『Confounding Factors in Phylogenetic Analysis: A Simulation Study』

目

Simon Ho

（2008年7月18日刊行，VDM Verlag Dr. Müller, Saarbrücken，iv+87 pp.，ISBN:9783639046106 [pbk] → 版元ページ｜著者サイト）


【目次】
Preface 2

1. Introdoction 3

2. Hetero: A Program to Simulate the Evolution of DNA on a Four-taxon Tree 6

Introduction 6
Hetero: Description of the Program and its Features 7
Using Hetero to Teach Phylogenetic Inference 9
Conclusion 11

3. The Biasing Effect of Compositional Heterogeneity on Phylogenetic Estimates may be Underestimated 12

Introduction 12

4. Tracing the Decay of the Historical Signal in Biological Sequence Data 16

Introduction 16
Materials and Methods 17
Results 19
　Case I - The Null Case 19
　Case II - Rate Heterogeneity among Sister Lineages 22
　Case III - Compositional Heterogeneity among Sister Lineages 26
　Case IV - Rate and Compositional Heterogeneity among Sister Lineages 26
　Case V - Rate and Compositional Homogeneity among Sister Lineages 28
　Case VI - Rate Heterogeneity and Compositional Homogeneity among Sister Lineages 31
　Case VII - Rate Homogeneity and Compositional Heterogeneity among Sister Lineages 31
Case Study: Beta-Tubulin in Metazoa 33
Discussion 36

5. Estimation of Molecular Divergence Dates: Bias due to Compositional Heterogeneity 39

Introduction 39
Distance-Based Method 40
Maximum-Likelihood Quartet Method 44
Bayseian Inference 47
Relationship Between Estimation Bias and Compositional Disparity 48
Case Study: Divergence between Plantae and Metazoa 51
Discussion 52

6. A Survey of Compositional Variation in Metazoan Mitochondrial Genomes 54

Introduction 54
Materials and Methods 55
Results 58
　Ubiquity of DMP 62
　Strand Asymmetry 64
　Effects on Amino Acid Content 71
Discussion 72
　Abundance of Transfer RNAs 72
　Unequal tRNA Binding Affinities 72
　Asymmetric Repair and Replication 73
　Chemical Instability of DNA 73
　Implications for Analysis of mtDNA 73
　Conclusion 74


Bibliography 75