Rapid evolutionary innovation during an Archaean genetic expansion

  title={Rapid evolutionary innovation during an Archaean genetic expansion},
  author={Lawrence A. David and Eric J. Alm},
The natural history of Precambrian life is still unknown because of the rarity of microbial fossils and biomarkers. However, the composition of modern-day genomes may bear imprints of ancient biogeochemical events. Here we use an explicit model of macroevolution including gene birth, transfer, duplication and loss events to map the evolutionary history of 3,983 gene families across the three domains of life onto a geological timeline. Surprisingly, we find that a brief period of genetic… 
Tunneling through Time: Horizontal Gene Transfer Constrains the Timing of Methanogen Evolution
Molecular clock analyses of methanogenic Archaea, with age constraints derived from an HGT from within methanogens to the ancestor of Cyanobacteria, provide independent support for the hypothesis of an Eoarchaean biogenic methane greenhouse.
Ecological Insights from the Evolutionary History of Microbial Innovations
The geological timeline and physiological expectations are used to provide independent evidence in support of the evolutionary history of microbial traits and gene transition rates can be used to make predictions about the size and type of genes in a genome.
Horizontal gene transfer constrains the timing of methanogen evolution
Support for methanogenesis predating the Archaean is found by analysing horizontal gene transfer events between methanogenic Archaea and Cyanobacteria, which show methanogens diverging within Euryarchaeota no later than 3.51 billion years ago.
Microbial genomic trait evolution is dominated by frequent and rare pulsed evolution
The findings suggest that major bacterial lineages could have originated in quick bursts and pulsed evolution is a common theme across the tree of life despite the drastically different population genetic properties of bacteria, archaea and eukaryotes.
Ancestral genome estimation reveals the history of ecological diversification in Agrobacterium
This work used a phylogenetic approach accounting for the transfer of genes (or groups of genes) to estimate the history of genomes in Agrobacterium biovar 1, a diverse group of soil and plant-dwelling bacterial species, and identified clade-specific blocks of co-transferred genes encoding coherent biochemical pathways that may have contributed to the evolutionary success of key Agrobacteria clades.
Novel phylogenetic approaches to problems in microbial genomics
Three new phylogenetic methods for gaining insight into how microbes evolve are presented, including the algorithm AdaptML, which uses strain ecology information to identify genetically and ecologically-distinct bacterial populations, and GAnG, which can construct prokaryotic species trees from thousands of distinct gene trees.
Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces
It is shown that acquisition and retention of genes through LGT are surprisingly rare in the ubiquitous and biomedically important bacterial genus Streptomyces, with merely one gene acquired in StrePTomyces lineages every 100,000 years.
Modularized Evolution in Archaeal Methanogens Phylogenetic Forest
This study presented a modularized phylogenetic forest that describes a combination of complicated vertical and nonvertical evolutionary processes for methanogenic archaeal species.
Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations
The results demonstrate that lateral gene transfers, detected by probabilistic models of genome evolution, can be used as a source of information on the timing of evolution, providing a valuable complement to the limited prokaryotic fossil record.


Biogeochemical signatures through time as inferred from whole microbial genomes
Geochemi- cal signatures and phylogenetic relationships of prokaryotes from whole genome sequences are deduced and this link is used to infer geochemical aspects of the biosphere through time.
Prokaryotic evolution in light of gene transfer.
The role of recombination and HGT in giving phenotypic "coherence" to prokaryotic taxa at all levels of inclusiveness, the implications of these processes for the reconstruction and meaning of "phylogeny," and new views of proKaryotic adaptation and diversification based on gene acquisition and exchange are discussed.
The balance of driving forces during genome evolution in prokaryotes.
The results indicate that the majority of protein families have only been transmitted by vertical inheritance, and it is suggested that gene gain and gene loss in prokaryotes are balanced; thus, on average, prokarian genome size is kept constant.
Genomes in flux: the evolution of archaeal and proteobacterial gene content.
This work reconstructs the gene content of ancestral Archaea and Proteobacteria and quantify the processes connecting them to their present day representatives based on the distribution of genes in completely sequenced genomes.
History of biological metal utilization inferred through phylogenomic analysis of protein structures
The late evolving Zn-binding proteins are fundamental to eukaryotic cellular biology, and Zn bioavailability may have been a limiting factor in eucaryotic evolution.
Archean molecular fossils and the early rise of eukaryotes.
The presence of steranes, particularly cholestane and its 28- to 30-carbon analogs, provides persuasive evidence for the existence of eukaryotes 500 million to 1 billion years before the extant fossil record indicates that the lineage arose.
Modern proteomes contain putative imprints of ancient shifts in trace metal geochemistry
It is hypothesize that these conserved trends are proteomic imprints of changes in trace metal bioavailability in the ancient ocean that highlight a major evolutionary shift in biological trace metal usage.
The Evolution of Two-Component Systems in Bacteria Reveals Different Strategies for Niche Adaptation
It is found that many genomes carry a large repertoire of recently evolved signaling genes, which may reflect selective pressure to adapt to new environmental conditions and clear species-specific preferences for which mode is used.
Reassessing the first appearance of eukaryotes and cyanobacteria
The results eliminate the evidence for oxygenic photosynthesis ∼2.7 Gyr ago and exclude previous biomarker evidence for a long delay between the appearance of oxygen-producing cyanobacteria and the rise in atmospheric oxygen 2.45–2.32 billion years ago.
Horizontal gene transfer among genomes: the complexity hypothesis.
  • R. Jain, M. Rivera, J. Lake
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1999
It is proposed that a major factor in the more frequent horizontal transfer of operational genes is that informational genes are typically members of large, complex systems, whereas operational genes are not, thereby making horizontalTransfer of informational gene products less probable (the complexity hypothesis).