Oct 18, 2015

Gene tree discordance causes apparent substitution rate variation

BioRxiv : the Preprint Server for Biology
Fabio K Mendes, Matthew W Hahn

Abstract

Substitution rates are known to be variable among genes, chromosomes, species, and lineages due to multifarious biological processes. Here we consider another source of substitution rate variation due to a technical bias associated with gene tree discordance, which has been found to be rampant in genome-wide datasets, often due to incomplete lineage sorting (ILS). This apparent substitution rate variation is caused when substitutions that occur on discordant gene trees are analyzed in the context of a single, fixed species tree. Such substitutions have to be resolved by proposing multiple substitutions on the species tree, and we therefore refer to this phenomenon as "SPILS" (Substitutions Produced by Incomplete Lineage Sorting). We use simulations to demonstrate that SPILS has a larger effect with increasing levels of ILS, and on trees with larger numbers of taxa. Specific branches of the species trees are consistently, but erroneously, inferred to be longer or shorter, and we show that these branches can be predicted based on discordant tree topologies. Moreover, we observe that fixing a species tree topology when performing tests of positive selection increases the false positive rate, particularly for genes whose discordant...Continue Reading

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Mentioned in this Paper

Fracture, Incomplete
CD4 Antigens
Genome
Genes
Trees (plant)
Drosophila
Sorting - Cell Movement
Chemical Substitution
Convergence - Direction
Chromosomes

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