Bio 1B Lecture Outline please print and bring along Fall 2007 B D Mishler Dept of Integrative Biology 2 6810 bmishler berkeley edu Evolution lecture 4 Phylogenetic Analysis Cladistics Nov 9th 2007 Outline of lecture Overview of task in front of us An example of putting together characters to make a tree Summary of cladistic concepts and terms Going through the steps of phylogenetic analysis at a more detailed level looking at some of the difficulties Phylogenetic systematics The value of phylogenies in biology Overview How can we discover phylogenetic history You can t actually see phylogeny so how do you make inferences about it Think of a huge oak tree buried in a sand dune with only the tips of the twigs showing what would you do The concept of historical markers characters Need to find something that changed its condition along a lineage and survived in recognizable form to the present period of shared history a marker changing state Phylogenetic Reconstruction Need to find markers that can be hypothesized to have changed their state on some shared branch in the past and to have retained a recognizable record of the derived state to the present Evolution 4 pg 1 Phylogenetics explained homology a feature shared by two lineages because of descent from an ancestor that had the feature transformation a heritable change in a homology along a lineage from a prior state to a posterior state divergence the splitting of one lineage into two lineages reticulation the blending of two lineages into one lineage monophyly all and only descendants of a common ancestor QuickTime and a TIFF LZW decompressor are needed to see this picture An example of putting together characters to make a tree Like other areas of biology this one is loaded with terminology and quantitative methods yet the basic principle is quite simple The fundamental idea is known as the Hennig Principle and is as elegant and fundamental in its way as was Darwin s principle of natural selection It is indeed simple yet profound in its implications It is based on the idea of homology one of the most important concepts in systematics but also one of the most controversial What does it mean to say that two organisms share the same characteristic The modern concept is based on evidence for historical continuity of information homology would then be defined as a feature shared by two organisms because of descent from a common ancestor that had the feature Evolution 4 pg 2 Hennig s seminal contribution was to note that in a system evolving via descent with modification and splitting of lineages characters that changed state along a particular lineage can serve to indicate the prior existence of that lineage even after further splitting occurs The Hennig Principle follows from this homologous similarities among organisms come in two basic kinds synapomorphies due to immediate shared ancestry i e a common ancestor at a specific phylogenetic level and symplesiomorphies due to more distant ancestry Only the former are useful for reconstructing the relative order of branching events in phylogeny special similarities synapomorphies are the key to reconstructing truly natural relationships of organisms rather than overall similarity which is an incoherent mixture of synapomorphy symplesiomorphy and non homology QuickTime and a TIFF Uncompressed decompressor are needed to see this picture In the Hennigian system individual hypotheses of putative homology are built up on a character by character basis then a congruence test using a parsimony principle is applied to identify homoplasies i e apparent homologies that are not congruent with the plurality of characters Examine the data matrix in box 3 4 above and be sure you can see why those data support the cladogram shown Note that the pattern of overall similarity would give a different result and group E with A and B rather than with C and D this will be demonstrated on the powerpoint To see the effect of homoplasy consider a new character 13 with the distribution 10010 see next page Finally classifications are applied to the resulting branching diagram cladogram A corollary of the Hennig Principle is that classification should reflect reconstructed branching order only monophyletic groups should be formally named A strictly monophyletic group is one that contains all and only descendents of a common ancestor A paraphyletic group is one the excludes some of the descendents of the common ancestor See figure on previous page for the distinction between these two types of groups This elegant correspondence between synapomorphy homology and monophyly is the basis of the cladistic revolution in systematics Evolution 4 pg 3 QuickTime and a TIFF LZW decompressor are needed to see this picture More detail on some topics in Cladistics summary of the following The basic methodology of cladistics Groupings of organisms are based on their sharing of a recent common ancestor with a new trait shared by no other groups Choice of traits relative time fossils on cladograms Contrast ancestral and derived new traits Contrast homologous shared ancestry and analogous convergent traits Why do we want to draw evolutionary relationships Weaknesses of the hierarchical Linnaean classification system Appendix Cladistics terms and concepts synapomorphies monophyletic and paraphyletic groups sister taxa outgroup stem and crown groups etc Evolution 4 pg 4 The basic methodology of cladistics Our aim is to use cladistics to describe the evolutionary relationships of all living and fossil species We use anatomical developmental behavioral and genetic data on living and fossil species to draw evolutionary relationships in a systematic and unbiased way see Fig 25 11 6th and 7th In cladistics we use new derived traits shared by all descendants of a common ancestor synapomorphies to determine monophyletic groupings which include the common ancestor and all descendants terms are defined below Groupings of organisms are based on their sharing of a recent common ancestor with a new trait shared by no other groups Tunicates Fish Amphibians Mammals Reptiles birds Single jaw bone Amniotes Tetrapods Vertebrates Chordates See Figs 34 2 and 34 23 7th Fig 34 7 6th Choice of traits relative time fossils on cladograms Choice of traits in a cladistic analysis a cladogram is only as good as the traits used to construct the branching points However it does provide us with a potentially unbiased way to determine evolutionary relationships
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