Difference between revisions of "Phylogenetics: Distances Lab"
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All of these organisms except ''Anacystis'' and ''Olithodiscus'' have both chlorophylls a and b. It is probable (based on independent evidence) that all chlorophyll a/b-containing chloroplasts have a common endosymbiotic origin, so we would expect trees constructed from these data to show a branch separating ''Anacystis'' and ''Olithodiscus'' from everything else. The cyanobacterium ''Anacystis'' uses phycobilin accessory pigments rather than chlorophylls for photosynthesis, and the chromophyte alga ''Olithodiscus'' has chlorophylls a and c (but not b). | All of these organisms except ''Anacystis'' and ''Olithodiscus'' have both chlorophylls a and b. It is probable (based on independent evidence) that all chlorophyll a/b-containing chloroplasts have a common endosymbiotic origin, so we would expect trees constructed from these data to show a branch separating ''Anacystis'' and ''Olithodiscus'' from everything else. The cyanobacterium ''Anacystis'' uses phycobilin accessory pigments rather than chlorophylls for photosynthesis, and the chromophyte alga ''Olithodiscus'' has chlorophylls a and c (but not b). | ||
| + | == References cited == | ||
<references/> | <references/> | ||
Revision as of 18:58, 30 January 2007
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This article is still under construction. Expect it to change frequently until this notice is removed. |
| This article is part of an EEB course. Please do not edit the content of this page without the approval of the course instructor. |
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EEB 349: Phylogenetics |
| The goal of this lab exercise is to show you how to conduct various distance based analyses in PAUP* and SplitsTree |
Part A: Using PAUP* to check your answers for homework #3
Part B: Analysis of algae.nex
Download the data file algae.nex from here. This data file was originally used in a 1994 study by Lockhart et al.[1] and comprises eight 16S ribosomal RNA sequences:
| Anacystis | a cyanobacterium (has chlorophyll a but not b or c) |
| Olithodiscus | a chloroplast from a chromophyte alga (chlorophylls a and c) |
| Euglena | a chloroplast from a photosynthetic euglenophyte protist |
| Chlorella | a chloroplast from a a chlorophyte green alga |
| Chlamydomonas | a chloroplast from a chlorophyte green alga |
| Marchantia | a chloroplast from a thallose liverwort (non-vascular bryophyte land plant) |
| Oryza | a chloroplast from a monocot (the flowering plant rice) |
| Nicotiana | a chloroplast from a dicot (the flowering plant tobacco) |
All of these organisms except Anacystis and Olithodiscus have both chlorophylls a and b. It is probable (based on independent evidence) that all chlorophyll a/b-containing chloroplasts have a common endosymbiotic origin, so we would expect trees constructed from these data to show a branch separating Anacystis and Olithodiscus from everything else. The cyanobacterium Anacystis uses phycobilin accessory pigments rather than chlorophylls for photosynthesis, and the chromophyte alga Olithodiscus has chlorophylls a and c (but not b).
References cited
- ↑ Lockhart, P. J., M. A. Steel, M. D. Hendy, and D. Penny. 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Molecular Biology and Evolution 11:605-612.
