki (CASIZ 190436). C. Euplexaura sp. (CASIZ 220608). D. Swiftia torreyi (CASIZ 220958). Scale bars = 0.05 mm.
FIGURE 9 in A New Species of Gorgonian Octocoral from the Mesophotic Zone off the Central Coast of California, Eastern Pacific with a Key to Related Regional Taxa (Anthozoa, Octocorallia, Alcyonacea)
FIGURE 9. Map of the Pacific coast of the United States showing the geographical ranges of Chromoplexaura marki () and Chromoplexaura cordellbankensis sp. nov. (); arrow denotes type locality.
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