Bio 1B Spring 2008 Evolution section 1 of 4 Lecture 11 Updated 3 27 08 9 35 AM 11 Phylogenetic systematics Reading 7th edition 492 504 6th edition 492 502 The Linnaean system of classification is hierarchical Higher categories The major categories are domain kingdom phylum class order family genus species Intermediate categories exist such as subphylum and superfamily 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 because many species are allopolyploids 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 Bio 1B Spring 2008 Evolution section 2 of 4 Lecture 11 Updated 3 27 08 9 35 AM 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 A polyphyletic group is one that contains descendants of two or more different ancestral species that are not in the group All prokaryotes used to be classified in a single kingdom which was later discovered to be polyphyletic Now the Bacteria and the Archaea are distinct monophyletic domains p 540 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 Phylogenetic systematics is based on the cladogram not on the phylogenetic tree Finding the right 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 An example is given in Fig 25 11 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 as in Fig 25 11 In practice that is almost never possible because for a given set of characters and species there is no Bio 1B Spring 2008 Evolution section 3 of 4 Lecture 11 Updated 3 27 08 9 35 AM 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 Figure 25 15 works through an example in which the most parsimonious cladogram of four species is found In Figure 25 15 if species IV is known to be an outgroup then the branching order of the other three species can be inferred In the best fitting cladogram a group containing species I and II is monophyletic a group containing species II and III but not I is paraphyletic The goal of phylogenetic systematics cannot always be achieved There are a limited number of taxonomic levels genus family order etc Even if they are subdivided as they sometimes are into subfamilies subgenera tribes etc finding reasonable names for every possible subdivision may be
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