RT Journal Article
SR Electronic
T1 Terraces in Gene Tree Reconciliation-Based Species Tree Inference
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.04.17.047092
DO 10.1101/2020.04.17.047092
A1 Michael J. Sanderson
A1 Michelle M. McMahon
A1 Mike Steel
YR 2020
UL http://biorxiv.org/content/early/2020/04/18/2020.04.17.047092.abstract
AB Terraces in phylogenetic tree space are sets of trees with identical optimality scores for a given data set, arising from missing data. These were first described for multilocus phylogenetic data sets in the context of maximum parsimony inference and maximum likelihood inference under certain model assumptions. Here we show how the mathematical properties that lead to terraces extend to gene tree - species tree problems in which the gene trees are incomplete. Inference of species trees from either sets of gene family trees subject to duplication and loss, or allele trees subject to incomplete lineage sorting, can exhibit terraces in their solution space. First, we show conditions that lead to a new kind of terrace, which stems from subtree operations that appear in reconciliation problems for incomplete trees. Then we characterize when terraces of both types can occur when the optimality criterion for tree search is based on duplication, loss or deep coalescence scores. Finally, we examine the impact of assumptions about the causes of losses: whether they are due to imperfect sampling or true evolutionary deletion.Competing Interest StatementThe authors have declared no competing interest.