ArticleGenome research2010
Reconstructing ancestral gene content by coevolution.
Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- The Possible Crystallization Process in the Origin of Bacteria, Archaea, Viruses, and Mobile Elements.Biology · 2024Article
- A Closer Look at Non-random Patterns Within Chemistry Space for a Smaller, Earlier Amino Acid Alphabet.Journal of molecular evolution · 2022Article
- The essence of life revisited: how theories can shed light on it.Theory in biosciences = Theorie in den Biowissenschaften · 2022Article
- Review
- A Place for Viruses on the Tree of Life.Frontiers in microbiology · 2020Review
- Hidden Concepts in the History and Philosophy of Origins-of-Life Studies: a Workshop Report.Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life · 2019Review
- The indefinable term 'prokaryote' and the polyphyletic origin of genes.Journal of genetics · 2017Article
- Biophysical comparison of ATP synthesis mechanisms shows a kinetic advantage for the rotary process.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- One step beyond a ribosome: The ancient anaerobic core.Biochimica et biophysica acta · 2016Review
- The Phylogeny of Rickettsia Using Different Evolutionary Signatures: How Tree-Like is Bacterial Evolution?Systematic biology · 2016Article
- Cladograms with Path to Event (ClaPTE): a novel algorithm to detect associations between genotypes or phenotypes using phylogenies.Computers in biology and medicine · 2015Article
- The non-biological meaning of the term "prokaryote" and its implications.Journal of molecular evolution · 2015Article
- Modelling the efficiency of codon-tRNA interactions based on codon usage bias.DNA research : an international journal for rapid publication of reports on genes and genomes · 2014Article
- Article
- Evolution of gene neighborhoods within reconciled phylogenies.Bioinformatics (Oxford, England) · 2012Article
- Uncovering the co-evolutionary network among prokaryotic genes.Bioinformatics (Oxford, England) · 2012Article
- 2011 William Allan Award: development and evolution.American journal of human genetics · 2012Article
- Divergence and convergence in enzyme evolution: parallel evolution of paraoxonases from quorum-quenching lactonases.The Journal of biological chemistry · 2012Review
- Extensive Inter-Domain Lateral Gene Transfer in the Evolution of the Human Commensal Methanosphaera stadtmanae.Frontiers in genetics · 2012Article
- Virtual genomes in flux: an interplay of neutrality and adaptability explains genome expansion and streamlining.Genome biology and evolution · 2012Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Inferring the gene content of ancestral genomes is a fundamental challenge in molecular evolution. Due to the statistical nature of this problem, ancestral genomes inferred by the maximum likelihood (ML) or the maximum-parsimony (MP) methods are prone to considerable error rates. In general, these errors are difficult to abolish by using longer genomic sequences or by analyzing more taxa. This study describes a new approach for improving ancestral genome reconstruction, the ancestral coevolver (ACE), which utilizes coevolutionary information to improve the accuracy of such reconstructions over previous approaches. The principal idea is to reduce the potentially large solution space by choosing a single optimal (or near optimal) solution that is in accord with the coevolutionary relationships between protein families. Simulation experiments, both on artificial and real biological data, show that ACE yields a marked decrease in error rate compared with ML or MP. Applied to a large data set (95 organisms, 4873 protein families, and 10,000 coevolutionary relationships), some of the ancestral genomes reconstructed by ACE were remarkably different in their gene content from those reconstructed by ML or MP alone (more than 10% in some nodes). These reconstructions, while having almost similar likelihood/parsimony scores as those obtained with ML/MP, had markedly higher concordance with the coevolutionary information. Specifically, when ACE was implemented to improve the results of ML, it added a large number of proteins to those encoded by LUCA (last universal common ancestor), most of them ribosomal proteins and components of the F(0)F(1)-type ATP synthase/ATPases, complexes that are vital in most living organisms. Our analysis suggests that LUCA appears to have been bacterial-like and had a genome size similar to the genome sizes of many extant organisms.
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