I know there is lots of work using mitochondrial genes and DNA fingerprinting but with the cost of NGS coming down to reasonable levels wouldn't it be better to use this technique rather than concentrating on a couple of genes? I'm interested in determining the taxonomic relationships in an Australian endemic genera called Eremophila which has very little sequencing data and also a number of ploidy states. Any insights would be appreciated.
Although this is used for phylogenomic reconstruction of the pines, you can have a look at this article.
http://www.biomedcentral.com/content/pdf/1471-2148-12-100.pdf
Hello Bevan
I dont know about plants, but this one test monophyly on the lake Victoria Ciclids using NGS. I don`t know if is what you looking fore but can give you some ideas
http://onlinelibrary.wiley.com/doi/10.1111/mec.12023/full
Best
Thiago thanks for the link to that paper it has been most useful..Robert you have baited the hook and Ive taken it. Please tell us more abouit what you did and how, as this is exactly what I wish to do in Eremophila spp. and susp.
The Cichlids paper that Thiago linked is an excellent example. There are many approaches to using NGS technologies for both phylogenetics and taxonomical issues at a variety of phylogenetic levels. One of the most promising is RAD-seq as used in that Molecular Ecology paper. Other approaches are amplicon sequencing, and ultimately phylogenomics methods based on the full complement of protein-coding genes.
The good thing about RAD-seq is that it is relatively cheap and very useful for probing evolutionary questions, where taxon sampling is as important as depth of sequencing coverage.
Edit: I re-read your original post. With a number of ploidy states it might make things a bit trickier (i.e. assigning orthologues vs. paralogues) but there are a number of ways around this. I aim to use RAD-seq and other approaches for Australian endemic Nicotiana.
NGS approaches definitely have the power to sort these spp. and subsp. out :)
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