| Autore |
Bickel David R.
|
| Pubbl/distr/stampa |
Cham, Switzerland : , : Springer, , [2022]
|
| Descrizione fisica |
1 online resource (112 pages)
|
| Disciplina |
570.15195
|
| Collana |
SpringerBriefs in Systems Biology
|
| Soggetto topico |
Biometry
Molecular evolution
Phylogeny - Molecular aspects
|
| ISBN |
9783031119583
9783031119576
|
| Formato |
Materiale a stampa  |
| Livello bibliografico |
Monografia |
| Lingua di pubblicazione |
eng
|
| Nota di contenuto |
Intro -- Preface -- Why This Book? -- Brief Description -- Why the Subtitle ``A Hands-On Introduction with Uncertainty Quantification Corrected?'' -- Chapter-by-Chapter Synopsis -- Acknowledgments -- Contents -- 1 Introduction to Phylogenetic Trees -- 1.1 What Are Phylogenetic Trees All About? -- 1.2 Assumptions Behind Models of Molecular Phylogenetics -- 1.2.1 Common Ancestry -- 1.2.2 Molecular Clock Hypothesis -- 1.2.3 Statistical Assumptions -- 1.3 Exercises -- 2 Adaptation of the Molecular Clock: A Divergence Time Story -- 2.1 1960s: Starting the Clock -- 2.2 1970s: Neutralism Versus Selectionism -- 2.3 1980s: Fluctuating Rates -- 2.4 1990s: Confronting the Fossil Record -- 2.5 2000s: Molecular Punctuated Equilibrium -- 2.6 2010s: Integration of Data -- 2.7 2020s: Time Will Tell -- 2.8 Excursus: Models with Molecular Evolution over All Time Scales -- 2.8.1 Why Models with Evolution over All Time Scales? -- 2.8.2 Fractal point process models -- 2.8.3 Fractal-Rate Poisson Models -- 2.8.3.1 Generic Fractal-Rate Poisson Model -- 2.8.3.2 Gaussian Models of Rates -- 2.8.3.3 Diffusion Models of Rates -- 2.8.4 Multiplicative Model of Molecular Evolution -- 2.9 Exercises -- 2.10 Bibliographic Notes -- 3 Estimating Phylogenetic Trees -- 3.1 Substituter: The Poisson Game (3 Sequences of 12 Nucleotides Each) -- 3.1.1 Rules for Simulation Mode -- 3.1.1.1 Simulating Sequences -- 3.1.1.2 Sharing Selected Sequences with the Opposing Team -- 3.1.2 Rules for Estimation Mode -- 3.1.2.1 Distance-Based Tree Estimation -- 3.1.2.2 Estimating a Tree from Protein Sequences -- 3.1.2.3 Estimating a Tree from DNA Sequences -- 3.2 Relations of Different Types of Trees -- 3.3 Software for Tree Estimation -- 3.4 Sources of Uncertainty in Tree Estimates -- 3.4.1 Uncertainty About Common Ancestry -- 3.4.2 Uncertainty About the Topology.
3.4.3 Uncertainty About the Branch Lengths -- 3.4.4 Uncertainty About the Substitution Model -- 3.4.5 Uncertainty About the Tree Estimation Method -- 3.4.6 Uncertainty About the Statistical Method and Prior Probabilities -- 3.5 Excursus: Models of Nucleotide Substitution -- 3.5.1 Background Terminology -- 3.5.2 Discrete-Time Models [13.2]ewens2001statistical -- 3.5.3 Continuous-Time Models [13.3]ewens2001statistical -- 3.5.4 Further Reading -- 3.6 Exercises -- 4 Estimating Divergence Times -- 4.1 Confidence Intervals of Divergence Times -- 4.2 Uncertainty in Divergence Time Estimates -- 4.2.1 Sources of Uncertainty in Divergence Time Estimates -- 4.2.1.1 Uncertainty About Phylogenetic Trees -- 4.2.1.2 Uncertainty About Fluctuations in the Substitution Rate -- 4.2.1.3 Uncertainty About the Dates and Relations of Fossils -- 4.2.1.4 Uncertainty in Statistical Error -- 4.2.1.5 Uncertainty About Prior Distributions -- 4.2.2 Quantified Uncertainty in Divergence Time Estimates -- 4.2.3 Correcting Unquantified Uncertainty in Divergence Time Estimates -- 4.3 Excursus: Why Multiply Probabilities by the Proportion of Quantified Certainty? -- 4.4 Exercises -- 5 Estimating Common Ancestors -- 5.1 Notation for Conditional Probability -- 5.2 Estimating Ancestors in Substituter -- 5.2.1 Estimating an Ancestral DNA Sequence -- 5.2.2 Estimating an Ancestral Protein Sequence -- 5.3 Probabilities for the First Site of the Ancestral DNA Sequence -- 5.4 Maximum Likelihood for the First Site of the Ancestral DNA Sequence -- 5.5 Uncertainty in Ancestral Sequence Estimates -- 5.5.1 Sources of Uncertainty in Ancestral Sequence Estimates -- 5.5.1.1 Uncertainty About the Statistical Method and About Prior Probabilities -- 5.5.1.2 Uncertainty About the Model Assumptions -- 5.5.2 Correcting for Unquantified Uncertainty in Ancestral Sequence Estimates -- 5.6 Exercises.
6 Testing Hypotheses of Molecular Evolution -- 6.1 Maximum Genetic Diversity Hypothesis -- 6.2 Genetic Equidistance Phenomenon -- 6.3 Slow Clock Method -- 6.4 Questions Raised by Distinguishing Macroevolution from Microevolution -- 6.5 Exercises -- 7 Recommendations for Further Reading -- 7.1 Molecular Phylogenetics Books -- 7.1.1 Phylogenetics Books with Less Mathematics -- 7.1.1.1 Phylogenetic Trees Made Easy: A How-To Manual Hall2018main -- 7.1.1.2 An Introduction to Molecular Evolution and Phylogenetics bromham2016book -- 7.1.2 Phylogenetics Books with More Mathematics -- 7.2 Bioinformatics and Genomics Books -- 7.3 Imprecise Probability Books -- 7.4 Power Law Books -- A Probability Interpretation: Support by Data and Model Evidence -- A.1 An Evidential Generalization of Frequentist and Bayesian Probability -- A.2 Evidential Models and Evidential Support Distributions -- A.3 Imprecision Due to Uncertainty -- A.4 Evidential Sufficiency Distributions -- A.5 Special Case: Unquantified Uncertainty Corrected -- B Intermittent Point Processes -- B.1 Basics of Intermittency -- B.2 Hurst Exponent -- B.3 Fractal Renewal Processes -- C Poisson Processes with Lévy-Stable Substitution Rates -- C.1 Lévy-Stable Processes for Substitution Rates -- C.2 Point Process Models for Molecular Evolution -- C.2.1 Poisson-Stable Processes -- C.2.2 Poisson-Fractal Processes -- References -- Index.
|
| Record Nr. | UNINA-9910616213003321 |
Info
L'albero intricato : una nuova e radicale storia della vita [e-book] / David Quammen ; trad. di Milena Zemira Ciccimarra
