I need to construct a phylogenetic tree for 4 grasses (Festuca, Holcus, Anthoxanthum and Agrostis) and 4 forbs (Leucanthemum, Centaurea, Rumex and Plantago), but have little experience in plant phylogeny. What would be an appropriate outgroup for such a tree? I have used a Larix species, just as the first gymnosperm that came to mind. Any ideas about a more appropriate outgroup?
Also, which gene or genes would be best to use? My aim is to get a clear separation of plants and forbs, and perhaps in these groups, clear separations by family. I have tried vouchers with 5.8S rRNA, ITS 1 and 2 and 26S rRNA genes. Some reading of the relevant literature I have done suggests the following may be more appropriate:
rbcL gene, MATK gene and the trnL intron.
What gene and what outgrooup to use depend greately on what you want to do and on what level of taxonomy or phylogeny you want to reconstruct (species level, subspecies level, genus level or something else?). How many trees you want to build and based on what algorithm? In general you may to use outgroup not too far from your objects but more basal. Correct outgroup chosing is very important and depend on many factors. You may to check literature on this aspect and so try to find articles on similar research. If you will be so kind to clarify the main goal of your work, I'll provide you more detail information.
The earliest divergent group you will be sampling will be the grasses...you could start with additional monocots.
The angiosperm tree of life (from the Angiosperm Phylogeny Group) is an extremely useful resource. Here is a link to a tree - it is interactive, so you can click on orders and find families, an go from there.
http://www.mobot.org/MOBOT/research/APweb/
As for markers, I would start with rbcL and trnL-F. These are commonly used, so you can probably get accessions from GenBank for many taxa. Definitely a good idea to include as many taxa / markers as you can.
I hope that helps as a starting point.
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