Sunday, 1 March 2020

Review of that grassland waxcap identification support tool

It's almost six months now since I released that grassland waxcap identification support tool for field testing. I was pretty lucky with the timing: not long after publishing the tool, waxcaps in this part of the world went BOOM! By the time we got into October, there were just mushrooms everywhere.

This meant I had some good opportunities to test out the tool myself and I've been very pleased to also get feedback from others in the mycology community. So I'd like to start this post with a big THANK YOU to everyone who gave the tool a try during waxcap season and took the time to provide feedback really helpful.

Below is a summary of the feedback received and some thoughts on how the tool could perhaps refined further.

"Generally it is pretty good"

This seemed to be the general gist of the feedback: the tool works reasonably well, in most cases. But it does have some limitations and a few quirks.

I would also note that, given:
  1. the considerable variability that can be observed within some 'species', such as Parrot Waxcap Gliophorus psittacinus and Blackening Waxcap Hygrocybe conica (both widely recognised as representing 'species complexes', i.e. the descriptions which accompany these names are known to encompass a whole group of closely related but distinct species, albeit not yet fully resolved from a taxonomic point of view so we carry on using these broad names); AND
  2. the considerable similarity that can be observed between certain species, i.e. species which can look remarkably similar to each other in the field, but are in fact taxonomically distinct ...
... a tool like this always needs to be used with caution; with an eye on detailed descriptions (in Boertmann's book, or elsewhere) and awareness of when observation of microscopic features is advisable, to confirm an identification.

Interpreting waxcaps' features is still tricky

The 2019 season was a big learning opportunity for me and I'm still figuring out how to recognise and categorise some of the more subtle features of waxcaps, such as texture and smell. There is no substitute for going out with experienced mycologists who can point these features out to you: the more specimens you see and examine, the easier it gets to recognise and categorise their features. But even when you think you've 'got' them, the effects of wind, rain and drought can make it harder still to interpret what you're looking at.

The tool includes some basic information on waxcaps' different features (ID characters) with some photos for illustration, which will hopefully be helpful to beginners. You just need to click on the character heading to bring this up.

An example of the 'character help' - information which pops up when you click on one of the character headings. In this case, "blackening or reddening of fruit body". You can scroll down to access more illustrations of this feature.

I might add a note to the next version to point this out, as I think not all users realised this additional 'help' is available.

Some of the ID characters seemed more prone to cause occasional problems with identification than others:

Cap shape
I decided to keep this simple when I was developing the tool and just included 'acutely conical', as a category for bringing the usually-very-pointy species H. calyptriformis, H. citrinovirens, H. acutoconica and H. conica to the fore.

However, at least one user was tripped up by the conical-ness of another species H. punicea
– which I'd categorised as 'Cap shape: Other". This is one of more than ten species where Boertmann uses the term "broadly conical" as a descriptor of cap shape; I just lumped these all in with 'Cap shape: Other' when I was putting the tool together. These terms are rather subjective and if you've come across a particularly conical-looking example of H. punicea or H. aurantiosplendens, for example, and interpreted its shape as being 'acutely conical', then the tool may lead you off in the wrong direction.

A collection of Hygrocybe aurantiosplendens, identified and photographed by Peter Russell showing their 'broadly conical' caps. PHOTO © Peter Russell.

I'm not sure what to do about this. I could have a go at expanding the 'cap shape' character. But I think that might create more potential problems than it solves.

Cap colour
I tripped myself up with this character, when I was trying to get an identification on this specimen:

A waxcap! More details of this collection on an earlier blog, here.

I went with 'Cap colour: pale brown (inc. buff, fawn)'. Which led me off in a wrong direction. I should have gone with 'Cap colour: whiteish (inc. ivory, cream, pale buff)' which would have led me towards Slimy Waxcap Gliophorus irrigata. I'd never come across a pale specimen like this before, so hadn't immediately recognised it.

Buff / pale buff. We're getting into very subjective categories here. Even I couldn't remember what they're supposed to mean. And I made them up!

However, I can't see an obvious way to improve the categorisation of 'Cap colour'. When I was working on this aspect of the tool, I came to the conclusion there's no perfect way of handling the colour characteristics: colours vary in different dimensions (i.e. shade, brightness, etc) and people perceive colours differently. I think the categorisation I've ended up with is probably about as good as I can get it – given the current functionality of the Identikit toolkit.

I could perhaps just add 'pale brown (inc. buff, fawn)' as an option for the cap colour of G. irrigata...

Toasted Waxcap Cuphophyllus colemannianus is another species where the colour categorisation within the tool might potentially trip you up. 

Toasted Waxcap Hygrocybe colemanniana, recorded on a Sussex Fungus Group foray in 2018. What colour would you call this?

I've allowed for it to be 'warm brown (yellow-, orange- or red-brown)' or 'dark brown'. However, others have commented that they often come across 'whiteish' specimens, with a brown centre, or would describe the shade of brown in different terms.

Again, I'm not sure there are any obvious improvements I can make to the tool here. Perhaps it just needs to come with some advice about not relying too heavily on colour, when using the tool to inform identifications.

Stipe colour
Returning to H. aurantiosplendens for a moment, this is another example where subjectivity of colour categorisations could lead one astray. Currently the tool classifies the stipe colour for this species as 'Yellow', based on Boertmann's description of it being "sulphur-yellow, egg-yellow". But then 'egg-yellow' can be quite orangey, can't it?

Maybe I should include 'Orange' as an option for stipe colour, for H. aurantiosplendens – so it doesn't get ruled out if someone finds a particularly orangey-stiped example? But then, looking at photographs of collections online, they do look to me to be more yellow than orange...

I don't think I've ever seen H. aurantiosplendens myself, so I'd be interested to hear views on this from folk who have experience with this species. Would you ever describe its stipe as 'Orange'?

Is there a better way of categorising texture? 

It was suggested that splitting the categories describing texture, e.g. to include 'thickly viscid' and 'slightly viscid', could be useful when encountering species such as Glutinous Waxcap Hygrocybe glutinipes.

I might have a play around with the categorisation of texture (for the cap and stipe), and have a look at how other keys deal with this character, to see if I can come up with something better for a future version.

Cap size can be problematic

Two people shared experiences of finding specimens which were bigger than the typical dimensions specified for that species in the tool, in which case if you enter the observed cap width the correct name gets knocked down the list of probable species. So the tool is potentially misleading if you happen to find some unusually large waxcaps (which does happen sometimes, as evidenced by these giant Oily Waxcaps H. quieta, found by Simon Harding last November).

There are potentially two ways I could address this:
  1. Reduce the weighting given to the 'Cap size' character
  2. Change the dimensions for relevant species, to allow for outsize specimens
I think (2) is probably the better option, but I have no idea what I should change the dimensions to. So if anyone can advise on the species where this is likely to be an issue, and what would make for sensible maximum cap width that would be very helpful!

The weighting of ID features is very simplistic

Yes, it is. The Identikit toolkit, which I used to develop the tool, allows you to specify the weight to be given to the different ID characters. I opted to keep things simple and give them all equal weight.

This can be a cause of frustration at times, e.g. if you encounter a species which has one character which is a dead give-away, like the bright green colours in Parrot Waxcap Gliophorus psittacina – and the significance of this might get diluted in a long list of ID characters. But I didn't think there was enough consistency across the various species, in terms of which characters are the critical ones for identification purposes, to warrant devising some more complicated weighting formula.

It's also not possible, within the current functionality of the Identikit toolkit, to set it so the presence of a particular character will rule out other possibilities.

This means the user has to rely on their own judgement, when using the tool, regarding which characters are most pertinent to identifying the specimen they've got in front of them. The different visualisations are potentially helpful in this situation, as the 'single column key' and 'side by side comparison' allow you to look across the various species and see which ID characters are leading you in one direction, or another. 

I would say it's also worth familiarising yourself with one or more of the 'quick keys' to waxcaps that are out there (such as this one, hosted on the Aberystwyth University Waxcap Website) and Boertmann's list of 'species with outstanding features' (on pages 26-27 of his guide to the genus Hygrocybe, 2010), as they'll often get you to an identification quicker than a tool like this will do.

Some additional ID features would be useful

Judging by the feedback I received, there are a couple of species where additional ID characters would be helpful in leading users to an identification.

Gill colour

Oily Waxcap Hygrocybe quieta. PHOTO © Simon Harding.

A few people have fed back that gill colour would be a useful ID character, e.g. for Oily Waxcap Hygrocybe quieta, pictured here showing its distinctive salmon-tinted gills.

I can add this in to the next version of the tool.

Intervenose gills
Intervenose gills on Toasted Waxcap Cuphophyllus colemannianus.

Would be useful for Toasted Waxcap Cuphophyllus colemannianus, where it is a distinctive ID character. I think it should be straight forward to add this in.

Missing varieties could lead to misleading answers

I based the tool on the list of species in the JNCC Guidelines for the Selection of Biological SSSIs: Chapter 14, Non-lichenised Fungi. This means there are a couple of generally recognised varieties that aren't included, such as:
  • Hygrocybe glutinipes var. rubra
  • Hygrocybe laeta var. flava
So if you were to use this tool to try and identify one of these, it's probably going to lead you off in a wrong direction.

These are, however, both very rare in lowland grassland habitats – so the likelihood of this causing anyone significant problems with identification seems low.

Missing dune species could lead to misleading answers

I didn't include the species listed in the 'dune fungal assemblage' in the JNCC Guidelines, these are:
  • Hygrocybe aurantiolutescens
  • Hygrocybe conica var. conicoides
  • Hygrocybe olivaceonigra
Given that dune habitats can grade into grassland habitats, I think it would be useful to add these in.

H. aurantiolutescens is a Peter Orton species, originally described from Britain and recognised by French mycologists, from the dunes of Northern France (Martyn Ainsworth, pers comm); and it's not a concept that's recognised in Boertmann's book (he treats it as a synonym of H. acutoconica). So I shall need to ferret out a description of that species from somewhere, before I can update the tool.


Variability within species not fully represented by the characters listed

Parrot Waxcap Gliophorus psittacinus

I got thoroughly confused by these two collections during the waxcap season...

A collection from Henfield Churchyard.

A collection from fields in the West Weald. More details on an earlier blog, here.
After careful observation and examination of other fruit bodies nearby, I came to the conclusion they're both Parrot Waxcap Gliophorus psittacinus; they just happen to be specimens which aren't showing the green top to the stipe.

So the ID tool wasn't super helpful in this scenario as it specifies that G. psittacinus should have a 'green top' to the stipe; because Boertmann describes it as "almost always with green top".

I could change the tool, so it accommodates these less-often-observed forms. But I think that might make the tool slightly less helpful when encountering typical forms. Perhaps it just needs a stronger caveat that "sometimes waxcaps don't look like what they're supposed to"!?

Heath Waxcap Gliophorus laetus

A similar situation to G. psittacinus: Rob Foster advised me that G. laetus is often green at the top of the stem. Indeed, Boertmann notes that the stipe is "usually with grey, greyish violet top, which can even be bright violet or dark olive".

So perhaps I should add this option in. But I don't want to introduce a potentially unhelpful source of confusion for beginners who are still getting to grips with G. psittacinus, with its green top to the stipe...

I'd be interested to know how often mycologists encounter examples of G. laetus with green tones at the top of the stem, in Britain. 

Does anyone have a photograph of this feature – G. laetus with a green top to the stipe – which I could use to illustrate this ID character?

Other species characteristics

Mycologists who are very experienced in surveying waxcap grasslands may gain familiarity with species characteristics which are not necessarily documented in the literature. E.g. Rob Foster mentioned that, in his experience, Hygrocybe ingrata often blackens rather than reddens – a characteristic which is not noted in Boertmann's description. 

I think it would be unwise for me to attempt to incorporate all these possible characteristics. But it's worth highlighting to users of the tool that they may come across specimens which don't seem to exactly fit any of the species listed. And there could be different explanations for this:
  1. They've found an atypical specimen of that species
  2. Their collection represents diversity within the species which is not currently well documented in the literature.
  3. Their collection genuinely doesn't fit within any of the species concepts that this tool is based on: their collection is 'something else' (in which case DNA sequencing may be required to understand 'what it is', from a taxonomic point of view).
As is noted in the JNCC Guidelines: "... it should be borne in mind that these current names are merely a snapshot taken in a period of relatively rapid taxonomic change. The recognition of further species that are morphologically similar (but phylogenetically different) to one another is anticipated." 

Names 'out of date'

It was a conscious decision to use the species names used in Boertmann's book as the primary names within the tool, to make it easy to read across from the tool to the detailed descriptions in his book. If you click on the individual species, this will bring up additional information including the 'current taxon name' according to the JNCC Guidelines.

Opinions on the correct 'current name' will sometimes differ. So I think I will focus on referring to well-known and generally accepted species concepts / names (i.e. what's in Boertmann's book and the JNCC Guidelines), in the hope that everyone knows what these mean. And I won't try and stay bang up to date with the 'latest names'.

I would also like to add a note of thanks here to Richard Shotbolt who has been checking the species names are properly incorporated within the UK Species Inventory, and are therefore available for recording purposes in iRecord and the FRDBI

Response and feedback

The tool got a positive response on social media. My tweet about it gained nearly 9,000 impressions and prompted over 120 accounts to click through to the link which is LOADS compared to the level of interest I usually get. And my post on the British Mycological Society Facebook page got quite a few 'shares'. So that was nice. A number of people got in touch to say they'd tried it out, and had some success with it, which was very encouraging to hear.

The tool also featured in the last National Forum for Biological Recording newsletter, with a waxcap on the cover page.

I was very grateful to receive in-depth feedback on the tool from several people including waxcap specialists Rob Foster, Jon Dunkelman (co-author of the Grassland Fungi book) and Peter Russell. Also Aideen O'Doherty, and Jim Howell from Sussex Fungus Group who provided helpful comments on their experience with the tool.

Thanks again for all the feedback - I really appreciate it.

If anyone reading this is contemplating a similar project: go for it! The Identikit toolkit is straightforward to use. And even if it doesn't work, it's a great way to learn your way around a new group of species.