Comparative Energetics of Mammalian Thermoregulatory Physiology

Endothermy allows species to decouple body temperature from environmental temperatures but does not equate to endothermic species maintaining those constant temperatures. Instead, heterothermy fluctuating body temperatures, both in and outside of torpor is common and allows endotherms to expand the limits of thermoneutrality. Thermolability is likely to be more common in the tropics and subtropics, where species live within or above their thermoneutral zone. My dissertation research focused on the heterothermic-homeothermic continuum, specifically quantifying where on the continuum different species fall at certain times and why those species have evolved to be at those points. I quantified the thermal profile of Sundamys muelleri, a tropical, nocturnal rodent. S. muelleri increased evaporative water loss and subcutaneous body temperature at ambient temperatures of 33°C, indicating an upper thermal limit, although metabolic rate showed no increase up to the highest ambient temperature (38.2°C), suggesting this species will tolerate future climatic changes. I then studied the extremely thermally-labile Tenrec ecaudatus. Although there was a wide range of intraindividual variability in metabolic rate and body temperature at both the higher and lower ambient temperatures, I identified a lower thermal limit thermoneutrality of 19.1°C. I then investigated how detailed climate variables may affect thermolability in Chiropteran species across biogeographical zones. I quantified how thermolability phenotypes in bats are globally distributed but found no relationship between thermoregulatory variables of body temperature and lower thermal limits and climatic variables. The unique thermoregulatory adaptations in Chiroptera gives us insights into the physiology and evolution of thermolability in endotherms. Finally, I focused on thermolability at the limits of thermoneutrality in Rodentia, the most diverse and specious clade of Mammalia. Body temperatures at the upper limits of thermoneutrality and the differential between the upper limit and the body temperature at that limit increase with latitude. However, the thermoneutral zone was wider for species with ranges at latitudes closer to the equator than the poles. Lower latitude species have lower temperatures at upper thermal limits and maintain their body temperatures closer to those limits. Through my research we can see how thermolability is shaped by evolutionary history, phylogeny, biogeographical patterns, and climate

Habitat quality, torpor expression and pathogen transmission in little brown bats (Myotis lucifugus)

Protection of habitat can improve survival and reproductive fitness of threatened and endangered wildlife, particularly if that habitat helps individuals maintain energy balance. Temperate bats are heterothermic and rely on torpor to save energy during winter hibernation and, to a lesser extent, during summer. However, torpor delays parturition and slows lactation for females, and inhibits sperm production for males, so reproductive bats should select warm roosts to help them avoid torpor. Torpor may also slow healing rates, which could have implications for bats that survive the winter with white-nose syndrome (WNS), a devastating fungal skin disease impacting hibernating North American bats. WNS survivors must emerge from hibernation and initiate reproduction while also healing from extensive wing damage caused by the disease. Warm roosting habitat could help WNS survivors avoid torpor to heal and reproduce more quickly, enhancing population recoveries. However, reduced torpor expression and increased activity and exploration could increase the chance of bats acquiring pathogens and parasites from substrates in their environment. I tested the hypotheses that warm roosting habitat: 1) reduces use of torpor by endangered little brown bats (Myotis lucifugus); but 2) increases the risk of pathogen acquisition from substrates in the environment. I captured bats from a fall swarm and housed individuals in outdoor flight enclosures equipped with either four heated or four unheated roost boxes. I quantified torpor expression using skin temperature dataloggers and used ultraviolet (UV) fluorescent powder as a proxy pathogen which I applied to one of the four roost boxes in each tent. Bats provided with warm roosts used less torpor (p<0.0001), but the amount of time a bat spent in torpor (p=0.26), had no effect on intensity of infection with the proxy pathogen. My data highlight roost temperature as a driver of torpor expression in little brown bats but suggest that heated roosts will not speed rates of pathogen or parasite acquisition from the environment. This result supports the potential of enhancement of summer roosting habitat as a management strategy for WNS.Master of Science in Bioscience, Technology, and Public Polic

Thermal Imaging and Physiological Analysis of Cold-Climate Caribou-Skin Clothing

Protective clothing is essential for human existence in the Arctic, and caribou-skin clothing has played a pivotal&nbsp;role for millennia. Although people with northern experience often extol caribou-skin clothing, few scientific studies have investigated its properties. We used infrared thermal imaging in a pilot study to compare authentic caribou-skin clothing sewn by traditional Inuit seamstresses with two other types of cold-weather clothing: a standard-issue, Canadian army, winter uniform and an ensemble of modern retail clothing designed for extreme cold (a down anorak and snowmobile pants). To make the comparison, two subjects sequentially wore the three types of clothing—caribou skin, army uniform, and modern retail—in a still air, uniform thermal environment (where radiant temperatures of all environmental surfaces were equal to air temperature) at −21°C to −23°C (−6°F to −10°F). Thermal imaging quantifies the temperature of the outer surface of clothing, thereby providing key, functionally relevant information on the interface where clothing and environment meet. Under otherwise similar conditions, a low clothing surface temperature indicates superior clothing performance and a reduced rate of heat loss from the body to the environment. Caribou-skin clothing was similar to modern extreme-cold retail clothing: the whole-body composite surface temperature of our subjects wearing caribou-skin clothing was −22.1°C to −22.7°C, compared with −21.6°C in both subjects wearing the modern retail clothing. The army winter uniform (−18.9°C to −20.0°C) was inferior. These quantitative results were mirrored by the subjects’ subjective impressions. A particular advantage of thermal imaging is that it pinpoints locations in clothing where heat leaks occur. Although the two types of modern clothing exhibited heat leaks at zippered structures (even though fully closed), the caribou-skin clothing evaded such heat leaks by lacking such structures, because it is donned over the head. The integral hood characteristic of a caribou-skin parka was also superior in comparison to&nbsp;the detachable hood of the army uniform.Les vêtements de protection sont essentiels à l’existence humaine dans l’Arctique, et les vêtements en peau de caribou y jouent un rôle vital depuis des millénaires. Même si les gens qui ont évolué dans le Nord vantent souvent les mérites des vêtements en peau de caribou, peu d’études scientifiques ont été réalisées au sujet de leurs propriétés. Nous nous sommes servi d’imagerie thermique infrarouge dans le cadre d’une étude pilote visant à comparer les vêtements en peau de caribou authentique cousus par des couturières inuites traditionnelles à deux autres types de vêtements pour temps froid : un uniforme d’hiver standard de l’Armée canadienne et un ensemble de vêtements modernes du détail conçus pour des froids extrêmes (un anorak en duvet et des pantalons de motoneige). À des fins de comparaison, deux sujets ont porté, dans l’ordre séquentiel, les trois types de vêtements — vêtement en peau de caribou, uniforme de l’armée et vêtements modernes du détail — dans des conditions de vent nul thermique uniforme (où les températures radiatives de toutes les surfaces environnementales sont égales à la température de l’air) moyennant des températures allant de −21 °C à −23 °C (de −6 °F à −10 °F). L’imagerie thermique quantifie la température de la surface extérieure du vêtement, ce qui permet d’obtenir de l’information fonctionnellement pertinente et essentielle sur le point de rencontre du vêtement et de l’environnement. Dans des conditions par ailleurs semblables, la faible température du vêtement en surface indique un rendement supérieur pour ce vêtement et un taux réduit de perte de chaleur du corps à l’environnement. Les vêtements en peau de caribou ont donné des résultats semblables aux vêtements pour froid extrême modernes du détail : la température composite du corps entier de nos sujets portant les vêtements en peau de caribou variait de −22,1 °C à −22,7 °C, comparativement à −21,6 °C chez les deux sujets portant les vêtements modernes du détail. Les températures de l’uniforme d’hiver de l’armée étaient inférieures (de −18,9 °C à −20,0 °C).&nbsp;Ces résultats quantitatifs cadraient avec les impressions subjectives des sujets. Un des avantages particuliers de l’imagerie thermique, c’est qu’elle permet de repérer là où les pertes de chaleur se produisent dans les vêtements. Bien que les deux types de vêtements modernes perdaient de la chaleur à l’endroit des fermetures éclair (même si elles étaient fermées complètement), les vêtements en peau de caribou n’affichaient pas de telles pertes de chaleur en raison de l’absence de structures de ce genre parce que ces vêtements s’enfilent par la tête. Par ailleurs, il y a lieu de noter que la caractéristique intégrale du capuchon du&nbsp;parka en peau de caribou était également supérieure à celle du capuchon amovible de l’uniforme militaire

Thermal Imaging and Physiological Analysis of Cold-Climate Caribou-Skin Clothing

Protective clothing is essential for human existence in the Arctic, and caribou-skin clothing has played a pivotal role for millennia. Although people with northern experience often extol caribou-skin clothing, few scientific studies have investigated its properties. We used infrared thermal imaging in a pilot study to compare authentic caribou-skin clothing sewn by traditional Inuit seamstresses with two other types of cold-weather clothing: a standard-issue, Canadian army, winter uniform and an ensemble of modern retail clothing designed for extreme cold (a down anorak and snowmobile pants). To make the comparison, two subjects sequentially wore the three types of clothing—caribou skin, army uniform, and modern retail—in a still air, uniform thermal environment (where radiant temperatures of all environmental surfaces were equal to air temperature) at −21°C to −23°C (−6°F to −10°F). Thermal imaging quantifies the temperature of the outer surface of clothing, thereby providing key, functionally relevant information on the interface where clothing and environment meet. Under otherwise similar conditions, a low clothing surface temperature indicates superior clothing performance and a reduced rate of heat loss from the body to the environment. Caribou-skin clothing was similar to modern extreme-cold retail clothing: the whole-body composite surface temperature of our subjects wearing caribou-skin clothing was −22.1°C to −22.7°C, compared with −21.6°C in both subjects wearing the modern retail clothing. The army winter uniform (−18.9°C to −20.0°C) was inferior. These quantitative results were mirrored by the subjects’ subjective impressions. A particular advantage of thermal imaging is that it pinpoints locations in clothing where heat leaks occur. Although the two types of modern clothing exhibited heat leaks at zippered structures (even though fully closed), the caribou-skin clothing evaded such heat leaks by lacking such structures, because it is donned over the head. The integral hood characteristic of a caribou-skin parka was also superior in comparison to the detachable hood of the army uniform

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

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\u27s vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes

A genomic timescale for placental mammal evolution

The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral genome-wide phylogenomic signals using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes, and analyzed extensive catalogs of structural variants. Interordinal relationships exhibit relatively low rates of phylogenomic conflict across diverse datasets and analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades that radiated during the Cenozoic. Genomic time trees reveal an accumulation of cladogenic events before and immediately after the Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance and the K-Pg extinction in the placental radiation

Integrating gene annotation with orthology inference at scale

Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method that integrates structural gene annotation and orthology inference. TOGA implements a different paradigm to infer orthologous loci, improves ortholog detection and annotation of conserved genes compared with state-of-the-art methods, and handles even highly fragmented assemblies. TOGA scales to hundreds of genomes, which we demonstrate by applying it to 488 placental mammal and 501 bird assemblies, creating the largest comparative gene resources so far. Additionally, TOGA detects gene losses, enables selection screens, and automatically provides a superior measure of mammalian genome quality. TOGA is a powerful and scalable method to annotate and compare genes in the genomic era