Relaxed phylogenetics and dating with
uses heuristic search to optimise the TMRCAs of a phylogeny and the substitution rate.An uncorrelated relaxed molecular clock accounts for rate variation between lineages of the phylogeny which is parameterised using a Gamma-Poisson mixture model.
Let there be N individuals, and to keep this calculation simple, let the individuals be haploid (i.e. The probability that this new mutation will become fixed in the population is then 1/N, since each copy of the gene is as good as any other.Simulation studies have shown that increasing the number of fossil constraints increases the accuracy of divergence time estimation.Sometimes referred to as tip dating, tip calibration is a method of molecular clock calibration in which fossils are treated as taxa and placed on the tips of the tree.The basic logic of their analysis involved recognizing that if one species lineage had evolved more quickly than a sister species lineage since their common ancestor, then the molecular differences between an outgroup (more distantly related) species and the faster-evolving species should be larger (since more molecular changes would have accumulated on that lineage) than the molecular differences between the outgroup species and the slower-evolving species. Sarich and Wilson's paper reported, for example, that human (Homo sapiens) and chimpanzee (Pan troglodytes) albumin immunological cross-reactions suggested they were about equally different from Ceboidea (New World Monkey) species (within experimental error).This meant that they had both accumulated approximately equal changes in albumin since their shared common ancestor.