Phylogenetics: Distances Lab

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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 B: Analysis of algae.nex

Download the data file algae.nex. 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).