Fundamentals of molecular evolution:
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Sunderland, Mass.
Sinauer Assoc.
2000
|
| Edition: | 2. ed. |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XIV, 481 S. graph. Darst. |
| ISBN: | 0878932666 |
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| 245 | 1 | 0 | |a Fundamentals of molecular evolution |c Dan Graur ; Wen-Hsiung Li |
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| 264 | 1 | |a Sunderland, Mass. |b Sinauer Assoc. |c 2000 | |
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FUNDAMENTALS OF MOLECULAR EVOLUTION SECOND EDITION I U R-R B IRA 1 DAN
GRAUR WEN-HSIUNG LI TEL AVIV UNIVERSITY UNIVERSITY OF CHICAGO SINAUER
ASSOCIATES, INC., PUBLISHERS SUNDERLAND, MASSACHUSETTS CONTENTS PREFACE
XIII INTRODUCTION 1 "1 CHAPTER 1 GENES, GENETIC CODES, AND MUTATION 5
NUCLEOTIDE SEQUENCES 5 GENOMES AND DNA REPLICATION 8 GENES AND GENE
STRUCTURE 9 PROTEIN-CODING GENES 9 RNA-SPECIFYING GENES 22
POSTTRANSCRIPTIONAL MODIFICATIONS OFRNA 13 UNTRANSCRIBED GENES 13
PSEUDOGENES 14 AMINO ACIDS 15 PROTEINS 20 TRANSLATION AND GENETIC CODES
22 MUTATION 25 SUBSTITUTION MUTATIONS 26 RECOMBINATION 29 DELETIONS AND
INSERTIONS 32 INVERSIONS 35 MUTATION RATES 35 SPATIAL DISTRIBUTION OF
MUTATIONS 37 PATTERNS OF MUTATION 38 ARE MUTATIONS RANDOM? 38 FURTHER
READINGS 38 CHAPTER 2 DYNAMICS OF GENES IN POPULATIONS 39 CHANGES IN
ALLELE FREQUENCIES 40 NATURAL SELECTION 41 CODOMINANCE 43 DOMINANCE 44
OVERDOMINANCE AND UNDER- DOMINANCE 45 RANDOM GENETIC DRIFT 47 EFFECTIVE
POPULATION SIZE 52 GENE SUBSTITUTION 53 FIXATION PROBABILITY 54 FIXATION
TIME 55 RATE OF GENE SUBSTITUTION 57 VI CONTENTS VII GENETIC
POLYMORPHISM 57 GENE DIVERSITY 57 NUCLEOTIDE DIVERSITY 58 THE DRIVING
FORCES IN EVOLUTION 59 I THE NEO-DARWINIAN THEORY AND THE NEUTRAL
MUTATION HYPOTHESIS 61 TESTING THE NEUTRAL MUTATION HYPOTHESIS 63
FURTHER READINGS 65 CHAPTER 3 EVOLUTIONARY CHANGE IN NUCLEOTIDE
SEQUENCES 67 NUCLEOTIDE SUBSTITUTION IN A DNA SEQUENCE 67 JUKES AND
CANTOR'S ONE-PARAMETER MODEL 68 KIMURA'S TWO-PARAMETER MODEL 71 NUMBER
OF NUCLEOTIDE SUBSTITUTIONS BETWEEN TWO DNA SEQUENCES 74 NUMBER OF
SUBSTITUTIONS BETWEEN TWO NONCODING SEQUENCES 75 SUBSTITUTION SCHEMES
WITH MORE THAN TWO PARAMETERS 77 VIOLATION OF ASSUMPTIONS 79 NUMBER OF
SUBSTITUTIONS BETWEEN TWO PROTEIN-CODING GENES 79 INDIRECT ESTIMATIONS
OF THE NUMBER OF NUCLEOTIDE SUBSTITUTIONS 85 AMINO ACID REPLACEMENTS
BETWEEN TWO PROTEINS 86 ALIGNMENT OF NUCLEOTIDE AND AMINO ACID SEQUENCES
86 MANUAL ALIGNMENT BY VISUAL INSPECTION 87 THE DOT MATRIX METHOD 87
DISTANCE AND SIMILARITY METHODS 90 ALIGNMENT ALGORITHMS 94 MULTIPLE
ALIGNMENTS 97 FURTHER READINGS 98 CHAPTER 4 RATES AND PATTERNS OF
NUCLEOTIDE SUBSTITUTION 99 RATES OF NUCLEOTIDE SUBSTITUTION 100 CODING
REGIONS 101 NONCODING REGIONS 105 SIMILARITY PROFILES 107 CAUSES OF
VARIATION IN SUBSTITUTION RATES 108 FUNCTIONAL CONSTRAINTS 108
SYNONYMOUS VERSUS NONSYNONYMOUS RATES 110 VARIATION AMONG DIFFERENT GENE
REGIONS 111 VARIATION AMONG GENES 113 ACCELERATION OF NUCLEOTIDE
SUBSTITUTION RATES FOLLOWING PARTIAL LOSS OF FUNCTION 115 ESTIMATING THE
INTENSITY OF PURIFYING SELECTION 116 MUTATIONAL INPUT: MALE-DRIVEN
EVOLUTION 117 POSITIVE SELECTION 119 DETECTING POSITIVE SELECTION 119
PARALLELISM AND CONVERGENCE 121 PREVALENCE OF POSITIVE SELECTION 123
PATTERNS OF SUBSTITUTION AND REPLACEMENT 123 PATTERN OF SPONTANEOUS
MUTATION 124 PATTERN OF SUBSTITUTION IN HUMAN MITOCHONDRIAL DNA 127
PATTERNS OF AMINO ACID REPLACEMENT 128 WHAT PROTEIN PROPERTIES ARE
CONSERVED IN EVOLUTION? 130 VIII CONTENTS NONRANDOM USAGE OF SYNONYMOUS
CODONS 132 MEASURES OF CODON-USAGE BIAS 132 UNIVERSAL AND
SPECIES-SPECIFIC PATTERNS OF CODON USAGE 133 CODON USAGE IN UNICELLULAR
ORGANISMS 134 CODON USAGE IN MULTICELLULAR ORGANISMS 137 CODON USAGE AND
POPULATION SIZE 139 MOLECULAR CLOCKS 139 RELATIVE RATE TESTS 142
MARGOLIASH, SARICH, AND WILSON'S TEST 142 TAJIMA'S ID METHOD 144 TESTS
INVOLVING COMPARISONS OF DUPLICATE GENES 145 LOCAL CLOCKS 146 NEARLY
EQUAL RATES IN MICE AND RATS 146 LOWER RATES IN HUMANS THAN IN AFRICAN
APES AND MONKEYS 147 HIGHER RATES IN RODENTS THAN IN PRIMATES 148
EVALUATION OF THE MOLECULAR CLOCK HYPOTHESIS 150 CAUSES OF VARIATION IN
SUBSTITUTION RATES AMONG EVOLUTIONARY LINEAGES 151 ARE LIVING FOSSILS
MOLECULAR FOSSILS TOO? 153 "PRIMITIVE" VERSUS "ADVANCED": A QUESTION OF
RATES 153 PHYLETIC GRADUALISM VERSUS PUNCTUATED EQUILIBRIA AT THE
MOLECULAR LEVEL 154 RATES OF SUBSTITUTION IN ORGANELLEDNA 155 MAMMALIAN
MITOCHONDRIAL GENES 157 PLANT NUCLEAR, MITOCHONDRIAL, AND CHLOROPLAST
DNAS 157 SUBSTITUTION AND REARRANGEMENT RATES 160 RATES OF SUBSTITUTION
IN RNA VIRUSES 160 ESTIMATION MODELS 161 HUMAN IMMUNODEFICIENCY VIRUSES
162 FURTHER READINGS 163 CHAPTER 5 MOLECULAR PHYLOGENETICS 165 IMPACTS
OF MOLECULAR DATA ON PHYLOGENETIC STUDIES 165 ADVANTAGES OF MOLECULAR
DATA IN PHYLOGENETIC STUDIES 167 TERMINOLOGY OF PHYLOGENETIC TREES 167
ROOTED AND UNROOTED TREES 169 SCALED AND UNSEALED TREES 169 THE NEWICK
FORMAT 170 NUMBER OF POSSIBLE PHYLOGENETIC TREES 170 TRUE AND INFERRED
TREES 173 GENE TREES AND SPECIES TREES 174 TAXA AND CLADES 176 TYPES OF
DATA 177 CHARACTER DATA 177 ASSUMPTIONS ABOUT CHARACTER EVOLUTION 178
POLARITY AND TAXONOMIC DISTRIBUTION OF CHARACTER STATES 180 DISTANCE
DATA 180 METHODS OF TREE RECONSTRUCTION 181 DISTANCE MATRIX METHODS 182
UNWEIGHTED PAIR-GROUP METHOD WITH ARITHMETIC MEANS (UPGMA) 183
TRANSFORMED DISTANCE METHOD 185 CONTENTS IX SATTATH AND TVERSKY'S
NEIGHBORS- RELATIONS METHOD 186 SAITOU AND NEI'S NEIGHBOR-JOINING METHOD
189 MAXIMUM PARSIMONY METHODS 189 WEIGHTED AND UNWEIGHTED PARSIMONY 193
SEARCHING FOR THE MAXIMUM PARSIMONY TREE 194 MAXIMUM LIKELIHOOD METHODS
198 ROOTING UNROOTED TREES 200 ESTIMATING BRANCH LENGTHS 202 ESTIMATING
SPECIES DIVERGENCE TIMES 204 TOPOLOGICAL COMPARISONS 206 PENNY AND
HENDY'S TOPOLOGICAL DISTANCE 206 CONSENSUS TREES 206 ASSESSING TREE
RELIABILITY 208 THE BOOTSTRAP 209 TESTS FOR TWO COMPETING TREES 211
PROBLEMS ASSOCIATED WITH PHYLO- GENETIC RECONSTRUCTION 212 STRENGTHS AND
WEAKNESSES OF DIFFERENT METHODS 214 MINIMIZING ERROR IN PHYLOGENETIC
ANALYSIS 216 MOLECULAR PHYLOGENETIC EXAMPLES 217 PHYLOGENY OF HUMANS AND
APES 217 CETARTIODACTYLA AND SINE PHYLOGENY 225 THE ORIGIN OF
ANGIOSPERMS 228 MOLECULAR PHYLOGENETIC ARCHEOLOGY 230 PHYLOGENY OF THE
MARSUPIAL WOLF 232 IS THE QUAGGA EXTINCT? 232 THE DUSKY SEASIDE SPARROW
234 THE UNIVERSAL PHYLOGENY 237 THE FIRST DIVERGENCE EVENTS 238 THE
CENANCESTOR 243 ENDOSYMBIOTIC ORIGIN OF MITOCHONDRIA AND CHLOROPLASTS
245 FURTHER READINGS 247 CHAPTER 6 GENE DUPLICATION, EXON SHUFFLING, AND
CONCERTED EVOLUTION 249 TYPES OF GENE DUPLICATION 250 DOMAINS AND EXONS
250 DOMAIN DUPLICATION AND GENE ELONGATION 255 THE OVOMUCOID GENE 258
ENHANCEMENT OF FUNCTION IN THE OC2 ALLELE OF HAPTOGLOBIN 258 ORIGIN OF
AN ANTIFREEZE GLYCOPROTEIN GENE 260 PREVALENCE OF DOMAIN DUPLICATION 262
FORMATION OF GENE FAMILIES AND THE ACQUISITION OF NEW FUNCTIONS 262
RNA-SPECIFYING GENES 265 ISOZYMES 268 OPSINS 269 DATING GENE
DUPLICATIONS 271 GENE LOSS 273 UNPROCESSED PSEUDOGENES 274 UNITARY
PSEUDOGENES 275 NONFUNCTIONALIZATION TIME 276 THE GLOBIN SUPERFAMILY 278
PREVALENCE OF GENE DUPLICATION, GENE LOSS, AND FUNCTIONAL DIVERGENCE 281
X CONTENTS EXON SHUFFLING 283 MOSAIC PROTEINS 283 PHASE LIMITATIONS ON
EXON SHUFFLING 286 EXONIZATION AND PSEUDOEXONIZATION 289 DIFFERENT
STRATEGIES OF MULTIDOMAIN GENE ASSEMBLY 290 THE "INTRONS-EARLY" VERSUS
"INTRONS-LATE" HYPOTHESES 291 INTRON SLIDING 292 THE RELATIVE FRACTION
OF "EARLY" AND "LATE" INTRONS 294 ALTERNATIVE PATHWAYS FOR PRODUCING NEW
FUNCTIONS 294 OVERLAPPING GENES 294 ALTERNATIVE SPLICING 296
INTRON-ENCODED PROTEINS AND NESTED GENES 299 FUNCTIONAL CONVERGENCE 299
RNA EDITING 301 GENE SHARING 302 MOLECULAR TINKERING 303 CONCERTED
EVOLUTION 304 MECHANISMS OF CONCERTED EVOLUTION 308 GENE CONVERSION 308
UNEQUAL CROSSING OVER 309 RELATIVE ROLES OF GENE CONVERSION AND UNEQUAL
CROSSING OVER 312 DETECTION AND EXAMPLES OF CONCERTED EVOLUTION 313 THE
A Y AND G Y-GLOBIN GENES IN THE GREAT APES 314 THE CONCERTED EVOLUTION
OF GENES AND PSEUDOGENES 315 FACTORS AFFECTING THE RATE OF CONCERTED
EVOLUTION 317 NUMBER OF REPEATS 318 ARRANGEMENT OF REPEATS 318 STRUCTURE
OF THE REPEAT UNIT 318 FUNCTIONAL REQUIREMENT 319 POPULATIONAL PROCESSES
320 EVOLUTIONARY IMPLICATIONS OF CONCERTED EVOLUTION 320 SPREAD OF
ADVANTAGEOUS MUTATIONS 320 RETARDATION OF PARALOGOUS GENE DIVERGENCE 321
GENERATION OF GENIE VARIATION 321 METHODOLOGICAL PITFALLS DUE TO
CONCERTED EVOLUTION 322 FURTHER READINGS 322 CHAPTER 7 EVOLUTION BY
TRANSPOSITION 323 TRANSPOSITION AND RETROPOSITION 323 TRANSPOSABLE
ELEMENTS 325 INSERTION SEQUENCES 326 TRANSPOSONS 327 TAXONOMIC,
DEVELOPMENTAL, AND TARGET SPECIFICITY OF TRANSPOSITION 328 AUTONOMY OF
TRANSPOSITION 329 RETROELEMENTS 329 RETROVIRUSES 330 RETROPOSONS AND
RETROTRANSPOSONS 330 RETRONS 333 PARARETROVIRUSES 333 EVOLUTIONARY
ORIGIN OF RETROELEMENTS 334 RETROSEQUENCES 336 RETROGENES 336
SEMIPROCESSED RETROGENES 338 RETROPSEUDOGENES 338 SEQUENCE EVOLUTION OF
RETROPSEUDO- GENES 341 CONTENTS XX LINES AND SINES 343 SINES DERIVED
FROM 7SL RNA 344 SINES DERIVED FROM TRNAS 346 WHERE THERE'S A SINE,
THERE'S A LINE 347 DNA-MEDIATED TRANSPOSABLE ELEMENTS AND TRANSPOSABLE
FOSSILS 349 RATE OF SINE EVOLUTION 349 GENETIC AND EVOLUTIONARY EFFECTS
OF TRANSPOSITION 349 HYBRID DYSGENESIS 354 TRANSPOSITION AND SPECIATION
357 EVOLUTIONARY DYNAMICS OF TRANS- POSABLE ELEMENT COPY NUMBER 358
HORIZONTAL GENE TRANSFER 359 HORIZONTAL TRANSFER OF VIROGENES FROM
BABOONS TO CATS 361 HORIZONTAL TRANSFER OFP ELEMENTS BETWEEN DROSOPHILA
SPECIES 363 PROMISCUOUS DNA 365 FURTHER READINGS 366 CHAPTER 8 GENOME
EVOLUTION 367 C VALUES 368 THE EVOLUTION OF GENOME SIZE IN PROKARYOTES
368 THE MINIMAL GENOME 371 THE ANALYTICAL APPROACH 371 THE EXPERIMENTAL
APPROACH 373 GENOME MINIATURIZATION 374 GENOME SIZE REDUCTION FOLLOWING
ENDOSYMBIOSIS 374 GENOME SIZE REDUCTION IN PARASITES 375 GENOME SIZE IN
EUKARYOTES AND THE C VALUE PARADOX 375 MECHANISMS FOR GLOBAL INCREASES
IN GENOME SIZE 380 POLYPLOIDIZATION 380 POLYSOMY 382 THE YEAST GENOME
382 POLYPLOIDY OF THE VERTEBRATE GENOME 384 MAINTENANCE OF NONGENIC DNA
384 THE HYPOTHESES 386 THE EVIDENCE 387 WHY DO SIMILAR SPECIES HAVE
DIFFERENT GENOME SIZES? 388 THE REPETITIVE STRUCTURE OF THE EUKARYOTIC
GENOME 389 LOCALIZED REPEATED SEQUENCES 390 DISPERSED REPEATED SEQUENCES
392 REPETITIVE SEQUENCES AS A CAUSE OF VARIATION IN GENOME SIZE 394
MECHANISMS FOR REGIONAL INCREASES IN GENOME SIZE 395 GENE DISTRIBUTION
397 HOW MANY GENES ARE THERE, WHERE ARE THEY, AND DO WE NEED THEM? 397
GENE NUMBER EVOLUTION 400 CHROMOSOMAL EVOLUTION 402 CHROMOSOMES,
PLASMIDS, AND EPISOMES 402 EVOLUTION OF CHROMOSOME NUMBER IN PROKARYOTES
402 CHROMOSOME NUMBER VARIATION IN EUKARYOTES 403 MECHANISMS FOR CHANGES
IN GENE ORDER AND GENE DISTRIBUTION AMONG CHROMOSOMES 404 COUNTING GENE
ORDER REARRANGEMENT EVENTS 406 XII CONTENTS GENE ORDER REARRANGEMENTS IN
BACTERIA 408 GENE ORDER REARRANGEMENTS IN EUKARYOTES 410 GENE ORDER AS A
PHYLOGENETIC CHARACTER 411 GC CONTENT IN BACTERIA 412 CHIROCHORES 415
COMPOSITIONAL ORGANIZATION OF THE VERTEBRATE GENOME 417 THE DISTRIBUTION
OF GENES AND OTHER GENETIC ELEMENTS AMONG ISOCHORES 420 ORIGIN OF
ISOCHORES 422 EMERGENCE OF NONUNIVERSAL GENETIC CODES 425 FURTHER
READINGS 427 APPENDIX 1 SPATIAL AND TEMPORAL FRAMEWORKS OF THE
EVOLUTIONARY PROCESS 429 APPENDIX II BASICS OF PROBABILITY 437
LITERATURE CITED 441 INDEX 467 TAXONOMIC INDEX 479 |
| any_adam_object | 1 |
| author | Graur, Dan Li, Wen-Hsiung |
| author_facet | Graur, Dan Li, Wen-Hsiung |
| author_role | aut aut |
| author_sort | Graur, Dan |
| author_variant | d g dg w h l whl |
| building | Verbundindex |
| bvnumber | BV013112604 |
| classification_rvk | WH 2600 |
| classification_tum | BIO 110f BIO 220f DAT 899f |
| ctrlnum | (OCoLC)247081355 (DE-599)BVBBV013112604 |
| dewey-full | 572.838 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 572 - Biochemistry |
| dewey-raw | 572.838 |
| dewey-search | 572.838 |
| dewey-sort | 3572.838 |
| dewey-tens | 570 - Biology |
| discipline | Biologie Informatik |
| edition | 2. ed. |
| format | Book |
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| indexdate | 2024-07-20T07:51:48Z |
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| isbn | 0878932666 |
| language | English |
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| open_access_boolean | |
| owner | DE-703 DE-19 DE-BY-UBM DE-91G DE-BY-TUM DE-20 DE-526 DE-11 DE-188 DE-B16 |
| owner_facet | DE-703 DE-19 DE-BY-UBM DE-91G DE-BY-TUM DE-20 DE-526 DE-11 DE-188 DE-B16 |
| physical | XIV, 481 S. graph. Darst. |
| publishDate | 2000 |
| publishDateSearch | 2000 |
| publishDateSort | 2000 |
| publisher | Sinauer Assoc. |
| record_format | marc |
| spelling | Graur, Dan Verfasser aut Fundamentals of molecular evolution Dan Graur ; Wen-Hsiung Li 2. ed. Sunderland, Mass. Sinauer Assoc. 2000 XIV, 481 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier biologie moleculaire inriac code genetique inriac evolution inriac genomique inriac phylogenetique inriac sequence nucleotide inriac Évolution moléculaire ram Molekulargenetik (DE-588)4039987-4 gnd rswk-swf Phylogenie (DE-588)4076110-1 gnd rswk-swf Evolution (DE-588)4071050-6 gnd rswk-swf Molekularbiologie (DE-588)4039983-7 gnd rswk-swf Matériel didactique Evolution (DE-588)4071050-6 s Molekularbiologie (DE-588)4039983-7 s DE-604 Molekulargenetik (DE-588)4039987-4 s Phylogenie (DE-588)4076110-1 s DE-188 Li, Wen-Hsiung Verfasser aut HEBIS Datenaustausch Mainz application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=008933223&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Graur, Dan Li, Wen-Hsiung Fundamentals of molecular evolution biologie moleculaire inriac code genetique inriac evolution inriac genomique inriac phylogenetique inriac sequence nucleotide inriac Évolution moléculaire ram Molekulargenetik (DE-588)4039987-4 gnd Phylogenie (DE-588)4076110-1 gnd Evolution (DE-588)4071050-6 gnd Molekularbiologie (DE-588)4039983-7 gnd |
| subject_GND | (DE-588)4039987-4 (DE-588)4076110-1 (DE-588)4071050-6 (DE-588)4039983-7 |
| title | Fundamentals of molecular evolution |
| title_auth | Fundamentals of molecular evolution |
| title_exact_search | Fundamentals of molecular evolution |
| title_full | Fundamentals of molecular evolution Dan Graur ; Wen-Hsiung Li |
| title_fullStr | Fundamentals of molecular evolution Dan Graur ; Wen-Hsiung Li |
| title_full_unstemmed | Fundamentals of molecular evolution Dan Graur ; Wen-Hsiung Li |
| title_short | Fundamentals of molecular evolution |
| title_sort | fundamentals of molecular evolution |
| topic | biologie moleculaire inriac code genetique inriac evolution inriac genomique inriac phylogenetique inriac sequence nucleotide inriac Évolution moléculaire ram Molekulargenetik (DE-588)4039987-4 gnd Phylogenie (DE-588)4076110-1 gnd Evolution (DE-588)4071050-6 gnd Molekularbiologie (DE-588)4039983-7 gnd |
| topic_facet | biologie moleculaire code genetique evolution genomique phylogenetique sequence nucleotide Évolution moléculaire Molekulargenetik Phylogenie Evolution Molekularbiologie Matériel didactique |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=008933223&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT graurdan fundamentalsofmolecularevolution AT liwenhsiung fundamentalsofmolecularevolution |