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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>
Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation
<p>Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility to comparative biologists. To establish a robust evolutionary timescale for all ~6000 living species of mammals, we developed credible sets of trees that capture root-to-tip uncertainty in topology and divergence times. Our 'backbone-and-patch' approach to tree-building applies a newly assembled 31-gene supermatrix to two levels of Bayesian inference: (i) backbone relationships and ages among major lineages, using fossil node- or tip-dating; and (ii) species-level 'patch' phylogenies with non-overlapping in-groups that each correspond to one representative lineage in the backbone. Species unsampled for DNA are either excluded ('DNA-only' trees) or imputed within taxonomic constraints using branch lengths drawn from local birth-death models ('completed' trees). Joining time-scaled patches to backbones results in species-level trees of extant Mammalia with all branches estimated under the same modeling framework, thereby facilitating rate comparisons among lineages as disparate as marsupials and placentals. We compare our phylogenetic trees to previous estimates of mammal-wide phylogeny and divergence times, finding that (i) node ages are broadly concordant among studies, and (ii) recent (tip-level) rates of speciation are estimated more accurately in our study than in previous 'supertree' approaches where unresolved nodes led to branch length artifacts. Credible sets of mammalian phylogenetic history are now available for download at <a href="http://vertlife.org/phylosubsets">http://vertlife.org/phylosubsets</a>, enabling investigations of long-standing questions in comparative biology.</p>
The location of solar farms within England's ecological landscape: implications for biodiversity conservation
<p>Data associated to the article entitled 'The location of solar farms within England's ecological landscape: implications for biodiversity conservation'. </p> <p> </p>
Supplementary file 1 from: Moliner Cachazo L, Makati K, Chadwick MA, Catford JA, Price BW, Mackay AW, Guiry MD, Murray-Hudson M, Murray-Hudson F (2023) A review of the freshwater diversity in the Okavango Delta and Lake Ngami (Botswana): taxonomic composition, ecology, comparison with similar systems and conservation status. Aquatic Sciences
<p>Dataset with 2,204 freshwater species from the Okavango Delta and Lake Ngami (Botswana), with additional 355 species found in other areas of Botswana that are likely to be present in the study region. The dataset covers the following groups: amphibians, birds, fishes, macroinvertebrates, macrophytes, mammals, reptiles, phytoplankton, and zooplankton. The following information is given for each species: status in the Okavango Delta and Lake Ngami (present/potentially present); conservation status globally, Phylum, Class, Order, Family, Genus, species name, cited synonyms, common name, habitat, presence in high water, presence in low water, ecology, distribution in continental Africa, confirmed locations in the Okavango Delta, site coordinates, references, notes.</p>
Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation
Open the record for dataset details and reuse information.
Survey data for "Remote Sensing & GIS Training in Ecology and Conservation"
<p>This file provides the raw data of an online survey intended at gathering information regarding remote sensing (RS) and Geographical Information Systems (GIS) for conservation in academic education. The aim was to unfold best practices as well as gaps in teaching methods of remote sensing/GIS, and to help inform how these may be adapted and improved. A total of 73 people answered the survey, which was distributed through closed mailing lists of universities and conservation groups.</p>
CONSERVATION BIOLOGY AND BEHAVIORAL ECOLOGY OF NOCTURNAL MAMMALS OF TAITA HILLS, KENYA
<p>Sound samples from PhD dissertation by Hanna Rosti</p><p>These sound samples include calls of following species</p><p>S1 Paragalago rondoensis, Saadani National Park, Tanzania, recorded by C. Hemp</p><p>S2 Paragalago orinus, Pugu Tanzania, recorded by A. Perkin</p><p>S3 Paragalago cocos, Shimba Hills National Reserve, Kenya, recorded by H. Rosti</p><p>S4 Paragalago zanzibaricus zanzibaricus, Zanzibar, Jozani, Tanzania, recorded by H. Rosti</p><p>S5 Paragalago zanzibaricus udzunwensis, Matundu, recorded by P. Honess</p><p>S6 Paragalago granti, Mdimba, Tanzania, recorded by S. Bearder</p><p>S7 Taita dwarf galago from Mbololo forest, Taita Hills, Kenya, recorded by H. Rosti</p><p>S8 Taita dwarf galago from Ngangao forest, Taita Hills, Kenya, recorded by H. Rosti</p><p>S9 Paragalago cocos, Diani Beach Kenya, recorded by H. Rosti</p><p>S10 Taita tree hyrax singing, Mbololo forest, Taita Hills, Kenya, recorded by H. Rosti</p><p>S11 Long 22 min recording of Taita tree hyrax singing, Mbololo forest, Taita Hills, Kenya, recorded by H. Rosti</p><p>S12 Rock hyrax song, Israel. Recorded by A. Ilany</p><p>S13 Strangled thwack from Taita Hills, Kenya, recorded by H. Rosti</p><p>S14 Dendrohyrax arboreus calls from Nanuyki, Kenia, recorded by H. Rosti</p><p>S15 Dendrohyrax dorsalis calls from Ostrava Zoo, Czechia, recorded by H. Rosti</p>
Fig. 6 in Hornets (Vespidae: Vespinae) of Singapore: ecology, identification, and national conservation assessment
Fig. 6. Nests of Vespa affinis in Singapore. A & B, mature nest in a tree and on a metal beam of a plant nursery respectively, C, lateral view of an embryo nest, D, multiple queens in an early embryo nest. (Photographs: Kam-Yung Soh, John Lee, and Zestin Soh).
Fig. 8 in Hornets (Vespidae: Vespinae) of Singapore: ecology, identification, and national conservation assessment
Fig. 8. Vespa analis in Singapore. A: dorsal view of a worker visiting flowers of Syzygium zeylanicum; B: mature nest built on a Caryota mitis palm; C: lateral view of a worker. (Photographs: Zestin Soh and Janice Ang).
Fig. 1 in Hornets (Vespidae: Vespinae) of Singapore: ecology, identification, and national conservation assessment
Fig. 1. Provespa anomala in Singapore. A, worker resting in a public lavatory in a forested park; B, worker capturing a small insect at a light trap at night; C, a swarm congregating under a shelter in a probable swarm-founding event; D, unusual occurrence of a worker attracted to shrimp paste in the day. (Photos: Marcus Ng, John Lee).
Fig. 3 in Hornets (Vespidae: Vespinae) of Singapore: ecology, identification, and national conservation assessment
Fig. 3. Vespa affinis in Singapore. A: worker capturing a flower-visiting sweat bee (Lasioglossum sp.); B: workers scavenging from a dead fish left behind at a fishing ground; C: worker with an insect caught in a spider's web; D: worker nectaring from flowers of Leea rubra. (Photos: Lim Yu Jun, Marcus Ng and Zestin Soh).
Fig. 7. The hoverfly Milesia vespoides, a in Hornets (Vespidae: Vespinae) of Singapore: ecology, identification, and national conservation assessment
Fig. 7. The hoverfly Milesia vespoides, a Batesian mimic of Vespa affinis and V. tropica, at Windsor Nature Park in January 2022. (Photograph by Yue Teng Lee).
Fig. 10 in Hornets (Vespidae: Vespinae) of Singapore: ecology, identification, and national conservation assessment
Fig. 10. Vespa multimaculata feeding on inflorescences of a palm (Arecaceae) in Selangor, Malaysia in September 2022. (Photographs: Mike Hooper).
Fig. 4 in Hornets (Vespidae: Vespinae) of Singapore: ecology, identification, and national conservation assessment
Fig. 4. Comparison of the clypeus of Vespa affinis (A) and V. tropica (B). The white arrows point to the clypeal apices, bordering a medial emargination, which are semi-circular protuberances in V. affinis but more strongly produced as triangular projections in V. tropica. (Photographs: John Lee).
Fig. 7 in Fishermen's local ecological knowledge on Southeastern Brazilian coastal fishes: contributions to research, conservation, and management
Fig. 7. Ordination plot of the correspondence analysis (first two axes) based on fishermen's answers about fishing season of the nine studied fish species in the southeastern Brazilian coast: Absa = Abudefduf saxatilis; Boru = Bodianus rufus; Cala = Caranx latus; Epma = Epinephelus marginatus; Haau = Haemulon aurolineatum; Heba = Hemiramphus balao; Kysp = Kyphosus spp.; Mifu = Micropogonias furnieri; Sesp = Seriola spp.
Fig. 6 in Fishermen's local ecological knowledge on Southeastern Brazilian coastal fishes: contributions to research, conservation, and management
Fig. 6. Ordination plot of the correspondence analysis (first two axes) based on fishermen's answers about migratory routes of the nine studied fish species in the southeastern Brazilian coast: Absa = Abudefduf saxatilis; Boru = Bodianus rufus; Cala = Caranx latus; Epma = Epinephelus marginatus; Haau = Haemulon aurolineatum; Heba = Hemiramphus balao; Kysp = Kyphosus spp.; Mifu = Micropogonias furnieri; Sesp = Seriola spp.
Fig. 4 in Fishermen's local ecological knowledge on Southeastern Brazilian coastal fishes: contributions to research, conservation, and management
Fig. 4. Trophic chain based on those food items and predators most cited by fishermen in the southeastern Brazilian coast for a) reef fishes and b) pelagic fishes. Numbers are percent of interviewed fishermen who mentioned each feeding interaction. Fish sizes are not in scale. Those feeding interactions that agree with reported feeding habits of these fishes in the biological literature are marked *(Randall, 1967; Berkeley & Houde, 1978; Menezes & Figueiredo, 1980; Sazima, 1986; Pipitone & Andaloro, 1995; Barreiros & Santos, 1998; Vasconcellos & Gasalla, 2001; Silvano, 2001; Silvano & Güth, 2006; Figueiredo & Vieira, 2005; Gibran, 2007).
Fig. 3 in Fishermen's local ecological knowledge on Southeastern Brazilian coastal fishes: contributions to research, conservation, and management
Fig. 3. Main habitats of fishes according to fishermen in the southeastern Brazilian coast: percentages of fishermen who mentioned each habitat category are in Appendix 1. Double-headed arrows indicate that fishes occur in both habitats in horizontal space (e.g. open ocean and reefs), up and down arrows indicate that fishes occur in both habitats in vertical space (e.g., near the bottom and at the surface). Fish sizes are not in scale.
Fig. 1 in Fishermen's local ecological knowledge on Southeastern Brazilian coastal fishes: contributions to research, conservation, and management
Fig. 1. Ordination plot of the correspondence analysis (first two axes) based on fishermen answers about uses of the nine studied fish species in the southeastern Brazilian coast: Absa = Abudefduf saxatilis; Boru = Bodianus rufus; Cala = Caranx latus; Epma = Epinephelus marginatus; Haau = Haemulon aurolineatum; Heba = Hemiramphus balao; Kysp = Kyphosus spp.; Mifu = Micropogonias furnieri; Sesp = Seriola spp.
Fig. 2 in Fishermen's local ecological knowledge on Southeastern Brazilian coastal fishes: contributions to research, conservation, and management
Fig. 2. Ordination plots of the correspondence analysis (first two axes) based on fishermen answers about fishing methods and baits of the nine studied fish species in the southeastern Brazilian coast: Absa = Abudefduf saxatilis; Boru = Bodianus rufus; Cala = Caranx latus; Epma = Epinephelus marginatus; Haau = Haemulon aurolineatum; Heba = Hemiramphus balao; Kysp = Kyphosus spp.; Mifu = Micropogonias furnieri; Sesp = Seriola spp.
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.