Mutagenetic tree models

Mutagenetic trees are a class of graphical models designed for accumulative evolutionary processes. The state spaces of these models form finite distributive lattices. Using this combinatorial structure, we determine the algebraic invariants of mutagenetic trees. We further discuss the geometry of mixture models. In particular, models resulting from mixing a single tree with an error model are shown to be identifiable. Accumulative evolutionary processes Some evolutionary processes can be described as the accumulation of non-reversible genetic changes. For example, the process of tumor development of several cancer types starts from the set of complete chromosomes and is characterized by the subsequent accumulation of chromosomal gains and losses, or by losses of heterozygosity [Vogelstein et al., 1988, Zang, 2001]. Mutagenetic trees, sometimes also called oncogenetic trees, have been applied to model tumor development in patients with different types of cancer, such as renal cancer [Desper et al., 1999, von Heydebreck et al., 2004], melanoma [Radmacher et al., 2001] and ovarian adenocarcinoma [Simon et al., 2000]. For glioblastoma and prostate cancer, tumor progression along the mutagenetic tree has been shown to be an independent cytogenetic marker of patient survival [Rahnenführer et al., 2005]. Amino acid substitutions in proteins may also be modeled as permanent under certain conditions, such as a very strong selective pressure. For example, the evolution of human immunodeficiency virus (HIV) under antiviral drug therapy exhibits this behavior.