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Phylogenomics

An Introduction

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Publisher:

Springer

Pages: 222
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Recommend to library

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Hardcover - 9783319540627

07 June 2017

€105.49

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Ebook - 9783319540641

01 June 2017

€83.29

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This unique textbook provides a clear and concise overview of the key principles of the complex field of phylogenomics, with a particular focus on sequencing technologies that are crucial to studying and understanding...

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This unique textbook provides a clear and concise overview of the key principles of the complex field of phylogenomics, with a particular focus on sequencing technologies that are crucial to studying and understanding interrelations in evolutionary genomics. It includes chapters dedicated to the analysis of nucleotide sequences using assembling and alignment methods and also discusses the main strategies for phylogenetic studies, systematic errors and their correction. This highly readable textbook is intended for graduate students and young researchers with an interest in phylogenetics and evolutionary developmental biology.

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Highly readable overview on the main theoretical and practical aspects of Phylogenomics

Particular focus on the latest sequencing technologies

Must-have book for students and young researchers interested in evolutionary genomics

1. Genomes
01.1 Prokaryotes vs. Eukaryotes
01.2 Genome Structure
01.3 Genome Sizes
01.4 Human Genome and Ancient DNA (Neandertaler, Denisova)
2. Genomes of Organelles
02.1 Mitochondria
02.2 Plastids
02.3 Outlook Obligate Endosymbionts
3. Transcriptomes
03.1 mRNA
03.2 Transcripts
03.3 Expression Level
03.4 Alternative Splicing
4. Sequencing Techniques
04.1 Sanger
04.2 Illumina
04.3 454
04.4 PacBio
04.5 Outlook Nanopore Sequencing
5. Genome Sequencing Strategies
05.1 Whole Genome Shotgun
05.2 RADseq
05.3 Target Enrichment
05.4 RNAseq
6. Assembly and Mapping
06.1 Assembling Strategies (kmer vs OLC)
06.2 Data Quality and Filtering
06.3 Re-Sequencing and Mapping
06.4 De novo Assembly Genome
06.5 De novo Assembly Transcriptome
7. Locating Genes
07.1 Orthology vs. Paralogy
07.2 BLAST and Successors
07.3 Hidden Markov Profile
07.4 Ortholog Conjecture
8. Alignment
08.1 Alignment Strategies
08.2 Alignment Masking
9. Phylogenetic Analysis
09.1 Distance Measurements
09.2 Maximum Parsimony
09.3 Maximum Likelihood
09.4 Bayesian Inference
09.5 Supermatrix vs. Single Gene Analysis (Gene Trees vs. Species Trees)
10. Systematic Errors in phylogenetic Analysis
10.1 Prediction: Evolutionary Models
10.2 Heterogenity Nucleotide/Amino Acid-Composition
10.3 Variation of substitution rate between the lines
10.4 Variation of substitution rate over time
10.5 New Approaches to Correct systematic Errors
11. Genome-wide Characteristics
11.1 Gene Order
11.2 Mobile Elements
11.3 microRNAs
11.4 Differences in the genetic code
12. Index
13. References
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Prof. Dr. Christoph Bleidorn Georg-August-University Göttingen Johann-Friedrich-Blumenbach Institute for Zoology & Anthropology Animal Evolution and Biodiversity Göttingen, Germany christoph.bleidorn@gmail.com

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Prof. Dr. Christoph Bleidorn Georg-August-University Göttingen Johann-Friedrich-Blumenbach Institute for Zoology & Anthropology Animal Evolution and Biodiversity Göttingen, Germany christoph.bleidorn@gmail.com

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