University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 5-2016 A Quantitative Genetic Analysis of Limb Segment Morphology in Humans and Other Primates: Genetic Variance, Morphological Integration, and Linkage Analysis Brannon Irene Hulsey University of Tennessee - Knoxville, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Part of the Biological and Physical Anthropology Commons Recommended Citation Hulsey, Brannon Irene, "A Quantitative Genetic Analysis of Limb Segment Morphology in Humans and Other Primates: Genetic Variance, Morphological Integration, and Linkage Analysis. " PhD diss., University of Tennessee, 2016. https://trace.tennessee.edu/utk_graddiss/3710 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Brannon Irene Hulsey entitled "A Quantitative Genetic Analysis of Limb Segment Morphology in Humans and Other Primates: Genetic Variance, Morphological Integration, and Linkage Analysis." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Anthropology. Graciela S. Cabana, Major Professor We have read this dissertation and recommend its acceptance: Benjamin M. Auerbach, Lorena M. Havill, Andrew Kramer, Richard L. Jantz, Charles C. Roseman, Arnold M. Saxton Accepted for the Council: Carolyn R. Hodges Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) A Quantitative Genetic Analysis of Limb Segment Morphology in Humans and Other Primates: Genetic Variance, Morphological Integration, and Linkage Analysis A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Brannon Irene Hulsey May 2016 Copyright © 2016 by Brannon Irene Hulsey All rights reserved. ii ACKNOWLEDGEMENTS There are many people that, without whom, this project would not have been completed. My sincere and heartfelt thanks goes out to each of them for their assistance and support. To begin, thank you to Graciela Cabana for being an exceptionally supportive and patient advisor. I am grateful for the opportunities she has provided for me, from trusting me to help set up and maintain the Molecular Anthropology Laboratories at the University of Tennessee, to financially supporting me in ancient DNA training and dissertation data collection, to including me in various projects, presentations, and publications. I feel lucky to have had such an avid supporter in the academic arena that always provided an optimistic lens to view my work and allowed me to weave the demands of a dissertation into my very busy personal life. Thank you also to my other UT committee members. Ben Auerbach provided statistical guidance and helped frame my work in the current literature. Richard Jantz, Andy Kramer, and Arnold Saxton each provided theoretical and statistical support through conversation and course work. And, thank you to the Department of Anthropology at UT for partially funding this work with the Kneberg-Lewis Award. This project has afforded me the opportunity to work with several other committee members who are affiliated with different institutions. Thanks to Lorena Havill who granted access to the baboon skeletal collection at the Texas Biomedical Research Institute (TBRI) and who provided technical assistance, both from her own vast knowledge and by connecting me with the many brilliant people at TBRI (more on that below). And, many thanks to Charles Roseman at the University of Illinois Urbana-Champaign for providing endless statistical support iii and helping me unravel the intricacies of R. Your patience with my many questions is much appreciated! I would also like to thank the many other researchers and colleagues who are not on my committee that provided essential data, advice, and assistance. Thank you to Michael Crawford for providing access to the Mennonite data and to his former students Kristin Young and Anne Justice for their hospitality while I visited the University of Kansas. Many thanks to Dennis O’Rourke for allowing me to use the Sukhumi Baboon data. Thank you to Mark Algee-Hewitt for assistance in deciphering computer networking and helping me make computers “talk” to one another, a feat which was formerly so far outside my realm of knowledge I didn’t even know where to begin. I am also indebted to a number of people at the TBRI: to Michael Mahaney for data access, to Debbie Newman for pedigree construction and SOLAR programming, to Charles Peterson and Linda Freeman-Shade for SOLAR assistance, to Jennifer Harris, Shayna Levine, and Ashan Choudary for general lab assistance, and to Courtney Roush and Tanya Lerma for assistance in bone cleaning. I also am extremely thankful for Jennifer Guida and Frankie West who each took time out of their summers to travel to San Antonio with me and spend a month cleaning baboon bones. You are both amazing women, and I appreciate you! In addition, there are several people in the San Antonio area who provided me with meals to eat and/or beds to sleep in: thank you Victoria Castellanos, Kate and Robert Crosby, Justin Schneider, Ellen Quillen, and Blake and Sarah Walsh. I am immensely thankful for my extremely supportive friends and family, without whom I would have fallen flat on my face a long time ago. Thank you to my parents, Jeffrey and Susan Jones, and my brother, Matthew, for your unending love and understanding, especially when I iv repeatedly told you not to ask me how the dissertation was going or when I would graduate. Thank you to my in-laws, Ron and Barbara Hulsey, for treating me like your own daughter and always agreeing to come into town and watch the kids when I needed to travel for conferences or data collection (or to go on a two-week journey to South Africa). Many thanks to my friends, both those within the academic world that understand the craziness that is grad school and dissertation writing and those outside of academia who love me and help me remember the bigger picture of life. The emotional support you have all provided is unparalleled. And a special thank you goes to my church family for always reminding me that my value in life does not come from what I do, but who I am. The community and support that I have found among the people of First Baptist Church Knoxville will always hold a special place in my heart. Finally, there are really not words to express my love and gratitude for my amazing husband, Wade. Thank you for following me to Knoxville. Thank you for supporting me, emotionally, physically, financially, and spiritually, as I have grown and changed during my time in grad school. Thank you for being my best friend and biggest fan. You rock my face off! And, thank you for our beautiful children, Samuel, Ava, and this new little one growing in my belly. v ABSTRACT Limb segment lengths (and, by extension, limb proportions) are widely studied postcranial features in biological anthropology due to the seemingly consistent phenotypic patterning among human and fossil hominin groups. This patterning, widely presumed to be the result of adaptation to thermoregulatory efficiency, has led to the assumption among biological anthropologists that limb proportions in humans are phenotypically stable unless long periods of extreme environmental conditions force adaptive change. Because these traits are considered stable, they have been used to inform multiple areas of anthropological inquiry, including investigations of phylogenetic relationships and fossil species identification, locomotor behavior and the evolution of bipedalism, and migration patterns. The problem with this assumption is that phenotypic patterns may not accurately reflect evolutionary processes, and even if they do, there is no reason to expect phenotype to respond to natural selection solely. Investigations of phenotypic variation need to incorporate genetic variation and covariation to better understand the processes that produced observable patterns, including evolutionary processes. However, the incorporation of genetic parameters is often difficult given that knowledge of familial relationships are required. Therefore, the goal of this project is to use a quantitative genetics approach to estimate the genetic variance and covariance in limb segment lengths and then begin the task of identifying genes which may influence this normal variation. These tasks are accomplished using multiple large, pedigreed samples of primate species, including humans. Linkage analysis on a baboon sample, a well-accepted model vi organism for humans, is used to identify regions of the genome which may influence limb segment variation. The results presented here suggest that 1) while patterns of genetic and phenotypic variance and covariance across limb segments are broadly similar, there are differences in the details, and 2) while patterns of genetic and phenotypic variance and covariance within and among limb segments generally adhere to expectations set forth by developmental and evolutionary-based hypotheses,