I am working on the phylogenetic analysis for communities of plants and arthropods.
A standardized protocol of building phylogenetic tree for plant species list that was widely used in studies. In brief, by reading a species list into R, using "plantlist" package in R to get one verified "Family/Genus/Species" list, and then reading the one into an online platform - phylomatic ( http://phylodiversity.net/phylomatic/ ) to get a .tre file.
However, I have no idea of building a phylogenetic tree for arthropod. Is there a sort of open online platform or software in producing one arthropod's phylogenetic tree? I had one athropod species list.
If no one, how abut effective way(s) of building the tree.
Thanks a lot.
Shimin Gu
I am not aware of any platform such as 'Phylomatic' (for plants) for obtaining a phyogeny of a list of arthropod species. You will have to infer a tree yourself with data available in GenBank; if you are lucky all your species will have sequences available for the same gene(s). Otherwise, you will have to generate your own data.
Once you have your data for the same gene(s), you will have to align your sequences per gene, determine the best partition and models of evolution, and then estimate your phylogeny. There are plenty of resources out there to guide you. Here are a couple of links:
A good intro to estimating phylogenies, although a bit outdated:
-https://cals.arizona.edu/mycoherb/arnoldlab/teaching/advmycol/baldauf.pdf
If you want to jump to the practical aspects, you should check this book of Barry G. Hall, apparently there is a new edition coming later this year:
-https://www.amazon.com/Phylogenetic-Trees-Made-Easy-How/dp/0878936068
I hope it helps!
Your question is rather unclear. Do you intend to build a phylogenetic tree from scratch or extract a subset from an existing larger phylogeny using a list of species? If it is the former, then you will need actual data, not just species names. If it is the latter, perhaps you can extract a tree from the tree of life project? The following links may be of use:
Article Treehouse: a user-friendly application to obtain subtrees fr...
https://phylot.biobyte.de/
https://itol.embl.de/itol.cgi
I have looked at the arthropods over many years and find Darwinian solutions of a tree to be over-contrived and better solved as Created kinds. For example the Hexapoda appear from nowhere in the Carboniferous, with trachea, so not linked to earlier aquatic arthropods. Likewise the Miriapoda in the Devonian. The groups, I assume, are Trilobita, Crustacea, Miriapoda, Hexapoda (most), but excepting: Amphiesmenoptera (because of their scaled wings), Hymenoptera (because of their altruistic nurture), Coleoptera (structure and hardened forewings). We assume (www.earthhistory.org.uk) that the fossils tell the story of recovery after a Hadean wipe out. Maybe too radical for those needing to get marks in assessments, but thinking outside the box! This whole new paradigm assumes decaying speed of light, which scientific community has recently been looking into, and Higgs Boson energy field of quantum chromodynamics.
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