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 1 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 2 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 1970s developed the computer algorithms seeks to minimize the total amount of evolutionary change that has occurred assumes that homoplasy is rare seeks to find the tree that requires the fewest number of character state changes the tree of choice is the shortest tree often called the