title: Evolution of DNA or amino acid sequences with dependent sites.
abstract: A framework is outlined to study the evolution of DNA or amino acid sequences, if sequence sites do not evolve independently. The units of evolution are nonoverlapping subsequences of length l. Each subsequence evolves independently of the others, but within a subsequence the sequences show a Markov order one dependency. We describe an algorithm to mimic the evolution of such sequences. The influence of dependencies between sites on distance estimates and the reliability of tree reconstruction methods is investigated. We show that an inappropriate model of sequence evolution in the tree reconstruction process will lead to a nonempty Felsenstein zone. Finally, we describe a method to infer l from sequence data. Examples from the evolution of DNA sequences as well as from amino acids are given.
authors.affiliation: Institute for Zoology, University of Munich, Germany.
authors.forename: A
authors.initials: A
authors.lastname: von Haeseler
authors.forename: M
authors.initials: M
authors.lastname: Schöniger
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence / Q000235:genetics; D000818:Animals; D001483:Base Sequence / Q000235:genetics; D004272:DNA, Mitochondrial / Q000737:chemistry; D019143:Evolution, Molecular; D008390:Markov Chains; D008957:Models, Genetic; D009010:Monte Carlo Method; D018995:Myosin Heavy Chains / Q000737:chemistry; D011336:Probability; D012335:RNA, Ribosomal; D014907:Whales
chemical_list: D004272:DNA, Mitochondrial; D012335:RNA, Ribosomal; D018995:Myosin Heavy Chains