Probability models for DNA sequence evolution:
Saved in:
| Main Author: | |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
New York [u.a.]
Springer
2008
|
| Edition: | 2. ed. |
| Series: | Probability and its applications
|
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Item Description: | Literaturverz. S. 223 - 237 |
| Physical Description: | XII, 431 S. graph. Darst. |
| ISBN: | 9780387781686 |
Staff View
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| 100 | 1 | |a Durrett, Richard |d 1951- |e Verfasser |0 (DE-588)121396789 |4 aut | |
| 245 | 1 | 0 | |a Probability models for DNA sequence evolution |c Richard Durrett |
| 250 | |a 2. ed. | ||
| 264 | 1 | |a New York [u.a.] |b Springer |c 2008 | |
| 300 | |a XII, 431 S. |b graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 490 | 0 | |a Probability and its applications | |
| 500 | |a Literaturverz. S. 223 - 237 | ||
| 650 | 4 | |a Base Sequence | |
| 650 | 4 | |a Evolution, Molecular | |
| 650 | 4 | |a Evolutionary genetics |x Statistical methods | |
| 650 | 4 | |a Models, Genetic | |
| 650 | 4 | |a Nucleotide sequence |x Statistical methods | |
| 650 | 4 | |a Probabilities | |
| 650 | 4 | |a Probability | |
| 650 | 4 | |a Variation (Biology) |x Statistical methods | |
| 650 | 0 | 7 | |a Stochastisches Modell |0 (DE-588)4057633-4 |2 gnd |9 rswk-swf |
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Record in the Search Index
| _version_ | 1817711153603674112 |
|---|---|
| adam_text |
Contents
Preface
.
V
1
Basic
Models. 1
1.1
ATGCs
of life
. 1
1.2
Wright-Fisher model
. 5
1.2.1
The coalescent
. 8
1.2.2
Shape of the genealogical tree
. 11
1.3
Infinite
alíeles
model
. 14
1.3.1
Hoppe's urn, Ewens' sampling formula
. 15
1.3.2
Chinese restaurants and sufficient statistics
. 20
1.3.3
Branching process viewpoint
. 26
1.4
Infinite sites model
. 29
1.4.1
Segregating sites
. 31
1.4.2
Nucleotide diversity
. 39
1.4.3
Pairwise differences
. 40
1.4.4
Folded site frequency spectrum
. 43
1.5
Moran
model
. 46
1.5.1
Fixation probability and time
. 47
1.5.2
Site frequency spectrum mean
. 50
2
Estimation and Hypothesis Testing
. 53
2.1
Site frequency spectrum covariance
. 53
2.2
Estimates of
θ
. 59
2.3
Hypothesis testing overview
. 63
2.4
Difference statistics
. 65
2.4.1
Tájimat
D.
65
2.4.2
Fu
and Li's
D.
67
2.4.3
Fay and Wu's
Η
. 69
2.4.4
Conditioning
onS„
. 71
2.5
The HKA test
. 72
2.6
McDonald-Kreitman test
. 78
X
Contents
3
Recombination
. 83
3.1
Two loci
. 83
3.1.1
Sample of size
2. 83
3.1.2
Sample of size
η
. 87
3.2
m
loci
. 90
3.2.1
Samples of size
2. 91
3.2.2
Samples of size
η
. 91
3.2.3
Pairwise differences
. 93
3.3
Linkage disequilibrium
. 97
3.4
Ancestral recombination graph
.101
3.4.1
Simulation
.105
3.4.2
Two approximate algorithms
.107
3.5
Counting recombinations
.
Ill
3.6
Estimating recombination rates
.114
3.6.1
Equations for the two-locus sampling distribution
.115
3.6.2
Simulation methods
.118
3.6.3
Composite likelihood estimation of
ρ
.120
3.7
Haplotypes and hot spots
.122
4
Population Complications
.125
4.1
Large family sizes
.125
4.2
Population growth
.130
4.2.1
Exponential growth
.131
4.2.2
Sudden population expansion
.134
4.3
Founding effects and bottlenecks
.138
4.4
Effective population size
.143
4.5
Matrix migration models
.146
4.5.1
Strobeck's theorem
.148
4.5.2
Fast migration limit
.149
4.6
Symmetric island model
.150
4.6.1
Identity by descent
.150
4.6.2
Mean and variance of coalescence times
.152
4.6.3
Effective population sizes
.153
4.6.4
Large
η
limit
.154
4.7
Fixation indices
.157
5
Stepping Stone Model
.161
5.1
d
= 1.
Exact results
.161
5.2
d
= 1
and
2,
Fourier methods
.165
5.3
d
= 2.
Coalescence times
.172
5.3.1
Random walk results
.172
5.3.2
Samples of size
2.175
5.3.3
Fixation indices Fst
.177
5.4
d
= 2.
Genealogies
.179
5.4.1
Simulation results
.181
Contents
XI
5.5
d
= 1,
Continuous models
.183
5.6
d =
2,
Continuous models
.188
6
Natural Selection
.191
6.1
Directional selection
.191
6.1.1
Fixation probability
.192
6.1.2
Time to fixation
.194
6.1.3
Three phases of the fixation process
.197
6.1.4
Ancestral selection graph
.199
6.2
Balancing selection
.201
6.3
Background selection
.211
6.4
Muller's ratchet
.219
6.4.1
Evolutionary advantages of recombination
.220
6.4.2
Sex, epistasis, and Kondrashov
.222
6.5
Hitchhiking
.225
6.6
Better approximations
.234
6.7
Recurrent sweeps
.241
6.7.1
Nucleotide diversity
.241
6.7.2
Genealogies
.243
6.7.3
Segregating sites
.245
7
Diffusion Processes
.249
7.1
Infinitesimal mean and variance
.250
7.2
Examples of diffusions
.252
7.3
Transition probabilities
.258
7.4
Hitting probabilities
.262
7.5
Stationary measures
.268
7.6
Occupation times
.273
7.7
Green's functions
.276
7.8
Examples
.280
7.9
Conditioned processes
.287
7.10
Boundary behavior
.293
7.11
Site frequency spectrum
.298
7.11.1
Poisson
random field model
.300
7.12
Fluctuating selection
.304
8
Multidimensional Diffusions
.313
8.1
К
alíele
model
.313
8.1.1
Fixation probabilities and time
.315
8.1.2
Stationary distributions
.318
8.2
Recombination
.322
8.2.1
A clever change of variables
.323
8.2.2
Time-dependent behavior
.326
8.2.3
Equilibrium when there is mutation
.329
8.3
Hill-Robertson interference
.334
XII Contents
8.4
Gene
duplication
.341
8.5
Watterson's double recessive null model
.343
8.6
Subfunctionalization
.347
9
Genome Rearrangement
.355
9.1
Inversions
.355
9.1.1
Breakpoint graph
.355
9.1.2
Hurdles
.358
9.2
When is parsimony reliable?
.362
9.2.1
Phase transition
.365
9.2.2
Bayesian approach
.367
9.3
Nadeau and Taylor's analysis
.370
9.4
Genomic distance
.375
9.4.1
Graph distance
.375
9.4.2
Bayesian estimation
.377
9.5
Midpoint problem
.382
9.6
Genome duplication
.389
9.6.1
Yeast
.389
9.6.2
Maize
.393
9.6.3
Arabidopsis thaliana
.396
References
.399
Index
.427 |
| adam_txt |
Contents
Preface
.
V
1
Basic
Models. 1
1.1
ATGCs
of life
. 1
1.2
Wright-Fisher model
. 5
1.2.1
The coalescent
. 8
1.2.2
Shape of the genealogical tree
. 11
1.3
Infinite
alíeles
model
. 14
1.3.1
Hoppe's urn, Ewens' sampling formula
. 15
1.3.2
Chinese restaurants and sufficient statistics
. 20
1.3.3
Branching process viewpoint
. 26
1.4
Infinite sites model
. 29
1.4.1
Segregating sites
. 31
1.4.2
Nucleotide diversity
. 39
1.4.3
Pairwise differences
. 40
1.4.4
Folded site frequency spectrum
. 43
1.5
Moran
model
. 46
1.5.1
Fixation probability and time
. 47
1.5.2
Site frequency spectrum mean
. 50
2
Estimation and Hypothesis Testing
. 53
2.1
Site frequency spectrum covariance
. 53
2.2
Estimates of
θ
. 59
2.3
Hypothesis testing overview
. 63
2.4
Difference statistics
. 65
2.4.1
Tájimat
D.
65
2.4.2
Fu
and Li's
D.
67
2.4.3
Fay and Wu's
Η
. 69
2.4.4
Conditioning
onS„
. 71
2.5
The HKA test
. 72
2.6
McDonald-Kreitman test
. 78
X
Contents
3
Recombination
. 83
3.1
Two loci
. 83
3.1.1
Sample of size
2. 83
3.1.2
Sample of size
η
. 87
3.2
m
loci
. 90
3.2.1
Samples of size
2. 91
3.2.2
Samples of size
η
. 91
3.2.3
Pairwise differences
. 93
3.3
Linkage disequilibrium
. 97
3.4
Ancestral recombination graph
.101
3.4.1
Simulation
.105
3.4.2
Two approximate algorithms
.107
3.5
Counting recombinations
.
Ill
3.6
Estimating recombination rates
.114
3.6.1
Equations for the two-locus sampling distribution
.115
3.6.2
Simulation methods
.118
3.6.3
Composite likelihood estimation of
ρ
.120
3.7
Haplotypes and hot spots
.122
4
Population Complications
.125
4.1
Large family sizes
.125
4.2
Population growth
.130
4.2.1
Exponential growth
.131
4.2.2
Sudden population expansion
.134
4.3
Founding effects and bottlenecks
.138
4.4
Effective population size
.143
4.5
Matrix migration models
.146
4.5.1
Strobeck's theorem
.148
4.5.2
Fast migration limit
.149
4.6
Symmetric island model
.150
4.6.1
Identity by descent
.150
4.6.2
Mean and variance of coalescence times
.152
4.6.3
Effective population sizes
.153
4.6.4
Large
η
limit
.154
4.7
Fixation indices
.157
5
Stepping Stone Model
.161
5.1
d
= 1.
Exact results
.161
5.2
d
= 1
and
2,
Fourier methods
.165
5.3
d
= 2.
Coalescence times
.172
5.3.1
Random walk results
.172
5.3.2
Samples of size
2.175
5.3.3
Fixation indices Fst
.177
5.4
d
= 2.
Genealogies
.179
5.4.1
Simulation results
.181
Contents
XI
5.5
d
= 1,
Continuous models
.183
5.6
d =
2,
Continuous models
.188
6
Natural Selection
.191
6.1
Directional selection
.191
6.1.1
Fixation probability
.192
6.1.2
Time to fixation
.194
6.1.3
Three phases of the fixation process
.197
6.1.4
Ancestral selection graph
.199
6.2
Balancing selection
.201
6.3
Background selection
.211
6.4
Muller's ratchet
.219
6.4.1
Evolutionary advantages of recombination
.220
6.4.2
Sex, epistasis, and Kondrashov
.222
6.5
Hitchhiking
.225
6.6
Better approximations
.234
6.7
Recurrent sweeps
.241
6.7.1
Nucleotide diversity
.241
6.7.2
Genealogies
.243
6.7.3
Segregating sites
.245
7
Diffusion Processes
.249
7.1
Infinitesimal mean and variance
.250
7.2
Examples of diffusions
.252
7.3
Transition probabilities
.258
7.4
Hitting probabilities
.262
7.5
Stationary measures
.268
7.6
Occupation times
.273
7.7
Green's functions
.276
7.8
Examples
.280
7.9
Conditioned processes
.287
7.10
Boundary behavior
.293
7.11
Site frequency spectrum
.298
7.11.1
Poisson
random field model
.300
7.12
Fluctuating selection
.304
8
Multidimensional Diffusions
.313
8.1
К
alíele
model
.313
8.1.1
Fixation probabilities and time
.315
8.1.2
Stationary distributions
.318
8.2
Recombination
.322
8.2.1
A clever change of variables
.323
8.2.2
Time-dependent behavior
.326
8.2.3
Equilibrium when there is mutation
.329
8.3
Hill-Robertson interference
.334
XII Contents
8.4
Gene
duplication
.341
8.5
Watterson's double recessive null model
.343
8.6
Subfunctionalization
.347
9
Genome Rearrangement
.355
9.1
Inversions
.355
9.1.1
Breakpoint graph
.355
9.1.2
Hurdles
.358
9.2
When is parsimony reliable?
.362
9.2.1
Phase transition
.365
9.2.2
Bayesian approach
.367
9.3
Nadeau and Taylor's analysis
.370
9.4
Genomic distance
.375
9.4.1
Graph distance
.375
9.4.2
Bayesian estimation
.377
9.5
Midpoint problem
.382
9.6
Genome duplication
.389
9.6.1
Yeast
.389
9.6.2
Maize
.393
9.6.3
Arabidopsis thaliana
.396
References
.399
Index
.427 |
| any_adam_object | 1 |
| any_adam_object_boolean | 1 |
| author | Durrett, Richard 1951- |
| author_GND | (DE-588)121396789 |
| author_facet | Durrett, Richard 1951- |
| author_role | aut |
| author_sort | Durrett, Richard 1951- |
| author_variant | r d rd |
| building | Verbundindex |
| bvnumber | BV035031516 |
| callnumber-first | Q - Science |
| callnumber-label | QH438 |
| callnumber-raw | QH438.4.S73 |
| callnumber-search | QH438.4.S73 |
| callnumber-sort | QH 3438.4 S73 |
| callnumber-subject | QH - Natural History and Biology |
| classification_rvk | SK 950 WH 2600 |
| classification_tum | BIO 107f |
| ctrlnum | (OCoLC)213855666 (DE-599)BVBBV035031516 |
| dewey-full | 572.8380727 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 572 - Biochemistry |
| dewey-raw | 572.8380727 |
| dewey-search | 572.8380727 |
| dewey-sort | 3572.8380727 |
| dewey-tens | 570 - Biology |
| discipline | Biologie Mathematik |
| discipline_str_mv | Biologie Mathematik |
| edition | 2. ed. |
| format | Book |
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| id | DE-604.BV035031516 |
| illustrated | Illustrated |
| index_date | 2024-07-02T21:49:58Z |
| indexdate | 2024-12-06T17:00:41Z |
| institution | BVB |
| isbn | 9780387781686 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-016700495 |
| oclc_num | 213855666 |
| open_access_boolean | |
| owner | DE-355 DE-BY-UBR DE-19 DE-BY-UBM DE-91G DE-BY-TUM DE-11 DE-29T DE-83 DE-20 |
| owner_facet | DE-355 DE-BY-UBR DE-19 DE-BY-UBM DE-91G DE-BY-TUM DE-11 DE-29T DE-83 DE-20 |
| physical | XII, 431 S. graph. Darst. |
| publishDate | 2008 |
| publishDateSearch | 2008 |
| publishDateSort | 2008 |
| publisher | Springer |
| record_format | marc |
| series2 | Probability and its applications |
| spelling | Durrett, Richard 1951- Verfasser (DE-588)121396789 aut Probability models for DNA sequence evolution Richard Durrett 2. ed. New York [u.a.] Springer 2008 XII, 431 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Probability and its applications Literaturverz. S. 223 - 237 Base Sequence Evolution, Molecular Evolutionary genetics Statistical methods Models, Genetic Nucleotide sequence Statistical methods Probabilities Probability Variation (Biology) Statistical methods Stochastisches Modell (DE-588)4057633-4 gnd rswk-swf DNS-Sequenz (DE-588)4150352-1 gnd rswk-swf Wahrscheinlichkeit (DE-588)4137007-7 gnd rswk-swf Mathematisches Modell (DE-588)4114528-8 gnd rswk-swf Wahrscheinlichkeitstheorie (DE-588)4079013-7 gnd rswk-swf Populationsbiologie (DE-588)4046800-8 gnd rswk-swf Ökologie (DE-588)4043207-5 gnd rswk-swf Genetische Variabilität (DE-588)4264352-1 gnd rswk-swf Evolution (DE-588)4071050-6 gnd rswk-swf DNS-Sequenz (DE-588)4150352-1 s Evolution (DE-588)4071050-6 s Stochastisches Modell (DE-588)4057633-4 s DE-604 Genetische Variabilität (DE-588)4264352-1 s Wahrscheinlichkeit (DE-588)4137007-7 s 1\p DE-604 Ökologie (DE-588)4043207-5 s Populationsbiologie (DE-588)4046800-8 s 2\p DE-604 Wahrscheinlichkeitstheorie (DE-588)4079013-7 s 3\p DE-604 Mathematisches Modell (DE-588)4114528-8 s 4\p DE-604 Erscheint auch als Online-Ausgabe 978-0-387-78169-3 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016700495&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk 2\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk 3\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk 4\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk |
| spellingShingle | Durrett, Richard 1951- Probability models for DNA sequence evolution Base Sequence Evolution, Molecular Evolutionary genetics Statistical methods Models, Genetic Nucleotide sequence Statistical methods Probabilities Probability Variation (Biology) Statistical methods Stochastisches Modell (DE-588)4057633-4 gnd DNS-Sequenz (DE-588)4150352-1 gnd Wahrscheinlichkeit (DE-588)4137007-7 gnd Mathematisches Modell (DE-588)4114528-8 gnd Wahrscheinlichkeitstheorie (DE-588)4079013-7 gnd Populationsbiologie (DE-588)4046800-8 gnd Ökologie (DE-588)4043207-5 gnd Genetische Variabilität (DE-588)4264352-1 gnd Evolution (DE-588)4071050-6 gnd |
| subject_GND | (DE-588)4057633-4 (DE-588)4150352-1 (DE-588)4137007-7 (DE-588)4114528-8 (DE-588)4079013-7 (DE-588)4046800-8 (DE-588)4043207-5 (DE-588)4264352-1 (DE-588)4071050-6 |
| title | Probability models for DNA sequence evolution |
| title_auth | Probability models for DNA sequence evolution |
| title_exact_search | Probability models for DNA sequence evolution |
| title_exact_search_txtP | Probability models for DNA sequence evolution |
| title_full | Probability models for DNA sequence evolution Richard Durrett |
| title_fullStr | Probability models for DNA sequence evolution Richard Durrett |
| title_full_unstemmed | Probability models for DNA sequence evolution Richard Durrett |
| title_short | Probability models for DNA sequence evolution |
| title_sort | probability models for dna sequence evolution |
| topic | Base Sequence Evolution, Molecular Evolutionary genetics Statistical methods Models, Genetic Nucleotide sequence Statistical methods Probabilities Probability Variation (Biology) Statistical methods Stochastisches Modell (DE-588)4057633-4 gnd DNS-Sequenz (DE-588)4150352-1 gnd Wahrscheinlichkeit (DE-588)4137007-7 gnd Mathematisches Modell (DE-588)4114528-8 gnd Wahrscheinlichkeitstheorie (DE-588)4079013-7 gnd Populationsbiologie (DE-588)4046800-8 gnd Ökologie (DE-588)4043207-5 gnd Genetische Variabilität (DE-588)4264352-1 gnd Evolution (DE-588)4071050-6 gnd |
| topic_facet | Base Sequence Evolution, Molecular Evolutionary genetics Statistical methods Models, Genetic Nucleotide sequence Statistical methods Probabilities Probability Variation (Biology) Statistical methods Stochastisches Modell DNS-Sequenz Wahrscheinlichkeit Mathematisches Modell Wahrscheinlichkeitstheorie Populationsbiologie Ökologie Genetische Variabilität Evolution |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016700495&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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