Abstract
Incomplete lineage sorting (ILS) gives rise to stochastic variation in the topology of a gene tree and hence introduces false duplication events when gene tree and species tree reconciliation method is used for inferring the duplication history of a gene family. We quantify the effect of ILS on inference of gene duplication by examining the expected number of false duplication events inferred from reconciling a random gene tree, which occurs with a probability predicted in coalescent theory, and the given species tree. We computationally analyze the relationships between the number of false duplication events inferred on a branch and its length in a species tree, and the relationships between the expected number of false duplication events in a species tree and its topological parameters. This study provides evidence that inference of gene duplication based on tree reconciliation was affected by ILS to a greater extent on an asymmetric species tree than on a symmetric one. Our findings also suggest that the bias caused by ILS in reconciliation-based inference of gene duplication might not be negligible. Hence, when gene duplication is inferred via tree reconciliation or any other method that takes gene tree topology into account, the ILS-induced bias should be examined cautiously.
Published Version
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