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Lecture 2: Phylogenetics

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Lecture 2: Phylogenetics IB 168: Systematics of Vascular Plants Spring 2009 Key concepts -- Lecture 2 (1/26/09) and part of Lecture 3 (1/28/09) As noted in the 1st lecture, a primary goal of systematics is discovery of evolutionary lineages at all levels in the "tree of life," which involves resolving phylogeny = evolutionary relationships among a group of organisms (higher-level genealogy; patterns of evolutionary descent). Phylogeny, which often has an openly branching tree-like pattern, can be contrasted with relationships that are primarily net-like or reticulate, as expected within populations of organisms. The boundary between levels of evolutionary divergence where relationships conform to openly-branching vs. net-like patterns is not necessarily sharp, especially in plants, which often retain capability of hybridization after long periods of evolutionary divergence from one another. Relationship (phylogenetic or tokogenetic) refers to recency of common ancestry, NOT overall similarity. For example, in the figure below, B and C are more closely related to one another than either is to A because B & C share a more recent common ancestor than does A & C or A & B. out1 out2 A B C g j f i e c e ? h a d ? b Phenetics, in contrast to phylogenetics, is concerned with overall similarity among organisms, not their relationships. Branching diagrams based on overall similarity (phenograms or networks) will not reflect phylogeny unless the characters used to construct them have evolved at ~constant rates throughout the organismal group (i.e., across lineages). For example, in the above figure, A & B are more similar to one another than either is C and would be grouped together to the exclusion of C based on a phenetic, as opposed to phylogenetic, criterion. Types of evolutionary relationship Anagenesis -- transformational evolution in a linear series from one (ancestral) species to the next (descendant) species. A to B to C. Not generally realistic to hypothesize such relationships among a set of contemporary taxa. taxon taxon taxon A B C Cladogenesis -- branching of evolutionary lineages in a tree-like pattern (as in figure on previous page). Rather than hypothesize ancestor-descendant relationships among modern taxa, cladogenetic relationships are expressed in terms of sister-groups (closest relatives). In discussing contemporary species, the terms "ancestral" and "derived" are applied in systematics to particular characteristics of organisms, not to the organisms themselves. Reticulate evolution -- merging of divergent evolutionary lineages via hybridization; very important in vascular-plant evolution, as we will see. In the example below, C has been formed from hybridization of ancestral taxa on the lineages leading to A and B. A C B Types of evolutionary groups -- Formally recognized groups at any rank (e.g., division, class, order, family, genus, species, subspecies, or variety) are referred to by systematists as taxa (a rank-neutral term) (taxon, singular). Monophyletic groups include all descendants of a common ancestor; also known as clades, evolutionary lineages, or holophyletic groups. All systematists recognize monophyletic groups. In the example below, groups A+B+C and B+C are each monophyletic because each includes all descendants of a common ancestor (MRCA = most recent common ancestor). out1 out2 A B C MRCA of B+C MRCA of A+B+C Sister groups are closest relatives based on common ancestry. In the tree above, B and C are sister groups and A is the sister group of B + C. Polyphyletic groups are artificial, without genealogical integrity; the result of taxonomic error (faulty “diagnostic” characteristics are shared due to independent origins of those features rather than common ancestry). Systematists in general agree that polyphyletic groups should not be recognized. For example, in the tree above, a group including out1 and taxon C would be polyphyletic. Paraphyletic groups -- Include some but not all descendants of a common ancestor; also known as grades. Shared characteristics may be due to common ancestry and members of such groups may be more similar to one another than to excluded groups that also descend from the same, most recent common ancestor. These groups are avoided by most systematists because they are misleading about relationships and limit the utility of taxonomy for comparative biology, which often relies on sister-group comparisons. Many traditionally recognized plant groups (and plant groups based on phenetic criteria) have proven to be paraphyletic, as expected if rates of character evolution often vary across lineages. In the example above, a grouping of either taxa A & B or of taxa A & C would be paraphyletic. Evidence for phylogenetic relationships Characters are independent, heritable variables, the values of which are a set of mutually-exclusive character-states (=characteristics). Characters, by this definition, represent different lines of evidence about relationship; systematists try to include as many characters as possible in phylogenetic analyses (with the proviso that some characters are inappropriate for a particular question -- those characters may be evolving at the wrong rate to be useful or they may lack sufficiently discrete character-states, etc.). Parsimony is a commonly used criterion for estimating phylogeny. The branch of systematics concerned with parsimony to resolve phylogenetic relationships is often referred to as cladistics. As the number of taxa in the analysis increases, the number of possible trees increases astronomically; computer-based algorithms generally must be used to search for the most parsimonious trees (those with the fewest character changes or evolutionary steps) in analyses including more than a few taxa. The ingroup is the set of taxa whose relationships are being estimated; the outgroup is the taxon or set of taxa that is used to root the phylogenetic tree -- prior information is needed to show that the outgroup is more distantly related to the ingroup than the members of the ingroup are to one another. The tree below is the most parsimonious reconstruction of relationships based on the taxon-by-character matrix below the tree. Outgroup taxa are designated "out1" and "out2" and are known to fall outside the ingroup (taxa A, B, C). What was not known before this hypothetical analysis was the relationships among A, B, and C. Note that one of the characters ("e") is inconsistent with the tree topology (only one of two possible reconstructions of that character's evolution is shown). out1 out2 A B C g j f i e c e ? h a d ? b Characters Taxa a b c d e f g h i j out1 0 0 0 0 0 0 0 0 0 0 out2 1 0 0 0 0 0 0 0 0 0 A 1 1 0 0 1 0 1 0 0 0 B 1 1 0 1 0 0 0 1 0 0 C 1 1 1 1 1 1 0 1 1 1 .
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