Phylograms

Phylograms are a type of phylogenetic tree in which the lengths of the branches are proportional to the amount of evolutionary change along that lineage. In a phylogram, longer branches indicate more change, while the topology shows relationships among taxa. This contrasts with cladograms, where branch lengths carry no quantitative meaning.

Phylograms are typically inferred from molecular data (DNA, RNA, or protein sequences) or from morphological character matrices. Branch lengths are estimated using models of character evolution and methods such as distance-based approaches, maximum likelihood, and Bayesian inference. The units of branch length are usually substitutions per site for molecular data, or inferred numbers of changes for morphological data. When rates of evolution differ among lineages, a phylogram may not reflect actual divergence times.

Rooting matters: phylograms can be rooted or unrooted. When rooted with an outgroup or when calibrated with a molecular clock, branch lengths can be interpreted as cumulative change or as time, respectively. If branch lengths are scaled to time, the tree is called a chronogram; if scaled to change, it is a phylogram.

Limitations include sensitivity to model assumptions, rate variation, and data quality. Saturation, incomplete lineage sorting, and horizontal gene transfer can bias branch lengths. Confidence measures such as bootstrap values help assess support for branches.

Applications include comparing evolutionary rates, dating divergences when calibrated, and annotating clades with inferred amounts of molecular change. Software packages commonly used to construct and visualize phylograms include MEGA, RAxML, BEAST, MrBayes, and R libraries such as Ape and Phytools.