The Evolutionary Biology of Vision in \u3ci\u3eDaphnia\u3c/i\u3e

Eyes have attracted the attention of evolutionary biologist since the field’s infancy. In On the Origin of Species, in fact, Darwin famously remarked on the proposition that natural selection could engineer the eye, saying “[it is] absurd in the highest possible degree.” Though, he goes on to explain, beautifully and simply, how his theory of evolution by natural selection could produce such an organ. Indeed, eyes are remarkable examples of complex information acquisition systems that have evolved from simple beginnings. Eyes allow animals to extract environmental information from light, which informs physiological and behavioral responses to resources, predation, and mates. The morphological and physiological features of eyes define the absolute bounds of visual capabilities. These characteristics of eyes highlight why they are particularly interesting from an evolutionary perspective: variation affects what and how environmental information can be collected and processed, thereby potentially altering many of the animal’s ecological interactions. While a rich literature has documented myriad facets of eye evolution, there remain many areas that merit more investigation. The aim of my thesis is to broaden our understanding of the evolution of vision by exploring three related, yet different, aspects using the ecological model organism, Daphnia. I present a study that examines the ecological factors that potentially influence eye morphology. Second, I present a study that demonstrates fitness variation associated with eye diameter, and pair these observations with information on genetic variation of eye diameter. Lastly, I present a study evaluating the evolution of opsins—the gene largely responsible for vision—in Daphnia

Visual Search and Target Selection Using a Bounded Optimal Model of State Estimation & Control

Visual attention and motor control are tightly coupled in domains requiring a human operator to interact with a visual interface. Here, we integrate a boundedly optimal visual attention model with two separate motor control models and compare the predictions made by these models against perceptual and motor data collected from human subjects engaged in a parafoveal detection task. The results indicate that humans use an optimal motor control policy limited by precision constraints – humans executed ballistic movements using near-optimal velocity (i.e., bang-bang control), but imprecision in those movements often caused participants to overshoot their targets, necessitating corrective action. Motor movements did not reflect response hedging, but rather a perceptual-motor policy permitting ballistic movements to a target only after localization confidence exceeded a threshold. We conclude that a boundedly-optimal perceptual-motor model can predict aspects of human performance visual search tasks requiring motor response

Evaluating Outer Segment Length as A Surrogate Measure of Peak Foveal Cone Density

Adaptive optics (AO) imaging tools enable direct visualization of the cone photoreceptor mosaic, which facilitates quantitative measurements such as cone density. However, in many individuals, low image quality or excessive eye movements precludes making such measures. As foveal cone specialization is associated with both increased density and outer segment (OS) elongation, we sought to examine whether OS length could be used as a surrogate measure of foveal cone density. The retinas of 43 subjects (23 normal and 20 albinism; aged 6–67 years) were examined. Peak foveal cone density was measured using confocal adaptive optics scanning light ophthalmoscopy (AOSLO), and OS length was measured using optical coherence tomography (OCT) and longitudinal reflectivity profile-based approach. Peak cone density ranged from 29,200 to 214,000 cones/mm2(111,700 ± 46,300 cones/mm2); OS length ranged from 26.3 to 54.5 μm (40.5 ± 7.7 μm). Density was significantly correlated with OS length in albinism (p \u3c 0.0001), but not normals (p = 0.99). A cubic model of density as a function of OS length was created based on histology and optimized to fit the albinism data. The model includes triangular cone packing, a cylindrical OS with a fixed volume of 136.6 μm3, and a ratio of OS to inner segment width that increased linearly with increasing OS length (R2 = 0.72). Normal subjects showed no apparent relationship between cone density and OS length. In the absence of adequate AOSLO imagery, OS length may be used to estimate cone density in patients with albinism. Whether this relationship exists in other patient populations with foveal hypoplasia (e.g., premature birth, aniridia, isolated foveal hypoplasia) remains to be seen

The effects of ractopamine-HCl (optaflexx) on performance, carcass characteristics, and meat quality of finishing feedlot heifers

Beta-adrenergic agonists are commonly used in livestock production to accelerate growth by enhancing lean tissue gain. These compounds repartition nutrients away from fat deposition and toward protein accretion. Generally, increased growth is associated with ractopamine feeding, which improves feed conversion and increases body weight gain. However, little data exists on the effects of ractopamine-HCl on live performance or carcass characteristics of beef heifers. Data released from Elanco Animal Health indicate that differences between gender may exist in response to ractopamine, and therefore appropriate strategies for the administration of this compound must be defined for heifers independent of those for steers. The objective of this study was to determine the effects of Optaflexx, when fed for different dosages over different durations, on finishing heifer performance

Liat1, an arginyltransferase-binding protein whose evolution among primates involved changes in the numbers of its 10-residue repeats

The arginyltransferase Ate1 is a component of the N-end rule pathway, which recognizes proteins containing N-terminal degradation signals called N-degrons, polyubiquitylates these proteins, and thereby causes their degradation by the proteasome. At least six isoforms of mouse Ate1 are produced through alternative splicing of Ate1 pre-mRNA. We identified a previously uncharacterized mouse protein, termed Liat1 (ligand of Ate1), that interacts with Ate1 but does not appear to be its arginylation substrate. Liat1 has a higher affinity for the isoforms Ate1^(1A7A) and Ate1^(1B7A). Liat1 stimulated the in vitro N-terminal arginylation of a model substrate by Ate1. All examined vertebrate and some invertebrate genomes encode proteins sequelogous (similar in sequence) to mouse Liat1. Sequelogs of Liat1 share a highly conserved ∼30-residue region that is shown here to be required for the binding of Liat1 to Ate1. We also identified non-Ate1 proteins that interact with Liat1. In contrast to Liat1 genes of nonprimate mammals, Liat1 genes of primates are subtelomeric, a location that tends to confer evolutionary instability on a gene. Remarkably, Liat1 proteins of some primates, from macaques to humans, contain tandem repeats of a 10-residue sequence, whereas Liat1 proteins of other mammals contain a single copy of this motif. Quantities of these repeats are, in general, different in Liat1 of different primates. For example, there are 1, 4, 13, 13, 17, and 17 repeats in the gibbon, gorilla, orangutan, bonobo, neanderthal, and human Liat1, respectively, suggesting that repeat number changes in this previously uncharacterized protein may contribute to evolution of primates

Eyes Over Puget Sound: Producing Validated Satellite Products to Support Rapid Water Quality Assessments in Puget Sound

Eyes Over Puget Sound (EOPS) is a rapid communication and outreach product developed by the Washington State Department of Ecology that provides a concise synthesis of near real-time data sources in Puget Sound, WA. Monthly EOPS reports summarize aerial photographic surveys, in-situ ferry observations, satellite products, CTD profiles, and mooring data within 2-days of completing each aerial survey. To facilitate the rapid development and synthesis of satellite information products, EOPS developed a framework for producing regionally-tuned products; validated using coincident ferry-based measurements of chlorophyll fluorescence, turbidity, CDOM fluorescence, temperature, and salinity. Daily ferry transects provide a consistent suite of high-resolution measurements necessary to characterize small-scale spatio-temporal variability across the large optical gradients that are present. Ferry data are made available within 24 hours and allow validation efforts to be performed on a daily-, sensor-, and image-specific basis. This framework has been used to validate and merge satellite products from a variety of platforms including MERIS, MODIS, HICO, and Landsat. Future efforts will utilize EOPS-validated satellite products to refine coupled 3-D hydrodynamic/water quality models currently being developed for the region

Decomposition of Reaching Movements Enables Detection and Measurement of Ataxia

Technologies that enable frequent, objective, and precise measurement of ataxia severity would benefit clinical trials by lowering participation barriers and improving the ability to measure disease state and change. We hypothesized that analyzing characteristics of sub-second movement profiles obtained during a reaching task would be useful for objectively quantifying motor characteristics of ataxia. Participants with ataxia (N=88), participants with parkinsonism (N=44), and healthy controls (N=34) performed a computer tablet version of the finger-to-nose test while wearing inertial sensors on their wrists. Data features designed to capture signs of ataxia were extracted from participants’ decomposed wrist velocity time-series. A machine learning regression model was trained to estimate overall ataxia severity, as measured by the Brief Ataxia Rating Scale (BARS). Classification models were trained to distinguish between ataxia participants and controls and between ataxia and parkinsonism phenotypes. Movement decomposition revealed expected and novel characteristics of the ataxia phenotype. The distance, speed, duration, morphology, and temporal relationships of decomposed movements exhibited strong relationships with disease severity. The regression model estimated BARS with a root mean square error of 3.6 points, r2 = 0.69, and moderate-to-excellent reliability. Classification models distinguished between ataxia participants and controls and ataxia and parkinsonism phenotypes with areas under the receiver-operating curve of 0.96 and 0.89, respectively. Movement decomposition captures core features of ataxia and may be useful for objective, precise, and frequent assessment of ataxia in home and clinic environments

Marine seismic surveys and ocean noise : time for coordinated and prudent planning

Marine seismic surveys use intense (eg >= 230 decibel [dB] root mean square [RMS]) sound impulses to explore the ocean bottom for hydrocarbon deposits, conduct geophysical research, and establish resource claims under the United Nations Convention on the Law of the Sea. The expansion of seismic surveys necessitates greater regional and international dialogue, partnerships, and planning to manage potential environmental risks. Data indicate several reasons for concern about the negative impacts of anthropogenic noise on numerous marine species, including habitat displacement, disruption of biologically important behaviors, masking of communication signals, chronic stress, and potential auditory damage. The sound impulses from seismic surveys - spanning temporal and spatial scales broader than those typically considered in environmental assessments - may have acute, cumulative, and chronic effects on marine organisms. Given the international and transboundary nature of noise from marine seismic surveys, we suggest the creation of an international regulatory instrument, potentially an annex to the existing International Convention on the Prevention of Pollution from Ships, to address the issue.Publisher PDFPeer reviewe