Advisor: Maryellen Ruvolo Randall Vincent Collura

Molecular Evolution of Genes

Related to Primate Encephalization and Energetics

Abstract

Interest in brain size clearly stems from the greatly enlarged brains of humans relative to our ape relatives. Understanding the molecular mechanisms that underlie this dramatic change (along with others in human evolution) is one of the major goals of molecular anthropology. Analyses in this thesis investigate molecular genetic changes related to increased brain size in the anthropoid primates and humans in particular. An analysis of the evolution of mitochondrial DNA in the primates reveals that mitochondrial proteins of anthropoids (monkeys, apes and humans) show dramatic differences in both the number and positions of variable sites when compared to those of other mammals, including non-anthropoid primates. These changes have serious implications for using mitochondrial sequences as molecular clocks for estimating divergence dates. However, a simple and reliable approach to using mitochondrial DNA to date primate divergences is presented.

Genes that have been shown to be responsible for human genetic disorders involving brain size reduction and/or changes in cerebral development are investigated next. Two published papers are presented that examine the evolution of the structure (amino acid sequence) of specific genes (ASPM and AHI1) that may have been involved in hominid brain expansion and development. Evidence of evolutionary selection is detailed along the branch leading to modern humans as well as other branches of the primate tree.

The use of microarray technology in cross-species studies illuminates an area of evolutionary divergence that has been neglected because of the difficulty in obtaining data. Human to chimpanzee differences in the expression of genes in different tissues, including brain, are examined and compared to human to chimpanzee structural divergence between these genes. Brain tissue seems to be different than other tissues in the overall magnitude of human to chimpanzee expression differences, the overall amount of protein structural change in tissue specific genes and in the overall relationship between protein expression and structural differences. Both protein expression and structural differences are lower, on average, than in other tissues and, at least in some comparisons, there is a weak, but still significant, negative association between these two kinds of change.

Table of Contents

Abstract iii

Acknowledgements vii

Chapter 1 1

General Introduction - Relative brain size in the primates

Chapter 2 12

The Evolution of Primate Mitochondrial DNA

Part 1 - Chapter Introduction 13

Part 2 - Isofunctional Remodeling of Anthropoid Primate 15

Mitochondrial Proteins

Introduction 16

Results and Discussion 17

Materials and Methods 36

Part 3 – A simpler approach to molecular dating using 39

mitochondrial DNA

Chapter 3 54

Accelerated Evolution of Brain Size and Development Related

Genes in the Hominoids

Chapter Introduction 55

*Paper 1: Accelerated evolution of the ASPM gene controlling 58

brain size begins prior to human brain expansion.

Introduction 60

Results 61

Discussion 77

Materials and Methods 81

#Paper 2: Abnormal cerebellar development and axonal 87

decussation due to mutations in AHI1 in Joubert syndrome

Methods 104

References (numbered) 112

Discussion and literature review 115

Conclusions 124

Chapter 4 125

The Relationship Between Gene Expression Divergence and

Protein Divergence in Humans and Chimpanzees

Chapter Introduction 126

Part 1 – Original paper draft 127

Introduction 127

Results and Discussion 131

Materials and Methods 146

Part 2 – Revised analysis 148

Introduction 148

Discussion 165

**Part 3 – Further analyses 168

Results 169

Discussion 173

Methods 175

Chapter 5 177

Conclusions

References Cited 181

Appendix 1 193

List of taxa used in Chapter 2 with accession numbers

Appendix 2 199

Chapter 2, Figure S1

Appendix 3 201

Chapter 2, Figure S2

Appendix 4 202

Chapter 2, Figure S3

Appendix 5 204

Chapter 4, Figure S4

*Paper 1:

Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion. Kouprina N, Pavlicek A, Mochida GH, Solomon G, Gersch W, Yoon YH, Collura R, Ruvolo M, Barrett JC, Woods CG, Walsh CA, Jurka J, Larionov V. PLoS Biol. May 2004; 2(5):E126. Epub 2004 Mar 23.

#Paper 2:

Abnormal cerebellar development and axonal decussation due to mutations in AHI1 in Joubert syndrome. Russell J Ferland, Wafaa Eyaid, Randall V Collura, Laura D Tully, R Sean Hill, Doha Al-Nouri, Ahmed Al-Rumayyan, Meral Topcu, Generoso Gascon, Adria Bodell, Yin Yao Shugart, Maryellen Ruvolo & Christopher A Walsh Nature Genetics 36, 1008 - 1013 2004

**Chapter 4, ≥Further analyses≤

Genomic and evolutionary analyses of asymmetrically expressed genes

in human fetal left and right cerebral cortex. Tao Sun, Randall V. Collura, Maryellen Ruvolo, and Christopher A. Walsh In Press at Cerebral Cortex