UIUC IB 201 - Phylogenetics: Constructing Phylogenetic Trees

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1 Genetics and Evolution IB 201 Phylogenetics: Constructing Phylogenetic Trees The next two lectures consider phylogenetics and the methods of reconstructing the history of relationships among organisms. This knowledge sets the groundwork for all the other subdisciplines in evolutionary biology, including evolutionary genetics. Phylogenetic trees are constructed from currently living (extant) organisms, and we use species as the basic units in this reconstruction. We will discuss later exactly what a species is; most of you already have an idea. Species are not independent entities—they are connected by descent from a common ancestor. They are connected by a lineage, a genealogy. A genealogy or lineage of species is known as a phylogeny, and the scientific discipline concerned with reconstructing the phylogenies of organisms is called phylogenetics (a part of the overall discipline called Systematics). Terms Phylogenetics: study of historical/genealogical relationships among organisms (taxa) Phylogeny: graphical representation of historical/genealogical relationships; a branching diagram Tree topology (phylogenetic tree, cladogram): a branching diagram that represents the genealogical relationships among taxa Taxon (pl. taxa): a group of organisms with an assigned name; can be a species name (Bombus impatiens), family name (e.g., Apidae), order name (e.g., Hymenoptera). A tree is represented by Tips: the species used in constructing the tree (currently extant, or extinct) Branches: ancestral populations of a species over time Nodes: the point where a species splits into two or more descendant populations History of Phylogenetics (Cladistics) Wilhelm (Willi) Hennig (1913-1976) • Phylogenetic relationships determined only by possession of synapomorphies (shared, derived characters) • Only monophyletic groups are recognized—i.e., those that contain all the descendants of a common ancestor [a paraphyletic group is missing some of the descendants of a common ancestor] [a polyphyletic group does not contain the most recent common ancestor of the taxa]2 Inferring a phylogenetic tree was done by hand in the early days. Only a few taxa and a few characters were used. Today, computers are needed to handle the large data sets used to reconstruct phylogenies. Principles of Estimating Relationships The basic concept is simple: closely related taxa should share the most traits • Each trait or character used in the reconstruction of relationships must be independent of one another • Characters must be homologous among all the taxa under study, and be divisible into at least two (usually more) homologous character states Many kinds of characters can be used for inferring relationships among organisms, e.g., Morphology DNA Behavior Use only shared, derived traits to group taxa because these provide a unique marker for species that originate from the ancestor in which the trait appeared. Phylogenetic Inference Seeks to recover the historical genetic patterns of relationships among organisms Principles 1. use shared derived features, not shared ancestral features 2. assume similar features are homologous until shown otherwise 3. treat shared, derived character states as markers of relatedness The same basic logic is used for all kinds characters, including morphology, DNA and behavior Terms Homology: correspondence (morphological, molecular, behavioral) inherited through common ancestry Apomorphy: derived character Synapmorphy: shared, derived character—informative for phylogenetic estimation Autapomorphy: uniquely derived character—non-informative for phylogeny Symplesiomorphy: shared ancestral character—non-informative for phylogeny Character: any phenotypic trait of an organism (tongue length, head shape, nucleotide position #50, degree of social behavior, and so on. Character state: variant (presumed to be homologous) forms of a character; coded as 0s, 1s, 2s, etc., if morphological trait, coded as G, A, T, or C, if characters are DNA sequences (also can code as different amino acids), and so on. Homoplasy: • Convergence: correspondence or similarity between characters that is not due to common ancestry; could be due to sharing similar environment. Common in nature and often a source of error in phylogenetic estimation • Parallelism: development of the same derived state in separate lineages from the same or a similar ancestral state—similar concept as convergence.3 Direction of Changes on a Tree In addition to identifying only shared, derived (synapomorphic) traits (that are homologous) for reconstructing a phylogeny, it is also important to know how the trait changed through time—that is, one needs to know the polarity. Sometimes fossils can help provide information on how a character changes through time, but we have very few fossils compared to all the changes in organisms that have occurred through time. Therefore, determining the direction of change in a character is best done through outgroup analysis. Outgroup Analysis: the character state in the group of interest (the ingroup) is compared to the character state in members outside that group, in a group that is closely related to the ingroup (outgroup). The outgroup state, if it also occurs within one or more of the members of the ingroup, is thought to be the ancestral state for a given character. Finding characters that are homologous and not convergent, as well as knowing which are the most closely related outgroups, requires considerable knowledge of the taxonomy and classification of the ingroup of interest. What to do if there is conflict among the different characters used to reconstruct a phylogeny? Tree reconstruction from multiple independent characters may run into problems if not all characters show the same phylogenetic relationships—i.e., if they imply different tree topologies. This occurs as a result of homoplasy (convergence, parallelism, and reversals of character states on a tree), which represents noise or error in the data set. Noise or conflict (lack of congruence among all the characters) in a data set is not uncommon in phylogenetic analysis. The more characters used in the analysis, the more likely it becomes. Several criteria have been proposed, but the most commonly used criterion for resolving conflict among characters is known as the parsimony criterion. Parsimony (developed in part by J. S. Farris in the


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UIUC IB 201 - Phylogenetics: Constructing Phylogenetic Trees

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