Peziza systematics

The problem with research papers is that unless you are a specialist in the field, you cannot really make sense of it. Even when the abstract states that “We have shown blah blah wibble wibble”, the truth is that the blah blah wibble wibble is usually subject to various assumptions, and simplifications, which the non specialist will struggle to interpret. A good example is a paper I came across concluding that various Peziza species are con-specific. It was based on DNA analysis, which I did not understand, having no training in biological sciences (I was a quantum physicist by training) so I had no idea whether or not the conclusions were cast iron. In a recent post Andreas indicated that they had drawn conclusions based on limited DNA analysis, and in fact it was not as clear cut as the abstract suggested.

Anyway, we seem to be going somewhat off topic …

As leif has correctly pointed out we had veered well off topic (myself included 😳 ). The paper on Peziza which he mentioned can be downloaded at https://dash.harvard.edu/bitstream/handle/1/3153301/Pfister_PhylogeneticDiversityCore.pdf?sequence=1” class=”bbcode_url”>https://dash.harvard.edu/bitstream/handle/1/3153301/Pfister_PhylogeneticDiversityCore.pdf?sequence=1.

I think one should point out that papers like these are peer-reviewed and one is likely to be shot down in flames if there are too many assumptions and simplifications. I’m sure someone versed in quantum physics (of all subjects) would agree that no conclusions in science can be viewed as ‘cast iron’. In fairness to the authors their “Conclusions” in that paper are qualified, and they do point out the gene areas other than ITS which might prove worth studying (I haven’t searched the subsequent literature to see if any such further work has been done). What does come out of that paper is that use of habitat as an identifying character can be problematical – hence the wide variation in the habitat range of the species they consider as Peziza varia which includes “P. cerea” on plastered walls which many mycologists (myself included) have happily recorded, often without microscopical examination.

In passing the “Discussion” opens with:

“There are weaknesses in the dataset but these do not appear to be a result of inclusion of ambiguously aligned regions, which could have added noise or been misleading. All phylogenetic resolution receiving even moderate bootstrap support from either of the datasets tested, is compatible with results from all datasets and did not effect [sic] conclusions in this study” (my underlining). I assume the “effect” is a slip and “affect” was intended – there is a subtle difference in this context.

The term “bootstrap” which often occurs in these papers refers to the degree of probability that a hypothesis / proposed relationship between taxa contains least errors (I think that doesn’t oversimplify – I stand to be corrected). It is analogous to “Occam’s Razor” https://en.wikipedia.org/wiki/Occam’s_razor” class=”bbcode_url”>https://en.wikipedia.org/wiki/Occam’s_razor – in that Wiki-article, within the paragraph entitled Biology, the paragraph starting “It is among the cladists that Occam’s razor is to be found . . . . ” is relevant here.

I’ll get mi’ coat . . .

Chris