Search for: All records

ABSTRACT Quantifying the relative importance of genomic and epigenomic modulators of phenotype is a focal challenge in comparative physiology, but progress is constrained by availability of data and analytic methods. Previous studies have linked physiological features to coding DNA sequence, regulatory DNA sequence, and epigenetic state, but few have disentangled their relative contributions or unambiguously distinguished causative effects (‘drivers’) from correlations. Progress has been limited by several factors, including the classical approach of treating continuous and fluid phenotypes as discrete and static across time and environment, and difficulty in considering the full diversity of mechanisms that can modulate phenotype, such as gene accessibility, transcription, mRNA processing and translation. We argue that attention to phenotype nuance, progressing to association with epigenetic marks and then causal analyses of the epigenetic mechanism, will enable clearer evaluation of the evolutionary path. This would underlie an essential paradigm shift, and power the search for links between genomic and epigenomic features and physiology. Here, we review the growing knowledge base of gene-regulatory mechanisms and describe their links to phenotype, proposing strategies to address widely recognized challenges. 

In this paper, we introduce a creative pipeline to incorporate physiological and behavioral data from contemporary marine mammal research into data-driven animations, leveraging functionality from industry tools and custom scripts to promote scientific insights, public awareness, and conservation outcomes. Our framework can flexibly transform data describing animals’ orientation, position, heart rate, and swimming stroke rate to control the position, rotation, and behavior of 3D models, to render animations, and to drive data sonification. Additionally, we explore the challenges of unifying disparate datasets gathered by an interdisciplinary team of researchers, and outline our design process for creating meaningful data visualization tools and animations. As part of our pipeline, we clean and process raw acceleration and electrophysiological signals to expedite complex multi-stream data analysis and the identification of critical foraging and escape behaviors. We provide details about four animation projects illustrating marine mammal datasets. These animations, commissioned by scientists to achieve outreach and conservation outcomes, have successfully increased the reach and engagement of the scientific projects they describe. These impactful visualizations help scientists identify behavioral responses to disturbance, increase public awareness of human-caused disturbance, and help build momentum for targeted conservation efforts backed by scientific evidence. 

Marine mammals possess impressive breath-holding capabilities made possible by physiological adjustments during dives. Studying marine mammals in their natural environment unravels vital information about these physiological adjustments particularly when we can monitor altered dive behavior in response to stressful situations such as human-induced oceanic disturbances, presence of predators and altered prey distributions. An important indicator of physiological status during submergence is the change in oxygen saturation in the muscles and blood of these mammals. In this work, we aim to investigate oxygen storage and consumption in the muscles of free-diving elephant seals when exposed to disturbances such as sonar or predator sounds while they are at sea. Optical oxygen sensors are a mature technology with multiple medical applications that provide a way to measure oxygenation changes in biological tissues in a minimally invasive manner. While these sensors are well calibrated and readily available for humans, they are still inadequate for marine mammals primarily due to a very small number of test candidates and therefore little data is available for validation and calibration. We propose a probe geometry and associated mathematical model for measuring muscle oxygenation in seals based on near infrared diffuse transport with no need for calibration. A prototype based on this concept has been designed and tested on humans and rats. We use the test results to discuss the advantages and limitations of the approach. We also detail the constraints on size, sensor location, electronics, light source properties and detector characteristics posed by the unique biology of seals. 

Nitric oxide (NO) is a potent vasodilator, which improves perfusion and oxygen delivery during tissue hypoxia in terrestrial animals. The vertebrate dive response involves vasoconstriction in select tissues, which persists despite profound hypoxia. Using tissues collected from Weddell seals at necropsy, we investigated whether vasoconstriction is aided by downregulation of local hypoxia signaling mechanisms. We focused on NO–soluble guanylyl cyclase (GC)-cGMP signaling, a well-known vasodilatory transduction pathway. Seals have a lower GC protein abundance, activity, and capacity to respond to NO stimulation than do terrestrial mammals. In seal lung homogenates, GC produced less cGMP (20.1 ± 3.7 pmol·mg protein−1·min−1) than the lungs of dogs (−80 ± 144 pmol·mg protein−1·min−1 less than seals), sheep (−472 ± 96), rats (−664 ± 104) or mice (−1,160 ± 104, P < 0.0001). Amino acid sequences of the GC enzyme α-subunits differed between seals and terrestrial mammals, potentially affecting their structure and function. Vasoconstriction in diving Weddell seals is not consistent across tissues; perfusion is maintained in the brain and heart but decreased in other organs such as the kidney. A NO donor increased median GC activity 49.5-fold in the seal brain but only 27.4-fold in the kidney, consistent with the priority of cerebral perfusion during diving. Nos3 expression was high in the seal brain, which could improve NO production and vasodilatory potential. Conversely, Pde5a expression was high in the seal renal artery, which may increase cGMP breakdown and vasoconstriction in the kidney. Taken together, the results of this study suggest that alterations in the NO-cGMP pathway facilitate the diving response. 

Vocal production learning (“vocal learning”) is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical, and neurophysiological data from the Egyptian fruit bat (Rousettus aegyptiacus) with analyses of the genomes of 215 placental mammals. First, we identified a set of proteins evolving more slowly in vocal learners. Then, we discovered a vocal motor cortical region in the Egyptian fruit bat, an emergent vocal learner, and leveraged that knowledge to identify active cis-regulatory elements in the motor cortex of vocal learners. Machine learning methods applied to motor cortex open chromatin revealed 50 enhancers robustly associated with vocal learning whose activity tended to be lower in vocal learners. Our research implicates convergent losses of motor cortex regulatory elements in mammalian vocal learning evolution.