2 PhylogenyThe evolutionary relationships among organisms; thepatterns of lineage branching produced by the trueevolutionary history of the organisms beingconsidered
3 What is Molecular Phylogeny? is the inference of lines of ancestry for organismsbased on DNA, RNA, or protein sequences for thoseorganisms obtained in the laboratoryWe can infer relation betweenOrganism to OrganismGenes of different organismsOr genes within one organism
4 Gene function prediction SpeciationOrigin of genes & gene transfer
5 The tree of lifeA phylogenetic tree, also known as a tree of life or simplya phylogeny, describes branching relationships amongspecies, showing which species shares its most recentcommon ancestor with which other species.
6 Rooted trees Unrooted trees infers the existence of an actual common ancestor and definesthe evolutionary paths leading to the development of eachorganism.It provides an indication of the direction of theevolutionary process, defining ancestral and derived charactersor speciesUnrooted treesshows only the evolutionary relationships between theorganisms in the tree, and does not actually infer theplacement of a common ancestor in the structure orthe evolutionary path used to obtain the currentrelationships
11 Molecular Clocksconcept based on the assumption that mutationsoccur at some regular, more or less predictablerate.
12 Evolutionary Tree Construction Methods Maximum ParsimonyMaximum LikelihoodDistances / transformed distances
13 Maximum ParsimonyAttempt to create an evolutionary tree for the organismsin question by using the minimum number of evolutionary steps
14 Phylogenetic inference using parsimony proceeds in two stages: Infer the unrooted tree for a set of species. An unrooted treeshows the branching relations between the species but does notshow the position of the deepest common ancestor. It is aphylogenetic tree with the time dimension removed.2. Locate the root. This means calculating character polarity for agroup: finding the shared derived homologies which revealwhether A evolved from B or the other way round.
15 How can we infer the unrooted tree? Imagine there are four species: human, chimpanzee,magnolia tree and amoeba.Write out all the possible unrooted trees for the species;that is (a), (b) and (c)
16 count the minimum number of evolutionary events (that is, changes in character states) implied by eachThe best estimate of the true unrooted tree is the onerequiring the least evolutionary change.Suppose we know that 1000 characters are shared in all four species, that each species has 10 characters unique to itself and that 100 characters are shared between humans and chimps, but are absent in amoebas and magnolias
17 the 1000 common characters could have evolved once each in the common ancestor of all four species and been retained throughoutthe phylogeny; that would require a total of 1000 evolutionaryevents. Each species' 10 unique characters can have evolved in thelineage leading to that species, making 40 evolutionary events.The smallest number of events to produce the distribution of charactersbetween humans and chimps is 200: they could have evolved separately inthe human lineage and in the chimp lineage (100 events in each, making 200).=1240 evolutionary events.
18 In (c), however, the 100 characters shared by humans and chimps only need to have evolved once, in the common ancestor of humansand chimps, and would not have to be lost again; (c) therefore onlyrequires 1140 events.(c) is therefore the most parsimonious unrooted tree, and (accordingto the principle of parsimony) the best estimate of the realunrooted tree.
20 Distance is a principle of phylogeny referring to the quantitatively measured difference between two groups of organisms, such as two species.Distance can be measured in two ways:The difference between the phenetic appearance of two groups(phenetic distance).The difference in their gene frequencies (genetic difference).Distance is simply a more precise method of the 'look more similar' approachwhich classifies human and chimpanzees (opposite) as having a more recentcommon ancestor than humans and rabbits because they share more pheneticcharacters.
21 The distances method creates a matrix of all distances (difference scores) between all organisms for which the tree isto be constructed.Having calculated the matrix, the pair of organisms which have thesmallest distance score are connected, with a root in between themThe average of the distances from each member of the pair to athird node is use for the next iteration of the distances matrix.The process is repeated, until all organisms have been placed inthe tree.There is an extremely critical assumption when creating a tree likethis, and that is that there is a "molecular clock" and that allorganisms are mutating at the same rate.
22 Maximum LikelihoodMaximum likelihood methods create all possible trees containing theset of organisms in question, and then uses statistics to evaluatewhich tree is most likely.
23 Steps in Phylogeny construction BLASTConvert to FASTACLUSTALXTreeview