- Title Pages
- Foreword and introduction
- Introduction to the Meeting in Kristineberg, Sweden
- Contributors
- CHAPTER 1 The early days of paleogenetics: connecting molecules to the planet
- CHAPTER 2 Ancestral sequence reconstruction as a tool to understand natural history and guide synthetic biology: realizing and extending the vision of Zuckerkandl and Pauling
- CHAPTER 3 Linking sequence to function in drug design with ancestral sequence reconstruction
- CHAPTER 4 Probabilistic models and their impact on the accuracy of reconstructed ancestral protein sequences
- CHAPTER 5 Probabilistic ancestral sequences based on the Markovian model of evolution: algorithms and applications
- CHAPTER 6 Estimating the history of mutations on a phylogeny
- CHAPTER 7 Coarse projections of the protein-mutational fitness landscape
- CHAPTER 8 Dealing with uncertainty in ancestral sequence reconstruction: sampling from the posterior distribution
- CHAPTER 9 Evolutionary properties of sequences and ancestral state reconstruction
- CHAPTER 10 Reconstructing the ancestral eukaryote: lessons from the past
- CHAPTER 11 Using ancestral sequence inference to determine the trend of functional divergence after gene duplication
- CHAPTER 12 Reconstruction of ancestral proteomes
- CHAPTER 13 Computational reconstruction of ancestral genomic regions from evolutionarily conserved gene clusters
- CHAPTER 14 Experimental resurrection of ancient biomolecules: gene synthesis, heterologous protein expression, and functional assays
- CHAPTER 15 Dealing with model uncertainty in reconstructing ancestral proteins in the laboratory: examples from archosaur visual pigments and coralfluorescent proteins
- CHAPTER 16 Using ancestral gene resurrection to unravel the evolution of protein function
- CHAPTER 17 A thermophilic last universal ancestor inferred from its estimated amino acid composition
- CHAPTER 18 The resurrection of ribonucleases from mammals: from ecology to medicine
- CHAPTER 19 Evolution of specificity and diversity
- Conclusion and a way forward
- Index
Reconstructing the ancestral eukaryote: lessons from the past
Reconstructing the ancestral eukaryote: lessons from the past
- Chapter:
- (p.103) CHAPTER 10 Reconstructing the ancestral eukaryote: lessons from the past
- Source:
- Ancestral Sequence Reconstruction
- Author(s):
Mary J. O'Connell
James O. McInerney
- Publisher:
- Oxford University Press
Reconstructing ancestral proteins relies heavily on accurate phylogeny reconstruction. This is a challenging area particularly for early eukaryote evolution. Despite decades of extensive studies to resolve the structure of the deepest branches of the Eukaryota, a generally accepted phylogenetic reconstruction has not been achieved. This chapter explores the relationships of the three crown eukaryota and the root of the animal kingdom itself. It describes the methodological developments that have aided the field of early eukaryote evolution and the biases that exist in certain methods and data.
Keywords: eukaryote evolution, phylogenetic reconstruction, three crown eukaryota, ancestral proteins
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- Title Pages
- Foreword and introduction
- Introduction to the Meeting in Kristineberg, Sweden
- Contributors
- CHAPTER 1 The early days of paleogenetics: connecting molecules to the planet
- CHAPTER 2 Ancestral sequence reconstruction as a tool to understand natural history and guide synthetic biology: realizing and extending the vision of Zuckerkandl and Pauling
- CHAPTER 3 Linking sequence to function in drug design with ancestral sequence reconstruction
- CHAPTER 4 Probabilistic models and their impact on the accuracy of reconstructed ancestral protein sequences
- CHAPTER 5 Probabilistic ancestral sequences based on the Markovian model of evolution: algorithms and applications
- CHAPTER 6 Estimating the history of mutations on a phylogeny
- CHAPTER 7 Coarse projections of the protein-mutational fitness landscape
- CHAPTER 8 Dealing with uncertainty in ancestral sequence reconstruction: sampling from the posterior distribution
- CHAPTER 9 Evolutionary properties of sequences and ancestral state reconstruction
- CHAPTER 10 Reconstructing the ancestral eukaryote: lessons from the past
- CHAPTER 11 Using ancestral sequence inference to determine the trend of functional divergence after gene duplication
- CHAPTER 12 Reconstruction of ancestral proteomes
- CHAPTER 13 Computational reconstruction of ancestral genomic regions from evolutionarily conserved gene clusters
- CHAPTER 14 Experimental resurrection of ancient biomolecules: gene synthesis, heterologous protein expression, and functional assays
- CHAPTER 15 Dealing with model uncertainty in reconstructing ancestral proteins in the laboratory: examples from archosaur visual pigments and coralfluorescent proteins
- CHAPTER 16 Using ancestral gene resurrection to unravel the evolution of protein function
- CHAPTER 17 A thermophilic last universal ancestor inferred from its estimated amino acid composition
- CHAPTER 18 The resurrection of ribonucleases from mammals: from ecology to medicine
- CHAPTER 19 Evolution of specificity and diversity
- Conclusion and a way forward
- Index
