17 de março de 2022

A note on curating fungal names on iNat, and my personal policies.

Currently there are no globally authoritative sources of taxonomy for fungi we can use as a taxon framework for iNat. SpeciesFungorum and MycoBank are often quoted as sources, but they are not. That is not their primary role and the managers of those resources do not claim to provide that service and they do not have the resources to do it. So please do not assume that because these resources say something different to iNat that they are right and iNat is wrong. The fungal equivalent of Plants of the World Online does not exist, although some individual groups are associated with maintained checklists. Consequently, in most cases, the curation of fungi is carried out by referring to the primary literature together with some evaluation of whether the stated opinions are agreed by consensus within the mycological community. Not all published changes are universally adopted by mycologists, especially where a monophyletic genus is split into several genera, often without easily observed separating characters, or where a phylogenetic analysis is not supported, or based on too few genes and/or inadequate or inappropriate taxon sampling. So, the latest publication is not always accepted in the longer term. To avoid flip-flopping names we should wait until consensus acceptance is clear - at least for controversial changes (a recent treatment splitting Cortinarius comes to mind). Likewise, opinions of heterotypic synonymy for fungal species are often rather fluid, certainly in the absence of sequences of type material.

It is a demanding task to try and maintain the currency of the iNaturalist fungal names and should only be done by those with access to the primary literature (often behind paywalls or expensive technical volumes) and have the expertise to interpret that literature. There are relatively few of fungal curators who can, and are prepared, to do that for the 20,000 species currently listed in the iNat dictionary.

The iNat list of 20,000 fungal names (plus synonyms) is still a small fraction of all fungal names. In total there are over 570,00 published names of fungi. 350,000 of those were published before 1950. Many older names are not associated with type material, or that material is in poor condition, and often the original descriptions lack sufficient detail to enable a sensible modern interpretation. These names are best forgotten unless they become officially resurrected through re-typification and description. Similarly, many names published up to the current day are supported by just the type collection, and perhaps a few paratypes. Many of these species are the province of dedicated specialists, perhaps needing confirmation by sequence. They may not be seen again for decades and may never have associated iNat observations.

New fungal species are currently described at a rate of about 50 per week and iNat observers will never record the vast majority. There is no point adding all these new names because they have been recently published.

For these reasons I personally will not add names to the iNaturalist dictionary simply because they are 'missing'. Every extra name creates an additional curatorial overhead. If you ask for a name to be added, then please provide a link to the observation that requires the name.

Likewise, I do not think it appropriate to add names because they are listed in some regional checklist. If those checklists have received recent revision, and every entry validated, then perhaps itis justifiable, even in the absence of associated observations. However, many regional lists contain the old, superfluous names I mention above. They are of no value in my opinion, certainly within the iNat framework.

Any name that is requested for addition should be checked to ensure it is listed in the global fungal nomenclature databases. IndexFungorum and MycoBank are the two that are easily accessible. These databases do contain authoritative and up to date nomenclatural information. That is, they tell you if the name was validly and legitimately published, together with any required orthographic corrections to the original spelling. Remember nomenclature (satisfying the rules of the International Code of Nomenclature for Algae, Fungi and Plants - ICN) is not the same as taxonomy (the opinion on the correct name for an organism). In certain cases, invalid or illegitimate names may be added to iNat. My rule is that if it’s in IF/MycoBank then it can be added, as long as it is really needed..

I will not add unpublished names to the iNat ditcionary, and that is iNat policy, and often debated on the forum. Neither will I add recently published names where the registered names have not been released by IF/MycoBank. There is always the possibility the original orthography is incorrect, or some other issue impacts on the eventual availability of the name.

In my opinion those curating fungal names should have a good grasp of the ICN rules and understand there are some fundamental differences between ICZN and ICN. For example, new combinations under ICN are nomenclatural acts, requiring valid/legitimate publication - noting that these terms mean different things under ICN and ICZN. That is not true under ICZN where new combinations can be created by anybody, anywhere. The iNat Taxon Swap page even has a convenient flag that can be ticked to create these combinations for subordinate taxa - and that tick box can generate havoc for names treated under ICN. For fungi it is now also necessary for nomenclatural acts to be registered in IndexFungorum or MycoBank. Non-registered or incorrectly registered names are not validly published.

It is worth noting that modern mycology relies entirely on phylogenetic data to make sense of taxonomy. If some published taxonomic opinion (synonyms and hierarchical classification) dates from before about 1995 then be very cautious about the interpretation.

The hierarchical classification of fungal names in iNat (genera in families, orders, classes, phyla) should stick to the 'standard' used within IndexFungorum if possible. Deviations should be documented.

IndexFungorum does not incorporate any infra-generic classifications and we should only implement them in iNat where they are supported by recent phylogenetic-based revisions. Many pre-molecular classifications will be paraphyletic and we should not use them. If you add an infra-generic/supra-specific rank name then make sure you also include the nominate species and all the others proposed in the literature. Do not leave names 'hanging'.

If you are asking for a species to be added to a genus which contains an infrageneric classification, then please provide some indication of the parent infra-taxon for the species. We need to know where to graft it.

Species complexes in iNat have a specific definition. Do not lump a bunch of species together in a complex simply because they look similar. Often the phylogenies do not support that. Within iNat a species complex must refer to a group of closely related species within a monophyletic group. By definition the use of the term 'complex' means the species within the complex are cryptic, i.e. they are macro-morphologicaly similar, may overlap in range and are therefore difficult to resolve (certainly from photos). I do not think we should introduce species complexes simply as a way of referring to phylogenetic clades. That would be a slippery slope to anarchy. They should be used sparingly and have some utility within iNat - as a container for unresolvable species. In addition, when a complex is introduced, it must have the nominate species included, and all the other species supported in the literature (from well supported phylogenies).

Finally, every name to be added should be checked against the literature to determine if the name is currently accepted (by consensus) and a reasonable scan of the literature to determine the current synonymy. Quite often iNat already contains synonymic names that may need a taxon swap. Over the last few months, I have made many hundreds of taxon swaps to try and tidy up the legacy of un-curated names in iNat. It is a time-consuming process that is far from complete.

Please (other curators) do not add to our problem by adding names without checking their status as outlined here.

Posted on 17 de março de 2022, 04:12 AM by cooperj cooperj | 5 comentários | Deixar um comentário

07 de maio de 2020

Identifying fungi in New Zealand

First up some statistics to put the problem into perspective. Most fungi in New Zealand have not been described, do not have names, and so cannot be identified as species on iNaturalist.

Numbers of fungi in New Zealand

The diversity of fungal species in an area shows a very strong correlation with the diversity of plant species. A conservative and widely used global estimate indicates there are at least six fungal species for every vascular plant species on earth. In New Zealand the vascular plants are relatively well-known, and we have about 2,200 indigenous species. Using this 6:1 ration we can therefore estimate there are at least 13,000 species of indigenous fungi. We might expect a similar pattern for introduced fungi, and introduced plants found in the wild. We know the number of introduced and naturalised plants is about 2,500 and many will have specific associated introduced fungi, but perhaps not as high as a 6:1 ratio for indigenous species. By some estimates there are an additional 40,000 introduced cultivated plant species in gardens etc, which may harbor yet more plant-specific fungi. We cannot reliably estimate the total numbers of introduced fungi associated with introduced plants but it will be very significant. The total number of fungal species in New Zealand is likely to be over 20,000.

Those are the estimates, but what do we actually know? To date we have described about 6,000 native fungal species and cataloged around 2,000 species that were clearly introduced. This comparison of estimates versus knowns indicates we have described less than half of our total number of indigenous fungi and that is likely to be a significant underestimate, and we know little about the large number of introduced species. Many of these fungi will be small, inconspicuous forms.

For the larger forms (mainly basidiomycete - agarics, brackets and so on, but excluding the ascomycete lichens) we have described about 2,000 indigenous species and we know about a significant number of introduced species, mainly in urban/agricultural/modified habitats. eDNA data from environmental soil samples compared with sequence ‘barcode’ data on known species support the estimate that less than half of our indigenous species have been described, even though this group is conspicuous. New Zealand has never committed adequate resource to the professional effort required to describe our native fungi, and there are relatively few trained mycologists to carry out the task. Some species could go extinct before we even document them. However, in recent years we have documented around 1,000 of these undescribed species, in the sense that we have sequenced collections and we know what they look like. Some of them even have unofficial 'tag names'. iNat observers have made important contributions to that effort to document the unknown. The task of formally describing these species is significant and there are few mycologists able to commit time to that task. Most of these undescribed species won’t have proper names any time soon. iNaturalist will only accept published names and so many of the species can be recognised but not named on iNaturalist.

To summarize again, we have an estimated 4,000 species of larger fungi that people are likely to see and photograph in natural habitats. 2,000 of those species have names and another 1,000 are known but undescribed. Urban/agricultural/modified habitats are dominated by fewer introduced species (most of the common observations on iNat fall into this category). Of our indigenous species over 40% are endemic, known only from New Zealand, with the remaining indigenous species shared with Australia, less often Asia or South America and elsewhere. Our indigenous fungi have many look-alike species in the northern hemisphere, but they are not the same. Historically our look-alike indigenous fungi were called by northern hemisphere names, but modern phylogenetic analysis almost always shows that is not the case. Our urban introduced fungi are mainly from Europe, Australia and much fewer from North America. Between 35% and 45% of our recorded fungi have been introduced by humans.

When you flick through a guide-book or website to track down a name for your observation just keep these facts in mind. Most of our species will not be included in guide books and many similar species probably aren't mentioned. Many entries in existing guide books are also incorrectly identified, and most unverified, and unverifiable without associated preserved collection. The majority of species cannot be reliably named from photographs alone because there are many species that look more or less identical, especially to the untrained eye, and differ consistently only in microscopic characters, and sometimes only in their sequences.  

Which fungi should I photograph when I’m out?

Please resist the temptation to photograph everything you see because there is little point! You have the best chance of being able to identify something, or getting somebody on iNat to identify something, if you follow some simple rules. Only make records of fungi that look in good condition, where there are a range of fruitbodies from immature to mature, and where you can get good photos. You need to catch them just at the right time. If they are old, rotten, or it has been dry for a long time, raining hard, or there have been frosts then it is 'game over' because fruitbodies change and become unrecognizable. Sure, you can take a casual phone-camera snap of a mushroom and upload to iNaturalist. Sometimes it will be a distinct species we can identify, and it may be a useful record telling us something about occurrence and changes in distribution. Most of the time however it is better to ‘walk on by’, especially if you are a beginner trying to learn.  

What should I photograph?

As I’ve said, reliably identifying most fungi from photographs is difficult but there are things that increase the probability of correct identification. Photos are needed in their habitat, not taken home and put on a dinner plate (see my comments later about edibility). Conversely aesthetically pleasing photographs of fungi in their natural habitat often don't show the necessary details for identification. Photos are needed showing ALL the relevant features close-up and with a good colour balance, lighting and focus, and some sense of scale. If possible use natural lighting with a tripod/time exposures if necessary, and resist the temptation to use HDR which makes species look unrealistic. We need to see the cap, stem, gills, the way the gills are attached to the stem, the stem base, any ring, and the way it is attached to the substrate. Remove it with a fixed blade knife so we can see an intact stem base. Removing a fruitbody to photograph these details will not affect the population. The fungus will have already released millions of spores and the fruitbody is just the 'apple on the tree'. The body of the fungus is the hyphae running through the soil and is unaffected by removing a few fruitbodies and turning them upside down (and leaving them there).

Field notes

The photos are just one aspect of recording fungi, and a relativley small part. You should include notes about the habitat. Was it a native habitat and if so what kind? Was it forest, scrub, grassland, dunes etc. If it was forest/scrub then what kind of forest? Was it beech, tea-tree, podocarp or mixed? Or was a modified habitat like farmland, urban parks & gardens etc? We need to know any specific associated species - guessed-at if it is a potential ectomycorrhizal species (you need to know your trees). We need to know substrate (soil, wood on a living tree, dead wood etc). The texture of the fungus (tough, fragile, crumbly etc). We need to know any odour, the taste (a small bit on the tongue will not kill you – except maybe the Death Cap – which we do have in NZ), any changes to the flesh colour on exposure to air. Ideally, we need to now the colour of the spores from a spore print.

Identifying fungi

I can't offer any good advice on NZ field guides or websites for fungi, not that we have many, because I don't use them. Their accuracy is variable and the coverage necessarily relatively restricted. I refer to the technical literature and verified material in the national collection.

Tracking down the correct identification for a species is often hard work and not just a matter of comparing a few photos. It is not just the problem of the vast numbers involved, or all the undescribed species. Fungal species are remarkably variable in their appearance depending on growth conditions and inherent ‘phenotypic plasticity’. You need to be able to recognise the key characters that can be relied upon, and recognise when something isn't 'normal' due to age, weather conditions etc. You need to develop familiarity with species in all their forms. It requires years of dedication to become proficient in identifying fungi. Most of our fungi cannot be named reliably from photographs alone. We have many superficially similar species that vary only in microscopic characters.

The iNaturalist 'Computer Vision' (CV) system is remarkable but often fails badly for fungi and should not be trusted. Fungal identification runs much deeper than superficial visual similarity. In particular you should avoid accepting suggestions that don't have 'seen locally' against them. These 'non local' suggestions are generally found only in the northern hemisphere. In addition the CV has been trained on northern records that are often incorrectly identified and refer to multiple different species. Fungi are generally difficult to identify correctly - anywhere. These 'loose' identifications have reached Research Grade in such numbers that they pollute the CV training set. Errors become self-propagating when people select and confirm these broad suggestions based on poor data. Our native species may look similar to these imprecise suggestions from the north, but they are rarely the same. And finally, most of our native fungi in New Zealand are not included in the CV training set and so they cannot be suggested. The CV model is heavily biased toward species in densely populated northern hemisphere regions with lots of observers and identifiers.

In New Zealand we also have a problem with the species that have been described in the past. Often the original descriptions are inadequate or ambiguous or they don’t recognise the full range of variability. Our understanding has improved rapidly since around the turn of the century because of gene sequencing technology that provides a more objective approach to defining species concepts, including the range of morphological variability within a species. Species concepts and descriptions from the last century, and/or not supported by sequence data, should be treated cautiously because they are often misleading. The process of disentangling, refining and improving the confusing historical work is ongoing. All this leads to uncertainty in identification and sometimes persistence of incorrect assertions and ongoing debate. Disagreements may seem confusing, annoying and unhelpful to many. From my perspective it is good science in action, although sometimes frustrating when faced with entrenched dogma founded on 20th century work. To re-iterate: definitive identification based only on photographs is often impossible. All we can provide is varying degrees of probability about it being this species or that species based on circumstantial evidence. Often it is only possible to give a reliable identification at the level of genus, family or higher.  

If you really want identifications to be as accurate as possible then you will need a high-power microscope (x1000) with an attached camera and some key chemicals like Potassium hydroxide solution and Melzer's reagent. You will need to learn how to prepare samples of tissue for examination and you will need to learn what the relevant micro-characters look like. You will need access to the technical literature (often expensive books or journal articles behind paywalls) and you will need to develop an understanding of the large amount of technical jargon. The ultimate identification method is gene/genome sequencing, which is becoming easier and cheaper, but nevertheless requires significant expertise to analyse the data appropriately. Mycology can become a very expensive and demanding hobby.

My Identifications

On iNaturalist I won't offer identification suggestions for any observation where the user has profile settings making observations, or the accompanying photographs, 'All Rights Reserved'. Unfortunately many new iNat users have those settings. See here for why I bypass those observations ...

https://inaturalist.nz/journal/cooperj/10306-creative-commons-licensing-on-images 

Sometimes I will also pass over observations that have been obscured by the user or where the accuracy > 10km because for my work I need good coordinates. Location data needs to be generally available, and not per observation on request. I will also pass over observations where the user has opted out of Community ID.

I use iNat data professionally for a number of purposes including improving my knowledge of poorly known and undescribed fungi, noting ranges and range extensions, and documenting threatened species. Those are my reasons for providing identifications on iNat, and l learn a lot by looking at the observations. I see more examples than I could ever hope to see personally, and far more than any previous professional mycologist in New Zealand. I use only the subset of observations where I have provided an identification. It is my way of 'tagging' a curated subset of data, and I don't always agree with the Community Identification. Generally I will be conservative when making suggestions, and so if I think there is some doubt then I will provide a genus or family-level ID. I admit that sometimes species-level identifications are probably possible if I were to do some background research, but I don't usually have the time for that. I don't often provide reasons for disagreement (I don't have the time for that either) but I will expand on specific issue if asked. Often my disagreements are because I have access to information not generally or easily available. I can understand the frustration that creates - but I can't ignore what I know. I am also not expert in all groups, although looking at fungi in Europe and New Zealand for over 40 years probably gives me some level of expertise. My knowledge of New Zealand fungi comes primarily from my own collections and the research I do, the research literature, and collections we hold in the PDD National Fungarium , and especially the subset we have gene-sequenced. I have examined over 16,000 collections and sequenced around 4,000 and examined nearly all the New Zealand type collections of agarics. Despite that background I also learn a lot through iNat. I am happy to change my identification if provided with evidence. People should not avoid contradicting my suggestions, and should not blindly agree with them either (an increasing problem on iNat). Blind agreement may seem like a good way of getting a record to Research Grade and saying "I trust your judgment" , especially for a group like fungi where there are very few people able to provide competent identifications. However blind agreement can also backfire badly when identifiers aren't competent. The result is the many erroneous Research Grade records that find their way into global resources like GBIF. That is why I only use my personally tagged subset of the data and I don't always use the Community ID. If I see that somebody has done the groundwork and taken good photos, of good material, and documented lots of field notes then I will often make more of an effort with my suggestion (when I'm not ultra busy). And finally, I respect the fact that the principle purpose of iNat is to promote engagement with nature and it is not to provide researchers like me with data. That is just an enormously valuable spin-off. So my comments and suggestions should be read with that in mind.  

My iNat Observations

I add examples of species from my collections as iNat observations. I collect specimens occasionally, and under the DOC and local authority permits we have to support taxonomic research. My iNat records are a small subset of the total. My specimens are deposited in the national collection, PDD, and may be searched for here SCD Home (landcareresearch.co.nz) Nearly all my collections are supported by sequence data. Some of that data associated with publications is deposited in GenBank, but most sequences are not deposited due to on-going discussions around biological data sovereignty in New Zealand.

Collections

It is very tempting to make collections of fungi and take them home – perhaps to eat them, make a spore print, do microscopy, make a reference collection etc. You should keep in mind that in many situations it is illegal to make such collections. You need written authorisation from the landowner (including DOC and local/regional council/iwi). Overseas visitors are not immune from prosecution and removal of material can and has resulted in visa cancellations and a ban on future entry to NZ.

https://www.inaturalist.org/pages/collecting-specimens-nz

Preserving Collections

If you do have permission to make collections then it is important to do that properly. You need to collect a range of fruitbodies in good condition showing different degrees of maturity and all from the same 'colony'. If there isn't a range of good fruitbodies in one spot then don't bother collecting them. They need to be dug-up/cut-out with a knife and not just pulled up. Often the stem base and associated mycelium has critical features. The collections need to be thoroughly documented, as described above for observations. The samples need to be wrapped carefully so they don't get squashed, don't get cross-contaminated with spores from other collections, and don't get too dirty. They need to be kept cool until you can process/look at them. If you intend to keep them in the longer term then they need to be thoroughly dried in a continuous air-flow. A fruit drier set on a temperature of 20- 40c is ideal. Any cooler and bacteria/molds will flourish. Any hotter and the DNA degrades. All fruitbodies need to be dried for at least 24 hours. Larger species need to be cut into thinner slices so they can dry properly and may take longer. They need to be packeted and documented appropriately. If you are keeping collections long-term then they need to be kept in a cool and dry environment otherwise they will be attacked by molds and mites and become useless. That means investing in permanent environmental control to reduce background humidity. Without that reduction then most collections are useless after about a decade. In the longer term the DNA naturally degrades and after 20 years it becomes difficult and expensive to get good DNA.

Edibility

I will generally not respond to questions on edibility but I will answer questions on toxicity. Many people will show allergic reactions to some fungi whilst others do not. Many fungi cause rapid gastric upset or vomiting, others are deadly, and some may have serious cumulative effects on blood and organs. When you buy a foodstuff from the supermarket you can be sure that health and safety measures have been considered. When you eat something from the  'wild', especially if you don't know precisely what it is, you are playing Russian Roulette. If you do eat something then make sure you take good records before you eat it. That will help the medics and eventually the coroner. Don't eat anything that isn't in pristine condition. Many fungi and moulds contain some of the most carcinogenic substances known (next to radioactivity). You will not die tomorrow but just give it a few years. Of course some (very few in New Zealand) are good edible species and not known to cause problems. Just make sure you are absolutely certain you have one of them.

The National Poisons Centre

https://poisons.co.nz/

Posted on 07 de maio de 2020, 08:32 AM by cooperj cooperj | 16 comentários | Deixar um comentário

31 de maio de 2017

Creative Commons Licensing on images

UPDATE March 2021 - in addition to my entry below here is another good reason you should addopt CC licensing .., https://www.inaturalist.org/blog/48165-we-want-you-to-license-your-inaturalist-photos-before-april-15th

https://www.inaturalist.org/blog/49564-inaturalist-licensed-observation-images-in-the-amazon-open-data-sponsorship-program

A number of NZ iNaturalist users apply the 'All rights reserved' license to their photographs. I have decided that from now on I will not provide identifications for such records. Restricting the use of the image in this way makes the record unusable from my perspective, as a scientist, and so I will bypass them. The image is the key piece of information allowing a record to be independently verified at any time in the future and independently of iNaturalist- a fundamental requirement in any area of research. Taxonomic opinions can, and do, change with time as we acquire better knowledge, and so on-going access to the original evidence is always required. 'All Rights Reserved' means the image cannot easily be part of the permanent package of evidence accompanying the record in any use external to iNaturalist, for example they are not uploaded to GBIF. I can understand the desire to derive potential income from images but I don't believe iNat is the place to promote them. If you want to share your records and images to support biodiversity research then adopt a Creative Commons Licence. I recommend CC-BY-NC, which means that your images can be used for non-commercial purposes and you will always be credited for the image, whatever the use. You can negotiate terms if somebody does want to use the image for commercial purposes. Although it is worth saying that even a CC-BY-NC license means the image will not be considered for use on Wikipedia because even that license is considered too restrictive.

For some users the adoption of 'All rights reserved' was probably an oversight when they setup their account. If you want to use a CC license by default then go to your Profile (menu top right of desktop web page), then 'Edit Account Settings and Profile' , scroll down to Licensing-Default Photo License, and tick one of the sensible options. I use CC-BY but I would recommend CC-BY-NC if you think your photos have commercial value. Then, most importantly, tick the box at the bottom that says 'Update existing photos with new license choices' . If you want to maintain 'All Rights Reserved' as the default setting because, for example you are a professional bird photographer, but also submit the occasional fungus, then you can change the license individually on each image for each record.

You may consider it not worth changing your License just to get fungal identifications from me, especially when many of my identifications are at genus level or above. There are reasons to consider and they concern your role as a Citizen Scientist in using iNaturalist. I actively try to look at all the NZ fungal records submitted to iNat (at least for non-bracket fungi). I want to be able to regularly collate the subset of records I can trust and use (and not necessarily accepting community IDs). I'd like to maintain a minimum quality for the data and to keep an eye out for new records of species, which we (every NZ citizen) are required, by law, to report to the government agencies. I want  a consistent quality so the data become fit-for-purpose for research work.

For example over the last year I have used iNat Citizen Science fungal data in the following ways ...

  • iNaturalist NZ images were used in a successful prototype demonstration of the use of Deep Convolutional Neural Networks for automated image recognition. This is a separate NZ based project to the one you may have seen from the iNat guys, and I am focused on biosecurity 'early warning' systems (e.g. detecting rust spores in the wind coming from Australia!)
  • Citizen Science data from iNaturalist NZ was initially included in a research paper investigating the role of ectomycorrhizal fungi and their relationship with host trees when introduced species enter a new area. Data from CS network in the UK and NZ were included. Results derived from a combined 2.2 million observations show species-partnering and hyphal foraging strategies are relaxed (or at least change) upon introduction of a tree into a new area.
  • The iNat community continues to highlight rarely encountered fungal species, facilitating taxonomic/biogeographical research and sequence characterisation (by me). Some of your records and your CC images have been/will be used to describe new species and next year Amanita sp 2 (the Noddy Flycap) will be published with iNat records (your records - if the images are CC)
  • Data (curated data) from iNat has been critical in assessing the threat status of fungi in NZ. This year it supported the inclusion of two NZ species on the IUCN red-list and contributed to DOC’s New Zealand Threat Classification Status (NZTCS). The new fungal list will be published next year
  • Important records this year include:

So, if you want to contribute to this kind of work, then make sure you don't use 'All Rights Reserved' on your fungal images.

Posted on 31 de maio de 2017, 08:45 PM by cooperj cooperj | 50 comentários | Deixar um comentário

14 de dezembro de 2016

Some notes on NZ Physalacriaceae

Posted on 14 de dezembro de 2016, 06:03 AM by cooperj cooperj | 0 comentários | Deixar um comentário

Some notes on NZ Marasmiaceae

Posted on 14 de dezembro de 2016, 06:02 AM by cooperj cooperj | 0 comentários | Deixar um comentário

Tricholomopsis in NZ

Posted on 14 de dezembro de 2016, 03:26 AM by cooperj cooperj | 0 comentários | Deixar um comentário

03 de dezembro de 2016

NZ species in Mycenella, Hemimycena, Atheniella and Mycena pp. (suborder Marasmineae incertae sedis)

Another one of my Mycological Notes - dodgy, not peer-reviewed, rough outlines ...
http://www.funnz.org.nz/node/128

Posted on 03 de dezembro de 2016, 08:34 AM by cooperj cooperj | 0 comentários | Deixar um comentário

28 de novembro de 2016

The family Porotheleaceae in NZ

I added a 'Mycological Notes' on this family to the FUNNZ site ...
http://www.funnz.org.nz/node/127

Posted on 28 de novembro de 2016, 10:52 PM by cooperj cooperj | 0 comentários | Deixar um comentário

06 de outubro de 2016

Strophariaceae sensu lato in NZ

[2021 March - an updated phylogeny of NZ Strophariaceae sensu lato is loaded on this record https://inaturalist.nz/observations/48212034

One of my earlier posts was ‘The Stropharia, Hypholoma, Pholiota, Leratiomyces, Clavogaster series in NZ’. This post covers the remaining genera in the strophariaceae in a broad sense. The genera included here may or may not reside in the family according to different views. I have deliberately excluded Hebeloma, Psathyloma and Naucoria (but included Galerina).

Keys to genera for fungi are becoming increasingly difficult to construct because in recent years genera are named or redefined based on phylogenetic entities, sometimes without a set of unique morphological characters separating them, or at least not characters that are easily seen. In reality, only keys to species work well. For that reason this key to genera should be used in conjunction with the key to species in the earlier post.

I’ve used micro-features in the key because, even without phylogenetic splitting, naming genera (and certainly species) purely by macro-morphology is often a betting game with poor odds. If you want to name fungi accurately then get a microscope.

Some jargon is used. Google the terms if you don’t know them. Chrysocystidia are a very useful micro-character in this group. It refers to the reaction of the cystidia to KOH solution. Some species will show yellow staining content. The dye Patent Blue is even more effective but difficult to obtain. It is sometimes sold in tablet form as a ‘dental revealer’ but banned in NZ. Beware species that have yellow cystidia anyway, without the addition of KOH, e.g. in Gymnopilus.

The keys, as usual, are rough and need refining. I’ll work on them as I get time.

The Genera

1

Pileipellis a trichoderm. Frb partialy secotioid. Sometimes in plant pots.

Tympanella galanthina

1’

Pileipellis hymeniform or a cutis. Frb secotioid or not.

2

2

Pileipellis hymeniform, often cracking on drying

3

2’

Pileipellis a cutis/trichoderm (but see also Agrocybe pediades)

4

3

Spores with germ pore

Agrocybe

3’

Spores without germ pore (Spores cruciate = Crucispora)

Cyclocybe

4

Stipe absent or laterally attached, small, Crepidotus-like

Deconica section Melanotus

4’

Stipe centrally attached (secotioid or not)

5

5

Spore print black/purplish

6

5’

Spore print brown

12

6

Pileus AND stipe glutinous in wet weather, on dung

Protostropharia semiglobata

6’

Pileus and stipe never glutinous. On dung or not

7

7

Clustered on wood or roots

Hypholoma

7’

Not clustered or if so then on soil

8

8

Well developed ring or ring zone

Stropharia

8’

No ring

9

9

Chrysocystidia absent

The secotioid C. virescens has chrysocystidia, but they are indistinct

10

9’

Chrysocystidia present. Frbs never blueing on bruising.

Hypholoma

10

Frbs red, secotioid or not

Leratiomyces

10’

Frbs brown, grey or blue, secotioid or not

11

11

Frbs usually blueing on bruising, secotioid or not

Psilocybe

11’

Secotioid or semi-secotioid, innately powder blue or yellowish

Clavogaster

12

Chrysocystida present (exceptions in other genera with Chrysocystidia:  Deconica baylissianum & D. novaezeandiae)

Pholiota & Protostropharia

12’

Chrysocystidia absent

13

13

Spores rough

14

13’

Spores smooth

15

14

Frb slender, often in mosses, sometimes on wood, spore print dull brown, taste mild.

Galerina pp.

14’

Frb more robust, on wood, spore print bright brown/orange, taste bitter

Gymnopilus

15

Pileus hygrophanous.

16

15’

Pileus not hygrophanous.

17

16

Growing on wood. Kuehneromyces brunneoalbescens has white flecks on a dark stem

Kuehneromyces brunneoalbescens & Galerina section Naucoriopsis (G. marginata group)

16’

Terrestrial in soil or grasses, or on dung.

Deconica

17

Pileus glabrous

Flammula ‘Matawai’

17’

Pileus with veil in slime, yellow/orange

Pholiota glutinosa

 

Agrocybe/Cyclocybe & Crucispora

Agrocybe acericola, A. howeana & A. puiggarii are all considered doubtfully present, based on inadequate material.

Agrocybe praecox is very common on wood chips, especially in spring. An endemic fungus recorded rarely (A. olivacea) is suspiciously similar to a recently described wood chip species (A. rivulosa) spreading in the northern hemisphere. Agrocybe arvalis has recently been confirmed as present. It is a species associated with sclerotia and may be confused with Hypholoma tuberosa (or vice versa). Cylocybe parasitica is the new name of Agrocybe parasitica, which itself is very close (same as) the confused pair A. cylindracea/aegerita of the northern hemisphere. An earlier name for C. parasitica might be A. chaxingu, which was obscurely published. Cyclocybe species are phylogenetically very different to the rest of Agrocybe. Interestingly Crucispora naucorioides, described by Egon Horak from New Zealand appears to be related to Cyclocybe based on sequences of a 2nd collection of this rare fungus. Crucispora, as the name suggests, has cruciate spores, unlike all the species below. C. naucorioides is the only species in the genus and has only been collected once in NZ, until recently.

Agrocybe pediades is common in NZ on soil/sand in open areas, especially areas manured (usually with rabbit pellets). It is variable in appearance. Material confirmed by sequences as this species has a surface ixocutis and the hymeniform nature of the partially gelatinised subpellis difficult to discern or absent. For that reason it has frequently been misidentified in NZ as the microscopically similar Deconica subcoprophila, but that species has a darker cap, often radially striate, and above all else has dark brown/violaceous spores, without the typical cinnamon coloration of the gills/spores of Agrocybe. Sometimes it is also confused with Stropharia coronilla , but that has a distinct grooved ring on the stem.  

1

With ring. Spores with or without germ pore.

2

1’

Without ring. Spores germ pore.

4

2

On living trees. Spores with a pore

Cyclocybe parasitica

2’

Not on living trees. Spores with or without pore

3

3

On wood chips. Pileus pale brown. Often in spring. Spores with a pore

Agrocybe praecox

3’

On soil. Pileus dark brown. Spores without pore.

Cyclocybe erebia

4

Pileus with velvety texture and pilocystidia. On wood chips.

Agrocybe putamimum

4’

Pileus smooth, without pilocystidia, usually on soil (sometimes manured)

5

5

Pileus wrinkled, with olivaceous hue (A. rivulosa without ring)

Agrocybe olivacea

5’

Pileus smooth, yellow/orange

6

6

Not growing frm a sclerotium

Agrocybe pediades

6'

Growing from a buried sclerotium and pleurocystidia with apical fingers

Agrocybe arvalis

 

Deconica

Some species originally placed in Psilocybe have been historically recorded and not include here. D. physaloides is a nom. dub. and Guzman’s concept, according to Noordeloos, is a mixture of species including D. subviscida and D. xeroderma. Relatives of both are known in NZ and material labelled D. physaloides has not yet been examined by me. NZ material labelled Psilocybe subcoprophila by Johnston et al., 1995, is annulate, related to D. merdaria, and included in the key as D. merdaria cf. Other NZ material labelled D. subcoprophila is a misidentification of Agrocybe pediades

Psilocybe brunneoalbescens was described from Tasmania under a very broad concept of Psilocybe that incorporated species better placed in several other genera. From the description it might be assumed to fit within the modern concept of Deconica, perhaps like D. montana aff. However, NZ collections identified as P. bruneoalbescens by Gen Gates and David Ratkowsky, and Tasmanian material are similar, and NZ material has sequences which fall within Kueheneromyces. The recombination K. brunneoalbescens was created.  It has a darker brown stem and sweet taste compared to similar Deconica species. It does not have a large germ-pore which is characteristic of northern hemisphere Kuehneromyces spp.

1

Minute, laterally attached to dead herbaceous stems

2 (section Melanotus)

1’

Not laterally attached

4

2

On dead Astelia leaves, spores > 10um, limoniform

D. citrispora

2’

Not on Astelia, spores smaller and not limoniform

3

3

Spores > 8um on average, Pileus opaque.  On wood. Indigenous D. vorax, introduced D. horizontalis

D. vorax/horizontalis

3’

Spores < 8um on average, Pileus translucent striate, on grasses

D. philipsii

4

Orange/tan, secotioid, Thaxterogaster-like but in alpine herbfields.

D. baylissianum

4’

Not secotioid

5

5

On dung or bare soil, litter/thin twigs

6

5’

On rotting wood (not twigs), Tubaria-like

D. xeroderma

6

On dung (or manured soil)

7

6’

On bare soil (not manured), litter, thin twigs

9

7

Pileus remaining hemispherical, orange brown. Stipe without ring. 

8

8

Spores > 14um in length. [not Guzman's concept, which = D. merdicola]

D. argentina ss Johnston

8'

Spores < 13um in length [currently without sequenced NZ material for evaluation] D. coprophila cf.

7’

Pileus becoming flattened, dark brown, stipe with distinct ring or ring-zone.

D. merdaria cf.

9

On decaying grass stems and moss

D. subviscida aff.

9’

On soil, litter

10

10

Spores mainly rhomboidal

D. novaezelandiae

10’

Spores broadly ellipsoid (see also Kuehneromyces brunneoalbescens)

D. montana aff.

 

Galerina

The moss/non-moss groups are phylogenetically different and will be split sometime, but Galerinas in general form multiple poorly resolved phylogenetic clades and more work is needed. The moss Galerinas are poorly known in NZ and names I’ve used will probably change. They are little more than sequence-informed guesses. We don't have the northern hemisphere species like G. hypnorum, G. calyptrata etc. These names are widely misused on iNat. We do have looka-like species. Amongst the wood inhabiting Galerina species with a ring we have G. patagonica (sensu Australasia) which is recorded from Australia and New Zealand. G. patagonica, as the name suggests, was described from South America but no sequences have been published to confirm the equivalence of the Australasian species assigned to this name. Australasian material tends to have a central nipple on the cap, but not always. There are 2 or 3 species within a complex with others known from Pacific Islands and the Subantarctic Islands. G. marginata cf. in the key is unrelated to the northern hemisphere species and may comprise two closely related species both found in NZ and Australia. One of these versions corresponds to Alec Wood's 2001 concept of G. rudericola with low spore ornamentation. I think it unlikley it is the same as the original version from North America.  The real G. marginata is deadly poisonous and contains the same toxins as the death-cap. G. patagonica and G. marginata cf. probably also contain the same toxins. 

1

With mosses

2

1’

On wood, soil or litter

6

2

Spores calyptrate

3

2’

Spores not calyptrate

4

3

Cheilocystidia cylindrical, not swollen at apex

G. neocalyptrata

3’

Cheilocystidia swollen at the apex. Phylogenetically different but morphology difference elusive.

G. subcerina,G austrocalyptiformis SS NZ

4

Pileus < 1cm. Spores rough

5

4’

Pileus > 1.5cm. Spores smooth

G. pumila

5

Pileus with pilocystidia

G. atkinsoniana

5’

Pileus without pilocystidia

G. vittiformis

6

On soil or litter

7

6’

On wood

8

7

On soil, often in plant pots, with ring or ring-zone. Thick walled cystidia, 4-spored

G. nana

7’

In litter, lower stipe dark, covered in white fibrils. 2-spored

G badipes

8 Stipe eccentric G. nothofaginia & G. eccentrica

8'

Stipe central

9

9

Spores smooth. 4-spored. Cheilocystidia swollen apex. Lower stipe with white fibrils

G sideroides

9’

Spores rough. Deadly poisonous group.

10

10

At least some cheilocystidia bifurcate

G. patagonica

10’

Cheilocystidia swollen but none bifurcate

G. marginata cf.

 

Gymnopilus

Gymnopilus junonius is one of the most frequently reported fungi in New Zealand due to its preference for growing in large clusters on cut stumps of Pinus radiata. Our species is the genuine G. junonius first described from Europe with sequences the same as collections from Australia, South America, and Europe. Asian material, under the name G. spectabilis, is a different species and the North American taxa under this name have recently been revised (Thorn et al, 2020). G. ventricosus from the home of Pinus radiata in California is certainly not the species present in NZ. Published sequence data is not yet available for the reported US blueing variants of ‘G. junonius’, which no doubt represents a different species. Many of our P. radiata-associated fungi are European in origin perhaps because our original P. radiata came from Australian stock, itself based on European stock and not direct from California.

All Gymnopilus species grow on wood, and the G. purpuratus complex often on wood chips. G. purpuratus was originally described from Australia but unfortunately the name is invalidly published. The related G. luteofolius (luteifolius) has been recorded in both New Zealand and Australia, often associated with (pine) wood chips but sequence data indicate this North American name has been misapplied elsewhere. A supported ‘species complex’ clade contains sequenced material labelled G. purpuratus, G. suberis, G. terricola, G. subpurpuratus, G. purpureosquamulosus, G. norfolkensis, ‘G. luteofolius’ (=G. suberis), G. igniculus, G. aeruginosus and G. hispdus. Certainly, ITS sequence data show NZ material in a clade with all material named G. purpuratus from Australia, Cook Islands and Switzerland, and genuine North American G. luteifolius in a different clade outside the complex. The similar G. dilepis forms a well-supported sister-clade and incorporates collections with several names (including another version of G. purpuratus).  Stable morphological characters separating the species in this group are difficult to assess. G. dilepis, described from Sri Lanka, seems to have dominant orange/yellow colours and in dry conditions any purple is present only as a scabrous colouring towards the cap centre, although it is said to have more diffuse magnta/purple colours under wet conditions. It usually has a distinct ring zone/remnants on the stem. At least that is what sequence verified collections imply. G. dilepis is often described with a purple cap which would make it difficult to separate from G. purpuratus, but I believe many of those identifications are incorrect. G. dilepis and G. purpuratus are certainly phylogeneticaly distinct and the shape of the cheilocystidia quite different in the two species.  Separating the similar G. luteifolius is more problematic. One opinion separates G. luteofolius with pleurocystidia from G. purpuratus without. NZ material of G. purpuratus does not possess pleurocystidia supporting the use of this name.   We have one poor NZ collection of a faintly blueing Gymnopilus species as a weed in a mushroom farm and it has a sequence in this complex. For this taxon I have tentatively settled on the name G. megaspora (having started with G. cyanopalmicola). Sequence data indicate it is closely related to (same as) European collections of G. igniculus and (one group of) material labelled G. purpureosquamulosus. There is no doubt that a multi-gene analysis, more collections, and a better assessment of stable morphological characters are required to clarify this species complex globally. In my opinion it is likely (and preferable) that we recognise fewer species with infra-specific biogeographical variation, and with considerable phenotypic variability.

Several species can exhibit off-centre stems and the character is not diagnostic, e.g. for G.crociphyllus described as eccentric-stemmed.

Gymnopilus allochrous is an unpublished name and I have not found a description. The characters in the key come from material with a sequence identical to one named G. allochrous from Australia.

[Jan 2019] The key doesn't work well because the character 'perispore' creeps back in after being discarded. In addition we have the second collection of a species closely related to the Australian G. tyallus/eucalyptorum which needs including. The presence of G. flavus in NZ, growing with exotic grasses, requires confirmation with deposited and sequenced material, but is possible.

 

1

Spores with a perispore, sometimes indistinct 

2

1' Spores without a perispore 3

2

Stipe lateral.  Spores 4.5 - 5.0 µm x 3.5 - 4.0 µm.

G. pyrrhum

2’

Stipe central to excentric. Spores 7 - 8 x 5 - 6 µm. G. ferruginosus, (collections without an obvious perispore) may be a synonym. Pileus rusty colour (if orange see G. austropicreus)

G. mesosporus

3

Partial veil a membranous annulus, frbs mostly large, bright orange, usually on pine stumps.

G. junonius

3’

Partial veil a fine cortina or absent. Frbs smaller, bright or not, modified habitats or not

4

4

Gills rust spotted at maturity. Veil present when young on lower stem. Gills pale to start. Spores 7-9 x 4-5

G. penetrans

4’

Gills not rust spotted at maturity. Veil absent. Gills brighter coloured from start. 

5

5

Pileus with blue, purple or reddish, rust brown colours.

6

5’

Pileus with yellow, golden or rusty orange colours. In some collections of G. dilepis the purple can be absent, so see also couplet 7

9

6

Pileus reddish rust brown, margin often lobed, fibrillose, spores strongly ornamented. Stipe sometimes eccentric. Natural habitats. G. mesosporus is a potential synonym.

G. ferruginosus

6’

Pileus or stipe with purple or cyanescent, sometimes fading, margin not lobed, spores more finely ornamented.

7 (purpuratus complex)

7

Pileus and stipe weakly cyanescent when bruised, fading.  Spores 8-11 µm x 6-8 µm. 

G. megaspora

7’

Pileus and stipe not cyanescent. Blue/green/purple colours innate. Spores smaller, 6-8.5 µm x 4-6 µm

8

8

Pileus usually brown, not scabrous. Purple colour persistent often dominant. Spores 7.5-8.7 µm x 4.8-5.7 µm

G. purpuratus

8’

Pileus usually orange, purple colours, if present at all, as scabrous cap centre. Ring remnant often present. . Spores. 6.3-7.2 µm x4.5-5.1 µm

G. dilepis

9

Spores 6.0 - 8.0 µm x 4.8 - 5.6 µm (and with an indistinct perispore). Pileus smooth.

G. austropicreus

9’

Spores without a perisporium

10

10

Spores 4.8 - 7.2 µm x 3.2 - 4.8 µm.

G. crociphyllus

10’

Spores mostly larger to 9 µm x 6um

11

11

Spore ornamentation very fine. Cheilocystidia abundant. Pileus yellowish brown, often with white flecks on perimeter. Stipe often with white silky coat.

G. allantopus

11’

Spore ornamentation medium. Cheilocystidia sparse. Colour bright orange/yellow, reminiscent of G. jononius.

G. allochrous ined.

 

Psilocybe

It is with hesitation that I say anything about Psilocybe. For obvious reasons species within the genus receive considerable scrutiny around the world. My knowledge is limited by comparison. Nevertheless, as a taxonomist I do have some comments I’ll throw out there.

Psilocybe alutacea was described from Tasmania on cow dung and, as Allan Rockefeller has pointed out, was misidentified as P. fimetaria in New Zealand. Sequence data indicate the same species is present in Argentina misidentified as P. pelliculosa. P. alutacea is surely not native to New Zealand but the real origin remains unclear. Sequence data indicate we may have several poorly defined species in the P. cyanescens complex. I think the P. cyanescens complex needs more work, globally. The current sampling of gene loci (ITS, LSU, EF-a) and proposed key morphological separation characters do not adequately resolve the differently named entities within the clade. Certainly, data based on ITS alone is not definitive and obscured by the presence of multiple different ITS PCR dominant copies (haplotypes) within the same species. I do think there may be closely related real ‘species’ involved, rather than over-splitting of a single broad species (P. cyanescens) because the secotioid P. weraroa sits within the group and is clearly morphologically quite different. However, having said that, the evidence suggests a recent divergence of P. weraroa, indicating how simple the gene switch must be from open mushroom to closed pouch. The current phylogenetic data indicate there might be two very similar but different semi-secotioid species, in addition to secotioid variability in P. weraora . These variants are called informally P. 'subsecotioides' but that has not been published and so not attributable to any specific taxon. They require more work to disentangle them from P. weraroa and confirm as real species. Some species do seem to have been historically over-lumped by several workers. Chang et al, 1992 lumped P. tasmaniana, P. australiana and P. eucalypta into P. subaeruginosa, but the equivalence of dung inhabiting and wood inhabiting species does not have much support, and I agree with other observers on this point. I also need more convincing that the current concept of P. subaeruginosa is the same as Cleland’s original concept. It might be correct, or it might not. Cleland did not designate a type for this species but lists some collections he assumed to be the same species. The original description says it occurs in grass with one collection on dung, which differs considerably from the common (but not universal) modern interpretation of a wood chip or myrtaceae litter associated species. Guzman & Watling studied Cleland’s material, including Cleland 13251, which they called the ‘type’ and demonstrated the presence of unusual and characteristic brown pleuro- and cheilocystidia. That specimen is currently missing from Cleland's collections at Adelaide. A formal lectotype AD 5603 (=Cleland 13256) from Belair National Park Australia has since been designated (Chang & Mills 1992), but without published details of the habitat and substrate of this critical collection which would allow us to narrow down the accepted species concept. Their lectotype apparently does not have brown cystidia. That treatment has received subsequent criticism (e.g. Stamets 1996). No examined NZ material labelled P. subaeruginosa has brown cheilo or pleurocystidia and no sequenced NZ material is so far identical to Australian collections under that name. Likewise at least some recently reported collections of Psilocybe tasmaniana on wood chips in Australia and NZ are not likely to be Roy Watling’s Australian species described on dung “cap to 2cm and without umbo or papilla” and is probably undescribed. Psilocybe allenii was described relatively recently and occurs convincingly in New Zealand based on sequence data. It is considered closely related to P. azurescens and P. cyanescens. A recent sequence of the type of P. azurescens is different to other sequenced taxa under that name. All of which just shows the current application of names in this clade is a bit random and requires more work. All the wood chip species fall out at my couplet 5. Species differentiation based on spore size, cheilocystidia length and cap morphology (used in some keys) does not work for me. If somebody can give me a key that works for all the named species in the P. cyanescens group I would be happy to test it. I think more sequence sampling of the dung, soil and wood species in southern Australia and Tasmania, and epitypification against sequenced and well described material is needed to resolve the use of several names of closely related species.

A phylogenetic tree including New Zealand species may be found attached to this observation ... https://inaturalist.nz/observations/1462023

 

1

On dung, stem with veilar remnants, sometimes bluing, similar to P. fimetaria. Deconica argentina/coprophila look may look a bit similar but without blueing. If cap with central nipple see P. angulospora.

P. alutacea

1’

Not on dung

2

2

Frb secotioid

P. weraroa

2’

Frb not secotioid

3

3

On soil

4

3’

On wood/wood chips

5

4

12 µm x 8um on average. Pileus 7-10 mm, with sharp umbo. In grassland.

P. semilanceata

4’

8 µm x 5 µm on average. Pileus 15-55mm, without sharp umbo. Phylogenetically and morphologically close (same as?) P. zapotecorum. Occasionally on wood.

P. aucklandiae

5 Spore length < 10um (9-9.5 x 6-7 µm on average) 6
5' Spore length > 10um. On wood chips in modified habitats (and probably all introduced). A species complex (exc. P. tasmaniana) with currently unreliable separating characters and species concepts. P. cyanescens, P. allenii, P. subaeruginosa, P. tasmaniana
6 On rotting wood in natural habitats. Cap without central papilla. Spores not angular in outline P. makarorae
6' On wood chips, greenhouse, plant-pots. Spores angular in outline. P. angulospora

 

Stropharia

S.rugosoannulata can have pale forms. S. caerulea is the correct name for many NZ records identified as S. aeruginosa (with others being Cortinarius rotundisporus!). S. cyanea auct is the same as C. caerulea (Bolton’s original concept of Agaricus cyanea is unclear). S. 'Kennedy' may be the same as, or closely related to S. formosa from Tasmania.

1

Pileus wine red to brown, smooth, frb large, often over 12cm

S. rugosoannulata

1’

Pileus other colours, smaller, under 8cm

2

2

Pileus with blue/green colours

S. caerulea

2’

Pileus yellowish or brown

3

3

Pileus yellowish, smooth, in grass, modified habitats. Stem with grooved ring.

S. coronilla

3’

Pileus brown, velutinate, unmodified habitats, stipe with rhizoids

S. ‘Kennedys Bush’

Posted on 06 de outubro de 2016, 03:33 AM by cooperj cooperj | 0 comentários | Deixar um comentário

Geastrum Earth-Stars in New Zealand

The genus Geastrum is easy to recognise, but like many fungal groups it is not so easy to identify species within the genus. Names like Geastrum triplex and G. saccatum are used indiscriminately everywhere. Most identifications adopting these names will be wrong.

My former colleague the late Ross Beever was interested in puffballs and their allies, and this current work builds on the collections and observations made by Ross (in the PDD national collection). I wanted to get this preliminary key ‘out there’ so it can be used, hopefully to recognise interesting collections for further work. Like many of my keys it was written for my own benefit, at least in this first instance. I do not know Geastrum very well (which is probably apparent) and the process of developing a key clarifies the concepts needed to separate species in my own mind. I will change this entry as more information becomes available, and I learn more. Like most genera you can only reliably identify species using a combination of macro and microscopic characters.

Good collections of Geastrum are needed for correct identification. By that I mean examples of the fruitbody from bulb stage to fully expanded, making a note of the colour of fresh material (any pinkish/red colouration of the flesh may fade). A fruitbody still attached to a piece of substrate is useful for characterising rhizomorphs. If material in the field looks old and knocked about then don’t bother attempting to identify it. A number of the key features are ephemeral and difficult to observe in weather-worn specimens. Read the terms in the short glossary to work out which features are key.

Geastrum was last revised in New Zealand by Cunningham in 1944 (Gasteromycetes of Australia and New Zealand). He recognised the following 7 species: G. pectinatum, G.plicatum, G. minus, G. limbatum, G. velutinum, G. triplex & G. floriforme. Like many authors he adopted names from the Northern Hemisphere. Although our species look similar to northern hemisphere species, and in many cases are closely related, the current sequence data suggest they are mostly localised in their distribution and probably indigenous. They are found in both natural and modified habitats, but there are some exceptions. G. floriforme might be introduced and is identical to the northern hemisphere species. In NZ this species favours dunes and alpine areas but isn't common in macrocarpa plantations, unlike many UK records where it is found under macrocarpa. On the other hand G. coronatum aff. and G. tenuipes, both like macrocarpa plantations, and G. velutinum aff. likes pine plantations. All of these species are not exclusively limited to these habitats and other Geastrum species occur in the same habitats. 

Because many of our species are near, but not the same as northern hemisphere species the names are followed by ‘aff.’ meaning ‘having and affinity with’ (phylogenetically and morphologically). Most are probably undescribed species. In some cases the sequence data indicate the names cover multiple species within a complex (G. velutinum aff. & G. saccatum aff.). The separate phylogenetic species within these complexes usually have no differentiating morphological characters (that I can find at the moment).

With reference to Cunningham's names his G. pectinatum/plicatum are treated here under the name G. tenuipes. It is possible that collections with a stalk, sulcate peristome and non-ridged apophysis may turn out to be different to collections posessing a ridged apophysis and a new name will be required for that species. Likewise G. minus is generally treated as a synonym of G. quadrifidum and here would key out under G. coronatum aff. It is likely that smaller versions of G. minus auct. NZ (of which there are a few collections) represent a good species which is likely to be G. austrominimum. More collections are needed to genetically characterise G. minus in NZ (in section quadrifida). There have been no confirmed collections since 1926. G. limbatum is now generally treated as a synonym of G. coronatum. A number of collections have been historically identified as G. triplex but on closer examination they represent G. lageniforme, G. australe or G. minutisporum aff. as well as G. triplex aff. The latter species is distinctly larger than any of the others. The presence of a residual fractured collar of pseudoparenchymatous material around the endoperidium has been shown not to be a unique and reliable feature of G. triplex (the so-called collared Geastrum), and I haven't used it as a character. G. triplex was described from Indonesia is a tropical species of south-east Asia. The name is used broadly and imprecisely elsewhere.

A number of names were added subsequent to Cunningham's 1944 treatment. A collection of G. drummondii was incorrectly identified. G. morganii was represented by a single collection which was used in an exhibit and not returned to PDD (duh!) but another collection related to G. morganii has been identified. G. fimbriatum has been recorded quite often but it is possible all these records refer to one of the species in our G. saccatum complex. G. fenestratum is generally regarded as a synonym of G. fornicatum and in New Zealand probably refers to G. setiferum aff.

Modern phylogenetic treatments by Zamora and colleagues (e.g. Zamora et al., 2015. Integrative taxonomy reveals an unexpected diversity in Geastrum section Geastrum (Geastrales, Basidiomycota); Persoonia, 34: 130–165 & Zamora et al., 2014. Systematics of the genus Geastrum (Fungi: Basidiomycota) revisited; Taon, 63: 477–497) have opened up the black-box of Geastrum. They provided a phylogenetic framework to place species, and some new characters assist in identifying them. In some cases reliable identification of NZ species, even to the broad ‘species complexes’ treated here, is not easy. In particular the G. saccatum/G. lageniforme groups are difficult to separate without observation of the form of crystals attached to the rhizomorphs attached to the fruitbodies, which are often not collected. 

As mentioned above, a preliminary phylogenetic analysis of a number of NZ collections show they are closely related to some recently named southern hemisphere relatives and I have adopted those names, with the ‘aff.’ because they aren’t the same (to re-iterate what aff. means). Thus G. setiferum was named in 2002 from South America and G. minutisporum also from South America in 2016 and in both cases our species are phylogenetically close and do have different characters. They need new names. The numbers in brackets after a species name in the key refer to the Zamora classification (in the following table)and the position of representative sequences of NZ material in that classification.

It isn’t easy to incorporate photographs into this journal entry so those will have to wait.

NZ Trial Key to Geastrum

1

Endoperidial body with a stalk (sometimes quite short).

2

1’

Endoperidial body sessile. 

4

2

Persistome sulcate or radially ridged fibrillose, clearly delineated. Stalk with apophysis. Base of endoperidium usually ridged (apophysis), sometimes with a torn collar.

 G  tenuipes (7d)

2’

Persistome fibrillose but without ridges, not delineated. Mycelial layer encrusting debris (hypogeous). Stalk without apophysis.

3

3

Endoperidium surface silky, usually pale steel grey, sometimes with white flecks of crystals. Stoma edge fibrillose. Without apophysis.  Endoperdium to 2cm diam.  Without long endoperidial setae.

Within Cunningham’s NZ collections there are records of G minus, with an endoperdium < 7 mm diam. which are not G coronatum and not G quadrifidum and probably represent G austrominumum.

G coronatum aff. (7b)

3’

Endoperidium surface minutely furfuraceous, without flecks of white crystal, pale tan. Stoma edge torn. Often with apophysis. Endoperdium with thick-walled setae > 70um. Stalk often short but present.

G setiferum aff. (6)

4

Flesh becoming pink. Endoperidium tomentose 

5

4’

Flesh not becoming pink. Endoperidium smooth or tomentose/pruinose

8

5

Peristome not delineated (concolorous). Rhizomorph crystals in rosettes. Endoperidium minutely tomentose. Stoma edge torn.

6

5’

Persistome delineated. Spores < 6um. Rhizomorph crystals prism shaped. Stoma edge fibrillose.

7

6

Spores > 8um diam., setae short. Not encrusting litter. Peristome concolorous but raised/sunk.

G australe (4)

6’

Spores < 7um. Peristome not differentiated at all.

G rufescens aff.  (4)

7

Mycelial layer finely tomentose and encrusting debris towards perimeter. On soil, not wood. Spores 2-3um. Bulb morphology unknown. Endoperidium minutely furfuraceous. Emergent setae short, < 50um. See also PDD100967 under G. velutinum.

G minutisporum aff. (10a)

7’

Not encrusting debris. Mycelial layer coarsely felty. Spores 3.5-4.5 um. Bulb without beak. Endoperidium smooth. Emergent setae absent. The NZ G. velutinum complex consist of at least 4 species for which no separating characters have been found, except  PDD100967 with very small spores, 2.4um on average.

G velutinum s.l. 4 spp. (10b)

8

Rays hygroscopic (the thin white petal-like rays totally enclose the dried frb). Hypogeous frb. Mycelial layer not encrusting soil (peels off rapidly). Peristome not delineated. Coastal and dry areas. Spores 5.5-7um

G floriforme (11)

8’

Not hygroscopic. Peristome delineated or not.

9

9

Endoperidium >= 20mm diam. Peristome ±delineated. Stoma with silvery/greyish fibres. Endoperidium flecked minutely white with crystals (characters of PDD95584). Spores > 4um. I’m not convinced the ‘collar’ character you will see mentioned elsewhere is good for diagnosis. If spores > 8um then see G. australe

G triplex aff. (14)

9’

Endoperidium < 20mm diam.  Spores < 4 um on average

10

10

Peristome sulcate and conical. Endoperidium slightly pruinose. Mycelial layer encrusting debris.

G. morganii aff. (2c)

10’

Peristome fimbriate/fibrillose

11

11

Peristome not delineated. Mycelial layer encrusting debris. Presence requires confirmation by sequencing. Some sequenced material named G fimbriatum is actually G saccatum s.l.

G fimbriatum? (5)

11’

Peristome delineated. Mycelial layer absent or present (and then not encrusting debris)

12

12

Rays not sharply acute and drying hook-like. Rhizomorph crystals acicular. Mycelial layer a persistent weak pale brown mycelium towards perimeter (unlike G. saccatum ss)  but hardly encrusting debris. Basidia bladder-like (not seen in NZ material). Surface of bulb +- felty. Endoperidium minutely furfuraceous, with short, inflated setae [but surface smooth setae absent and smaller spores in PDD97802 sp.3 ]. Sp.1 and sp2. Are morphologically identical.  See also G fimbriatum auct NZ

G saccatum aff. 3 spp. (2b)

12'

Rays acute and drying like sharp hooks. Rhizomorph crystals horn-like (thin, cylindrical, ridged/irregular surface). Mycelial layer totally absent and under surface white/smooth (unlike G. lageniforme ss). Basidia lageniform ('Florence flask' - Google it) (not seen in NZ material). Surface of bulb smooth. Peristome delineated. Endoperidium smooth, no bladder-like setae.

G lageniforme aff. (2a)

The Zamora et al classification of Geastrum, and NZ representatives

#

Section

Subsection

Colls

1

Campestria

 

 

2a

Corollina

Lageniformia

G lageniforme aff.

2b

Corollina

Marginata  

G saccatum aff. 3 spp.

2c

Plicostomata

 

 G. morganii aff.

3

Elegantia

 

 

4

Exareolata

 

G rufescens aff.  , G australe

5

Fimbriata

 

G fimbriatum?

6

Fornicata

 

G setiferum aff.

7a

Geastrum

Arenaria

 

7b

Geastrum

Geastrum

G coronatum aff.

7c

Geastrum

Quadrifida

 G austrominimum?

7d

Geastrum

Sulcostomata

G tenuipes

8

Hariotia

 

 

9

Hieronymia

 

 

10a

Myceliostroma

Epigaea

G minutisporum aff.

10b

Myceliostroma

Velutina

G velutinum s.l. 4 spp.

11

Papillata

 

G floriforme

12

Pseudolimbata

 

 

13

Schmidelia

 

 

14

Trichaster

 

G triplex aff.

Glossary

Apophysis – collar/ring like swelling on stalk or junction of endoperidium and stalk.

Binding litter - The outer mycelial layer can bind litter or not, and this is a key feature. This doesn’t mean lumps of substrate that can be trapped by rays bent backwards. It means fine material firmly embedded within and stuck to the mycelial layer on underside of the rays. It is an indication the closed fruitbody was hypogeous (buried), and not sitting on the surface before it opened. However, soil encrusted layer may flake off, as a whole or in bits, and so I find this a difficult character to be absolutely certain about. The point of attachment of the fruitbody is often smooth, so don’t be fooled by that.

Endoperdium – the globe-like structure in the centre of the earth-star, specifically the skin of that structure. The texture of the surface is a useful feature. In some species it is obviously smooth/polished, but in most species it is superficially matt and under a lens either looks smooth or minutely hairy (tomentose), sometimes with aggregations of white crystals.

Exoperidium – The outer skin of the fruitbody can form three major layers. The outer mycelial layer (which can be simple or double), a middle fibrous later, and an inner pseudoparenchymatous (fleshy) layer. Outer and inner layers are evanescent, flaking off, sometimes lost entirely. Any pinkish colour to the fleshy layer is an important feature. The exoperidium splits into petal-like rays, which fold back.

Fornicate – rays arched downward and tips attached to remains of a separated exoperidial layer forming a basin in the soil. In some species the rays arch downward but without a separated cup layer.

Hygroscopic – You need to wet dried material to see the rays open out and then close up again as it dries. However, dried fruitbodies of hygroscopic species will be closed with the rays entirely covering the endoperidium so it isn’t visible. In non-hygroscopic fruitbodies the closed rays won’t cover over the endoperidium.

Mesoperidum – sometimes seen as a transient layer on surface of fleshy layer and surface of endoperidium, but usually dispersing rapidly.

Peristome – the circular zone around mouth, often different to rest of endoperidium (delineated) in either colour, texture, or raised/sunken. The area can be radially fibrillose, sulcate (ridged/pleated/folded) or smooth. Sometimes the term seems to have been used to refer just to the edge of the stoma rather than the circular zone surrounding the mouth.

Rhizomorphs - the rope-like hyphae connecting the fruitbody to the mycelium in the soil. They often have small (microscopic) crystals stuck to them, and the shape/form of these crystals is very useful fo separating groups. 

Saccate – an endoperidium sitting inside exoperidium at maturity, i.e. the globe is sitting in a bowl, not pushed up and exposed. Conversely the endoperidium looking like it is sitting on an upturned bowl (and then often with a stalk).

Stalk – between the endoperidium and exoperidium. Present or absent, and with or without an apophysis. Sometimes difficult to see without a vertical section.

Stoma – mouth where spores emerge. Edge of the stoma may be regular, fibrillose or ragged.

Posted on 06 de outubro de 2016, 02:06 AM by cooperj cooperj | 3 comentários | Deixar um comentário