Abstract
BackgroundThe shape of phylogenetic trees has been used to make inferences about the evolutionary process by comparing the shapes of actual phylogenies with those expected under simple models of the speciation process. Previous studies have focused on speciation events, but gene duplication is another lineage splitting event, analogous to speciation, and gene loss or deletion is analogous to extinction. Measures of the shape of gene family phylogenies can thus be used to investigate the processes of gene duplication and loss. We make the first systematic attempt to use tree shape to study gene duplication using human gene phylogenies.ResultsWe find that gene duplication has produced gene family trees significantly less balanced than expected from a simple model of the process, and less balanced than species phylogenies: the opposite to what might be expected under the 2R hypothesis.ConclusionWhile other explanations are plausible, we suggest that the greater imbalance of gene family trees than species trees is due to the prevalence of tandem duplications over regional duplications during the evolution of the human genome.
Highlights
The shape of phylogenetic trees has been used to make inferences about the evolutionary process by comparing the shapes of actual phylogenies with those expected under simple models of the speciation process
Gene family trees are more unbalanced than expected under the Equal-Rate Markov model (ERM) model but substantially more balanced than expected under the proportional-todistinguishable arrangements (PDA) model
This can be confirmed for the ERM model because the individual pIm scores can be combined using Fisher's method to yield an overall p-value that the trees have been drawn from an ERM distribution [[27] pp.794–797], which is significantly rejected for our data (χ2 = 1693.9, df = 1430, P < 0.0001)
Summary
The shape of phylogenetic trees has been used to make inferences about the evolutionary process by comparing the shapes of actual phylogenies with those expected under simple models of the speciation process. Molecular phylogenies for gene families (e.g. figure 1a) usually display sequences for different orthologous groups of proteins [1] from one or more species These trees can show a complicated tapestry of orthology and paralogy, and nodes on such trees may represent either gene duplications or speciations (figure 1, [2]): both are splitting events, producing daughter lineages that have independent evolutionary histories (at least in the absence of gene conversion or introgression [3]). Gene sequences from a completely sequenced (page number not for citation purposes)
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