Reconstructing evolution: new mathematical and computational advances
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Oxford
Oxford Univ. Press
2007
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | Includes bibliographical references and index |
| Beschreibung: | XXIX, 318 S. graph. Darst. 24 cm |
| ISBN: | 9780199208227 |
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Datensatz im Suchindex
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|---|---|
| adam_text | Reconstructing Evolution
New Mathematical and Computational Advances
Edited by
OLIVIER GASCUEL AND MIKE STEEL
OXTORD
UNIVERSITY PRESS
CONTENTS
List of Contributors xxvi
I Evolution in Populations 1
1 Trees of genes in populations 3
Joseph Felsenstein
1 1 Introduction 3
1 2 Effects of evolutionary forces on coalescent trees 7
121 Population growth 7
122 Migration 8
123 Coalescents with recombination 9
124 Natural selection 11
1 3 Inference methods 12
131 Earlier inference methods 13
132 The basic equation 13
133 Rescaling times 14
134 How many coalescent trees? 15
135 Monte Carlo integration 15
136 Importance sampling 15
137 Independent sampling 16
138 Correlated sampling 18
139 Sampling from approximate distributions 20
1 3 10 Ascertainment and SNPs 20
1 3 11 Bayesian samplers 21
1 3 12 Future extensions 21
1 4 Programmes 23
1 5 The wave of the future 25
2 The evolutionary analysis of measurably evolving
populations using serially sampled gene sequences 30
Allen Rodrigo Gregory Ewing and Alexei Drummond
2 1 Introduction 30
2 2 Constructing phylogenetic trees from serially sampled data 33
221 Estimation of the expected number of substitutions in
each interval, or a uniform substitution rate 34
xx
CONTENTS
222 Correction of pairwise distances
223 Clustering using UPGMA
224 Trimming back branches
225 sUPGMA and serial sample miscellany
2 3 Maximum-likelihood estimation of evolutionary rates
231 Single rate dated tips
232 Multiple rates dated tips
233A few last words about likelihood and serial samples
2 4 The serial coalescent
2 5 Estimating population size and substitution rates under the
s-coalescent
251 Changing population sizes and skyline plots
2 6 Estimating migration rates
2 7 Where to next?
II Models of sequence evolution
3 Modelling the variability of evolutionary processes
Olivier Gascuel and Stephane Guindon
3 1 Introduction
311 Among-site heterogeneity
312 Mixing among-site and time-dependent variability
3 2 Mathematical tools and concepts
321 Markovian models of sequence evolution: the basis and
assumptions
322 Neyman (two-state, DNA), GTR (DNA), WAG (protein),
and NY1 (codon) models
323 Trees and likelihood calculations
324 Accounting for among-site variability using mixture models
325 Gamma-based rate across sites models and NY3 (codon)
models
326 Accounting for among-site and time variability using
Markov-modulated Markov (MMM) models
327 On/Off (two-state, DNA), covarion-like (DNA) and
compound codon models
3 3 Biological data sets
331 The role of Deficiens and Globosa genes in flower
development
332 The singular dynamics of the envelope gene evolution
during HIV-1 infection
3 4 The models in action: analysis of protein coding sequences
341 Among-site heterogeneity
342 Application: classification of sites into selection regimes
I
xxi
xxii CONTENTS
343 Among-site and lineage heterogeneity in a unified
framework 94
3-4 4 Application: visualization of time-dependent variations at
individual sites 96
3 5 Discussion 99
4 Phylogenetic invariants 108
Elizabeth S Allman and John A Rhodes
4 1 Introduction 108
4 2 Phylogenetic models on a tree 113
4 3 Edge invariants and matrix rank 115
4 4 Vertex invariants and tensor rank 118
4 5 Algebraic geometry and computational algebra 121
4 6 Invariants for specific models 126
461 Group-based models 126
462 The general Markov model 128
463 The strand symmetric model 129
464 Stable base distribution models 130
4 7 Invariants and statistical tests 131
4 8 Invariants and maximum-likelihood 132
4 9 Invariants and identifiability of complex models 135
4 10 Other directions 139
4 10 1 A tree construction algorithm 139
4 10 2 Invariants for gene order models 140
4 11 Concluding remarks 141
III Tree shape, speciation, and extinction 147
5 Some models of phylogenetic tree shape 149
Arne 0 Mooers, Luke J Harmon, Michael G B Blum, Dennis H J
Wong, and Stephen B Heard
5 1 Introduction 149
5 2 Background 150
5 3 Yule and Hey models 151
54A= function(trait) 153
55A= function(age) 154
56A= function(time) 156
5 7 The neutral model 157
58A= function(iV) 160
5 9 Concluding remarks 162
5 10 Appendix 163
CONTENTS xxiii
6 Phylogenetic diversity: from combinatorics
to ecology 171
Klaas Hartmann and Mike Steel
6 1 Introduction and terminology 171
6 2 Definitions and combinatorial properties 172
621 The strong exchange property 174
622 Generalized Pauplin formula 174
623 Exclusive molecular phylodiversity 175
6 3 Biodiversity conservation 175
631 Simple indices 177
632 Noah s Ark Problem 178
633 Conservation time scale 181
634 Further algorithmic results 182
635 Extensions to the NAP 183
6 4 Loss of phylogenetic diversity under extinction models 184
641 Relationship between PD and time under an extinction
process 186
6 5 Tree reconstruction using PD 188
651 Tree reconstruction from Pf-values over an abelian group 189
6 6 Concluding comments 192
IV Trees from subtrees and characters 197
7 Fragmentation of large data sets in phylogenetic analyses 199
Michael J Sanderson, Cecile Ane, Oliver Eulenstein, David
Fernandez-Baca, Junhyong Kim, Michelle M McMahon, and Raul
Piaggio-Talice
7 1 Introduction 199
7 2 Basic definitions 203
7 3 Strategies for handling fragmentation of data sets 205
731 Strategy 1 Post-processing collections of trees 205
732 Strategy 2 Pre-processing by grove identification 206
733 Strategy 3 Pre-processing by clustering or optimization
strategies 211
7 4 Conclusions 213
8 Identifying and defining trees 217
Stefan Griinewald and Katharina T Huber
8 1 Introduction 217
8 2 From biology to mathematics 218
821 Evolutionary trees and X-trees 218
822 Characters and (partial) partitions 219
xxiv CONTENTS
823 Homoplasy and displaying 220
824 Question (Q) restated 221
8 3 Defining trees in terms of chordal graphs 222
831 Partition intersection graphs and restricted chordal
completions 222
832 Minimal restricted chordal completions and distinguishing
edges 225
8 4 Defining trees in terms of closure rules 226
841 Quartet closure rules 228
842 Split closure rules 230
843 The semi-dyadic closure and homoplasy-free evolution 232
8 5 Identifying trees in terms of chordal graphs 234
851 Restricted chordal completions revisited 235
852 Strongly distinguishing 236
8 6 Identifying trees in terms of quartets 238
861 The quartet graph 238
862 Small identifying quartet sets 240
8 7 Conclusion 241
V From trees to networks 245
9 Split networks and reticulate networks 247
Daniel H Huson
9 1 Introduction 247
9 2 Consensus networks and super networks 249
9 3 Split networks from sequences and distances 255
9 4 Hybridization and reticulate networks 260
9 5 Recombination networks 267
10 Hybridization networks 277
Charles Semple
10 1 Introduction 277
10 1 1 Preliminaries 279
10 2 Hybridization networks 280
10 3 A characterization of MINIMUM HYBRIDIZATION 282
10 3 1 Rooted subtree prune and regraft operation and
agreement forests 283
10 3 2 Characterizations of MINIMUM HYBRIDIZATION and
MINIMUM RSPR 285
10 3 3 Comparing drspR (7, T ) and h(T T ) 288
10 3 4 Algorithms for constructing rSPR sequences and
hybridization networks from agreement forests 290
CONTENTS XXV
10 4 Algorithmic applications of agreement forests 291
10 4 1 Reduction rules 292
10 42A simple divide-and-conquer algorithm for MINIMUM
HYBRIDIZATION 295
10 4 3 Galled-trees 299
10 5 Recombination networks 301
10 6 Hybridization networks in real time 304
10 6 1 Temporal representations 304
10 6 2 Time-ordered rooted subtree prune and regraft operations 306
10 7 Computational complexity 308
10 8 Concluding remarks 309
Index 315
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| spelling | Reconstructing evolution new mathematical and computational advances ed. by Olivier Gascuel ... Oxford Oxford Univ. Press 2007 XXIX, 318 S. graph. Darst. 24 cm txt rdacontent n rdamedia nc rdacarrier Includes bibliographical references and index Évolution (Biologie) - Modèles mathématiques Mathematisches Modell Evolution (Biology) Mathematical models Evolution (DE-588)4071050-6 gnd rswk-swf Phylogenie (DE-588)4076110-1 gnd rswk-swf Mathematisches Modell (DE-588)4114528-8 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Evolution (DE-588)4071050-6 s Mathematisches Modell (DE-588)4114528-8 s DE-604 Phylogenie (DE-588)4076110-1 s DE-188 Gascuel, Olivier 1956- Sonstige (DE-588)122915712 oth HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=018766608&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Reconstructing evolution new mathematical and computational advances Évolution (Biologie) - Modèles mathématiques Mathematisches Modell Evolution (Biology) Mathematical models Evolution (DE-588)4071050-6 gnd Phylogenie (DE-588)4076110-1 gnd Mathematisches Modell (DE-588)4114528-8 gnd |
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| title | Reconstructing evolution new mathematical and computational advances |
| title_auth | Reconstructing evolution new mathematical and computational advances |
| title_exact_search | Reconstructing evolution new mathematical and computational advances |
| title_full | Reconstructing evolution new mathematical and computational advances ed. by Olivier Gascuel ... |
| title_fullStr | Reconstructing evolution new mathematical and computational advances ed. by Olivier Gascuel ... |
| title_full_unstemmed | Reconstructing evolution new mathematical and computational advances ed. by Olivier Gascuel ... |
| title_short | Reconstructing evolution |
| title_sort | reconstructing evolution new mathematical and computational advances |
| title_sub | new mathematical and computational advances |
| topic | Évolution (Biologie) - Modèles mathématiques Mathematisches Modell Evolution (Biology) Mathematical models Evolution (DE-588)4071050-6 gnd Phylogenie (DE-588)4076110-1 gnd Mathematisches Modell (DE-588)4114528-8 gnd |
| topic_facet | Évolution (Biologie) - Modèles mathématiques Mathematisches Modell Evolution (Biology) Mathematical models Evolution Phylogenie Aufsatzsammlung |
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