Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data

Abstract

Background: As genomes evolve after speciation, gene content, coding sequence, gene expression, and splicing all diverge with time from ancestors with close relatives. A minimum evolution general method for continuous character analysis in a phylogenetic perspective is presented that allows for reconstruction of ancestral character states and for measuring along branch evolution.

Results: A software package for reconstruction of continuous character traits, like relative gene expression levels or alternative splice site usage data is presented and is available for download at http://www.rossnes.org/phyrex. This program was applied to a primate gene expression dataset to detect transcription factor binding sites that have undergone substitution, potentially having driven lineage-specific differences in gene expression.

Conclusion: Systematic analysis of lineage-specific evolution is becoming the cornerstone of comparative genomics. New methods, like phyrex, extend the capabilities of comparative genomics by tracing the evolution of additional biomolecular processes.

Figure 1

While comparing gene expression values between extant species averages over several branches of a phylogenetic tree, considering change along a branch based upon consideration of ancestral character states increases the signal to noise ratio, resulting in a test with more power to detect causative changes.

Figure 2

The rules for setting the intervals for ancestral character states are shown diagramatically. If an intersection exists among values at connected nodes, it is the minimum evolution range. If not, the range is the distance between the closest possible values from connected nodes.

Figure 3

A sample reconstruction of relative gene expression values is shown as the algorithm progresses. Along branch values are then obtained by subtracting the more recent node from the more ancient node. The successive values at each node reflect the values obtained moving up and down the tree as they reach convergence.

Figure 4

A similar reconstruction of ancestral promoter sequences is shown, using a standard method. Changes along branches in Figure 3 can then be compared with changes along the same branch in Figure 4.

Figure 5

The distribution of gene expression values from Enard et al. [7] obtained with phyrex is shown for the lineage leading from the last common ancestor of human and chimpanzee to human.

Figure 6

Similarly to Figure 5, the distribution of gene expression values from Enard et al. [7] obtained with phyrex is shown for the lineage leading from the last common ancestor of human and chimpanzee to chimpanzee.