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60 results for “Pinnipeds”
Data: Approaching a population level assessment of body size in pinnipeds using drones, an early warning of environmental degradation.
<p>Data and R sctipts for measuring harbour seal body sizes and estimating mass based on .shp files containing outlines. Associated with the manusctipt currently titled "Approaching a population level assessment of body size in pinnipeds using drones, an early warning of environmental degradation."</p> <p>1_Seal_Volume_Function.R: A function for the estimation of length, width, and ellipsoid volume of harbour seals from georeferenced polygons representing individual outlines 2_Polygon_Process.R: This script uses the curved_length_vol function (1_Seal_Volume_Function.R) to process a folder full of .shp file subfolders containing georeferenced polygons representing individual outlines and outputs a .csv with estimates of length, width, and ellipsoid volume for each individual. 3_Calibration.R: This script processes and calibrates summarized harbor seal measurements based on reference to known individuals</p> <p>CSV_Files: Folder containing data files</p> <p>Known_Seals.csv: True measurments of length and mass for known seals with derived estimates of 'true' width and volume. Drone based estimates of length, width, simple and complex volume for the same individuals, information on pose.</p> <p>measurments.csv: Drone based estimates of length, width, simple and complex volume for all individuals.</p> <p>Pup_growth.csv: Data on pup mass by age from Harding et al. 2005 (<a href="https://doi.org/10.1111/j.0269-8463.2005.00945.x" rel="nofollow">https://doi.org/10.1111/j.0269-8463.2005.00945.x</a>).</p> <p>Slottsskogen_Data.csv: True and drone based measurments for individual captive harbour seals taken on two seperate occasions.</p> <p>Summarised_Weights.csv: True measurments of length, girth, and mass for harbour seals.</p>
Pinniped metatree data and scripts
<p>This is a copy of relevant data from the pinniped metatree project. Below explains the file structure of the folder.</p> <p>## InputData</p> <p>Folder containing the following subfolders:</p> <p>### Molecular_Data</p> <p>Folder containing two subdirectories (fulton and Lopes), each of which contains a further two subdirectories (mrp and xml) that contain the Matrix Representations with Parsimony (MRP) nexus files and XML files (see below), respectivly, for the two molecular studies used as backbone constraints</p> <p>### MRP</p> <p>Matrix Representations with Parsimony (MRPs) obtained by re-analysing each morphological input data set under parsimony and retaining only unique biparitions until all such biparitions have been sampled.</p> <p>### NEXUS</p> <p>The original character-taxon matrices for each morphological input data set.</p> <p>### TNT</p> <p>TNT format input files used for reanalysis of each morphological input dataset. Each file contains the relevant commands to run the analyses.</p> <p>### XML</p> <p>XML files that record important metadata about each input data set, particularly data set dependence and taxonomic reconciliation.</p> <p><br> ## metatree_files</p> <p>Folder containing the metatree data organised in the following subfolders:</p> <p>### Consensus_trees</p> <p>Folder containing Strict (SCC) and Majority Rule (MRC) trees before (STR_***) and after (no prefix) safely reinserting taxa</p> <p>### Files</p> <p>All files output by running the metatree function to assemble a reconciled complete MRP matrix over all input datasets:</p> <p>#### Character weights </p> <p>weights for each character</p> <p>#### DataSetWeights.txt </p> <p>information of the contribution of each dataset to the overall analysis </p> <p>#### FULL.nex / FULL.tnt</p> <p>MRP files in nexus and tnt format containing all taxa (not used in main analysis)</p> <p>#### STR.nex / STR.tnt</p> <p>Safely reduced input files in nexus and tnt format. The tnt format file is the one used in main analyses.</p> <p>### STR.tnt</p> <p>text file containing safely removed taxa and the rules used to reinsert them</p> <p>#### TaxonomyTreee.tre</p> <p>newick string containing the paleobiology database taxonomy for PanPinnipeds in tree form. Used in the metatree analysis as a very downweighted input.</p> <p><br> ### MPTS</p> <p>Folder containing all most parsimonious trees before and after Safe Taxonomic Reinsertion</p> <p>### tnt</p> <p>MPTs from each of 1000 independent TNT searches (.tnt) and associated search info from screen output (.txt) </p> <p><br> ### README.md</p> <p>This file.</p> <p>### Scripts</p> <p>The set of R scripts used to generate the metatree</p> <p>#### BuildBeastXML.R</p> <p>A function used to assemble a nexus file, starting tree, topology constraints, and age priors for BEAST input. Is sourced by the file CreateBeastInput_Script.R</p> <p>#### Build_Metatree_Files_Combined.R</p> <p>Script to read in input files from input_files folder and assemble MRP matrices for generation of metatree</p> <p>#### CreateBeastInput_Script.R</p> <p>Script to read in a set of input files contained in the TimeTree folder and output a set of files that can be used to build a BEAST XML for Fossilized Birth Death tip dating analyses with a relaxed molecular clock</p> <p>#### makemrpandscandmpts.R</p> <p>Utility script to read the output of TNT for each source study, produce separate MPT and Strict Cosensus files, and generate an MRP file that can be used for input into the metatree function</p> <p>#### process_beast_output.R</p> <p>Script to read combined, post-burnin output from beast and find the median tree under the Kendall-Colijn distance metric. This tree is used in subsequent macroevolutionary analyses.</p> <p>#### runtntoutputcollator.R</p> <p>Utility script to read the output from TNT analysis of the ensemble MRP matrix, find all unique shortest trees, and assemble a combined MPT file, consensus trees, and perform safe taxonomic reinsertion. </p> <p>### TimeTree</p> <p>Files and Folders related to BEAST time-tree inference. Organized as follows:</p> <p>#### BEAST_Run</p> <p>Folder containing input xml file, log and tree files from the two independent MCMC analyses, combined post-burnin log and tree files, and the median tree from the combined posterior sample.</p> <p>#### partitionFinder</p> <p>PartitionFinder input and output files used to identify the appropriate partitioning scheme and evolutionary models for the augmented Fulton and Strobeck alignment. </p> <p>#### strictclockrun</p> <p>xml and output files from a short analysis of extant pinnipeds only under a strict molecular clock. The posterior mean root height divided by the approximate age of crown pinnipeds was used to define a mean for the lognormal prior on the relaxed molecular clock in the main analysis</p> <p>#### MRC.tre</p> <p>The majority Rule Consensus metatree used to derive topological constraints for the BEAST analysis</p> <p>#### pinnipeds_extant_beast.nex</p> <p>augmented version of the Fulton and Strobeck alignment used in BEAST analysis</p> <p>#### Taxa_FAD.csv</p> <p>Stratigraphic uncertainty associated with the first appearances of fossil taxa. Used to define age ranges for fossils for the Fossilized Birth Death analysis.</p> <p> </p> <p><br> ### TimeTreeInference</p> <p>Folder containing the R scripts and temporal data used to build the timetrees as well as the following subfolders:</p> <p>#### Dangerous</p> <p>Subfolder containing the results for the Dangerous timetree analyses.</p> <p>#### Risky</p> <p>Subfolder containing the results for the Risky timetree analyses.</p> <p>#### Safe</p> <p>Subfolder containing the results for the Safe timetree analyses.</p>
Research methods and Comparative examination of pinniped craniofacial musculature and its role in aquatic feeding
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Data from: Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds
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Hiding in plain sight: The biomolecular identification of pinniped use in medieval manuscripts – MALDI and mtDNA data set
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Pinniped comparative survival data
<p>Survival rates are a central component of life-history strategies of large vertebrate species. However, comparative studies seldom investigate interspecific variation in survival rates with respect to other life-history traits, especially for males. The lack of such studies could be due to the challenges associated with obtaining reliable datasets, incorporating information on the 0-1 probability scale, or dealing with several types of measurement error in life-history traits, which can be a computationally intensive process that is often absent in comparative studies. We present a quantitative approach using Bayesian phylogenetically controlled regression with the flexibility to incorporate uncertainty in estimated survival rates and quantitative life-history traits while considering genetic similarity among species and uncertainty in relatedness. As with any comparative analysis, our approach makes several assumptions regarding the generalizability and comparability of empirical data from separate studies. Our model is versatile in that it can be applied to any species group of interest and include any life-history traits as covariates. We used an unbiased simulation framework to provide "proof of concept" for our model and applied a slightly richer model to a real-data example for pinnipeds. Pinnipeds are an excellent taxonomic group for comparative analysis, but survival rate data are scarce. Our work elucidates the challenges associated with addressing important questions related to broader ecological life-history patterns and how survival-reproduction tradeoffs might shape evolutionary histories of extant taxa. Specifically, we underscore the importance of having high-quality estimates of age-specific survival rates and information on other life-history traits that reasonably characterize a species for accurately comparing across species.</p>
Raw images, annotations, and vvipr code archive to support 'Evaluating thermal and color sensors for automating detection of penguins and pinnipeds in images collected with an unoccupied aerial system''
<p>Images, annotations, and code archived here were used in the paper "Evaluating a machine learning approach to detect penguins and pinnipeds in thermal and color images collected with an unoccupied aerial system" submitted for publication in Drones. The files contain raw thermal and color images of aggregations of gentoo (<em>Pygoscelis papua</em>) and chinstrap (<em>P. antarcticus</em>) penguins and Antarctic fur seals (<em>Arctocephalus gazella</em>). All images were collected with the Flir DuoPro R camera (Teledyne FLIR LLC, Wilsonville, OR, U.S.A.), carried into flight under an APH-28 hexacopter (Aerial Imaging Solutions, LLC, Old Lyme, CT, U<strong>.</strong>S<strong>.</strong>A<strong>.)</strong> at Cape Shirreff, Livingston Island, Antarctica (60.79 °W, 62.46 °S), during the austral summer of 2019-20. All aerial surveys occurred under the Marine Mammal Protection Act Permit No. 20599 granted by the Office of Protected Resources/National Marine Fisheries Service, the Antarctic Conservation Act Permit No. 2017-012, NMFS-SWFSC Institutional Animal Care and Use Committee Permit No. SWPI 2014-03R, and all domestic and international UAS flight regulations. The annotations of the images were conducted using VIAME desktop software (v 0.16.1 or later;<a href="https://github.com/VIAME/VIAME">https://github.com/VIAME</a>) or the online using the DIVE interface (https://viame.kitware.com/). Model results were assessed with the vvipr code (v.0.3.2), archived here and available online (https://github.com/us-amlr/vvipr/releases/tag/v0.3.2).</p> <p> </p>
Pinniped comparative survival data
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Data from: Molecular discovery of filarial nematode DNA in an endangered wild pinniped
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Año Nuevo Island Animal Count: analyzing citizen science pinniped counts from drone imagery
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Pinniped censuses at Año Nuevo, California, 1967-2017
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Data from: Evolution of age at primiparity in pinnipeds in the absence of the quality-quantity trade-off in reproduction
Age at primiparity (AP) is a key life history trait which is crucial to the evolution of life-history strategies. This trait is particularly interesting in pinnipeds (walrus, eared seals and true seals), which are monotocous animals. Thus, the commonly observed trade-off between offspring quality and quantity does not apply to this taxon. Therefore, comparative studies on the evolution of AP might shed light on other important evolutionary correlates when litter size is fixed. Using phylogenetic generalised least squares analyses, we found a strong negative and robust correlation between relative birth mass (mean pup birth mass as a proportion of mean adult female mass) and AP. Rather than trading-off an early start of reproduction with light relative offspring mass, this result suggests that pinnipeds exhibit either faster (i.e. higher relative offspring mass leading to shorter lactation length, and thus shorter inter-birth interval) or slower life histories and that an early AP and a heavy relative offspring mass co-evolved into a comparatively fast life history strategy. On the other hand, AP was positively related to lactation length: a later start of reproduction was associated with a longer lactation length. Consequently, variation in AP in pinnipeds seems to be affected by an interplay between costs and benefits of early reproduction mediated by relative investment into the single offspring via relative birth mass and lactation length.
Data from: Disentangling the contribution of sexual selection and ecology to the evolution of size dimorphism in pinnipeds
The positive relationship between sexual size dimorphism (SSD) and harem size across pinnipeds is often cited as a textbook example of sexual selection. It assumes that female aggregation selected for large male size via male-male competition. Yet, it is also conceivable that SSD evolved prior to polygyny due to ecological forces. We analysed eleven life history traits in 35 pinniped species to determine their co-evolutionary dynamics and infer their most likely evolutionary trajectories contrasting these two hypotheses. We find support for SSD having evolved prior to changes in the mating system, either as a consequence of niche partitioning during aquatic foraging or in combination with sexual selection on males to enforce copulations on females. Only subsequently did polygyny evolve, leading to further coevolution as the strength of sexual selection intensified. Evolutionary sequence analyses suggest a polar origin of pinnipeds and indicate that SSD and polygyny are intrinsically linked to a suite of ecological and life history traits. Overall, this study calls for the inclusion of ecological variables when studying sexual selection and argues for caution when assuming causality between coevolving traits. It provides novel insights into the role of sexual selection for the co-evolutionary dynamics of SSD and mating system.
Fig. 7 in Can You Hear Me Now? A Comparative Survey Of Pinniped Auditory Apparatus Morphology
Fig. 7. Representative Carnivore Basicrania of Types of Auditory Bullae: A — Ursus, representation of Type A; B — Canis, representation of Type B (one third the scale). Al — alisphenoid; Bo — basioccipital; Bs — basisphenoid; Eam — external auditory meatus; Ect — ectotympanic, outlined with red dotted line; Ent — rostral + caudal entotympanic, marked with blue; Exo — exoccipital; Ma — mastoid process of petrosal; P — promontorium; Sq — squamous portion of temporal bone; pos. car. — can. posterior opening of the carotid canal; pos. lac. for. — posterior lacerate foramen which is known as the jugular foramen (modified from Tedford, 1976).
Fig. 1 in Can You Hear Me Now? A Comparative Survey Of Pinniped Auditory Apparatus Morphology
Fig. 1. Comparisons of Reptilian and Mammalian Ears: A — Pelycosaur; B — Early mammal; C — Reptilian middle ear; D — Mammalian middle ear (modified from Pearson Education Inc).
Fig. 8. A in Re-Evaluation Of Morphological Characters Questions Current Views Of Pinniped Origins
Fig. 8. A — Allodesmus kelloggi, LACM 4320, holotype, mounted skeleton, Natural History Museum of Los Angeles County; B — Zalophus, Clark Park, CA; C — Allodesmus kelloggi, forelimb, Buena Vista Museum of Natural History, Bakersfield, CA. Forelimb (D) and hindlimb (E — reversed, left, adult male) of Monachus tropicalis (USNM 22543). Arrow indicates middle phalanx in the V digit of the hindlimb.
Fig. 10 in Re-Evaluation Of Morphological Characters Questions Current Views Of Pinniped Origins
Fig. 10. Dorsal views of skulls of modern representative of pinnipeds (modified from Howell, 1929; King, 1983 b) of: A — otariids (supraorbital process of the frontal bone is large and shelf-like); B — phocids (supraorbital process is absent); C — odobenids (supraorbital process is absent also).
Fig. 8 in Arthropod parasites of Antarctic and Subantarctic birds and pinnipeds: A review of host-parasite associations
Fig. 8. Distribution of the number of parasite species/subspecies recorded in relation to the number of host species known to breed at the different Antarctic sub-regions, excluding stragglers and contaminants. Legend: AAP = Antarctic Peninsula (including South Shetland Islands and Palmer Archipelago), AWS = Antarctica Weddell Sea sector, AAT = Antarctica Atlantic Ocean sector (including Bouvet Island), AIW = Antarctica Indian Ocean West sector, AIE = Antarctica Indian Ocean East sector, ARS = Antarctica Ross Sea sector (including Scott and Balleny Islands), APW = Antarctica Pacific Ocean West sector, APE = Antarctica Pacific Ocean East sector (including Peter I Island), SOI = South Orkney Island, SGI = South Georgia Island, SSI = South Sandwich Islands, PEI = Prince Edward Islands, CRI = Crozet Islands, KEI = Kerguelen Islands, HMI = Heard and McDonald Islands.
Data from: Disentangling the contribution of sexual selection and ecology to the evolution of size dimorphism in pinnipeds
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Data from: Evolution of age at primiparity in pinnipeds in the absence of the quality-quantity trade-off in reproduction
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