Phylogenetics and dating
However, it is quite feasible to determine the sequence of a defined area of a particular chromosome.Typical molecular systematic analyses require the sequencing of around 1000 base pairs.The base sequences for the haplotypes are then compared.In the simplest case, the difference between two haplotypes is assessed by counting the number of locations where they have different bases: this is referred to as the number of substitutions (other kinds of differences between haplotypes can also occur, for example, the insertion of a section of nucleic acid in one haplotype that is not present in another).Molecular phylogenetics and molecular evolution correlate. Molecular evolution is the process of selective changes (mutations) at a molecular level (genes, proteins, etc.) throughout various branches in the tree of life (evolution).Molecular phylogenetics makes inferences of the evolutionary relationships that arise due to molecular evolution and results in the construction of a phylogenetic tree. Work with protein electrophoresis began around 1956.
BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. BEAST is built on a large body of prior work and appropriate citations for individual modules, models and components will be listed when BEAST is run.
The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree.
Molecular phylogenetics is one aspect of molecular systematics, a broader term that also includes the use of molecular data in taxonomy and biogeography.
In principle, since there are four base types, with 1000 base pairs, we could have 4 distinct haplotypes.
However, for organisms within a particular species or in a group of related species, it has been found empirically that only a minority of sites show any variation at all, and most of the variations that are found are correlated, so that the number of distinct haplotypes that are found is relatively small.
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We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results. Users are strongly advised to join the BEAST mailing-list.