Hi There,
Does anyone know how to get a phylogeny (with branch length, and good to be in newick format) for flowering plants ?
And how to get a subset phylogeny from that big phylogeny?
Many thanks in advance.
Kind Regards,
Lhl
I recently worked on a figure for a paper with my research group where I did the exact same thing you are asking. There are no basic plant newick files out there. You can search google for newick files to published papers: I spent days searching for newick files of plant phylogenies and what I found was not appropriate for what we wanted to show. Additionally, for plants, there are few newick files including branch lengths.
In the end I constructed my own phylogeny with data from Phytozome. There are a lot of duplicated genes so I searched for genes with low copy number. I selected 41 genes from all of the plants with sequenced genomes and then concatenated them and aligned them, inspected by eye, and made a phylogenetic tree. Basic phylogenetics. This ended up being much faster than the time I spent searching for the perfect newick file on the web.
You want a subset of that big phylogeny? I don't quite understand your question. But if you're asking how to show a specific clade within the phylogeny of flowering plants, after you construct (or select) a phylogeny, simply select those branches in a tree viewing program like TreeView or (my favorite) FigTree.
If you're adventurous and in a hurry and see exactly what you want on the web, you can try TreeSnatcher, but I'm not a fan (at least I think the learning curve is high, which is a little ridiculous for a program whose intent is to be a shortcut).
There are multiple large consortia with funding to resolve plant relationships. Don't just download the raw data and try to construct a tree because these groups have already gone through all the computational and statistical hurdles to do that. If you just want to create a small phylogram as a figure, that is different.
There was a recent phylogeny of green plants published using a supermatrix approach and you can download all the data (i.e., matrices, alignments, etc.) from the BigPlant website. This is just one study though, and you can find more trees from Dryad, TreeBASE, The Open Tree of Life, in addition to the other sources mentioned. The best place to start would be to look at the paper related to that first link and follow their citations to find other large-scale plant phylogenetic studies.
You might also find useful datasets and trees for angiosperms in the Phylota browser
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Hi Josh,
Thank you very much for your kind response.
My purpose is to find a complete (as complete as possible) flowering plants phylogeny.
And in my analysis a few steps would be focused on certain lineages (including around 200 species, for example). I was actually also trying to find a way to extract the topology (It is certainly good to have branch length information) for certain species out of the big phylogeny.
I agree with your suggestion to construct a phylogeny from scratch using molecular data as done by the following studies.
Soltis D., Smith S.A., Cellinese N., Wurdack K.J., Tank D.C., Brockington S.F., Refulio-rodriguez N., Walker J.B., Moore M.J., Carlsward B.S., Bell C., Latvis M., Crawley S., Black C., Diouf D., Xi Z., Rushworth C.A., Gitzendanner M.A., Sytsma K.J., Qiu Y., Hilu K., Davis C., Sanderson M.J., Beaman R.S., Olmstead R., Judd W., Donoghue M., & Soltis P. 2011. Angiosperm phylogeny: 17 genes, 640 taxa. American Journal of Botany, .
Smith SA, Beaulieu JM, Stamatakis A, Donoghue MJ (2011) Understanding angiosperm diversification using small and large phylogenetic trees. American Journal of Botany 98(3): 404-414. doi:10.3732/ajb.1000481
AND
http://phylota.net/pb/Download.htm
By the way, how many species are you processing?
Kind Regards,
Lhl
Currently, i am focusing on those studies of large phylogeny.
No problem Lhl, my pleasure. Sounds like you have a good model with the data from Doug Soltis et al 2011 paper, I guess you saw all the data is here. Looks like a good resource for building a large phylogenetic tree.
In addition to all the usual database suspects (NCBI, EMBL, etc.) I really like JGI's Phytozome for genome data, the Plant Genome Duplication Database (for picking apart gene duplication events and helping to choose which gene for phylogenetics) and there is some data at the Floral Genome Project website run by some of my collaborators. These tend to be the ones I use the most.
The projects I am working on are variable: sometimes we want a small phylogenetic tree of just a few taxa, other times we want to show many genes across all the sequenced plant genomes. One of genes I am actively investigating averages about 40 copies in dicot genera, so the analyses can get large.
If you want to pick my brain about my further thoughts, feel free to email me (my email is listed in my profile here).
Hi Josh,
Thanks for being so generous to sharing your thoughts and recommending resources.
And i guess I will bother you again at some point in the future.
Cheers
Lhl
No problem, my pleasure. Best of luck to you!