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). | ||
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Revision as of 18:41, 30 January 2007
| 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 study by Lockhart (1994) 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).
