期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 26, 期 8, 页码 1901-1908出版社
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msp102
关键词
gene families; mixture model; parasites; maximum likelihood; phylogenetics
资金
- Biotechnology and Biological Sciences Research Council [BB/E019005/1]
- Biotechnology and Biological Sciences Research Council [BB/E019005/1] Funding Source: researchfish
- BBSRC [BB/E019005/1] Funding Source: UKRI
Gene families are frequently gained and lost from prokaryotic genomes. It is widely believed that the rate of loss was accelerated for some but not all gene families in lineages that became parasites or endosymbionts. This leads to a form of heterotachy that may be responsible for the poor performance of phylogeny estimation based on gene content. We describe a mixture model that accounts for this heterotachy. We show that this model fits data on the distribution of gene families across bacteria from the COG database much better than previous models. However, it still favors an artifactual tree topology in which parasites form a clade over the more plausible 16S topology. In contrast to a previous model of genome dynamics, our model suggests that the ancestral bacterium had a small genome. We suggest that models of gene family gain and loss are likely to be more useful for understanding genome dynamics than for estimating phylogenetic trees.
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