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Ecology and conservation of socially learned foraging tactics in odontocetes
<h3>Overview</h3> <p>This package contains the data and R code to replicate the analyses and figures of the review article, "Ecology and conservation of socially learned foraging tactics in odontocetes", submitted to the special issue of Philosophical Transactions B, "Animal Culture: conservation in a changing world". </p> <p>Metadata for CSV files used for analyses are provided below, and detailed instructions on running code are available at: https://github.com/JoaoVallePereira/Toothed_Whales_Forag_Tactics. For full description of variables, see supplemental material associated with publication. </p> <div> <h3>Main data table - dataTable_Forag_Tactics.csv</h3> </div> <table> <tbody> <tr> <th>Variable</th> <th>Class</th> <th>Description</th> </tr> </tbody> <tbody> <tr> <td>common_name</td> <td>Character</td> <td>The common name of the species exhibiting the foraging tactic</td> </tr> <tr> <td>latin_name</td> <td>Character</td> <td>The Latin name of the species exhibiting the foraging tactic</td> </tr> <tr> <td>country</td> <td>Character</td> <td>The country that has jurisdiction over the region where the foraging tactic occurs</td> </tr> <tr> <td>region</td> <td>Character</td> <td>The region where the foraging tactic occurs</td> </tr> <tr> <td>animal_identity_data</td> <td>Character</td> <td>Whether identity information for the individual(s) exhibiting the foraging tactic is available</td> </tr> <tr> <td>number_of_animals</td> <td>Character</td> <td>The number of different individuals exhibiting the foraging tactic</td> </tr> <tr> <td>foraging_category</td> <td>Character</td> <td>The broad foraging category that the specific foraging tactic most closely aligns with</td> </tr> <tr> <td>foraging_tactic</td> <td>Character</td> <td>The specific foraging tactic</td> </tr> <tr> <td>tactic_driver</td> <td>Character</td> <td>The key factor influencing or determining the observed foraging tactic</td> </tr> <tr> <td>human_induced</td> <td>Character</td> <td>Whether the foraging tactic is human-induced or not</td> </tr> <tr> <td>prey_category</td> <td>Character</td> <td>The type of prey being targeted during the foraging tactic</td> </tr> <tr> <td>habitat</td> <td>Character</td> <td>The type of habitat in which the foraging tactic is exhibited</td> </tr> <tr> <td>prey_category</td> <td>Character</td> <td>The type of prey being targeted during the foraging tactic</td> </tr> <tr> <td>putative_specialised_foraging_tactic</td> <td>Character</td> <td>Foraging tactics having both individual identity information and evidence of being shared among conspecifics</td> </tr> <tr> <td>putative_cultural_foraging_tactic</td> <td>Character</td> <td>Foraging tactics with positive evidence of social learning</td> </tr> <tr> <td>transmission_direction</td> <td>Character</td> <td>How the foraging tactic is transmitted, given positive evidence of social learning</td> </tr> <tr> <td>nature_of_social_learning_evidence</td> <td>Character</td> <td>The type of evidence for social learning</td> </tr> <tr> <td>culture_acknowledgement</td> <td>Character</td> <td>The type of evidence for social learning</td> </tr> <tr> <td>evidence_for_discreteness_significance</td> <td>Character</td> <td>Evidence for differences in diet or foraging techniques that are stable</td> </tr> <tr> <td>threat_acknowledgement</td> <td>Character</td> <td>Whether the reviewed studies acknowledge anthropogenic threats</td> </tr> <tr> <td>threat_category</td> <td>Character</td> <td>For studies that acknowledge anthropogenic threats and impacts, the type of IUCN-CMP first-level threat classification</td> </tr> <tr> <td>threat_subcategory</td> <td>Character</td> <td>For studies that acknowledge anthropogenic threats and impacts, the type of IUCN-CMP second-level threat classification</td> </tr> <tr> <td>threat_direction</td> <td>Character</td> <td>Whether the acknowledged threats were considered a threat to or a consequence of the foraging tactic</td> </tr> <tr> <td>conservation_actions_acknowledgement</td> <td>Character</td> <td>Whether the reviewed studies acknowledge existing or proposed conservation actions related to the foraging tactic</td> </tr> <tr> <td>existing_conservation_actions_category</td> <td>Character</td> <td>Existing conservation actions related to the foraging tactic, the type of IUCN-CMP first-level action classification</td> </tr> <tr> <td>existing_conservation_actions_subcategory</td> <td>Character</td> <td>Existing conservation actions related to the foraging tactic, the type of IUCN-CMP second-level action classification</td> </tr> <tr> <td>proposed_conservation_actions_category</td> <td>Character</td> <td>Proposed conservation actions related to the foraging tactic, the type of IUCN-CMP first-level action classification</td> </tr> <tr> <td>proposed_conservation_actions_subcategory</td> <td>Character</td> <td>Proposed conservation actions related to the foraging tactic, the type of IUCN-CMP second-level action classification</td> </tr> <tr> <td>references</td> <td>Character</td> <td>Reviewed primary and secondary literature used to fill out metrics for the foraging tactic</td> </tr> </tbody> </table> <div> <h3> </h3> <h3>Maps data table - dataTable_Forag_Tactics_map.csv</h3> </div> <table> <tbody> <tr> <th>Variable</th> <th>Class</th> <th>Description</th> </tr> </tbody> <tbody> <tr> <td>common_name</td> <td>Character</td> <td>The common name of the species exhibiting the foraging tactic</td> </tr> <tr> <td>latin_name</td> <td>Character</td> <td>The Latin name of the species exhibiting the foraging tactic</td> </tr> <tr> <td>orca_ecotype</td> <td>Character</td> <td>The orca ecotypes exhibiting the foraging tactic</td> </tr> <tr> <td>country</td> <td>Character</td> <td>The country that has jurisdiction over the region where the foraging tactic occurs</td> </tr> <tr> <td>region</td> <td>Character</td> <td>The region where the foraging tactic occurs</td> </tr> <tr> <td>latitude</td> <td>Numeric</td> <td>The latitude where the foraging tactic occurs</td> </tr> <tr> <td>longitude</td> <td>Numeric</td> <td>The longitude where the foraging tactic occurs</td> </tr> <tr> <td>putative_specialised_foraging_tactic</td> <td>Character</td> <td>Foraging tactics having both individual identity information and evidence of being shared among conspecifics</td> </tr> <tr> <td>foraging_category</td> <td>Character</td> <td>The broad foraging category that the specific foraging tactic most closely aligns with</td> </tr> <tr> <td>tactic_cat_fact</td> <td>Factor (10 levels)</td> <td>The broad foraging category that the specific foraging tactic most closely aligns with</td> </tr> <tr> <td>evidence_for_discreteness_significance</td> <td>Character</td> <td>Evidence for differences in diet or foraging techniques that are stable</td> </tr> </tbody> </table>
Odontocete detections and corresponding values of environmental variables in the Hawaiian Archipelago
<p>This dataset contains detections of echolocation clicks at two sites in the Hawaiian Archipelago. These sites are Hawaii and Manawai (also known as Pearl and Hermes Reef). Echolocation clicks have been labeled using a neural network classifier that was trained and tested on data from the Hawaiian Islands and can successfully identify many species of regionally present odontocetes. During the labeling process, clicks were grouped into five-minute bins and each bin was given a class label. The data provided here is further binned at a daily level, where counts of a given class represent the number of five-minute bins within a given day that were labeled as that class. One file is provided per site, and files are in .csv format that can be read using any desired coding language. </p> <p>In addition to acoustic counts, values for environmental variables considered in the corresponding manuscript are provided in the CSV files. The final file in this dataset contains satellite-derived chlorophyll-a concentration values from NASA MODIS for the Hawaiian region (used to create Supplementary Fig. 1). Details on all variables and how they were accessed can be found in the manuscript and in the README file accompanying this dataset. </p>
Figure 3 in A new odontocete (Inioidea, Odontoceti) from the late Neogene of North Carolina, USA
Figure 3. Isoninia borealis (gen. nov., sp. nov.). (a) CMM-V-4061 in dorsal view; anterior to top of figure. (b) Single CT-scan image through CMM-V-4061 in posterior view as indicated by the transverse white line in (a) to which the corresponding arrow is pointing. (c) Single CT-scan image in posterior view through the anterior part of the nasals as indicated by the white line in (a). (d) Single CT-scan image in posterior view through the vertex showing the os suturarum or a fold in the frontals as indicated by the white line in (a). (e) CMM-V-4061 in left lateral view. (f) CMM-V-4061 in ventral view; anterior to top of figure. Specimen lightly coated with sublimed ammonium chloride. CT-scan images (b–d) are adjusted to the scale bar to the left below (a). The scale bar for (e) and (f) is to the left below (f).
Figure 2 in A new odontocete (Inioidea, Odontoceti) from the late Neogene of North Carolina, USA
Figure 2. Isoninia borealis (gen. nov., sp. nov.). (a) Partial skull CMM-V-4061 in dorsal view lightly coated with sublimed ammonium chloride. (b) Interpretative drawing of (a).
Figure 1 in A new odontocete (Inioidea, Odontoceti) from the late Neogene of North Carolina, USA
Figure 1. Stratigraphy of the marine late Miocene to Pliocene of North Carolina, USA, showing the Cobham Bay Member of the Eastover Formation, from which CMM-V-4061, the holotype and only known specimen of Isoninia borealis (gen. nov., sp. nov.), is thought to be derived. From Geisler et al. (2012), which they modified from Ward and Andrews (2008).
Figure 2 in Acoustic documentation of temperate odontocetes in the Bering and Chukchi Seas
Figure 2. (A) Map of the acoustic detections attributed to northern right whale dolphins at sites M2 and M5 with dotted lines denoting historical range extents. (B) A spectrogram from 10 November 2012, at M2 of a downsweeping, harmonic click/buzz at 0.5 s with is characteristic of northern right whale dolphins (despite being masked by the ping of another instrument on the mooring). Spectrogram settings are: window = Hanning, Nfft = 512, overlap = 99%, min dB = 11 dB, dB spread = 35 dB.
Figure 3 in Acoustic documentation of temperate odontocetes in the Bering and Chukchi Seas
Figure 3. (top) Map of acoustic detections attributed to Pacific white-sided dolphins at M2, M5, and CH with dotted lines denoting historical range extents. Number of files with detections each day are in parentheses if>1. (bottom) A spectrogram from 25 October 2009, at M2 of buzzes with peaks and notches as expected for Pacific white-sided dolphins according to Soldevilla et al. (2008). Spectrogram settings are: window = Hanning, Nfft = 1,024, overlap = 99%, min dB = 12 dB, dB spread = 42 dB.
Figure 1 in Acoustic documentation of temperate odontocetes in the Bering and Chukchi Seas
Figure 1. (A) Map of acoustic detections attributed to Risso's dolphins at sites M2, M5, and CH with dotted lines denoting historical range extents. (B) A spectrogram from 31 March 2010, at M2 zoomed into clicks attributed to Risso's dolphins because peaks and notches are centered near the expected frequencies reported in Soldevilla et al. (2008). Spectrogram settings are: window = Hanning, Nfft = 2,048, overlap = 99%, min dB = 10 dB, dB spread = 40 dB.
Fig. 5. A in Whale lice (Isocyamus deltobranchium & Isocyamus delphinii; Cyamidae) prevalence in odontocetes off the German and Dutch coasts - morphological and molecular characterization and health implications
Fig. 5. A: Ulcerative lesion with whale lice in harbour porpoise (Phocoena phocoena); B: rake marks with whale lice on pilot whale (Globicephala melas).
Fig. 4 in Whale lice (Isocyamus deltobranchium & Isocyamus delphinii; Cyamidae) prevalence in odontocetes off the German and Dutch coasts - morphological and molecular characterization and health implications
Fig. 4. Maximum likelihood phylogeny tree produced with MEGA (version X), sequences in red box from this study. Bootstrap values (n = 1000 replicates) above 50% are shown above the branches.
Fig. 3 in Whale lice (Isocyamus deltobranchium & Isocyamus delphinii; Cyamidae) prevalence in odontocetes off the German and Dutch coasts - morphological and molecular characterization and health implications
Fig. 3. (A) Isocyamus deltobranchium and (B) Isocyamus delphinii showing the characteristic accessory gills (asterisk).
Fig. 2. A in Whale lice (Isocyamus deltobranchium & Isocyamus delphinii; Cyamidae) prevalence in odontocetes off the German and Dutch coasts - morphological and molecular characterization and health implications
Fig. 2. A: Isocyamus deltobranchium adult male ventral view showing genitalia and accessory gills; B: Isocyamus deltobranchium adult female dorsal view; C: Isocyamus deltobranchium adult female ventral view showing genitalia and broodpouch; D: adult female ventral view with juveniles in brood pouch, all sampled from a stranded harbour porpoise (Phocoena phocoena) on the Dutch coast.
Fig. 6 in Whale lice (Isocyamus deltobranchium & Isocyamus delphinii; Cyamidae) prevalence in odontocetes off the German and Dutch coasts - morphological and molecular characterization and health implications
Fig. 6. Intralesional whale lice (arrow) in lesion with mild hyperplasia of the adjacent epidermis and granulation tissue in the superficial dermis (scale bar 2 mm).
Fig. 2 in Specificity of Stenurus (Metastrongyloidea: Pseudaliidae) infections in odontocetes stranded along the north-west Spanish coast
Fig. 2. (A–B) Stenurus minor: posterior end of a male (A) with an undivided bursa and broad spicules and of a female (B) with a finger-shaped cuticular process on the anterior lip of the vulva (➨) and first stage larvae (L1) in the uterus (⇨). (C–D) Stenurus globicephalae: posterior end of a male (C) and a female (D) with multiple cuticular swellings (➨) and L1 in the uterus (⇨). (E–F) Stenurus ovatus: posterior end of a male (E) with a divided bursa showing three rays and a female (F) showing a conical terminal process (➨) and a cuticular swelling (⇨).
Fig. 1 in Specificity of Stenurus (Metastrongyloidea: Pseudaliidae) infections in odontocetes stranded along the north-west Spanish coast
Fig. 1. Nematodes found in the pterygoid sinuses during the necropsy of a short-finned pilot whale (Globicephala macrorhynchus).
Fig. 3 in Specificity of Stenurus (Metastrongyloidea: Pseudaliidae) infections in odontocetes stranded along the north-west Spanish coast
Fig. 3. Bipartite multigraph relating the three Stenurus species with their hosts. The width of the links (gray arrows) represents the mean parasitic load on each host.
Odontocete detections and corresponding values of environmental variables in the Hawaiian Archipelago
Open the record for dataset details and reuse information.
Data from: The largest freshwater odontocete: a South Asian river dolphin relative from the Proto-Amazonia
<p>Several dolphin lineages have independently invaded freshwater systems. Among these, the evolution of the South Asian river dolphin <em>Platanista </em>and its closest relatives (Platanistidae) remains virtually unknown as fossils are scarce. Here, we describe <em>Pebanista</em> <em>yacuruna</em> gen. et sp. nov., a fossil dolphin from the Miocene proto-Amazonia of Peru, recovered in phylogenies as the closest relative of <em>Platanista</em>. Morphological characters such as an elongated rostrum and large supraorbital crests, along with ecological interpretations, indicate that this new taxon was fully adapted to freshwater environments. <em>Pebanista</em> constitutes the largest freshwater odontocete known, with an estimated body length of 3 meters. It highlights the ample resource availability in the region, supporting biotic diversity during the Early to Middle Miocene. The finding of <em>Pebanista</em> in proto-Amazonian layers attests that platanistids ventured into freshwater ecosystems not only in South Asia, but also in South America, long before and independently of modern Amazon River dolphin <em>Inia</em>, during a crucial moment for the evolution of the Amazonian realm.</p>
Fig. 1 in Whale lice (Isocyamus deltobranchium & Isocyamus delphinii; Cyamidae) prevalence in odontocetes off the German and Dutch coasts - morphological and molecular characterization and health implications
Fig. 1. Map of German and Dutch coast with sampling locations of harbour porpoises and pilot whale.
Table 2 in Acoustic documentation of temperate odontocetes in the Bering and Chukchi Seas
<p><i>Table 2.</i> Mean frequencies and standard deviation (kHz) of click and buzz peaks and notches classified as Risso’ s (Gg) or Pacific-white sided (Lo) dolphins on PALs as compared to the testing and training data sets of Soldeville <i>et al</i>. (2008).</p><table><tbody><tr><th></th><th>Peak No. Mean kHz (SD)</th><th>Notch No. Mean kHz (SD)</th></tr></tbody><tbody><tr><th></th><td>1</td><td>2</td><td>3</td><td>4</td><td>1</td><td>2</td><td>3</td></tr><tr><th>Soldevilla</th></tr><tr><th>training Gg</th><td>22.1(0.7)</td><td>25.6(0.7)</td><td>30.3(0.8)</td><td>39.0(0.8)</td><td>19.8(0.7)</td><td>27.5(0.9)</td><td>35.8(1.1)</td></tr><tr><th>Soldevilla</th></tr><tr><th>test Gg</th><td>22.4(0.8)</td><td>25.5(1.0)</td><td>30.5(1.1)</td><td>38.8(1.1)</td><td>19.6(1.3)</td><td>27.7(1.1)</td><td>35.9(1.2)</td></tr><tr><th>PAL Gg</th><td>21.3(1.2)</td><td>24.9(1.1)</td><td>31.1(1.4)</td><td>38.9(1.1)</td><td>19.9(1.3)</td><td>27.1(1.5)</td><td>34.6(1.6)</td></tr><tr><th>Soldevilla</th></tr><tr><th>training Lo</th><td>22.1(0.6)</td><td>26.7(1.0)</td><td>33.1(1.4)</td><td>37.3(1.1)</td><td>19.5(0.9)</td><td>24.5(0.8)</td><td>29.8(1.4)</td></tr><tr><th>Soldevilla</th></tr><tr><th>test Lo</th><td>22.2(0.6)</td><td>26.6(0.9)</td><td>33.7(1.4)</td><td>37.3(1.4)</td><td>19.0(1.1)</td><td>24.5(0.9)</td><td>29.7(1.4)</td></tr><tr><th>PAL Lo</th><td>21.5(0.6)</td><td>26.4(1.1)</td><td>32.9(1.1)</td><td>37.4(0.9)</td><td>19.3(0.9)</td><td>24.2(1.4)</td><td>29.8(1.4)</td></tr></tbody></table>
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