Difference between revisions of "Phylogenetics: Distances Lab"
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== Part B: Analysis of algae.nex == | == Part B: Analysis of algae.nex == | ||
− | '''Download the data file [http://hydrodictyon.eeb.uconn.edu/phylogenetics/labs/Spring2005/data/algae.nex | + | '''Download the data file algae.nex from [http://hydrodictyon.eeb.uconn.edu/phylogenetics/labs/Spring2005/data/algae.nex here].''' This data file was originally used in a study by Lockhart (1994) and comprises eight 16S ribosomal RNA sequences: |
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Revision as of 18:40, 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. |
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).