Ch 19t - Chapter 19: Molecular Phylogenetics Molecular...

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Chapter 19: Molecular Phylogenetics Molecular Genetics Lecture Outlines -- C.M. Kearney This chapter is about finding relationships between groups, species or higher taxa using molecular techniques. This information can be used to track the evolution of a virus during an epidemic or to estimate how a particular organism evolved over a few thousand years or a few million years. The clues for all this are found in the sequences of the genome. These are core techniques in bioinformatics, since the relationships of various genes is always of practical interest. Fig. 19.2: Previously, phylogenists decided which morphological characteristics were best for determining relationships, and they separated species based on these few characteristics . Phenetics changed that by including as many measurable characters as possible and weighting them equally. Then came cladistics, which gives greater weight to characters which are were more significant in the evolution of the organism. It's phenetics with "fudge factors" from the fossil record. For example, wings are not a good character with which to separate higher taxa, such as birds from mammals, since bats also have wings, via convergent evolution. Ancestral characters are the basic plan from which all succeeding organisms developed. Five toes per foot is an example, from which some groups made modifications and others didn't, but there isn't a general progression from five to fewer toes. Therefore, humans aren't more closely related to lizards than to horses (one toe). When sequence data became available, it was recognized that this was the ultimate data for phenetics analysis. Why is sequence data generally superior to morphological characters in determining relationships? What are the character states dealt with in sequence data? In the early days, genome data for phylogeny came from immunological data, protein electrophoresis, and hybridization data. How were these data obtained and interpreted? Fig. 19.3: Why does DNA yield more information than protein sequence data? Fig. 19.4: You can show the relationships between several species graphically using a phylogenetic tree. What's the difference between a rooted and an unrooted tree? External nodes are the actual species you have DNA for. Internal nodes are the presumed ancestors. Fig. 19.5: To make a rooted tree, you need an outgroup -- what is that? What are inferred and true trees? True tree is unknown, so all our trees are inferred. Fig. 19.6: What is a clade? Groups that fit together phylogenically What is a "monophyletic" group of DNA sequences? Groups that come from the same origin The opposites of these are polyphyletic and paraphyletic. Like pigs and horses Fig. 19.7: What are gene and species trees? Fig. 19.8:
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This note was uploaded on 07/21/2008 for the course BIO 4306 taught by Professor Kearney during the Fall '08 term at Baylor.

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Ch 19t - Chapter 19: Molecular Phylogenetics Molecular...

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