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the ends of branches of the evolutionary tree rather than about its roots. There was once an idea that, given a species, there would be a tendency to homogenization of the many copies of the blue print for making ribosomes. (Ribosomes are the molecular machines that read the DNA directions for making proteins and manufacture said proteins.) Because so many proteins are needed all the time, there are lots of copies of the ribosome blueprints in a given fungal genome.
Expectations of homogeneity were not met in reality. ..especially in Amanita reality. Lots of amanitas have multiple different copies of ribosome blueprints. How exactly this came about is still open to some debate. It has a practical impact on whether or not a readable gene sequence can be obtained from a given specimen of a given species.
Obtaining a “proposed fungal barcode” sequence from some species is relatively easy. A sequence can be read with relative easy and with few (if any) characters that are ambiguous. In the case of other species the “proposed fungal barcode” simply cannot be obtained by the simplest, direct method. The results that come back from the sequencing lab are analogous to a recording of a large chorus where multiple singers have divergent copies of the music….chaos.
It was hoped that more conserved (less changeable) parts of the ribosome blueprint would be more reliable for tree building; however, increased experience show that these “more conserved parts” also have their problems including the chorus-with-mixed-music problem just described.
Hence the search for moderately mutate-able genes of which there are NOT two or more copies in the genome. In the recent work of Sanchez-Ramirez (2015 papers on the movement of Caesareae genes around the world in the last few 10’s of millions of years), an effort was made to find new genes of this sort and to deploy them in the research.
By the way, according to Sanchez-Ramirez, the Caesareae may be 50,000,000 years old. And based on that hypothesis, then Amanita may be 100,000,000 years old or more. I’m very happy that my cartoons of dinosaurs kicking over amanitas are now plausible visions of 10’s of millions of years of Amanita history. :)
First, it is important to keep in mind that the most extensive Amanitaceae tree published to date, or soon to be published, is still a hypothesis based on a small fraction of the genome of roughly 20% of amanitas and that the sampling is not evenly distributed across the world or across the sections of the genus.
What part of the genome is to be used is currently being investigated extensively. And preferences are moving away from the DNA that is the blue print for ribosomes to singly occurring protein-encoding genes. So we continue to be in a transition concerning what is best practice and what methods are likely to make hypotheses more plausible and less liable to disruptions caused by the genes themselves and the software that aligns them and builds trees.
In month or so there will be a paper opposing the splitting of the genus Amanita based on a rather thorough reassessment of the research of Wolfe, Tulloss & Pringle (2012) concerning what appears to be an early diverging group of amanitas…including the majority of the species that Dr. Bas (1969) assigned to subsect. Vittadiniae. The group cannot be separated off as a section, or subgenus, or genus for several reasons, which need to be treated at length (i.e., not here). Some of the questions you’ve asked are treated in the paper…although probably not answered. At least the paper spends some effort trying to assess existing hypotheses and suggests that the results of the Wolfe et al. paper pose complex additional questions rather than offering a simple vision of two clear cut types of carbon absorbing “life styles”.
… for an exhaustive answer. Does the existence of such hybrid forms suggests that all extant species in subgenus Amanita share a common ancestor?
I’ve been wondering for a while about the evolution of the genus Amanita. If I correctly recall your comments from a few years back, sect. Lepidella is the most ancient one (lack of color, existence of non-mycorrhizal relic species) and sect. Vaginatae is a “baby” [build ’em faster, cheaper, but not necessarily better :-)]. Could Lepidella be the basal section for the entire genus, or is the picture more complicated than that?
I am curious to find out about the molecular clocks of the sections and their respective “denizens” as well as the gross structure of the Amanita genealogy tree. Perhaps some of that data and its discussion already exists on your website…
…that are earliest diverging according to some rough trees. It took me awhile to understand that the similar A. murinoflammeum was in section Amanita and, not Caesareae. You have lit on exactly the same problem that I had in that case. Eventually, we found specimens with slight bulbs in the sacks.
Their closest relatives include the two truffle-like amanitas that used to be in the genus Amarrendia before it was merged with Amanita. Notice that there is a slighly radicating base to the stem in some of the collections of the present species. Sometimes there is an obconic base to the stem and volva.
These are very curious critters. Lucy sent me at least three collections of this species and a gray-brown-capped specimen that might be closer to A. umbrinella. I look forward to seeing the DNA for the other collections.
suggests it is genetically similar to, but distinct from, both A. umbrinella and A. murinoflammeum. As to an attempt to derive a “proposed fungal barcode” (nrITS sequence), it appears that we have good partial sequences for the two ends of that locus; but there is a large and sudden gap in the middle, possibly due to extensive ambiguity (multiple distinct copies of the gene in the organism).
A little news.
I worked up the spores for this collection and the similar collections you collected on 1.iii.2013. The spore data and your images suggest that all of the material could be assigned to roseolamellata.
I have just written to Santiago Sanchez to ask if he extracted DNA from samples I sent to him of the dried material from this observation and others. He did cite sequences of two genes from one of your collections collected on 3.iv.2011 in his paper on the Caesareae published recently. The genes in question and links to GenBank for the sequences are here:
in the “GenBank nos.” data field near the top of the technical tab.
This material has been accessioned to Rod’s herbarium and sampled for DNA sequencing.
collections from Australia because they have yielded DNA, but didn’t have all the available morphological data on the WAO website.
These were found considerably north of your collecting area and are more like taxa of SE Asia (rather bright colors…reds and yellows):
Dr. Roy Halling says he can get me the related images for these taxa later this week.
My point in trying to simply specify the subgenus with inamyloid spores was that the proper sectional treatment of this material is not completely clear to me from its morphology. It shares some characteristics with Amanita murinoflammeum, which according to some preliminary DNA examination several years ago was not part of the Caesareae; on the other hand the volval sack in the present case is more distinct and persistent than in the case of murinoflammeum.
The simplest thing is to see what sequencing of this material will tell us.
Morphologically, there are several links to murinoflammeum. Among these are the spore size and shape, the red-brown pigment of the cap surface, the short marginal striations on the cap, a stem that is pinkish at the top on the exterior surface, the presence of both a persistent saccate volva and partial veil, and the occasional appearance of a stipe that is narrow at top and bottom and bowed outward near mid-stipe.
I reached this point after reviewing spores and macromorphology of all three collections that you sent me. Other MO numbers are 129727 and 129661, I think.
This is fascinating material.
Created: 2013-03-03 06:22:29 EET (+0200)
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