Bioinformatics

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Phylogenetics

Genome Scan

FST

The correlation of allelic states between individuals from the same population. The history of a population can be thought of as a series of genealogies describing the relationships between every individual at a certain point in the genome. For a neutrally evolving metapopulation FST reflects the pattern of coalescence times of those genealogies. In particular, FST = (T – T0) / T where T0 is the average coalescence time for a pair of alleles drawn from the same deme and T is the average coalescence time for a pair of alleles drawn from the metapopulation as a whole. FST varies across the genome; the mutations that happened to occur in the population and the individuals that happened to be sampled will give rise to variation in FST at different points in the genome.

Genealogical hierarchy

The genealogical hierarchy exist as a consequence of the spatial distribution of reproduction in species. The levels within the hierarchy ascend with increasing size and geographic range and are each subjected to corresponding factors in the ecological hierarchy. The lowest level in the genealogical hierarchy is the organism, especially in its reproductive sense. These organisms participate the reproduction of the overall species. The next level up in the hierarchy are 'deme' who are the interbreeding local population of a species. These can be thought of as specific regional variations of the species that interbreed. The next and second highest level in the hierarchy are species. The final and highest level in the genealogical hierarchy are monophyletic taxa, who all share and come from an common ancestor.

Deme

In biology, a deme, in the strict sense, is a group of individuals that belong to the same taxonomic group.[1] However, when biologists, and especially zoologists, use the term ‘deme’ they usually refer to it as the definition of a gamodeme:[2] a local group of individuals (from the same taxon) that interbreed with each other and share a gene pool.[1] The latter definition of a deme is only applicable to sexual reproducing species, while the former is more neutral and also takes asexual reproducing species into account, such as certain plant species. In the following sections the latter (and most frequently used) definition of a deme will be used. In evolutionary computation, a "deme" often refers to any isolated subpopulation subjected to selection as a unit rather than as individuals.

Brownian Motion

The basic model for the evolution of continuous characters on phylogenies is Brownian Motion, in which characters follow a constant-rate random walk with no trend. BM can model drift, drift-mutation balance, or even selection in a rapidly changing environment.

Ornstein–Uhlenbeck Model

In the past 20 years, various extensions of Brownian Motion have been proposed. The most significant advance was the development of the Ornstein–Uhlenbeck model, which adds a pull toward a central value to BM. OU was designed to model stabilizing selection in an analogy with adaptive landscapes in population genetics, but is more generally assumed to model adaptive evolution over phylogenies

Homoplasy

Heterotachy

Protein Folding

Missense Mutation

A missense mutation is a mistake in the DNA which results in the wrong amino acid being incorporated into a protein because of change, that single DNA sequence change, results in a different amino acid codon which the ribosome recognizes. Changes in amino acid can be very important in the function of a protein. But sometimes they make no difference at all, or very little difference. Sometimes missense mutations cause amino acids to be incorporated, which make the protein more effective in doing its job. More frequently, it causes the protein to be less effective in doing its job. But this is really the grist of evolution, when missense mutations happen, and therefore small changes, frequently small changes in proteins, happen, and it happens to be that it improves the function of a protein. That will sometimes give the organism that has it a competitive advantage over its colleagues and be maintained in the population.

Mutation spectrum

The mutation spectrum of an organism is the rate at which different types of mutations occur at different sites in the genome. The mutation spectrum matters because the rate alone gives a very incomplete picture of what is going on in a genome. For instance, mutations might occur at the same rate in two lineages, but the rate alone would not tell us if the mutations were all base substitutions in one lineage and all large-scale rearrangements in the other. Even within base substitutions, the spectrum can still be informative because a transition substitution is different from a transversion. The mutation spectrum also allows us to know whether mutations happen in coding or noncoding regions. There is a systematic difference in rates for transitions (Alpha) and transversions (Beta).