Evolution of Morphology: Modifications to Size and Pattern The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Uygur, Aysu N. 2014. Evolution of Morphology: Modifications to Size and Pattern. Doctoral dissertation, Harvard University. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:12274611 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Evolution of Morphology: Modifications to Size and Pattern A dissertation presented by Aysu N. Uygur to The Division of Medical Sciences in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Genetics Harvard University Cambridge, Massachusetts May, 2014 iii © 2014 by Aysu N. Uygur All Rights Reserved iv Dissertation Advisor: Dr. Clifford J. Tabin Aysu N. Uygur Evolution of Morphology: Modifications to Size and Pattern Abstract A remarkable property of developing organisms is the consistency and robustness within the formation of the body plan. In many animals, morphological pattern formation is orchestrated by conserved signaling pathways, through a process of strict spatio-temporal regulation of cell fate specification. Although morphological patterns have been the focus of both classical and recent studies, little is known about how this robust process is modified throughout evolution to accomodate different morphological adaptations. In this dissertation, I first examine how morphological patterns are conserved throughout the enourmous diversity of size in animal kingdom. We explore scaling of patterning to variations in embryonic size, and focus on the patterning of ventral neurons in the neural tube dorso-ventral axis in three avian species that are drastically different in size: Zebra Finch, Chick and Emu. We find that although the three species end up with comparable proportions of neuronal domains, the dynamics of patterning are very different due to differential response to the morphogen Sonic hedgehog, which mediates cell fate induction along the D-V axis. This difference in response to morphogen across species is intrinsic to cells, and downstream of the pathway receptor Smoothened. iii In the second part of this work, I explore developmental mechanisms involved in modifying conserved morphological patterns in order to adapt to a new function throughout evolution. Loss of digits in the tetrapod limbs is one such adaptation that has arose repeatedly as tetrapods occupied and adapted to different habitats. We focus on comparisons between mouse, the three-toed desert rodent Jerboa, and three species of hooved ungulates. We find that digit loss occurs early during limb development prior to chondrogenesis, either during patterning with down regulation of Ptc1 expression, or post-patterning through expansive cell death in the limb. Our findings demonstrate that mechanisms to alter pattern are flexible, and can either happen at time of patterning or subsequently. Taken together, this dissertation explores evolution of modifications to morphological patterns. The first part focuses on how alterations to size can evolve while conserving pattern, and the second part explores how strictly conserved patterns are modified to accomodate adaptations to function. iv Table of Contents Abstract ......................................................................................................................... iii List of Figures and Tables .......................................................................................... vii Acknowledgments........................................................................................................ ix Chapter One: Introduction ............................................................................................ 1 On Growth and Pattern ......................................................................................................................... 2 Part 1. Scaling Morphogen Mediated Patterns to Variations in Size ............................................. 3 Morphogen Mediated Pattern Formation ........................................................................................ 3 Pattern and Size ................................................................................................................................. 5 Sonic hedgehog signaling cascade in the neural tube ................................................................. 7 Patterning of the neural tube by a gradient of SHH .................................................................... 10 Chick, Zebra finch and Emu as model species for comparative studies of Shh morphogen gradient .............................................................................................................................................. 17 Conclusion ......................................................................................................................................... 18 Part 2. Modifications to Pattern: An Introduction to Evolution of Pentadactyly and a Reduction to Digit Number ..................................................................................................................................... 18 Origins of Limbs and Autopoda .......................................................................................................... 19 Ancestral Polydactyly ......................................................................................................................... 24 Evolutionary History of Digit Loss ..................................................................................................... 33 Human oligodactyly ............................................................................................................................ 43 Conclusion .......................................................................................................................................... 45 References ............................................................................................................................................... 47 Chapter Two: Scaling Pattern to Variations in Size during Vertebrate Neural Tube Development ................................................................................................................ 58 Summary ................................................................................................................................................. 60 Introduction ............................................................................................................................................. 61 Results ..................................................................................................................................................... 64 Discussion ............................................................................................................................................... 88 Materials and Methods ............................................................................................................................ 89 References ............................................................................................................................................... 94 v Chapter Three: Patterning and Post-patterning Modes of Evolutionary Digit Loss in Mammals .................................................................................................................. 96 Summary ................................................................................................................................................. 98 Introduction ............................................................................................................................................. 98 Results ..................................................................................................................................................... 99 Methods Summary ................................................................................................................................ 117 References ............................................................................................................................................. 119 Chapter Four .............................................................................................................. 123 Concluding Discussion ............................................................................................ 123 Pertaining to Chapter Two on Scaling Morphogen Mediated Patterns to Variations in Size ............... 124 Pertaining to Chapter Three on Digit Reduction in Vertebrate Limb Evolution .................................. 128 References ............................................................................................................................................. 133 Appendix .................................................................................................................... 135 vi List of Figures and Tables Chapter One: Introduction Figure 1.1 Sonic Hedgehog Signaling Pathway...............................................................8 Figure 1.2 Sonic hedgehog mediated patterning in the vertebrate neural tube………..12 Figure 1.3 Two phases of neural tube development in chick…………………………….16 Figure 1.4 Signaling events regulating growh and patterning