Rapid growth of genome data provides opportunities for updating microbial evolutionary
relationships, but this is challenged by the discordant evolution of individual genes. Here we …

Eukaryotes arose from prokaryotes, hence the root in the tree of life resides among the
prokaryotic domains. The position of the root is still debated, although pinpointing it would …

The accrual of genomic data from both cultured and uncultured microorganisms provides
new opportunities to develop systematic taxonomies based on evolutionary relationships …

The complexity and depth of the relationships between the three domains of life challenge
the reliability of phylogenetic methods, encouraging the use of alternative analytical tools …

Eukaryotes are typically depicted as descendants of archaea, but their genomes are
evolutionary chimeras with genes stemming from archaea and bacteria. Which prokaryotic …

Bacterial genomics has revolutionized our understanding of the microbial tree of life;
however, mapping and visualizing the distribution of functional traits across bacteria remains …

In order to explore microevolutionary trends in bacteria and archaea, we constructed a data
set of 41 alignable tight genome clusters (ATGCs). We show that the ratio of the medians of …

Bacterial and archaeal evolution involve extensive gene gain and loss. Thus, phylogenetic
trees of prokaryotes can be constructed both by traditional sequence-based methods (gene …

Reconstruction of the Tree of Life is a central goal in biology. Although numerous novel
phyla of bacteria and archaea have recently been discovered, inconsistent phylogenetic …

INTRODUCTION Bacteria are the most diverse and abundant cellular organisms on Earth,
and in recent years environmental genomics has revealed the existence of an enormous …