eDNA is here, it's just not evenly distributed

I worked with DNA for decades (although not strictly speaking eDNA - Environmental DNA), but earlier this year a paper was published that changed my world view (Environmental DNA metabarcoding of wild flowers reveals diverse communities of terrestrial arthropods. (2019) Ecology and Evolution, 9(4), 1665-1679 https://doi.org/10.1002/ece3.4809). I am in no doubt that in a generation's time, eDNA will have changed the way biological recording works, but what I struggle to see is what this will mean for the amateur naturalist.

Consequently, I was interested to come across LifeScanner - "LifeScanner employs DNA barcoding technology to identify insects, food, fur, or any animal tissue. Find out what you're eating, what's in your garden, or in your home." As far as I can make out, the service is only available in the USA & Canada. It's not clear to me exactly what range of taxa the service covers. It doesn't do plants but I'm not clear what arthropods, if any, are covered. Leaving that aside, the price is US$40 for four tests. Would I use a service like this for difficult spiders or springtails which can only identified by their DNA? Possibly, but at 10 quid a pop, not very often.

In the UK the closest thing we currently have is the NatureMetrics Great Crested Newt eDNA service. I'm not aware of any other UK consumer-level eDNA services, but if there are any, please let me know. PCRing your newt soup will cost you £170+VAT, well worth while if you don't want your garden turned into a supermarket car park. NatureMetrics also run a citizen science eDNA project, although I can't figure out exactly what this entails. So it seems that UK arthropod consumer level eDNA on demand is still some way away, but probably not too far. After that, it's all about commoditization and price reduction. And what that will do to field and identification skills is an open question...

Christmas has come early!

On Sunday evening I was going to bed, walked into the kitchen, turned the light on and found ... something crawling across the worktop. At first I thought it was a tiny harvestman, but since that didn't make any sense (it was late!), it had to be a spider. I presumed it must be Pholcus phalangioides but I popped it in a pot and went to bed. Looking at it in the morning it turned out to be a male Psilochorus simoni, although it took me a while to convince myself of that. This species is thought to be of American origin, imported first into France and then into Britain on wine bottles. There are only two previous VC55 records, one from the wine cellar of a very grand country house. I would like to point out that my wine cellar consists of a few bottles from Sainsbury's in the understairs cupboard, and that alone is pretty good evidence that this species is increasing in frequency. The only reason we don't have more records is because it is so easily confused with Pholcus phalangioides (he wrote, without any sense of irony.... ).

Oligolophus hanseni

Oligolophus hanseni is probably not uncommon, but it is difficult to identify, being very similar to Oligolophus tridens. Identification requires either examination with a very good hand lens or a microscope to see the that the trident and associated tubercles are different. Although the trident members of both species are quite small, in Oligolophus hanseni they are normally pale and on close inspection, tipped with black spines. In Oligolophus tridens the trident tubercles can be pale, or the same colour as the body. Oligolophus tridens can have no additional tubercles to the side of the trident and as few as two behind, but in Oligolophus hanseni there are normally more than this to the side and behind. In Oligolophus tridens the two rows of tubercles on the ocularium are often neatly delineated in white, giving the impression of two white eye-rings. In Oligolophus hanseni there are white patches on the ocularium, but these don't usually give the impression of two neat eye-rings. There are only seven previous records for VC55, but in reality I suspect this is quite a common species.

Benchmarking Spider Recording

Recently, I've been thinking a lot about occupancy models for invertebrates (see: Filling the White Holes). Other taxa, notably birds and butterflies (through the BTO Wetland Bird Survey and Butterfly Conservation's UK Butterfly Monitoring Scheme (UKBMS), respectively) have good negative data, i.e. an indication of where species are absent as well as where they are present. For most invertebrate taxa, partly because of lack of resource (recording effort) but mostly because of the inefficiency of recording, all we have are "White Holes" - gaps in the data which are difficult to interpret. The BAS Spider Recording Scheme does not include "negative data" because it's virtually impossible (without DNA approaches) to be certain a spider is truly absent from a particular area. This makes occupancy models difficult if not impossible to derive. The alternative is to fall back to benchmark species as indicators of recording coverage.

Following Filling the White Holes I had an interesting online chat with Geoffrey Hall who introduced me to the idea of axiophytes (it's a botany thing). BSBI gives the following criteria for axiophytes:

• 90% restricted to these conservation habitats
• Recorded in fewer than 25% of tetrads in the county

It seems that Pliny made it up (as so many other things) in his "Natural History". As far as I can tell, neither axioentomos nor axioarachnos exist, so I've just made up two new words (take that Pliny). The point is that axiowhatevers focus attention on presence (even if it is rare presence), rather than absence, so I still tend towards the idea of using a "universal" benchmark species rather than an axiomatic one. Clearly, the choice of a benchmark species is crucial. For springtails, I am happy to use Orchesella cincta, widely acknowledged to be the commonest species of springtail in lowland Britain. I would be amazed if this species was not present in every quadrat in VC55, it's identifiable in the field with no need to put it under a microscope. For spiders it's a little more complex. The obvious choice is Araneus diadematus. While this might seems to be the most obvious choice, it's only the 4th most commonly recorded species in VC55 (n=724) with only 39% of the count of the most frequently recorded species (Tenuiphantes tenuis, n=1,849). I'm pretty sure that this does not reflect the actual situation, but rather recording bias/snobbery (of which I am probably guilty). While the ubiquity of this species is a good reason to think that this is a valid choice, I needed to test the hypothesis. As a starting point I used quadrat mapping - arbitrarily dividing VC55 into a grid and looking at the number of records within each section. A 25x25 grid worked but the the intervals were a bit small and a 10x10 grid is more informative (all VC55 Spider records to end 2018):


The grid for Araneus diadematus looks like this:


To make sense of this, I converted the distributions into histograms:


The distributions look look similar, but to be sure, I ran some further analysis:


While there is a correlation between the Araneus diadematus distribution and the overall VC55 spider records dataset and this is statistically significant (p = 4.49e-11), it's not a great fit (R² = 0.48). In contrast, when I run the same exercise on the benchmark species I use for normalizing springtail recording effort (Orchesella cincta), I get an R² value of 0.87 (p = 2.2e-16), so that's a much better fit from a dataset which is nearly ten times smaller than the VC55 spider data. So I conclude that Araneus diadematus is a valid benchmark for VC55 spider recording - but it's not a great one. If you can think of a better candidate benchmark species, please let me know.


Acknowledgements:
All data Copyright Leicestershire and Rutland Environmental Records Centre.
Data visualization performed using the R platform, v. 3.6.1 (R Core Team (2014) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org).
J. Cann for assistance with data visualization.

Rainbow Dust [Book Review]

Rainbow Dust: Three Centuries of Delight in British Butterflies
Peter Marren
Vintage, 2016
ISBN: 1784703184

Cover blurb: "Rainbow Dust explores the ways in which butterflies delight and inspire us all, naturalists and non-naturalists alike. Beginning with the author's own experience of hunting and rearing butterflies as a boy, Peter Marren considers the special place of the butterfly in art, literature, advertising and science, and, latterly, our attempts to conserve them. Rainbow Dust takes in the controversy over collecting, the women who studied them and the curious details that lead to butterflies being feared as well as loved. This is a celebration of butterflies; one shot through with a sense of wonder but also of sorrow at what we are losing."

Peter Marren is now a highly respected nature writer best known for the excellent Bugs Britannia and Chasing the Ghost: My Search for all the Wild Flowers of Britain. Although I enjoyed reading Rainbow Dust and learned a lot from it, this is very much in the old school of nature writing, and personally, I enjoyed The Moth Snowstorm more and would recommend that over this book. Nevertheless, Rainbow Dust is still a good read and I recommend it.

Catching the red eye

The glowing red eyes of Drymus brunneus staring back at me from the leaf litter at Charnwood Lodge. It's not as scary as it looks, partly because it's a trick of the light, but mostly because this 4mm long ground bug feeds on mosses and fungi.

Scorpions at Charnwood Lodge?

Neobisium carcinoides

Actually no, but there are pseudoscorpions, related to true scorpions but in a separate Order of arthropods. Like true scorpions they are venomous, but they have venom glands in their chelicerae (pincers) rather than a sting in the tail. The good news is that at only 2-3mm long, they are completely harmless to humans, although not so to the springtails, mites, nematodes and other tiny organisms on which they feed. On a recent trip to Charnwood Lodge I found abundant Neobisium carcinoides in the leaf litter at two different locations. There are more than 3,300 species of pseudoscorpion worldwide, with more being discovered on a regular basis. Most live in leaf litter, moss and soils but some live in houses, such as the Book Scorpion, Chelifer cancroides, which feeds on booklice and so helps to preserve your library!


Charnwood Lodge

Neobisium carcinoides was last recorded at Charnwood Lodge in 1968. Although this species is easily overlooked I am surprised that it has not turned up in the many invertebrate surveys which have been conducted since then. The first County record dates from Buddon Wood in 1929, and John Crocker recorded it regularly on Charnwood in the 1960s. The most recent County record is from Beacon Hill in 2017 but like so many soil arthropods, this is very much a neglected group of organisms and they are undoubtedly widesprerad across the County. Please keep your eyes open for these tiny marvels!

Filling the White Holes

I'm growing increasingly obsessed with data that isn't there... Earlier this month Dom Greaves used the phrase White Holes on Twitter:



It stuck in my mind and I haven't been able to shift it. Previously, I've used R to plot heatmaps of VC55 (Leicestershire and Rutland) spider records (all VC55 spider records (>43k) to end 2018, data copyright Leicestershire and Rutland Environmental Records Centre) (click images for larger versions):



However, the problem with heatmaps is that they inevitably focus attention on where the data is, rather than where it is missing. As an attempt to try to switch the emphasis I tried quadrat mapping - arbitrarily dividing VC55 into a grid and looking at the number of records within each section. Initially I tried a 50x50 grid but with 43,000 records, that choked my computer. A 25x25 grid worked but the the intervals were a bit small and a 10x10 grid is more informative:



Conveniently, R gives the record counts for each tile:



and plotting a histogram of the counts draws attention to how skewed the distribution of records is. Result!



The method isn't prefect. The tiles and hence the counts are of unequal area where they overlap the VC55 boundary, but I don't know how you get around that, with the possible exception that plotting the data by parish rather than by quadrat might be better?

The other place I'm currently stuck is trying to turn unstructured data into occupancy models. This is another White Hole Problem, but one that continues to defeat me.


Acknowledgements:

• All data Copyright Leicestershire and Rutland Environmental Records Centre.
• Data visualization performed using the R platform, v. 3.6.1 (R Core Team (2014) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org).
• J. Cann for assistance with data visualization.

Gnathonarium dentatum

I'm not entirely sure where I'm going with this, but here's my first attempt to combine focus stacking with HDR.

Gnathonarium dentatum.