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closeHow did you calculate your phylogeny figures?
Posted by rmounce on 26 Jul 2012 at 19:38 GMT
Dear Authors,
You have five figures in this paper that depict phylogenies.
I assume these are some of the main findings of the paper(?).
How were these phylogenies determined?
I read the paper several times, including the methods section and could not find any reference to any phylogenetic method or phylogenetic program that I recognise. I don't claim to be familiar with all phylogenetic methods and programs ever produced, but it seems to me that the process of how these phylogenies were inferred is incompletely documented in this paper.
I would normally expect to see a mention of the method used to infer these phylogenies such as Maximum Likelihood (ML), Bayesian Inference (BI) or Maximum Parsimony (MP). As well as a mention of the program that the phylogenetic analyses were performed in e.g. PAUP*, TNT, MrBayes, POY, RAxML etc... Along with further methodological details so that the analysis could in theory be replicated by an independent investigator.
Without reporting this information it makes your results non-reproducible and less useful to others, so as a student of systematics myself, who re-uses published data, I feel it is important to further clarify the methods used here.
So, methodologically how did you arrive at these 'proposed' and 'validated' phylogenetic trees?
RE: How did you calculate your phylogeny figures?
gmagoon replied to rmounce on 26 Jul 2012 at 23:34 GMT
In the case of the non-recombining Y chromosome, single-nucleotide variants and small indels may be assumed to be binary, unique-event polymorphisms (UEPs) on the time scales of interest. Thus, it is simply a matter of logical inference to go from the sequencing results to phylogeny; the statistical methods mentioned are not necessary.