Phylogenomics: Intersection of Evolution and Genomics

  title={Phylogenomics: Intersection of Evolution and Genomics},
  author={Jonathan A. Eisen and Claire M. Fraser},
  pages={1706 - 1707}
Much has been gained from genomic and evolutionary studies of species. Combining the perspectives of these different approaches suggests that an integrated phylogenomic approach will be beneficial. 
Taking advantage of phylogenetic trees in comparative genomics
Phylogenomics can be regarded as evolution and genomics in co-operation. Various kinds of evolutionary studies, gene family analysis among them, demand access to genome-scale datasets. But it is al
Phylogenomics and the reconstruction of the tree of life
This work has demonstrated the power of the phylogenomics approach, which has the potential to provide answers to several fundamental evolutionary questions, but challenges for the future have also been revealed.
3 Phylogenomics for the Study of Fungal Biology
An overview of how different phylogenomic approaches can be used to address the study of fungal biology is provided, including the establishment of the phylogenetic position of a newly sequenced species, the detection of past evolutionary events shaping a given genome, or the prediction of putative functions of uncharacterized proteins.
Phylogenomics, Protein Family Evolution, and the Tree of Life: An Integrated Approach between Molecular Evolution and Computational Intelligence
The application of phylogenomics (phylogenetics and genomics) is focused on to improve functional prediction of genes and gene products, to understand the evolution of protein families, and to resolve phylogenetic relationships of organisms.
The synergistic effect of concatenation in phylogenomics: the case in Pantoea
It is argued that by using a concatenation-based approach in phylogenomics, one can obtain robust phylogenies due to the synergistic effect of the combined signal obtained from multiple genes, as the topology from a ≥70-gene concatenated species phylogeny is not driven by single genes, and this finding may also hold true for smaller datasets.
The ecological coherence of high bacterial taxonomic ranks
The ecological coherence of high bacterial taxa in the light of genome analyses is discussed and examples of niche differentiation between deeply diverging groups in terrestrial and aquatic systems are presented.
Fungal phylogenomics.A global analysis of fungal genomes and their evolution
It is determined that the species tree was mostly well supported but some nodes showed large discrepancies to most genes, which could partly be attributed to evolutionary events that result in topological changes in gene trees.
Evolutionary Relationships Among the Oryza Species
Advances in genomics are offering opportunities for resolving the origin of cultivated rice and clarifying phylogenetic and evolutionary relationships between the various Oryza species, with a special focus on the application of current advances ingenomics in understanding the various evolutionary dynamics.


Genome sequencing: Brouhaha over the other yeast
The sequencing of the fission-yeast genome allows researchers to compare it with that of its cousin, budding yeast, and to identify genes that may distinguish eukaryotes (such as yeast) from
Gastrogenomic delights: A movable feast
The complete genome sequences of Escherichia coli and Helicobacter pylori provide insights into the biology of these species.
Initial sequencing and analysis of the human genome.
The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates
A phylogenetic analysis of 28 proposed HGT genes, whose presence in the human genome had been confirmed by polymerase chain reaction (PCR), indicates that most putative H GT genes are present in more anciently derived eukaryotes and can be explained in terms of descent through common ancestry.
A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history.
An attempt to use a supertree method to build the phylogenetic tree of 45 organisms, with special focus on bacterial phylogeny, by performing a phylogenetic study of congruence of tree topologies, which allows the identification of a core of genes supporting similar species phylogeny.
Comparative Genome Sequencing for Discovery of Novel Polymorphisms in Bacillus anthracis
Comparison of the whole-genome sequence ofBacillus anthracis isolated from a victim of a recent bioterrorist anthrax attack with a reference reveals 60 new markers that include single nucleotide