Phylogenetics - Bioinformatics - Lecture Slides, Slides of Bioinformatics

Download Phylogenetics - Bioinformatics - Lecture Slides and more Slides Bioinformatics in PDF only on Docsity! Phylogenetics - Distance- Based Methods Docsity.com Phylogenetics • Attempts to infer the evolutionary history of a group of organisms or sequences of nucleic acids or proteins – Phylogenetic methods can be used for the study of evolutionary relationships between species of organisms as well as genes – Attempt to reconstruct evolutionary ancestors – Estimate time of divergence from ancestor Docsity.com History • Taxonomists used anatomy and physiology to group and classify organisms – Morphological features like presence of feathers or number of legs • When protein sequencing, and later DNA sequencing became common, amino acid and DNA sequences became the common way to contruct trees Docsity.com Phylogenetic Tree constructed from aa sequences of Cytochrome C protein QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Docsity.com The Big Picture • Determine the species or genes to be studied • Acquire homologous sequence data • Use multiple sequence alignment software like ClustalW to align • Clean up data by hand • Use phylogenetic analysis software like Phylip based on techniques we will study • Verify experimentally Docsity.com Phylogenetic Trees • Trees are composed of nodes and branches – Terminal or leaf nodes correspond to a gene or organism for which data has been collected – Internal nodes usually represent an inferred common ancestor that gave rise to two independent lineages sometime in the past Docsity.com Rooted and Unrooted Trees • Some trees make an inference about a common ancestor and the direction of evolution and some don’t – First type is called a rooted tree and has a single node designated as root which is the common ancestor – Second type is called an unrooted tree • Specifies only relationship between nodes and says nothing about direction of evolution Docsity.com Rooted and Unrooted Trees R A B C D E Time B C A E D Docsity.com Rooting Trees • Trees can be rooted by using the outgroup method previously mentioned, or by putting the root midway between the two most distant species as determined by branch length – Branch length measures the amount of difference that occurred along a branch – Assumes the species are evolving in a clock-like manner Docsity.com Rooting a Tree QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Docsity.com More Tree Terminology • Structure of a phylogenetic tree can be represented in Newick format using nested parentheses – (((B, C), (D, E)), A) • If we lack data to tell in which order two or more independent lineages occurred in the past, the tree may be multifurcating (more than two ancestors) otherwise, it is bifurcating (exactly two ancestors per interior node) Docsity.com Distance-Based Methods • Given such an input matrix we want to find an edge-weighted tree where the leafs of the tree correspond to the species and the distances measured between two leaves corresponds to the corresponding matrix value for the leaves Docsity.com UPGMA • UPGMA (Unweighted Pair Group Method with Arithmetic mean) is the oldest distance matrix method – Uses a distance matrix representing measure of genetic distance between pairs of species being considered – Clusters the two closest species – Compute new distance matrix using arithmetic mean to first cluster – Repeat until all species grouped Docsity.com UPGMA A B C E D A B C E D Docsity.com Transformed Distance Method • Several distance matrix-based alternatives to UPGMA allow different rates of evolution within different lineages – Oldest and simplest is the transformed distance method which takes advantage of an outgroup – Other lineages only evolve separately from each other after they diverged and since the outgroup diverged first we can use it as a frame of reference to compare how much the other lineages evolved by seeing when they diverged Docsity.com Neighbor’s Relation Method • One variant of UPGMA tries to pair species in such a way as to minimize the sum of the branch lengths – On a rooted tree, pairs of species separated from each other by only one node are called neighbors – We have important relationships between neighbors of a phylogenetic tree with four nodes Docsity.com Neighbor’s Relation Method A B C D a b d e c dAC + dBD = dAD + dBC = a + b + c + d + 2e = dAB + dCD + 2e dAB + dCD < dAC + dBD dAB + dCD < dAD + dBC The following hold for this tree Docsity.com