I have drawn the tree of my fungal population Rep-PCR, and I want to know how to read the results and what it means, I have use three primers Rep, ERIC, and BOX , and I am looking for genetic diversity. Any suggestions?
Dear Oadi
Trees only tell you how diversity is partitioned. From your graph, I would say you have two single outliers and the rest forms one group without any further clear structuring. Anyhow, it is good practice to estimate how many times the branching at each node is supported, which is usually done by bootstrapping (for a genetic distance matrix you could use "seqboot" from the Philip suite)
Hope this helps
Pablo
Dear Oadi,
The taxon 18 is really special and different it's an outgroup,
the other is a heterogeneous group divided into three groups, the first with only 11 taxon particular contribution to other taxa, the second group with 28 taxa and 29, the third group is to provide all other taxon. In the latter group it is obvious that the 27 taxa, 19 is 1 are particularly in this group with a clear distinction between on the one hand 27, 19 and secondly the 1. The other taxa are more or less together, but it is to notice that a lot of similarity between 7.20 and 24.23 and 15.13 taxon. Having said this tree has no statistical weight for there not been a bootstrap
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