Phylogenomic networks

doi:10.1016/j.tim.2011.07.001

Trends in Microbiology

Volume 19, Issue 10, October 2011, Pages 483-491

https://doi.org/10.1016/j.tim.2011.07.001 Get rights and content

Phylogenomics is aimed at studying functional and evolutionary aspects of genome biology using phylogenetic analysis of whole genomes. Current approaches to genome phylogenies are commonly founded in terms of phylogenetic trees. However, several evolutionary processes are non tree-like in nature, including recombination and lateral gene transfer (LGT). Phylogenomic networks are a special type of phylogenetic network reconstructed from fully sequenced genomes. The network model, comprising genomes connected by pairwise evolutionary relations, enables the reconstruction of both vertical and LGT events. Modeling genome evolution in the form of a network enables the use of an extensive toolbox developed for network research. The structural properties of phylogenomic networks open up fundamentally new insights into genome evolution.

Section snippets

Phylogenomics

The evolutionary history of a species is most commonly depicted as a bifurcating phylogenetic tree (see Glossary) comprising nodes and branches. The nodes in the tree correspond to contemporary species (external nodes) and their ancestors (internal nodes). The branches represent vertical inheritance linking ancestors with their descendants (Figure 1a). The accumulation of fully sequenced genomes since the early 2000s has enabled the practice of phylogenomics, that is, the study of phylogenetic

Networks

A network (or a graph) is a mathematical model of pairwise relations among entities. The entities (vertices or nodes) in the network are linked by edges representing the connections or interactions between these entities. In a coauthorship network, for example, the vertices signify scientists and the edges represent common publications to the scientists that they connect [22]. In an aviation network, airports are connected by flights [23]. Network approaches are common in almost all fields of

Phylogenetic networks

Networks are commonly used in phylogenetic research for the reconstruction of evolutionary processes that are non-tree-like in nature including hybridization, recombination, genome fusions and LGT [19]. The application of networks to phylogenetic data enables the modeling and visualization of reticulated evolutionary events that cannot be represented using a bifurcating phylogenetic tree 18, 19, 20, 21, 34, 35, 36. Network applications can also be used for tree-like (vertical inheritance only)

Phylogenomic networks of shared genes

Networks of shared genes are reconstructed from the presence/absence pattern of all orthologous protein families distributed across the genomes in the network 11, 46, 47, 48, 49, 50, 54. The vertices in the network are genomes (species) and the edges correspond to gene sharing between the genomes they connect. The gene sharing network reconstruction procedure includes the following steps: (i) selecting the genomes to be included in the network; (ii) sorting all proteins encoded in the selected

Phylogenomic LGT networks from shared genes

Phylogenomic LGT networks have been developed to study the lateral component in microbial evolution and are reconstructed from LGT events inferred from genomic data 11, 14, 48, 50, 51. Networks of laterally shared genes (LSG) are a special case of shared genes networks. These are designed specifically to study gene distribution patterns resulting from LGT during prokaryotic evolution. The vertices in the network are the external and internal nodes of a reference species phylogenetic tree. Edges

Phylogenomic LGT networks from trees

Phylogenomic LGT networks have also been reconstructed from LGT events detected in gene phylogenies 14, 51. As in the LSG network, the phylogenomic LGT network reconstruction requires a species tree that is considered as a reference for distinction between vertical inheritance and LGT. For the network reconstruction, a phylogenetic tree is reconstructed for each protein family. Branches (splits) in the protein family tree that are found in disagreement with the reference species tree are

Structural properties of phylogenomic networks

Structural properties of networks can be analyzed and understood using an extensive set of tools developed over the years 24, 26. Node connectivity, for example, is a measure that quantifies the extent to which a node is central within the network [26]. A similar measure, vertex centrality, quantifies the frequency in which the vertex occurs along the shortest path between any vertex pair in the network. The overall distribution of vertex centrality is commonly used to test for internal

Concluding remarks

Each of the different phylogenomic network types presented here offers a different insight into microbial genome evolution. Networks capture a substantial component of genome evolution, which is not tree-like in nature. Therefore, in biological systems where reticulated evolutionary events are common, phylogenomic networks offer a general computational approach that is more biologically realistic and evolutionarily more accurate. The prevalence of LGT during microbial and viral evolution makes

Acknowledgments

I thank Giddy Landan, Liat Shavit-Grievink, Ovidiu Popa, Thorsten Klösges and William Martin for their critical comments on the manuscript. This publication was funded in part by an ERC grant NETWORKORIGINS to William Martin.

Glossary

Conjugation: the transfer of DNA via proteinaceous cell-to-cell junctions in bacteria.
Degree (or connectivity): the number of edges that connect the node with other nodes.
Directed network: a network where the entities are connected by asymmetric relationships.
Edge (or link): related vertices are connected by an edge.
Gene copy number: the number of copies of a certain gene within the genome.
Gene transfer agents (GTA): phage-like DNA-carriers that are produced by a donor cell during the growth phase and

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Trends in Microbiology

ReviewMicrobial systems biologyPhylogenomic networks

Section snippets

Phylogenomics

Networks

Phylogenetic networks

Phylogenomic networks of shared genes

Phylogenomic LGT networks from shared genes

Phylogenomic LGT networks from trees

Structural properties of phylogenomic networks

Concluding remarks

Acknowledgments

Glossary

Trends Microbiol.

Phys. A

Mol. Cell

Adv. Math.

Gene

Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis

Genome Res.

Phylogenomics: intersection of evolution and genomics

Science

Lateral gene transfer and the nature of bacterial innovation

Nature

Direct visualization of horizontal gene transfer

Science

DNA uptake during bacterial transformation

Nat. Rev. Microbiol.

Mechanisms of, and barriers to, horizontal gene transfer between bacteria

Nat. Rev. Microbiol.

The ins and outs of DNA transfer in bacteria

Science

High frequency of horizontal gene transfer in the oceans

Science

The net of life: reconstructing the microbial phylogenetic network

Genome Res.

Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution

Proc. Natl. Acad. Sci. U.S.A.

Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes

BMC Evol. Biol.

The cobweb of life revealed by genome-scale estimates of horizontal gene transfer

PLoS Biol.

Highways of gene sharing in prokaryotes

Proc. Natl. Acad. Sci. U.S.A.

Genome-wide experimental determination of barriers to horizontal gene transfer

Science

Horizontal gene transfer among genomes: the complexity hypothesis

Proc. Natl. Acad. Sci. U.S.A.

The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transfer

Mol. Biol. Evol.

Application of phylogenetic networks in evolutionary studies

Mol. Biol. Evol.

survey of combinatorial methods for phylogenetic networks

Genome Biol. Evol.

Prokaryotic evolution and the tree of life are two different things

Biol. Direct

Getting a better picture of microbial evolution en route to a network of genomes

Philos. Trans. R. Soc. Lond. B: Biol. Sci.

The structure of scientific collaboration networks

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The worldwide air transportation network: anomalous centrality, community structure, and cities’ global roles

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Exploring complex networks

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Review
Microbial systems biology
Phylogenomic networks