Publications by authors named "TF Duda"

The Beaufort duct (BD) is a subsurface sound channel in the western Arctic Ocean formed by cold Pacific Winter Water (PWW) sandwiched between warmer Pacific Summer Water (PSW) and Atlantic Water (AW). Sound waves can be trapped in this duct and travel long distances without experiencing lossy surface/ice interactions. This study analyzes BD vertical and temporal variability using moored oceanographic measurements from two yearlong acoustic transmission experiments (2016-2017 and 2019-2020).

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Many venomous animals express toxins that show extraordinary levels of variation both within and among species. In snakes, most studies of venom variation focus on front-fanged species in the families Viperidae and Elapidae, even though rear-fanged snakes in other families vary along the same ecological axes important to venom evolution. Here we characterized venom gland transcriptomes from 19 snakes across two dipsadine rear-fanged genera ( and , Colubridae) and two front-fanged genera (, Viperidae; , Elapidae).

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A one-year fixed-path observation of seasonally varying subsurface ducted sound propagation in the Beaufort Sea is presented. The ducted and surface-interacting sounds have different time behaviors. To understand this, a surface-forced computational model of the Chukchi and Beaufort Seas with ice cover is used to simulate local conditions, which are then used to computationally simulate sound propagation.

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Conidae is a hyperdiverse family of marine snails that has many hallmarks of adaptive radiation. Hybridization and introgression may contribute to such instances of rapid diversification by generating novel gene combinations that facilitate exploitation of distinct niches. Here we evaluated whether or not these mechanisms may have contributed to the evolutionary history of a subgenus of Conidae (Virroconus).

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Background: Although mitochondrial DNA (mtDNA) of many animals tends to mutate at higher rates than nuclear DNA (nuDNA), a recent survey of mutation rates of various animal groups found that the gastropod family Bradybaenidae (suborder Helicina) shows a nearly 40-fold difference in mutation rates of mtDNA ([Formula: see text]) and nuDNA ([Formula: see text]), while other gastropod taxa exhibit only two to five-fold differences. To determine if Bradybaenidae represents an outlier within Gastropoda, I compared estimated values of [Formula: see text]/[Formula: see text] of additional gastropod groups. In particular, I reconstructed mtDNA and nuDNA gene trees of 121 datasets that include members of various clades contained within the gastropod subclasses Caenogastropoda, Heterobranchia, Patellogastropoda, and Vetigastropoda and then used total branch length estimates of these gene trees to infer [Formula: see text]/[Formula: see text].

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A fundamental understanding of the impact of petrochemicals and other stressors on marine biodiversity is critical for effective management, restoration, recovery, and mitigation initiatives. As species-specific information on levels of petrochemical exposure and toxicological response are lacking for the majority of marine species, a trait-based assessment to rank species vulnerabilities to petrochemical activities in the Gulf of Mexico can provide a more comprehensive and effective means to prioritize species, habitats, and ecosystems for improved management, restoration and recovery. To initiate and standardize this process, we developed a trait-based framework, applicable to a wide range of vertebrate and invertebrate species, that can be used to rank relative population vulnerabilities of species to petrochemical activities in the Gulf of Mexico.

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A fully three-dimensional (3D) omnidirectional numerical coupled mode model of acoustic propagation is detailed. A combination of normal mode and finite element computational methods is applied to produce the numerical results. The technique is tested in a strongly range-dependent ocean environment modeled after the Hudson Canyon.

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Three-dimensional (3D) underwater sound field computations have been used for a few decades to understand sound propagation effects above sloped seabeds and in areas with strong 3D temperature and salinity variations. For an approximate simulation of effects in nature, the necessary 3D sound-speed field can be made from snapshots of temperature and salinity from an operational data-driven regional ocean model. However, these models invariably have resolution constraints and physics approximations that exclude features that can have strong effects on acoustics, example features being strong submesoscale fronts and nonhydrostatic nonlinear internal waves (NNIWs).

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Species interactions are fundamental ecological forces that can have significant impacts on the evolutionary trajectories of species. Nonetheless, the contribution of predator-prey interactions to genetic and phenotypic divergence remains largely unknown. Predatory marine snails of the family Conidae exhibit specializations for different prey items and intraspecific variation in prey utilization patterns at geographic scales.

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It is predicted that Arctic Ocean acidity will increase during the next century as a result of carbon dioxide accumulation in the atmosphere and migration into ocean waters. This change has implications for sound transmission because low-pH seawater absorbs less sound than high-pH water. Altered pH will affect sound in the 0.

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Knowledge concerning the taxonomic diversity of marine organisms is crucial for understanding processes associated with species diversification in geographic areas that are devoid of obvious barriers to dispersal. The marine gastropod family Conidae contains many species complexes due to lack of clear morphological distinctiveness and existence of morphological intergradations among described species. Conus flavidus Lamarck, 1810 and Conus frigidus Reeve, 1848 are currently recognized as distinct taxa, but are often difficult to distinguish by morphological characters and include several synonyms, including Conus peasei Brazier, 1877.

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Background: Venomous organisms serve as wonderful systems to study the evolution and expression of genes that are directly associated with prey capture. To evaluate the relationship between venom gene expression and prey utilization, we examined these features among individuals of different ages of the venomous, worm-eating marine snail Conus ebraeus. We determined expression levels of six genes that encode venom components, used a DNA-based approach to evaluate the identity of prey items, and compared patterns of venom gene expression and dietary specialization.

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Article Synopsis
  • The study introduces a new classification for cone snails (family Conidae) based on molecular phylogenetic analyses of 329 species, challenging both traditional one-genus models and recent multi-family classifications.
  • The researchers propose placing all cone snails into one family (Conidae) with four main genera, where one genus alone contains approximately 85% of known species, highlighting distinct evolutionary lineages.
  • The new classification includes 71 subgenera and aims to simplify communication about these species by reducing the number of accepted genera and retaining the majority within the largest genus, facilitating better understanding of their relationships.
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Geographical heterogeneity in the composition of biotic interactions can create a mosaic of selection regimes that may drive the differentiation of phenotypes that operate at the interface of these interactions. Nonetheless, little is known about effects of these geographical mosaics on the evolution of genes encoding traits associated with species interactions. Predatory marine snails of the family Conidae use venom, a cocktail of conotoxins, to capture prey.

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This article documents the public availability of (i) transcriptome sequence data, assembly and annotation, and single nucleotide polymorphisms (SNPs) for the cone snail Conus miliaris; (ii) a set of SNP markers for two biotypes from the Culex pipiens mosquito complex; (iii) transcriptome sequence data, assembly and annotation for the mountain fly Drosophila nigrosparsa; (iv) transcriptome sequence data, assembly and annotation and SNPs for the Neotropical toads Rhinella marina and R. schneideri; and (v) partial genomic sequence assembly and annotation for 35 spiny lizard species (Genus Sceloporus).

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Background: Predatory marine gastropods of the genus Conus exhibit substantial variation in venom composition both within and among species. Apart from mechanisms associated with extensive turnover of gene families and rapid evolution of genes that encode venom components ('conotoxins'), the evolution of distinct conotoxin expression patterns is an additional source of variation that may drive interspecific differences in the utilization of species' 'venom gene space'. To determine the evolution of expression patterns of venom genes of Conus species, we evaluated the expression of A-superfamily conotoxin genes of a set of closely related Conus species by comparing recovered transcripts of A-superfamily genes that were previously identified from the genomes of these species.

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We present a large-scale molecular phylogeny that includes 320 of the 761 recognized valid species of the cone snails (Conus), one of the most diverse groups of marine molluscs, based on three mitochondrial genes (COI, 16S rDNA and 12S rDNA). This is the first phylogeny of the taxon to employ concatenated sequences of several genes, and it includes more than twice as many species as the last published molecular phylogeny of the entire group nearly a decade ago. Most of the numerous molecular phylogenies published during the last 15years are limited to rather small fractions of its species diversity.

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The propagation of weakly dispersive modal pulses is investigated using data collected during the 2004 long-range ocean acoustic propagation experiment (LOAPEX). Weakly dispersive modal pulses are characterized by weak dispersion- and scattering-induced pulse broadening; such modal pulses experience minimal propagation-induced distortion and are thus well suited to communications applications. In the LOAPEX environment modes 1, 2, and 3 are approximately weakly dispersive.

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An alternating direction implicit (ADI) three-dimensional fluid parabolic equation solution method with enhanced accuracy is presented. The method uses a square-root Helmholtz operator splitting algorithm that retains cross-multiplied operator terms that have been previously neglected. With these higher-order cross terms, the valid angular range of the parabolic equation solution is improved.

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Data collected during the 2004 Long-range Ocean Acoustic Propagation Experiment provide absolute intensities and travel times of acoustic pulses at ranges varying from 50 to 3200 km. In this paper a subset of these data is analyzed, focusing on the effects of seafloor reflections at the shortest transmission range of approximately 50 km. At this range bottom-reflected (BR) and surface-reflected, bottom-reflected energy interferes with refracted arrivals.

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A three-dimensional Cartesian parabolic-equation model with a higher-order approximation to the square-root Helmholtz operator is presented for simulating underwater sound propagation in ocean waveguides. The higher-order approximation includes cross terms with the free-space square-root Helmholtz operator and the medium phase speed anomaly. It can be implemented with a split-step Fourier algorithm to solve for sound pressure in the model.

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Motivated by measurements made in the 2004 Long-Range Ocean Acoustic Propagation Experiment (LOAPEX), the problem of mode processing transient acoustic signals collected on two nearby vertical line arrays is considered. The first three moments (centroid, variance, and skewness) of broadband distributions of acoustic energy with fixed mode number (referred to as modal group arrivals) are estimated. It is shown that despite the absence of signal coherence between the two arrays and poor high mode number energy resolution, the centroid and variance of these distributions can be estimated with tolerable errors using piecewise coherent mode processing as described in this paper.

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The results of mode-processing measurements of broadband acoustic wavefields made in the fall of 2004 as part of the Long-Range Ocean Acoustic Propagation Experiment (LOAPEX) in the eastern North Pacific Ocean are reported here. Transient wavefields in the 50-90 Hz band that were recorded on a 1400-m long 40 element vertical array centered near the sound channel axis are analyzed. This array was designed to resolve low-order modes.

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Sound at 85 to 450 Hz propagating in approximately 80-m depth water from fixed sources to a joint horizontal/vertical line array (HLA/VLA) is analyzed. The data are from a continental shelf area east of Delaware Bay (USA) populated with tidally generated long- and short-wavelength internal waves. Sound paths are 19 km in the along-shore (along internal-wave crest) direction and 30 km in the cross-shore direction.

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To understand the issues associated with the presence (or lack) of azimuthal isotropy and horizontal (along isobath) invariance of low-frequency (center frequencies of 600 Hz and 900 Hz) acoustic propagation in a shelfbreak environment, a series of experiments were conducted under the Autonomous Wide-Aperture Cluster for Surveillance component of the Shallow Water 2006 experiment. Transmission loss data reported here were from two mobile acoustic sources executing (nearly) circular tracks transmitting to sonobuoy receivers in the circle centers, and from one 12.5 km alongshelf acoustic track.

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