Abstract
The estimation of species trees from multiple genes is complicated by processes such as incomplete lineage sorting, duplication and loss, and horizontal gene transfer, that result in gene trees that differ from the species tree. Methods to estimate species trees in the presence of gene tree discord resulting from incomplete lineage sorting (ILS) have been developed and proved to be statistically consistent when gene tree discord is due only to ILS and every gene tree has the full set of species. Here we address statistical consistency of coalescent-based species tree estimation methods when gene trees are missing species, i.e., in the presence of missing data.
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