title: Maximum parsimony for tree mixtures.
abstract: With the number of sequenced genomes growing ever larger, it is now common practice to concatenate sequence alignments from several genomic loci as a first step to phylogenetic tree inference. However, as different loci may support different trees due to processes such as gene duplication and lineage sorting, it is important to better understand how commonly used phylogenetic inference methods behave on such "phylogenetic mixtures". Here we shall focus on how parsimony, one of the most popular methods for reconstructing phylogenetic trees, behaves for mixtures of two trees. In particular, we show that (i) the parsimony problem is NP-complete for mixtures of two trees, (ii) there are mixtures of two trees that have exponentially many (in the number of leaves) most parsimonious trees, and (iii) give an explicit description of the most parsimonious tree(s) and scores corresponding to the mixture of a pair of trees related by a single TBR operation.
authors.affiliation: Department of Combinatorics and Geometry, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 YueYang Road, Shanghai 200031. stefan@picb.ac.cn
authors.forename: Stefan
authors.initials: S
authors.lastname: Grünewald
authors.forename: Vincent
authors.initials: V
authors.lastname: Moulton
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D023281:Genomics; D008957:Models, Genetic; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA