Collection location: Cochise Co., Arizona, USA [Click for map]
soil under aspen and mixed conifers in area recovering from 2011 burn
|I’d Call It That||3.0||6.10||1|
sum(score * weight) /
(total weight + 1)
|I’d Call It That||3.0||5.19||1||(IGSafonov)|
sum(score * weight) /
(total weight + 1)
Please read my sequencing notes to find out which MO obs represent which taxon in my opinion. Yes, I saw your alignment. As I said it is missing the portion of ITS2 where there are significant differences between the two taxa. I regret that I am unable to continue this back and forth. You have your opinion and I have mine.
You continue mentioning Taxon 1 and Taxon 2 and “consistent differences” seen in their ITS sequences without referring to particular observations or posting sequence alignment and p-trees. This is not helpful, and I still have no idea what you are talking about.
I sent you alignments of your AZ leccinum MO248759, MO396881, MO251619, MO396887, MO396885 and MO286897, which IMO are all 1 species, likely L. vulpinum or its NA conifer-associated relative, based on the GenBank data (e.g., AF454580 from Europe). Is this Taxon 1 or 2 or neither?
A couple of caveats based on the pioneering research by den Bakker & Noordeloos. The ITS2 region in sect. Leccinum appears to be very conserved for many conifer- and hardwood-associated taxa. On the other hand, ITS1 seems like a much better marker for species ID; however, this region suffers from intraspecific variability related to the presence of mini-satellite tandem repeats and requires careful interpretation. Hence, neither sublocus would be useful for inferring evolutionary relationships in sect. Leccinum. We need better markers to study these red/orange-capped critters.
I continue to believe that there are two taxa represented by the 7 AZ collections. There are a small number of fixed consistent differences in ITS1 between what I’m calling taxon 1 and taxon 2. There are a large number of fixed consistent differences in ITS2 between the two taxa. IMO taxon 1 is not in the L. vulpinum, L. piceinum or L. insigne group based on a large number of fixed consistent differences in ITS2. I don’t think taxon 2 is in the L. vulpinum or L. piceinum group but the evidence is less clear since it is based on a small number of fixed consistent differences in ITS1. Since the ITS sequence of L. insigne lacks ITS1 it can’t be ruled out for taxon 2.
…the 6 listed collections are in the L. vulpinum group, unless we are dealing with a single species showing a phylogeographic pattern in the ITS locus. Another thought came across my mind when I remembered the recent development with Desarmillaria caespitosa, which is a of the European D. tabescens (I had to look up that term, LOL). In other words, these conifer-associated scaber stalks from the east Coast and AZ may have arisen through what’s called allopatric speciation. I think those long inserts/indels may have a story to tell. :-)
After reading and re-reading the early Leccinum papers from Europe, and doing quite a bit of sequence analysis work with my own collections through the gargantuan mess in GenBank, I am ready to give up on using ITS for scaber stalks identification and barcoding, particularly sect. Leccinum (phylogeny is out, of course). But what’s the alternative when there is an obvious dearth of accession of other loci for Leccinum in GenBank?!
Yes, I remember that one because I had to exclude it from my analysis, for its ITS sequence consists only of the last 58 characters of ITS2. Not really useful… Not sure if you got from a single read, like a long reverse read from LR3, or from two reads, but though it was a rather unusual fragment. I didn’t try to BLAST it because LSU lacks species resolution within Leccinum sections.
including the 7th AZ collection MO 326509, which include partial LSU and ITS2. Some of these may not be published on GenBank until tomorrow 5/12.
Of the six collections/sequences I referred to in the previous comment, only four had the ITS2 region available at the time I did my analysis. Those sequences are identical. I am not sure what 18 differences you are talking about unless they come from a collection/sequence I didn’t see.
and there are 18 fixed differences in ITS2 between the two groups that you did not look at in the alignment you sent me. It seems pretty clear that there are two taxa represented.
I aligned the ITS sequences associated with your six Leccinum sect. Leccinum observations:
…and I would say that they all represent the same species.
The sequence of my PA collection of Leccinum aff. vulpinum, obs 207392 (MW882080), is structurally very similar, if not identical, but is substantially shorter due to the presence of two long indels in ITS1 (120 & 116 bps) and one indel in ITS2 (46 bps).
This genus is still not well sorted in North America from what I can tell by Kuo’s recent study. Many of the names are suspect since they were based on subtle morphological differences— staining for example. What we need I think is a multi-locus study of the genus. I am attempting a tree but there are few reliable sequences on GB, the best are from den Bakker’s study of European Leccinum. The sequences of all of these AZ conifer associates are close to L. vulpinum.
PS See sequencing notes I added to the ITS sequence
Could these be L. ponderosum?