for normal protein function. Other approaches such as PhyloP and PhyloHMM incorporate statistical phylogenetics methods to compare probability distributions of substitution rates, which allows the detection of both conservation and accelerated mutation. First, a background probability distribution is generated of the number of substitutions expected to occur for a column in a multiple sequence alignment, based on a phylogenetic tree. The estimated evolutionary relationships between the species of interest are used to calculate the significance of any substitutions (i.e. a substitution between two closely related species may be less likely to occur than distantly related ones, and therefore more significant). To detect conservation, a probability distribution is calculated for a subset of the multiple sequence alignment, and compared to the background distribution using a statistical test such as a likelihood-ratio test or score test. P-values generated from comparing the two distributions are then used to identify conserved regions. PhyloHMM uses hidden Markov models to generate probability distributions. The PhyloP software package compares probability distributions using a likelihood-ratio test or score test, as well as using a GERP-like scoring system. Extreme conservation Ultra-conserved elements Ultra-conserved elements or UCEs are sequences that are highly similar or identical across multiple taxonomic groupings. These were first discovered in vertebrates, and have subsequently been identified within widely-differing taxa. While the origin and function of UCEs are poorly understood, they have been used to investigate deep-time divergences in amniotes, insects, and between animals and plants. Universally conserved genes The most highly conserved genes are those that can be found in all organisms. These consist mainly of the ncRNAs and proteins required for transcription and translation, which are assumed to have been conserved from the last universal common ancestor of all life. Genes or gene families that have been found to be universally conserved include GTP-binding elongation factors, Methionine aminopeptidase 2, Serine hydroxymethyltransferase, and ATP transporters. Components of the transcription machinery, such as RNA polymerase and helicases, and of the translation machinery, such as ribosomal RNAs, tRNAs and ribosomal proteins are also universally conserved. Applications Phylogenetics and taxonomy Sets of conserved sequences are often used for generating phylogenetic trees, as it can be assumed that organisms with similar sequences are closely related. The choice of sequences may vary depending on the taxonomic scope of the study. For example, the most highly conserved genes such as the 16S RNA and other ribosomal sequences are useful for reconstructing deep