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Molecular Phylogenetics Phylogenetics •In the lectures on molecular evolution we shifted our focus onto longer evolutionary times. Instead of thinking about time passing in generations, we want to consider millions of years instead. • Evolutionary theory states that groups of similar organisms are descended from a common ancestor. •We can use phylogenetic trees to visualise and analyse evolution over very long periods. • Phylogenetic systematics (cladistics) is a method of taxonomic classification based on their evolutionary history. •If we had complete, reliable information, we could draw the relationship of species as a branching tree, where each branching event represents a speciation event. • It was developed by Willi Hennig, a German entomologist, in 1950. Cladistic Methods • Evolutionary relationships are documented by creating a branching structure, termed a phylogeny or tree, that illustrates the relationships between the sequences. • Cladistic methods construct a tree (cladogram) by considering the various possible pathways of evolution and choose from among these the best possible tree. • A phylogram is a tree with branches that are proportional to evolutionary distances. time 1 NODE Hypothetical Taxonomic Unit C A BRANCH D B ROOT Operational Taxonomic Unit (OTU) A C B D E E time UNROOTED ROOTED There are two kinds of information contained within a phylogenetic tree: 1. Branching order (topology) indicates the relative closeness of different taxa Trees may be rooted (we know which taxa are older or younger), or unrooted 2. Branch lengths indicate the amount of divergence Cladogram Phylogram os o Monophyletic, paraphyletic, and polyphyletic groupings a ph Hair Grouping 2 se Grouping 1 ou an at R d Grouping 3 M Leopard um Bir Turtle H t sh ele Fi nc Am La ibia n Dr il ph D E G H J K D E G H J K D E G H J K Salamander Amniotic egg C F I C F I C F I Tuna Lamprey Four walking legs Hinged jaws Lancelet (outgroup) Vertebral column B B A (a) Monophyletic. In this tree, grouping 1, consisting of the seven species B– H, is a monophyletic group, or clade. A monophyletic group is made up of an ancestral species (species B in this case) and all of its descendant species. Only monophyletic groups qualify as legitimate taxa derived from cladistics. B A (b) Paraphyletic. Grouping 2 does not meet the cladistic criterion: It is paraphyletic, which means that it consists of an ancestor (A in this case) and some, but not all, of that ancestor’s descendants. (Grouping 2 includes the descendants I, J, and K, but excludes B–H, which also descended from A.) A (c) Polyphyletic. Grouping 3 also fails the cladistic test. It is polyphyletic, which means that it lacks the common ancestor of (A) the species in the group. Furthermore, a valid taxon that includes the extant species G, H, J, and K would necessarily also contain D and E, which are also descended from A. 2 Birds Molecular Evolution Crocodiles Snakes and lizards Turtles and tortoises REPTILES Mammals The reptiles group, which excludes birds, is a paraphyletic group. Reptiles + birds together form a monophyletic group. DNA is a good tool for taxonomy DNA sequences have many advantages over classical types of taxonomic characters: – Character states can be scored unambiguously – Large numbers of characters can be scored for each individual – Information on both the extent and the nature of divergence between sequences is available (nucleotide substitutions, insertion/deletions, or genome rearrangements) • Phylogenetics often makes use of numerical data, (numerical taxonomy) which can be scores for various “character states” such as the size of a visible structure or it can be DNA sequences. • Similarities and differences between organisms can be coded as a set of characters, each with two or more alternative character states. • In an alignment of DNA sequences, each position is a separate character, with four possible character states, the four nucleotides. We rarely, if ever, know the species relationship, so we infer the phylogeny from biological data – morphological or molecular (DNA, protein sequence) We can study evolutionary relationships by analysing DNA sequence divergence. Aims: 1. Discover order of sequence/species divergence 2. Discover time of divergences 3. Describe sequence of events in lineage 3 DNA sequences start evolving independently after speciation events. Sequences accumulate differences over time. most closely related organisms should be the most similar at the molecular level. Convergent evolution is a problem Convergent evolution of analogous burrowing characteristics Australian marsupial mole Homology vs. Analogy Human arm vs bat wing • Homology: similar by descent; likeness in structure is due to trait inherited from common ancestor. Example: human hand and bat wing • Analogy: correspondence in function between anatomical parts of different structure and origin. Examples: Marsupial mole vs N. American mole Porcupine quill and cactus spine. Divergence of species from a common ancestor Leopard Domestic cat Domestic cats did not evolve from leopards N. American mole (placental mammal) Common ancestor 4 •In terms of DNA comparison, the simplest measure of level of similarity is obtained by counting the number of nucleotide differences. This is much less ambiguous than methods using morphological characters. We can develop statistical models for the accumulation of differences. •The molecular clock can be used to estimate the relative time of divergence of several species based on the level of DNA sequence similarity in a given homologous gene. This information can be used to construct phylogenetic trees. •We prefer Molecular data over Morpholgical data because: 1.DNA is strictly heritable, whereas morphological characteristics will be affected by the environment (non-heritable differences) 2.DNA can be described unambiguously (sequence of base pairs) whereas there are often classification differences of morphological characters 3.We have clear models of how DNA and proteins evolve over time, but the models for morphological evolution are unclear 4.DNA /protein is more amenable to mathematical analysis 5.It is very easy to assess homology (relationship by descent) of DNA/protein sequences 6.Possible to perform very distant comparisons of DNA/protein •The DNA sequences are compared and the levels of similarity or dissimilarity are used to arrange the species’ relationships into the phylogenetic tree shown on the left. •The DNA sequences are aligned (lined up with each column corresponding to the same base-pair in the ancestor). This is often called a multiple alignment, and columns are often called sites in the alignment. 7.DNA is abundant (found in all life) 5