Huson D.H. Phylogenetic networks: concepts, algorithms and applications / D.H.Huson, R.Rupp, C.Scornavacca. - Cambridge: Cambridge University Press, 2011. - xii, 362 p.: ill. - Ref.: p.343-357. - Ind.: p.358-362. - ISBN 978-0-521-75596-2  Место хранения:   021 | Институт цитологии и генетики CO РАН | Новосибирск | Библиотека

Оглавление / Contents

Preface ..................................................... ix Part I Introduction ............................................. l 1 Basics ....................................................... 3 1.1 Overview ................................................ 3 1.2 Undirected and directed graphs .......................... 3 1.3 Trees ................................................... 7 1.4 Rooted DAGs ............................................. 8 1.5 Traversals of trees and DAGs ............................ 9 1.6 Taxa, clusters, clades and splits ...................... 11 2 Sequence alignment .......................................... 13 2.1 Overview ............................................... 13 2.2 Pairwise sequence alignment ............................ 13 2.3 Multiple sequence alignment ............................ 20 3 Phylogenetic trees .......................................... 23 3.1 Overview ............................................... 23 3.2 Phylogenetic trees ..................................... 24 3.3 The number of phylogenetic trees ....................... 27 3.4 Models of DNA evolution ................................ 29 3.5 The phylogenetic tree reconstruction problem ........... 32 3.6 Sequence-based methods ................................. 33 3.7 Maximum parsimony ...................................... 33 3.8 Branch-swapping methods ................................ 37 3.9 Maximum likelihood estimation .......................... 40 3.10 Bootstrap analysis ..................................... 43 3.11 Bayesian methods ....................................... 45 3.12 Distance-based methods ................................. 50 3.13 UPGMA .................................................. 52 3.14 Neighbor-joining ....................................... 54 3.15 Balanced minimum evolution ............................. 56 3.16 Comparing trees ........................................ 60 3.17 Consensus trees ........................................ 63 3.18 The Newick format ...................................... 66 4 Introduction to phylogenetic networks ....................... 68 4.1 Overview ............................................... 69 4.2 What is a phylogenetic network? ........................ 69 4.3 Unrooted phylogenetic networks ......................... 71 4.4 Rooted phylogenetic networks ........................... 76 4.5 The extended Newick format ............................. 81 4.6 Which types of networks are currently used in practice? .............................................. 83 Part II Theory ................................................. 85 5 Splits and unrooted phylogenetic networks ................... 87 5.1 Overview ............................................... 87 5.2 Splits ................................................. 88 5.3 Compatibility and incompatibility ...................... 90 5.4 Splits and clusters .................................... 91 5.5 Split networks ......................................... 93 5.6 The canonical split network ............................ 97 5.7 Circular splits and planar split networks ............. 102 5.8 Weak compatibility .................................... 105 5.9 The split decomposition ............................... 107 5.10 Representing trees in a split network ................. 121 5.11 Comparing split networks .............................. 122 5.12 T-theory .............................................. 122 6 Clusters and rooted phylogenetic networks .................. 127 6.1 Overview .............................................. 127 6.2 Clusters, compatibility and incompatibility ........... 128 6.3 Hasse diagrams ........................................ 132 6.4 Cluster networks ...................................... 133 6.5 Rooted phylogenetic networks .......................... 138 6.6 The lowest stable ancestor ............................ 140 6.7 Representing trees in rooted networks ................. 144 6.8 Hardwired and softwired clusters ...................... 146 6.9 Minimum rooted phylogenetic networks .................. 149 6.10 Decomposability ....................................... 150 6.11 Topological constraints on rooted networks ............ 156 6.12 Cluster containment in rooted networks ................ 168 6.13 Tree containment ...................................... 171 6.14 Comparing rooted networks ............................. 171 Part III Algorithms and applications .......................... 185 7 Phylogenetic networks from splits .......................... 187 7.1 The convex hull algorithm ............................. 187 7.2 The circular network algorithm ........................ 190 8 Phylogenetic networks from clusters ........................ 193 8.1 Cluster networks ...................................... 193 8.2 Divide-and-conquer using decomposition ................ 194 8.3 Galled trees .......................................... 198 8.4 Galled networks ....................................... 201 8.5 Level-к networks ...................................... 210 9 Phylogenetic networks from sequences ....................... 216 9.1 Condensed alignments .................................. 216 9.2 Binary sequences and splits ........................... 216 9.3 Parsimony splits ...................................... 218 9.4 Median networks ....................................... 219 9.5 Quasi-median networks ................................. 223 9.6 Median-joining ........................................ 227 9.7 Pruned quasi-median networks .......................... 232 9.8 Recombination networks ................................ 233 9.9 Galled trees .......................................... 240 10 Phylogenetic networks from distances ....................... 250 10.1 Distances and splits .................................. 250 10.2 Minimum spanning networks ............................. 251 10.3 Split decomposition ................................... 251 10.4 Neighbor-net .......................................... 254 10.5 T-Rex ................................................. 261 11 Phylogenetic networks from trees ........................... 265 11.1 Consensus split networks .............................. 265 11.2 Consensus super split networks for unrooted trees ..... 268 11.3 Distortion-filtered super split networks for unrooted trees ........................................ 273 11.4 Consensus cluster networks for rooted trees ........... 274 11.5 Minimum hybridization networks ........................ 275 11.6 Minimum hybridization networks and galled trees ....... 285 11.7 Networks from multi-labeled trees ..................... 287 11.8 DLT reconciliation of gene and species trees .......... 289 12 Phylogenetic networks from triples or quartets ............. 300 12.1 Trees from rooted triples ............................. 300 12.2 Level-fc networks from rooted triples ................. 302 12.3 The quartet-net method ................................ 308 13 Drawing phylogenetic networks .............................. 312 13.1 Overview .............................................. 312 13.2 Cladograms for rooted phylogenetic trees .............. 312 13.3 Cladograms for rooted phylogenetic networks ........... 316 13.4 Phylograms for rooted phylogenetic trees .............. 323 13.5 Phylograms for rooted phylogenetic networks ........... 324 13.6 Drawing rooted phylogenetic networks with transfer edges ................................................. 327 13.7 Radial diagrams for unrooted trees .................... 328 13.8 Radial diagrams for split networks .................... 329 14 Software ................................................... 332 14.1 Splits Tree ........................................... 332 14.2 Network ............................................... 333 14.3 TCS ................................................... 334 14.4 Dendroscope ........................................... 334 14.5 Other programs ........................................ 335 Glossary ................................................... 338 References ................................................. 343 Index ...................................................... 358