Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements.

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.

Non-Torpid Heterothermy in Mammals: Another Category along the Homeothermy-Hibernation Continuum.

Variability in body temperature is now recognized to be widespread among whole-body endotherms with homeothermy being the exception rather than the norm. A wide range of body temperature patterns exists in extant endotherms, spanning from strict homeothermy, to occasional use of torpor, to deep seasonal hibernation with many points in between. What is often lost in discussions of heterothermy in endotherms are the benefits of variations in body temperature outside of torpor. Endotherms that do not use torpor can still obtain extensive energy and water savings from varying levels of flexibility in normothermic body temperature regulation. Flexibility at higher temperatures (heat storage or facultative hyperthermia) can provide significant water savings, while decreases at cooler temperatures, even outside of torpor, can lower the energetic costs of thermoregulation during rest. We discuss the varying uses of the terms heterothermy, thermolability, and torpor to describe differences in the amplitude of body temperature cycles and advocate for a broader use of the term "heterothermy" to include non-torpid variations in body temperature.

Evolutionary constraint and innovation across hundreds of placental mammals.

Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.

High Body Temperature is an Unlikely Cause of High Viral Tolerance in Bats.

The global SARS-CoV-2 pandemic and the role of bats in zoonotic spillover have renewed interest in the flight-as-fever hypothesis, which posits that high body temperatures experienced by bats during flight contribute to their high viral tolerance. We argue that flight-as-fever is unlikely to explain why bats harbor more viruses than other mammals on the basis of two lines of reasoning. First, flight temperatures reported in the literature overestimate true flight temperatures because of methodologic limitations. Second, body temperatures in bats are only high relative to humans, and not relative to many other mammals. We provide examples of mammals from diverse habitats to show that temperatures in excess of 40 C during activity are quite common in species with lower viral diversity than bats. We caution scientists against stating the flight-as-fever hypothesis as unquestioned truth, as has repeatedly occurred in the popular media in the wake of the SARS-CoV-2 pandemic.

Transcriptional host-pathogen responses of Pseudogymnoascus destructans and three species of bats with white-nose syndrome.

Understanding how context (e.g., host species, environmental conditions) drives disease susceptibility is an essential goal of disease ecology. We hypothesized that in bat white-nose syndrome (WNS), species-specific host-pathogen interactions may partly explain varying disease outcomes among host species. We characterized bat and pathogen transcriptomes in paired samples of lesion-positive and lesion-negative wing tissue from bats infected with Pseudogymnoascus destructans in three parallel experiments. The first two experiments analyzed samples collected from the susceptible Nearctic Myotis lucifugus and the less-susceptible Nearctic Eptesicus fuscus, following experimental infection and hibernation in captivity under controlled conditions. The third experiment applied the same analyses to paired samples from infected, free-ranging Myotis myotis, a less susceptible, Palearctic species, following natural infection and hibernation (n = 8 sample pairs/species). Gene expression by P. destructans was similar among the three host species despite varying environmental conditions among the three experiments and was similar within each host species between saprophytic contexts (superficial growth on wings) and pathogenic contexts (growth in lesions on the same wings). In contrast, we observed qualitative variation in host response: M. lucifugus and M. myotis exhibited systemic responses to infection, while E. fuscus up-regulated a remarkably localized response. Our results suggest potential phylogenetic determinants of response to WNS and can inform further studies of context-dependent host-pathogen interactions.