『The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing, 2nd Edition』

Philippe Lemey, Marco Salemi, Anne-Mieke Vandamme (eds.)

(2009年3月刊行,Cambridge University Press, Cambridge, xxvi+723 pp., ISBN:9780521877107 [hbk] / ISBN:9780521730716 [pbk])

6年ぶりの大改定により,とても詳細な最新の「系統推定論ハンドブック」に変身した.いくつかの章とソフトウェアが削られて,代わりにベイズ推定や分岐年代推定などより新しいトピックスの章が挿入され,その結果,ページ数は第1版のおよそ2倍ほどに膨張した.内容的にも,分子系統学の方法論的な側面が強調されるようになったので,「系統推定論ハンドブック」と呼ぶべきだろう.

【目次】
List of contributors xix
Foreword xxiii
Preface xxv


Part I. Introduction 1

1. Basic concepts of molecular evolution / Anne-Mieke Vandamme 3

Part II. Data Preparation 31

2. Sequence databases and database searching / Guy Bottu, Marc Van Ranst and Philippe Lemey 33
3. Multiple sequence alignment / Des Higgins and Philippe Lemey 68

Part III. Phylogenetic Inference 109

4. Genetic distances and Nucleotide substitution models / Korbinian Strimmer, Arndt von Haeseler and Marco Salemi 111
5. Phylogenetic inference based on distance methods / Yves Van de Peer and Marco Salemi 142
6. Phylogenetic inference using maximum likelihood methods / Heiko A. Schmidt and Arndt von Haeseler 181
7. Bayesian phylogenetic analysis using MRBAYES / Fredrik Ronquist, Paul van der Mark and John P. Huelsenbeck 210
8. Phylogeny inference based on parsimony and other methods using PAUP* / David L. Swofford and Jack Sullivan 267
9. Phylogenetic analysis using protein sequences / Fred R. Opperdoes and Philippe Lemey 313

Part IV. Testing Models and Trees 343

10. Selecting models of evolution / David Posada 345
11. Molecular clock analysis / Philippe Lemey and David Posada 362
12. Testing tree topologies / Heiko Schmidt 381

Part V. Molecular Adaptation 405

13. Natural selection and adaptation of molecular sequences / Oliver G. Pybus and Beth Shapiro 407
14. Estimating selection pressures on alignments of coding sequences / Sergei L. Kosakovsky Pond, Art F. Y. Poon, and Simon D. W. Frost 419

Part VI. Recombination 491

15. Introduction to recombination detection / Philippe Lemey and David Posada 493
16. Detecting and characterizing individual recombination events / Mika Salminen and Darren Martin 519

Part VII. Population Genetics 549

17. The coalescent: population genetic inference using genealogies / Allen Rodrigo 551
18. Bayesian evolutionary analysis by sampling trees / Alexei Drummond and Andrew Rambaut 564
19. LAMARC: estimating population genetic parameters from molecular data / Mary K. Kuhner 592

Part VIII. Additional Topic 613

20. Assessing substitution saturation with DAMBE / Xuhua Xia and Philippe Lemey 615
21. Split networks: a tool for exploring complex evolutionary relationships in molecular data / Vincent Moulton and Katharina T. Huber 631


Glossary 654
References 672
Index 709