New Course: Computational Paleophysiology
Summer field & lab course on the methods scientists use to reconstruct the soft tissues and physiology of extinct animals. For more info go to the ' Phys Course ' page
Welcome to the homepage of the Farmer lab at the University of Utah. In this lab we study evolutionary biology. We primarily ask questions about major transitions and key innovations of vertebrates. We seek to understand how such transitions occurred through a sequence of small modifications from the ancestral conditions. To address these questions we integrate functional studies with phylogenetic analyses and data from the fossil record.
cg.frmr at gmail.com
The avian respiratory system is very interesting because seperate regions are responsible for moving air in and out of the body (the air-sacs) and for gas-exchange (the lung). In addition air moves in the same direction through the gas-exchange regions of the lung on inspiration as it does on exhalation due to aerodynamic mechanisms (Bernoulli effects, jetting, etc.). We are investigating when, why, and how unidirectional airflow in lungs evolved by studying air-flow patterns in the lungs of the sister group to birds, the crocodilians.
Birds and mammals are both warm-blooded animals, that is they produce enough heat through their own metabolism to keep their bodies warm when needed. In contast the majority of vertebrates are ectothermic and rely on heat sources and heat sinks to regulate their body temperature. The energetic cost of endothermy can be very large for small animals and therefore it is believed a selective benefit that outweighs this cost must exist. We are investigating the hypothesis that a major advantage of being warm blooded is that it allows parents to incubate embryos and neonates, which in turn reduces the time needed for development and growth to sexual maturity.
A key function of the cardiovascular system is to transport oxygen from the environment to the mitochondria of tissues where it is used in the burning of fuel to produce ATP. An animal's aerobic capacity determines whether or not the animal can sustain vigorous locomotion or must rely on bursts of activity that are unsustainable because of the production of lactic acid. A great aerobic capacity allows animals to migrate long distances, it expands their foraging ranges, enables sustained intraspecific competitions, or allows animals to outlast their predator or their prey. Hence the evolution of locomotor stamina opens up new niches. There are clear advantages to the evolution of locomotor stamina but what innovations were necessary to build the cardiopulmonary system of endurance athletes? How do the cardiovascular systems of sit-and-wait predators differ from thos of endurance athletes?
Shunts and Digestion in Crocodilians
Cardiac shunts and myocardial oxygenation
Venous Return
Gastralia are rib-like bones located in the ventral abdominal body wall. Among extant vertebrates, they are found in the New Zealand frog Leiopelma, in the tuatara ( Sphenodon ), some lizards, and in crocodilians. They are pleisiomorphic for amniotes but were lost in most lineages and greatly elaborated in archosauromorphs. Known as the cuirassal basket, we have found that these bones play a role during inspiration in the American alligator. We are investigating the potential role in ventilation in extinct archosaurs such as pterosaurs, theropod dinosaurs, and early birds such as Archeopteryx .
A specialized muscle mechanically coupled to the lung has evolved independently in mammals, crocodilians, some amphibians, and some turtles. This muscle is named the "diaphragmaticus" but is not homologous. Traditionally the function of the diaphragmaticus is thought to be ventilation, but we are finding the muscles help the animals maneuver underwater by moving the lungs within the body cavity to change the center of buoyancy relative to the center of mass and thereby affect pitch and roll.
Traditionally it is thought that the selective advantage of lungs in early fishes was that they allowed the animals to live in hypoxic aquatic habitats, which appeared to be widespread during the Devonian. However, the fishes that first evolved lungs lived in near-shore marine environments of the Silurian, and marine environments and not usually hypoxic. We have been investigating the hypothesis that the selective benefit of lungs is they provide oxygen to the heart, which lacks a coronary circulation and relies on lumenal blood to provide oxygen. Predictions of this hypothesis are being investigated with respect to the physiology and function of the cardiovascular system of extant air-breathing fishes, such as the gar ( Lepisosteus sp) and bowfin ( Amia calva ).
Ph.D. 1998. Brown University, Providence RI. Physiology, Donald Jackson (advisor)
B.A. 1987. University of Idaho, Moscow ID. Physics
Professional positions:
Contact Dr. Farmer if you would like a full CV: cg.frmr at gmail.com
Emma R. Schachner Ph.D.
Graduate Students:
Research Engineer:
Undergraduate Students:
Select Undergraduate Research Projects:
Coming soon...
Graduate Students
Undergraduate Students
Publications with students:
We analyze our CT Data using various different 3D modeling software programs.
The free DICOM viewer OsiriX is available here: http://www.osirix-viewer.com/
To download the original DICOM files of the CT and µCT scans follow the given links.
New Course: Computational Paleophysiology Summer 2012
To apply for a spot in this course email send your answers to the following questions to cg.frmr_gmail.com along with your name and a phone number that you can be reached at:
1) Tell us about your career stage and aspirations. How far along are you in your academic career? Upon graduating, do you aspire to graduate school, professional school, etc.? (200 words max)
2) Tell us why you are interested in taking this course. What do you hope to get out of it? Are there particular topics that you are interested in learning about? (500 words max)
3) What is your level of experience with fieldwork? Have you ever participated in a paleontological excavation? (250 words max)
4) List your previous math and physics courses and the grades you received.
The National Science Foundation
Society for the Study of Amphibians and Reptiles
Amphibiaweb
Society of Integrative and Comparative Biology
International Society of Vertebrate Morphology
Society of Vertebrate Paleontology
PUBLICATIONS
Farmer, C.G. 2011. On the Evolution of Vascular Patterns of Tetrapods. Journal of Morphology 272: in press but Epub available ahead of print: doi: 10.1002/jmor.10986
Reide, T., I.T. Tokuda, C.G. Farmer . 2011. Subglottal pressure and fundamental frequency control in contact calls of juvenile Alligator mississippiensis. Journal of Experimental Biology. 214: 3082- 3095 (cover).
Schachner, E.R., C.G Farmer , A.T. McDonald, P.Dodson. 2011. Evolution of the dinosauriform respiratory apparatus: new evidence from the postcranial axial skeleton. Anatomical Record 294:1532-1547.
Farmer, C.G. and K. Sanders. 2010. Unidirectional airflow in the lungs of alligators. Science. 327:338-340
Farmer, C.G . 2010. The provenance of the alveolar and parabronchial lungs: Insights from paleoecology and the discovery of cardiogenic, unidirectional airflow in the American alligator ( Alligator mississippiensis ). Physiological and Biochemical Zoology 83 (4): 561-575 (cover).
Torday, J.S., Powell, F.L., Farmer, CG , Orgeig, S., Nielsen, H.C., Hall, A.J. 2010. Leptin integrates vertebrate evolution: From oxygen to the blood-gas barrier. Respiration Physiology and Neurobiology 173S:S37-S42.
Uriona, TJ, Lyon, M., Farmer, CG . 2009. The importance of the diaphragmaticus to dive-time in the American alligator ( Alligator mississippiensis ). Zoology. 112 (4): 263-269.
Uriona, T.J., and C.G Farmer . 2008. Recruitment of the diaphragmaticus, ischipubis, and other respiratory muscles to control pitch and roll in the American alligator ( Alligator mississippiensis ). Journal of Experimental Biology 211(7):1141-1147 (cover).
Farmer, C.G. , TJ Uriona, M. Steenblik, D. Olsen, K. Sanders. 2008. The right-to-left shunt of crocodilians serves digestion. Physiological and Biochemical Zoology 81(2):125137, (cover).
Chan, B.K., Peterson, A.L., C.G Farmer. 2007. Predation of Dendrobates auratus larvae by Phelsuma laticauda. Herpetological Review 38(3): 321-322.
Uriona, T.J. and C.G Farmer. 2006. Contribution of the diaphragmaticus muscle to vital capacity in postprandial American alligators ( Alligator mississippiensis ). Journal of Experimental Biology 209(21): 4313-4318.
Farmer, C.G. 2006. On the Origin of Avian Air Sacs. Respiration Physiology and Neurobiology 154:89-106.
T.J. Uriona, C.G. Farmer, J. Dazely, F. Clayton, J. Moore. 2005. Structure and function of the esophagus of the American alligator ( Alligator mississippiensis ). Journal of Experimental Biology 208:3047-3053.
Farmer, C.G. 2003. Reproduction: the adaptive significance of endothermy. American Naturalist 162(6):826-840.
Farmer, C.G. and J.W. Hicks. 2002. The intracardiac shunt as a source of myocardial oxygen in a turtle, Trachemys scripta . Integrative and Comparative Biology 42(2):208-215.
Farmer, C.G. 2001. Parental care: A new perspective on the origin of endothermy. Pp. 389-412, In J.A. Gauthier and L.F. Gall, eds., New Perspectives on the Origin and Early Evolution of Birds: Proceedings of the International Symposium in Honor of John H. Ostrom. Peabody Museum of Natural History, Yale University. PDF
Carrier, D.R. and C.G. Farmer. 2000. The evolution of pelvic aspiration in archosaurs. Paleobiology 26(2):271-293.
Carrier, D.R. and C.G. Farmer. 2000. The integration of ventilation and locomotion in archosaurs. American Zoologist 40(1):87-100.
Farmer, C.G. 2000. Parental Care: The key to understanding endothermy and other convergent features in birds and mammal. American Naturalist 155 (3): 326-334.
Farmer, C.G. and D.R. Carrier. 2000. Pelvic aspiration in the American alligator ( Alligator mississippiensis ). Journal of Experimental Biology 203:1671-1678.
Farmer, C.G. and D.R. Carrier. 2000. Respiration and gas exchange during recovery in alligators. Respiration Physiology 120(1):81-87.
