2009/05/28 by Elizabeth S. Allman, Allman, Elizabeth S., Mark T. Holder +3
Biochemistry, Genetics and Molecular Biology · Earth and Planetary Sciences · #Evolution and Paleontology Studies #FOS: Biological sciences #Genetic diversity and population structure #Genomics and Phylogenetic Studies #Populations and Evolution (q-bio.PE) #q-bio.PE
paper · pdf · doi:10.48550/arxiv.0905.4542
31 pages, 4 figures; minor changes to reflect version to be published
openalex publication_date 2009/05/28 · arxiv created 2009/12/20 · arxiv updated 2010/01/07 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
As an alternative to parsimony analyses, stochastic models have been proposed (Lewis, 2001), (Nylander, et al., 2004) for morphological characters, so that maximum likelihood or Bayesian analyses may be used for phylogenetic inference. A key feature of these models is that they account for ascertainment bias, in that only varying, or parsimony-informative characters are observed. However, statistical consistency of such model-based inference requires that the model parameters be identifiable from the joint distribution they entail, and this issue has not been addressed. Here we prove that parameters for several such models, with finite state spaces of arbitrary size, are identifiable, provided the tree has at least 8 leaves. If the tree topology is already known, then 7 leaves suffice for identifiability of the numerical parameters. The method of proof involves first inferring a full distribution of both parsimony-informative and non-informative pattern joint probabilities from the parsimony-informative ones, using phylogenetic invariants. The failure of identifiability of the tree parameter for 4-taxon trees is also investigated.