Phylogenetic network
Encyclopedia
A phylogenetic network is any graph
used to visualize evolutionary relationships between nucleotide sequences, gene
s, chromosome
s, genome
s, or species
. They are employed when reticulate events such as hybridization, horizontal gene transfer
, recombination
, or gene duplication
and loss are believed to be involved. They differ from phylogenetic trees by the explicit modeling, by means of the addition of hybrid nodes (nodes with two parents) instead of only tree nodes (nodes with only one parent) . Phylogenetic tree
s are a subset of phylogenetic networks. Phylogenetic networks can be inferred and visualised with software such as SplitsTree
and, more recently, Dendroscope
. A standard format for representing phylogenetic networks is a variant of Newick format
which is extended to support networks as well as trees.
Many kinds and subclasses of phylogenetic networks have been defined based on the biological phenomenon they represent or which data they are built from (hybridization networks, usually built from rooted trees, recombination networks from binary sequences, median networks
from a set of split
s, optimal realizations and reticulograms from a distance matrix
), or restrictions to get computationally tractable problems (galled trees, and their generalizations level-k phylogenetic networks, tree-child or tree-sibling phylogenetic networks).
ary events, for example the geographical distribution of muskrat or fish populations of a given species among river networks, because there is no species
boundary to prevent gene flow between populations. Therefore, a more general phylogenetic network better depicts these situations.
Graph (mathematics)
In mathematics, a graph is an abstract representation of a set of objects where some pairs of the objects are connected by links. The interconnected objects are represented by mathematical abstractions called vertices, and the links that connect some pairs of vertices are called edges...
used to visualize evolutionary relationships between nucleotide sequences, gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
s, chromosome
Chromosome
A chromosome is an organized structure of DNA and protein found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions.Chromosomes...
s, genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
s, or species
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...
. They are employed when reticulate events such as hybridization, horizontal gene transfer
Horizontal gene transfer
Horizontal gene transfer , also lateral gene transfer , is any process in which an organism incorporates genetic material from another organism without being the offspring of that organism...
, recombination
Genetic recombination
Genetic recombination is a process by which a molecule of nucleic acid is broken and then joined to a different one. Recombination can occur between similar molecules of DNA, as in homologous recombination, or dissimilar molecules, as in non-homologous end joining. Recombination is a common method...
, or gene duplication
Gene duplication
Gene duplication is any duplication of a region of DNA that contains a gene; it may occur as an error in homologous recombination, a retrotransposition event, or duplication of an entire chromosome.The second copy of the gene is often free from selective pressure — that is, mutations of it have no...
and loss are believed to be involved. They differ from phylogenetic trees by the explicit modeling, by means of the addition of hybrid nodes (nodes with two parents) instead of only tree nodes (nodes with only one parent) . Phylogenetic tree
Phylogenetic tree
A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical and/or genetic characteristics...
s are a subset of phylogenetic networks. Phylogenetic networks can be inferred and visualised with software such as SplitsTree
SplitsTree
SplitsTree is a popular program for inferring phylogenetic trees or, more generally, phylogenetic networks from various types of data such as a sequence alignment, a distance matrix or a set of trees...
and, more recently, Dendroscope
Dendroscope
Dendroscope is an interactive computer software program written in Java for viewing Phylogenetic trees. This program is designed to view trees of all sizes and is very useful for creating figures...
. A standard format for representing phylogenetic networks is a variant of Newick format
Newick format
In mathematics, Newick tree format is a way to represent graph-theoretical trees with edge lengths using parentheses and commas. It was adopted by James Archie, William H. E. Day, Joseph Felsenstein, Wayne Maddison, Christopher Meacham, F...
which is extended to support networks as well as trees.
Many kinds and subclasses of phylogenetic networks have been defined based on the biological phenomenon they represent or which data they are built from (hybridization networks, usually built from rooted trees, recombination networks from binary sequences, median networks
Median graph
In mathematics, and more specifically graph theory, a median graph is an undirected graph in which any three vertices a, b, and c have a unique median: a vertex m that belongs to shortest paths between any two of a, b, and c.The concept of median graphs has long been studied, for instance by or ...
from a set of split
Split (phylogenetics)
A split in phylogenetics is a bipartition of a set of taxa, and the smallest unit of information in unrooted phylogenetic trees: each edge of an unrooted phylogenetic tree represents one split, and the tree can be efficiently reconstructed from its set of splits...
s, optimal realizations and reticulograms from a distance matrix
Distance matrix
In mathematics, computer science and graph theory, a distance matrix is a matrix containing the distances, taken pairwise, of a set of points...
), or restrictions to get computationally tractable problems (galled trees, and their generalizations level-k phylogenetic networks, tree-child or tree-sibling phylogenetic networks).
Microevolution
Phylogenetic trees also have trouble depicting microevolutionMicroevolution
Microevolution is the changes in allele frequencies that occur over time within a population. This change is due to four different processes: mutation, selection , gene flow, and genetic drift....
ary events, for example the geographical distribution of muskrat or fish populations of a given species among river networks, because there is no species
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...
boundary to prevent gene flow between populations. Therefore, a more general phylogenetic network better depicts these situations.
Software to compute phylogenetic networks
- Network, Free Phylogenetic Network Software. Network generates evolutionary trees and networks from genetic, linguistic, and other data.
- Phylogeny programs, some of which compute phylogenetic networks
- List of programs for phylogenetic network reconstruction, evaluation, visualization, etc.
- SplitsTreeSplitsTreeSplitsTree is a popular program for inferring phylogenetic trees or, more generally, phylogenetic networks from various types of data such as a sequence alignment, a distance matrix or a set of trees...
- DendroscopeDendroscopeDendroscope is an interactive computer software program written in Java for viewing Phylogenetic trees. This program is designed to view trees of all sizes and is very useful for creating figures...
- Network inferring on the T-REX server
- TCS, Phylogenetic networks from DNA sequences or nucleotide distances using statistical parsimony.
- NetTest, Characterization of phylogenetic networks.