Correcting the Apparent Mutation Rate Acceleration at Shorter Time Scales under a Jukes-Cantor Model
نویسندگان
چکیده
منابع مشابه
Correcting the apparent mutation rate acceleration at shorter time scales under a Jukes-Cantor model.
At macroevolutionary time scales, and for a constant mutation rate, there is an expected linear relationship between time and the number of inferred neutral mutations (the "molecular clock"). However, at shorter time scales, a number of recent studies have observed an apparent acceleration in the rate of molecular evolution. We study this apparent acceleration under a Jukes-Cantor model applied...
متن کاملIdentifiability of 3-Class Jukes-Cantor Mixtures
We prove identifiability of the tree parameters of the 3-class Jukes-Cantor mixture model. The proof uses ideas from algebraic statistics, in particular: finding phylogenetic invariants that separate the varieties associated to different triples of trees; computing dimensions of the resulting phylogenetic varieties; and using the disentangling number to reduce to trees with a small number of le...
متن کاملMaximum likelihood Jukes-Cantor triplets: analytic solutions.
Maximum likelihood (ML) is a popular method for inferring a phylogenetic tree of the evolutionary relationship of a set of taxa, from observed homologous aligned genetic sequences of the taxa. Generally, the computation of the ML tree is based on numerical methods, which in a few cases, are known to converge to a local maximum on a tree, which is suboptimal. The extent of this problem is unknow...
متن کاملClassifying and Counting Linear Phylogenetic Invariants for the Jukes-Cantor Model
Linear invariants are useful tools for testing phylogenetic hypotheses from aligned DNA/RNA sequences, particularly when the sites evolve at different rates. Here we give a simple, graph theoretic classification for each phylogenetic tree T, of its associated vector space I(T) of linear invariants under the Jukes-Cantor one-parameter model of nucleotide substitution. We also provide an easily d...
متن کاملComparative Genomics Via Phylogenetic Invariants For Jukes-Cantor Semigroups
We review the theory of invariants as it has been developed for comparing the DNA sequences of homologous genes from phylogenetically related species, with particular attention to the semigroups used to model sequence evolution. We also outline the computational theory of genome rearrangements, including the optimization problems in calculating edit distances between genomes and the simpler not...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Molecular Biology and Evolution
سال: 2012
ISSN: 0737-4038,1537-1719
DOI: 10.1093/molbev/mss172