Lectures 11 Monday, November 30, 2009 Phylogenetic tree (phylogeny) • Darwin and classification: In the Origin, Darwin said that descent from a common ancestral species could explain why the Linnaean system is hierarchical. Species in the same genus had a common ancestor more recently than species in different genera. The only figure in the Origin illustrated his idea. He introduced the idea of a phylogenetic tree. • A phylogenetic tree represents the history of most groups of species: For a phylogenetic tree to be a good description of the history of a group, the time it takes for new species to form (represented by the splitting of lineages) has to be very short compared to how long each species was present. The phylogeny of humans, chimps, gorillas and bonobos is typical and thought to be roughly accurate. • A few groups of plants, such as those in the genus Clarkia, do not have a tree-like history. The history of Clarkia and other such groups is reticulate (net-like) in which some species have two ancestors. • Information in a phylogenetic tree: The pattern of branching indicates ancestry. The branch lengths indicate times. • Cladogram: A cladogram summarizes the branching pattern but contains no information about times. Be sure to understand the difference between a phylogenetic tree and a cladogram. • A phylogenetic tree represents the pattern of evolution: A tree is a convenient summary of what actually happened. If you could replay the webcast of life, you could discover the tree that describes the true history of a group of species. Phylogenetic trees and classification • Darwin and taxonomy: Darwin did not address the practical problem of how to use evolutionary history to classify species into higher groups. The problem was then and is still that, although there is a phylogenetic tree that describes the history of most groups, the correct tree is usually not known. • With the advent of DNA sequencing, much effort is going into inferring the phylogenies of all major groups. The Tree of Life project (www.tolweb.org) is an international effort to join phylogenetic trees of different groups into a single tree that describes the overall pattern of evolution. • Terminology: A monophyletic group is one that contains an ancestral species and all of its descendants. Mammals are a monophyletic group. A monophyletic group is often called a clade. A paraphyletic group is one that contains an ancestral species and some but not all of its descendants. The family Pongidae(orangutans, chimpanzees, bonobos and gorillas) is paraphyletic. It does not include modern and extinct humans which are descended from a pongid ancestor. • Phylogenetic systematics: The overall goal is to make higher categories reflect evolutionary history by requiring that all taxa be monophyletic. In a phylogenetic classification, species in the same genus had a most recent common ancestor more recently than species in different genera in the same family, and so on. Finding the best cladogram • The problem is to determine the cladogram that describes the ancestry of a group. • A simple method and one that is easy to apply is parsimony, which is the only one discussed in this course. Other methods, including maximum likelihood, rely on statistical models that make it possible to infer branch lengths as well the branching pattern. • Parsimony: Parsimony assumes that changes in characters or the appearance of new characters occur very rarely. The underlying idea is to choose the tree that requires the fewest changes. • Counting evolutionary transitions requires that homologous characters be distinguished form analogous characters. Wings in different species of bats are homologous. Wings in bats and wings in birds are analogous. • A shared derived character is a character that is shared by every species in a group but is not shared with any species outside the group. The assumption of parsimony is that a shared derived character arose once in the ancestor of the group. Monophyletic groups can be distinguished by identifying shared derived characters. • In order to distinguish between shared primitive characters and shared derived characters, one or more outgroups are needed. Wings are a shared derived character of bats; fur is a shared primitive character. • Theory and practice: In theory, it should be possible to always find the correct cladogram by identifying a the right set of shared derived characters. In practice, that is almost never possible because, for a given set of characters and species, there is no cladogram that perfectly fits in the sense that only one change is needed for each character. • Shared derived characters are homologous. Characters that arose independently in different groups are analogous. The problem is that without knowing the cladogram, it may be difficult to know which characters are homologous and which are analogous. That is true whether the characters are morphological characters or differences in DNA sequence.DNA sequences provide many characters • There is increasing use of DNA sequences of gene from different species to infer phylogenetic trees. • Molecular clocks. • Population genetics tells us that on average differences in DNA sequence evolve at a roughly constant rate. • Different genes evolve at different rates, which makes them useful for analyzing species that diverged at different times in the past. • Ribosomal RNA evolves very slowly. The recognition that Archaea and Bacteria were quite different first came from the analysis of ribosomal RNA sequences. Once the groups were distinguished, phenotypic differences between them were then found. Table 27.2 summarizes the differences, but it will not be necessary to know those differences for this course. • Mitochondria in animals contain small circular DNA molecules (about 16,000 bases in length) that are inherited maternally. Animal mtDNA evolves more rapidly than nuclear DNA, so it is useful for examining
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