Journal archives for May 2020

May 07, 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 the associated and adequately preserved collections. 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. Sequencing provides a more objective approach to defining species concepts, including establishing 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. On the other hand, modern sequence-based approaches often reveal multiple similar species that are sometimes impossible to distinguish even after detailed microscopic examination. The process of disentangling, refining and improving the confusing historical work is ongoing, and the modern approach does not necessarily deliver the ability to easily identify species. 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, or a denial of modern approaches to fungal taxonomy. 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 ... 

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 ( 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.


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.

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.


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

Posted on May 07, 2020 08:32 AM by cooperj cooperj | 16 comments | Leave a comment