UPGMA stands for Unweighted Pair Group Method with Arithmetic Mean. UPGMA is a bottom up clustering method to create rooted phenetic trees (trees not based on sequence variants, but on morphological traits or other observable features). In a phylogenetic context, UPGMA assumes a constant rate of evolution.
UPGMA is the regarded as the most straight forward method of tree construction. It was originally developed for constructing taxonomic phenograms, but it can also be used to construct phylogenetic trees if the rates of evolution are approximately constant among the different lineages (Opperdoes 2004). UPGMA computes for each pair of taxons which pair has the smallest distance (i.e. least mutations), it the collapse that pair into one single taxon. This process is repeated until a root tree is derived. The assumed constant rate of mutations is believed to result in incorrect trees frequently (Anon. 2012).
References
– Opperdoes, Fred. 2004. Construction of a distance tree using clustering with the Unweighted Pair Group Method with Arithmetic Mean (UPGMA). Available at: http://www.icp.ucl.ac.be/~opperd/private/upgma.html. Accessed 1 November 2015.
– Anon. 2012. UPGMA. Sequentix. Available at: http://www.sequentix.de/gelquest/help/upgma_method.htm. Accessed 1 November 2015.