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Figure 1 in Relationships of cochlear coiling shape and hearing frequencies in cetaceans, and the occurrence of infrasonic hearing in Miocene Mysticeti
Figure 1. Cochlear anatomy and visualization of methods. (a) Three-dimensional rendering of the cochlea (shown as right) of Balaenoptera acutorostrata in apical view. (b) Same, virtually transected along the modiolus (mod) showing the primary and secondary bony laminae (bl1 and bl2, respectively). (c) Radii ratio method as applied in this study: circles superimposed onto basal and apical turns of a 2-D projection of the path tracing the basilar membrane within the cochlea. Dots represent three points on each circle for calculation of the respective radius. (d) Landmark-based geometric morphometrics: 3-D resampled path with landmarks 1 to 40.
Figure 3 in Relationships of cochlear coiling shape and hearing frequencies in cetaceans, and the occurrence of infrasonic hearing in Miocene Mysticeti
Figure 3. (a–g) Linear regressions for significant correlations of PC1 and PC2 with individual variables tested in this study.
Figure 2 in Relationships of cochlear coiling shape and hearing frequencies in cetaceans, and the occurrence of infrasonic hearing in Miocene Mysticeti
Figure 2. PCA plot of shape variation of cochlear coiling. Lines represent 95 % confidence ellipses for Mysticeti (red) and Odontoceti (blue). Shape change along the axes is shown as black landmark configurations against the average shape (in gray) in apical view and in profile. Known lowest hearing limits in Hz are given for extant cetaceans (see Table 2). Number in parentheses refers to a fetus. * denotes extinct mysticetes with presumed very low frequency hearing (50 Hz and below). ** denotes extinct mysticetes with presumed infrasonic hearing (below 20 Hz). Gray numbers represent identification numbers (ID) listed in Table 2. The specimens plotting outside of the ellipse are Megapteropsis robusta (ID12) and Eschrichtiidae indet. (ID6).
Figure 1 in Why we should develop guidelines and quantitative standards for using genetic data to delimit subspecies for data-poor organisms like cetaceans
Figure 1. Depiction of the divergence of lineages with four times (T1–T4) chosen to illustrate different levels of biological organization. At T1 the yellow lineage is found across the distribution and although there are likely Demographically Independent Populations (DIPs) that differ in frequencies of the blue, yellow, and red lineages, there are no discontinuities. At T2 some lineages may be diagnosable but likely do not yet appear to be separate lineages. At T3 three groups (the blue/green, yellow, and orange/red lineages) meet the subspecies definition (they are diagnosable and appear to be diverging separately). The divergence level is not sufficient that reconvergence can be ruled out. Between T3 and T4, barriers to gene flow change such that the yellow lineage comes into contact with the blue/green and red-dominated lineages. Blue has diverged in a manner by which gene flow does not resume and the green/yellow lineage dies out. The yellow lineage reconverges and persists alongside the red lineage with a small level of gene flow (orange). At T4 the blue lineage is a species evolving separately from the yellow/red species. The yellow/red species has two subspecies that are both diagnosable and partially diverged.
Figure 2 in Examining metrics and magnitudes of molecular genetic differentiation used to delimit cetacean subspecies based on mitochondrial DNA control region sequences
Figure 2. Relationship between ΦST and Nei's estimate of net divergence (dA) among cetacean population, subspecies, and species pairs estimated using mitochondrial DNA control region sequence data. Specific values mentioned in the text are numbered: 1 = Neophocaena species; 2 = killer whale populations. The three green squares in the left-hand side of the figure (ΦST <0.07) represent, from bottom to top, the subspecies comparisons for S. attenuata, S. longirostris, and L. obscurus, respectively.
Figure 1 in Examining metrics and magnitudes of molecular genetic differentiation used to delimit cetacean subspecies based on mitochondrial DNA control region sequences
Figure 1. Box and whisker plots showing median and 1st and 3rd quartiles, and minimum and maximum values for six metrics of genetic divergence among cetacean population, subspecies, and species pairs estimated using mitochondrial DNA control region sequence data.
Figure 3 in Guidelines and quantitative standards to improve consistency in cetacean subspecies and species delimitation relying on molecular genetic data
Figure 3. Flow diagram for subspecies delineation using combined quantitative and qualitative standards. The threshold values assume the user is evaluating a case relying on mtDNA control region data. Percent Diagnosable (PD) is the smallest strata-specific correct classification score in a given comparison (e.g., PD50 in two-strata comparisons in Archer et al. 2017). The second box in the second row (other evidence to meet subspecies definition) allows for subspecies delineation when both conditions are not met using mtDNA. This box could be used either for the case when one condition is met and one unmet or when both just barely miss meeting the standards. For example, consider the case with PD <95% and dA> 0.004. Diagnosability could be achieved with morphological data or nuclear data that are sufficient for subspecies but not for full species.
Figure 2. A in Guidelines and quantitative standards to improve consistency in cetacean subspecies and species delimitation relying on molecular genetic data
Figure 2. A comparison of the pairs of populations (red triangles), subspecies (green squares) and species (blue circles) estimated by Rosel et al. (2017a). Net nucleotide divergence (dA) is shown on a natural log scale to better illustrate differences between the pairwise comparisons at low levels of divergence. Bars show the central 95th-pecentile of the estimate distributions. The solid vertical line at dA = 0.020 delimits all but one species and correctly excludes all subspecies pairs. The vertical dashed line at dA = 0.004 delimits all populations from the higher taxonomic levels and correctly delimits seven of eleven subspecies. The horizontal dashed lines are two potential thresholds for percent diagnosable (80% and 95%) that are discussed in the text.
Online Appendix and Cetacean Datasets for: The Occurrence Birth-Death Process for combined-evidence analysis in macroevolution and epidemiology
<p>Phylodynamic models generally aim at jointly inferring phylogenetic relationships, model parameters, and more recently, the number of lineages through time, based on molecular sequence data. In the fields of epidemiology and macroevolution these models can be used to estimate, respectively, the past number of infected individuals (prevalence) or the past number of species (paleodiversity) through time. Recent years have seen the development of "total-evidence" analyses, which combine molecular and morphological data from extant and past sampled individuals in a unified Bayesian inference framework. Even sampled individuals characterized only by their sampling time, i.e. lacking morphological and molecular data, which we call occurrences, provide invaluable information to reconstruct the past number of lineages.</p> <p>Here, we present new methodological developments around the Fossilized Birth-Death Process enabling us to (i) incorporate occurrence data in the likelihood function; (ii) consider piecewise-constant birth, death and sampling rates; and (iii) reconstruct the past number of lineages, with or without knowledge of the underlying tree. We implement our method in the RevBayes software environment, enabling its use along with a large set of models of molecular and morphological evolution, and validate the inference workflow using simulations under a wide range of conditions.</p> <p>We finally illustrate our new implementation using two empirical datasets stemming from the fields of epidemiology and macroevolution. In epidemiology, we infer the prevalence of the COVID-19 outbreak on the Diamond Princess ship, by taking into account jointly the case count record (occurrences) along with viral sequences for a fraction of infected individuals. In macroevolution, we infer the diversity trajectory of cetaceans using molecular and morphological data from extant taxa, morphological data from fossils, as well as numerous fossil occurrences. The joint modeling of occurrences and trees holds the promise to further bridge the gap between between traditional epidemiology and pathogen genomics, as well as paleontology and molecular phylogenetics.</p>
Fig. 2 in Linear Transect Surveys Of Abundance And Density Of Cetaceans In The Area Near The Dzharylgach Island In The North-Western Black Sea
Fig. 2. Linear transect survey of cetaceans near the Dzharylgach Island in 2017 (lt, linear transect survey encounters; vis, additional visual observations).
Fig. 1 in Linear Transect Surveys Of Abundance And Density Of Cetaceans In The Area Near The Dzharylgach Island In The North-Western Black Sea
Fig. 1. Linear transect survey of cetaceans near the Dzharylgach Island in 2016 (lt, linear transect survey encounters; vis, additional visual observations).
Data from: Convergence and constraint in the cranial evolution of mosasaurid reptiles and early cetaceans
<p>The repeated return of tetrapods to aquatic life provides some of the best-known examples of convergent evolution. One comparison which has received relatively little focus is that of mosasaurids (a group of Late Cretaceous squamates) and archaic cetaceans (the ancestors of modern whales and dolphins), both of which show high levels of craniodental disparity, similar initial trends in locomotory evolution, and global distributions. Here we investigate convergence in skull ecomorphology during the initial aquatic radiations of these groups. A series of functionally informative ratios were calculated from 38 species, with ordination techniques used to reconstruct patterns of functional ecomorphospace occupation. The earliest fully aquatic members of each clade occupied different regions of ecomorphospace, with basilosaurids and early russellosaurines exhibiting marked differences in cranial functional morphology. Subsequent ecomorphological trajectories notably diverge: mosasaurids radiated across ecomorphospace with no clear pattern and numerous reversals, whereas cetaceans notably evolved towards shallower, more elongated snouts, perhaps as an adaptation for capturing smaller prey. Incomplete convergence between the two groups is present among megapredatory and longirostrine forms, suggesting stronger selection on cranial function in these two ecomorphologies. Our study highlights both the similarities and divergences in craniodental evolutionary trajectories between archaic cetaceans and mosasaurids, with convergences transcending their deeply divergent phylogenetic affinities.</p>
Recordings from: Evaluation of a coastal acoustic buoy for cetacean detections, bearing accuracy, and exclusion zone monitoring
<p>1.<span> </span>There is strong socio-political support for offshore wind development in US territorial waters, and construction is planned off several east coast states. Some of the planned development sites coincide with important habitat for critically endangered North Atlantic right whales. Both exclusion zones and passive acoustic monitoring are important tools for managing interactions between marine mammals and human activities. Understanding where animals are with respect to exclusion zones is important to avoid costly construction delays while minimizing the potential for negative impacts. Impact piling from construction of hundreds of offshore wind turbines likely requires exclusion zones as large as 10 km.</p> <p>2.<span> </span>We have developed a three-hydrophone passive acoustic monitoring system that provides bearing information along with marine mammal detections to allow for informed management decisions in real-time. Multiple units form a monitoring system designed to determine whether marine mammal calls originate from inside or outside of an exclusion zone. In October 2021 we undertook a full system validation, with a focus on evaluating the detection range and bearing accuracy of the system with respect to right whale upcalls. Five units were deployed in Mid-Atlantic waters and we played more than >3,500 simulated right whale upcalls at known locations to characterize the detection function and bearing accuracy of each unit. The modeled results of the detection function error were then used to compare the effectiveness of a bearing-based system to a single sensor that can only detect a signal but not ascertain directivity.</p> <p>3.<span> </span>Field trials indicated maximum detection ranges from 4–7.3 km depending on source and ambient noise levels. Simulations showed that incorporating bearing detections provides a substantial improvement in false alarm rates (6 to 12 times depending on number of units, placement, and signal to noise conditions) for a small increase in the risk of missed detections inside of an exclusion zone (1–3%). </p> <p>4.<span> </span>We show that the system can be used for monitoring exclusion zones and clearly highlight the value of including bearing estimation into exclusion zone monitoring plans while noting that placement and configuration of units should reflect anticipated ambient noise conditions.</p>
FIGURE 2. CMM-V-10108, a in A Miocene cetacean vertebra showing a partially healed longitudinal shear-compression fracture, possibly the result of domoic acid toxicity or failed predation
FIGURE 2. CMM-V-10108, a Miocene pathological cetacean vertebra associated with the one shown in Figures 5 and 6. A. Anterior view showing a major shear-compression fracture with comminution. B. right lateral view, and C. posterior view showing the intact fused epiphysis.
FIGURE 3. CMM-V-10108 in A Miocene cetacean vertebra showing a partially healed longitudinal shear-compression fracture, possibly the result of domoic acid toxicity or failed predation
FIGURE 3. CMM-V-10108, shear-fractured Miocene cetacean lumbar vertebra in three transverse CT-scan images. These CT-scan images cut through the vertebra in an anterodorsal-posteroventral direction. A. CT-scan image through the anterior portion of the vertebra showing the wide-open lumen of the shear-compression fracture. B. CT-scan image from approximately 1 cm behind A, showing the thickness of the periosteal reactive bone layer. C. CT-image at about the midpoint in the length of the vertebra showing the posterior-most part of the sheared base of the centrum compressed (telescoped) into the body of the centrum.
FIGURE 7. CMM-V-8522 in A Miocene cetacean vertebra showing a partially healed longitudinal shear-compression fracture, possibly the result of domoic acid toxicity or failed predation
FIGURE 7. CMM-V-8522, Otodus megalodon lower anterior tooth in labial view. This tooth was found touching one of the two pathological vertebrae (CMM-V-10108). Notice the spall-fracture marking the tip of the tooth. White scale bar equals 10 mm.
FIGURE 6. CMM-V-10108, a in A Miocene cetacean vertebra showing a partially healed longitudinal shear-compression fracture, possibly the result of domoic acid toxicity or failed predation
FIGURE 6. CMM-V-10108, a second Miocene pathological cetacean vertebra (also shown in Figure 5) associated with the one shown in Figures 2-4. A. CT-scan image towards the anterior end of the vertebra. B. CT-scan image at about the midpoint in the length of the vertebra showing the thickness of the periosteal reactive bone.
FIGURE 8 in A Miocene cetacean vertebra showing a partially healed longitudinal shear-compression fracture, possibly the result of domoic acid toxicity or failed predation
FIGURE 8. One possible way in which the shear-compression fracture occurred in CMM-V-10108. The posterior vertebral column was severely hyperflexed to such a degree that at least one of its vertebrae experienced a shear-compression fracture, and the periosteum was pulled away from most of the sides of both vertebrae. Artwork by Clarence (Shoe) Schumaker (CMM).
FIGURE 5. CMM-V-10108, a in A Miocene cetacean vertebra showing a partially healed longitudinal shear-compression fracture, possibly the result of domoic acid toxicity or failed predation
FIGURE 5. CMM-V-10108, a second Miocene pathological cetacean vertebra (CT-scans shown in Figure 6) associated with the one shown in Figures 2-4. A. Posterior view showing that the neural spine is incomplete and that the sides of the centrum are covered with periosteal reactive bone. B. ventral view to highlight the periosteal reactive bone. In B, the anterior end of the centrum is up.
FIGURE. 1 in A Miocene cetacean vertebra showing a partially healed longitudinal shear-compression fracture, possibly the result of domoic acid toxicity or failed predation
FIGURE. 1. The site along Calvert Cliffs where the two pathological cetacean vertebrae (CMM-V-10108) and associated Otodus megalodon tooth (CMM-V-8522) were found in situ in Shattuck-Zone 12. Looking north along the cliffs at Warrior's Rest. Photo by M. Ellwood.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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.