Bio 1B Lecture Outline (please print and bring along) Fall, 2007B.D. Mishler, Dept. of Integrative Biology 2-6810, [email protected] lecture #4 -- Phylogenetic Analysis (Cladistics) -- Nov. 9th, 2007• Outline of lecture:Overview of task in front of usAn example of putting together characters to make a treeSummary of cladistic concepts and termsGoing through the steps of phylogenetic analysis at a more detailed level, looking at some of the difficultiesPhylogenetic systematicsThe 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 -- charactersNeed to find something that changed its condition along a lineage, and survived in recognizable form to the present.Evolution #4, pg. 1period of period of shared historyshared historyPhylogenetic Phylogenetic Reconstruction:Reconstruction:Need to find markers that can be hypothesizedNeed to find markers that can be hypothesized to have changedto have changedtheir state on some shared branch in the past, and to have retainedtheir state on some shared branch in the past, and to have retaineda recognizable record of the derived state to the present.a recognizable record of the derived state to the present.a markera marker changing statechanging statePhylogenetics 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 statedivergence -- the splitting of one lineage into two lineagesreticulation - the blending of two lineages into one lineagemonophyly -- all and only descendants of a common ancestor• An example of putting together characters to make a treeLike 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 meanto 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. 2QuickTime™ and aTIFF (LZW) decompressorare needed to see this picture.Hennig's seminalcontribution was to note that in asystem evolving via descent withmodification and splitting oflineages, characters that changedstate along a particular lineage canserve to indicate the priorexistence of that lineage, even afterfurther splitting occurs. The"Hennig Principle" follows fromthis: homologous similaritiesamong organisms come in twobasic kinds, synapomorphies dueto immediate shared ancestry (i.e.,a common ancestor at a specificphylogenetic level), and symplesiomorphies due to moredistant ancestry. Only the formerare useful for reconstructing therelative order of branching eventsin phylogeny -- "specialsimilarities" (synapomorphies) arethe key to reconstructing trulynatural relationships of organisms,rather than overall similarity(which is an incoherent mixture ofsynapomorphy, symplesiomorphy,and non-homology). 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 ratherthan 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. 3QuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.QuickTime™ and aTIFF (LZW) decompressorare needed to see this picture.• More detail on some topics in Cladistics (summary of the following)• The basic methodology of cladisticsGroupings of organisms are based on their sharing of a recent common ancestor with anew 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 andfossil 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
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