rich burkmar's blog

Into the future: new FSC QGIS Plugin features

rich burkmar — Wed, 27 Feb 2019 11:06:26 +0000

Today we released a new version of the FSC QGIS Plugin (version 3.2.0 released 27th Februrary 2019). This feels like a real milestone for the FSC QGIS Plugin for a number of reasons. First is the sheer number of new quality features we've added, including:

ability to deal seamlessly with both British and Irish grid references;
ability to source records directly from Recorder 6 in the Biological Records tool;
a brand new tool to add British or Irish grid references, eastings/northings and lats/lons to any vector layer;
new ability of the OSGR tool to read random text containing grid references (Irish or British) from which the GRs are extracted and added to the grid squares temporary layer; and
ability to specify date/year columns in source layer in order to generate earliest and latest year columns in aggregated atlas data (which can then be used to style the layers).

There are other new features, improvements and bug fixes too. Most of the new features were added in direct response to the consultation which we carried out through this website and by direct feedback from users of the plugin at various meetings and conferences.

To find out how to use the new features, go to our online help pages and look at the pages for each tool: https://www.fscbiodiversity.uk/fsc-plugin-qgis-v3.

A second reason for the 'milestone' feeling is that another contributor, Ian Carle from the Hertfordshire Environmental Records Centre, was responsible for conceiving the idea and carrying out most of the coding for the new Recorder 6 feature. Ian has contributed code to the project before, but this is the first time we've had such a major contribution from another open source developer. It really showed us that collaborative open source development, managed through the GitHub platform, can work for the FSC QGIS Plugin.

Which brings us to the third reason for the 'milestone' tag: although I am moving from the Field Studies Council to the Biological Records Centre, I will continue to work on the FSC QGIS Plugin into the future. To formalise and facilitate this collaborative development, we've transferred the GitHub repository (the place we keep the open source code) from my personal account to the Field Studies Council's organisation account (https://github.com/FieldStudiesCouncil/QGIS-Biological-Recording-Tools). To help us manage the future development, we've taken the first steps to develop a collaborative governance structure by forming a 'steering group' for this project (and the FSC Identikit which will be treated similarly). The initial group consists of:

Rich Burkmar (BRC)
Charles Roper (FSC)
Martin Harvey (BRC)
Andy Cawthray (FSC)
Keiron Brown (FSC)
Charlie Bell (FSC)

This group will correspond informally via email etc rather than meet formally. This is in no way a 'closed' group - the project will remain open to collaborative development from anyone else and will, of course, continue to welcome suggestions from others on what direction the plugin should take in the future. So please feel free to correspond directly with any of these people if you've ideas or suggestions to make for the future of the plugin or, if you prefer, you can raise 'issues' via the GitHub platform. (Don't be mislead by the term 'issue' - you can also use GitHub issues to make suggestions or ask questions.)

I never been as excited about the future of the FSC QGIS Plugin as I am right now! QGIS continues to go from strength to strength and I hope that the new steering group for the FSC QGIS Plugin will help ensure that British and Irish biological recorders and ecologists continue to leverage the benefits of QGIS to the full!

Latest Identikit developments

rich burkmar — Thu, 20 Dec 2018 00:00:00 +0000

FSC Identikit is an open-source platform for building online ID resources, including multi-access keys, driven by spreadsheets of taxonomic/morphological knowledge.

Identikit’s roots are in FSC’s Tomorrow’s Biodiversity project (where it was called the ‘ID Framework’) but when that project completed at the end of 2017, Esmée Fairbairn agreed to fund development for a further year, enabling us to roll it forward into FSC’s BioLinks project.

2018 has been a year of intensive development of Identikit and Esmée Fairbairn’s support has enabled us to completely restructure the software ‘under the hood’ to add the capacity to deliver ID resources on mobile devices in the field – even where an internet connection is not available.

We published these ‘mobile-first’ features in November 2018 with the release of version 1.8.0 and have showcased the developments by publishing mobile-first implementations of our resources Harvestman of Britain and Ireland (https://harvestmen.fscbiodiversity.uk/) and The Conifers of Britain (https://conifers.fscbiodiversity.uk/). Other people have already taken advantages of the new features to publish mobile resources, including Nia Howells who has created a mobile-first multi-access key for British Froghoppers - https://identikit.fscbiodiversity.uk/howells/fh/m/.

The screenshots give a flavour for how the harvestmen resources look and feel in the new mobile-first implementation.

A feature of the Identikit software is that it is web-based which means that it can run on any mobile device that supports a ‘modern browser’ – we don’t have to create a version for Android, a version for Apple and so on. We’ve taken advantage of new (and developing) technologies to create a ‘Progressive Web App’ (PWA). As well as looking more like a native app than a website, once installed, a PWA can be invoked from an icon on your phones home screen – just like a standard app.

The PWA technologies enable the app to download all necessary images, knowledge-base files and so on, whilst within range of wifi and then use these in the field where no wifi or data are available.

Anyone can use FSC Identikit on their computer to develop a new ID resource just by creating a spreadsheet of taxonomic/morphological knowledge which Identikit then reads to generate the ID resources like the one shown above. No programming is required. The multi-access keys and other ID resources are driven by the content of the knowledge-base spreadsheets.

Just creating a resource for personal use can be a great learning experience that helps you get under the skin of a taxonomic group. For those who wish to take their resources further and make them available for other people to use, it isn’t complicated to publish an FSC Identikit resource on almost any website. For those without access to a hosting website, we may well be able to host their resources on our FSC Biodiversity projects website (as we did for Nia Howell's Froghopper key referred to above).

If you want to keep abreast of developments with FSC Identikit, the best way is to sign up to our dedicated Identikit email newsletter here: https://www.biodiversity.uk/identikit-signup. We've just published a new edition of the newsletter which discusses, amongst other things, features planned for the next release of the software.

If you just want to get started right away, then look here: /use-fsc-identikit-create-new-id-resources

To explore some resources created with Identikit, look here: /id-resources-built-fsc-identikit

As an important element of FSC BioLink’s digital outputs, FSC development and support for Identikit is planned until the end of 2022. We know of some exciting new ID resources being built by people using the FSC Identikit. We very much hope and expect that many more will become available over the course of the BioLinks project.

QGIS - is there something missing?

rich burkmar — Tue, 22 May 2018 08:46:53 +0000

If you are unfamiliar with QGIS and/or the FSC QGIS plugin, read on! But if you are familiar with them and eager to discuss your own ideas about what's missing in QGIS for UK biological recorders, skip to the end!

QGIS and biological recorders

At the recent NFBR conference at Preston Montford, Shropshire - a conference aimed squarely at biological recorders - I was surprised how many attendees, particularly those of younger generations, considered GIS to be central to their biological recording skillset. I'm really the last person that should be surprised by this - I can't imagine pursuing my own interest in biological recording without tools to spatially represent and analyse biological records - but many biological recorders of my generation pursue fulfilling interests in biological recording without going near GIS - that's something they leave for other people.

This generational shift must be influenced by a number of things, for example it is likely that a higher proportion of younger biological recorders want to pursue related careers where GIS skills are highly sought-after. Another influence must be the increasing exposure of younger generations to all sorts of digital technology, including GIS, from an early age and the increasing accessibility of high-quality GIS tools. Over recent years, QGIS has been a real game-changer in respect of making high-quality GIS more accessible. QGIS started life over 15 years ago and has since become the world's leading open-source desktop GIS. It started life as 'Quantum GIS' but the 'Quantum' part has officially been dropped in favour of a simple enigmatic 'Q'! Like scientific names, it doesn't really matter how you pronounce QGIS, as long as you say it with confidence! (Personally I favour 'kew-jiss'.)

The FSC QGIS plugin

Not only is QGIS freely available, but it supports a wide range of operating systems including Windows, Mac OS X, Linux and Unix. There is also an Android version under development. This means that choice of hardware and operating system is unlikely to restrict access to QGIS. One of the best features of QGIS is its extensibility: it is possible for any programmer with the requisite skills to contribute a QGIS 'plugin' that extends the functionality of QGIS to carry out particular tasks more efficiently. That's exactly what we did when we created the 'FSC TomBio QGIS plugin' for biological recorders as part of the FSC's Tomorrow's Biodiversity project.

The plugin plugs the gaps (pun intended) in QGIS when it comes to dealing with biological records - particularly those geocoded with Ordnance Survey grid references - as well as providing a number of other utilities for UK biological recorders, e.g. easy access to NBN Atlas data from within QGIS. The plugin has proved popular with over 25,000 downloads since its release in November 2014. The last release for version 2 of QGIS (version 2.8.0 of the plugin) has had over 4,700 downloads and our recent new release for version 3 of QGIS (version 3.0.0 of the plugin) has been downloaded over 300 times. The plugin was the winner of the 2017 CIEEM 'Best Practice Award for Knowledge Sharing'.

What other QGIS gaps could the FSC QGIS plugin fill?

When the FSC Tomorrow's Biodiversity project came to an end, we were thrilled to be able to roll our support for the plugin forward into the new FSC BioLinks project. This means that FSC will support the maintenance and development of the plugin until, at least, the end of 2022. The release of version 3.0.0 of the plugin was an early result of its adoption by the FSC BioLinks project, requiring major reworking to accommodate the new architecture of QGIS 3. The FSC QGIS Plugin was amongst the first to be 'ported' to QGIS version 3. But support from BioLinks will mean much more than simple maintenance of the current toolset.

We want to hear your ideas about what functionality you would like us to add to the plugin. For example one idea is to provide a direct link to MapMate so that records can be mapped directly from a local MapMate database without having to extract them first. But what would you like to see? We're interested in hearing your ideas - however simple or outlandish! We've created a short online consultation where you can give us feedback on which of the current tools in the plugin you find most useful; what works and what doesn't and what new features, if any, you'd like to see.

To have your say, participate in the short online consultation here: BioLinks FSC QGIS Plugin consultation. (The consultation was closed on 13th Feb 2019.)

The more responses we get, the more likely it is that the next phase of development of the plugin will meet the needs of our biological recording community, so please pass the link on to anyone that you believe might be interested in expressing their ideas and opinions. Here's to the next five years of the FSC QGIS plugin!

Want to know more about QGIS?

FSC offers a range of training courses in QGIS that provide a holistic and practical approach to using these tools for biological recording. More details on upcoming QGIS courses, along with courses to improve your surveying, mapping and recording skills, can be found on the FSC website.

Putting the invertebrates in order

rich burkmar — Thu, 05 Apr 2018 18:32:56 +0000

Guest blog by Siiri Hubbard and Nigel Kelly

Melville Louis Kossuth Dewey (1851-1931), was an American librarian, entrepreneur, womaniser, spelling reformer and inventor of a decimal-based system for the organisation of knowledge in libraries. He divided all knowledge into ten broad subject areas, such as science 500-599; divided each of those areas into ten, such as animals 590-599; divided each of those into ten, such as 598 birds; and so on, such as 598.9 raptors. Whether it’s books, reports or cdROMs, you can assign them a Dewey number, and all the items on similar subjects in your library and its catalogue come together. As the meerkat (599.742) says, “simples”.

Siiri, a member of FSC staff and a librarian from Estonia, and her librarian husband Nigel, worked on the Preston Montford Library during 2016. Much of it was already Deweyfied, albeit inconsistently. Our work was to clean up the past catalogue and the stock as much as possible. This meant far more than changing some Dewey numbers. The catalogue’s listing of titles, authors, editions and copies contained many errors and inconsistencies. As in all libraries, some items had gone missing over the years. Some had been updated by newer editions, and some were just disintegrating. 2,501 titles were catalogued electronically to international standards, and the catalogue is now available to all at Preston Montford. Whether looking for something on flood management, bryophytes or mustelids, you have a good chance of finding it in the library.

This year we returned to catalogue the Invertebrate Challenge Collection in the Wenlock building. This had not been fully catalogued, and being research-based, was more specialised than much of the Library collection. Part of the librarian’s skill is to know a little about a lot, so we gradually began to understand the differences between the odonata (595.733), trichoptera (595.745) and coleoptera (595.76). At 595.77, the impressively numerous types of diptera left us in awe of nature’s fecundity and ability to find adaptive niches. As non-biologists, we discovered the splendidly-named pseudo-scorpion (what is natural selection doing there?) and the broad-nosed weevil, and the privilege of being allowed by a volunteer researcher to view of the hairs and hooks on a springtail’s legs down a microscope.

The taxonomic reassignment of organisms is reflected by newer versions of the Dewey scheme. Thus the annelids have been moved from 595 to join the simpler invertebrates at 592. Protozoa, no longer being considered animals, have moved from 593 to 579, a home for refugees exiled from botany and zoology. To retain consistency with older items in the main library, we retained use of the older numbers; finding items on the same subject together is more important than taxonomic niceties. We also detected the possible bias of biologists to more attractive species: books and reports abounded on butterflies, caddis flies and snails, but there was little on fleas, mites, dung beetles or slugs.

The Collection contains a shelf of books by and about the great French entomologist, Jean-Henri Fabre (1823-1915). These are bound in the cloth covers of the time, many inlaid with their titles and illustrations of their content picked out in gold. The heat-taped and spiral-bound, paper scientific reports of more recent times seem flimsy and ephemeral in comparison.

The Invertebrate Collection has just over 400 titles. Its strength lies in being focused on invertebrates, and particularly insects. It has a greater proportion of more recent material than the main library. The main library has relied considerably on donation, and therefore reflects the enthusiasms and specialisms of donaters as much as systematic coverage of field studies. The Collection also has multiple copies of the FSC and similar core guides, suitable for use in courses. Collection items are in green in the catalogue.

So what is the value of a traditional library today to an organisation such as the Field Studies Council? Can past and present media be integrated in a useful way? Fundamentally, libraries and information storage are about users: you. Shelves of fine old books look nice, and we can feel warm and nostalgic about them, but if they are hardly ever used, we must ask why are we keeping them? They are taking up space and resources that might be better used. Whilst they contain timeless material (think of the New Naturalist series from the 1950-60s), they also include outdated information.

Electronic media have currency, immediate and remote accessibility, and easy portability into teaching and other documents. Serials (periodicals) and scientific reports are now frequently only available in electronic format. Yet, we became very aware of the wealth of engaging material to be found among the older items, and older can be right up to the 2000s. In addition, far from all material is published electronically even now, particularly small-scale but important, localised research. Electronic media are becoming ever more astounding and flexible, but just remember how frustrating it can be on a field trip to find you have a flat battery or no mobile signal. Then the durable, waterproofed FSC mini-guides really come into their own!

The newly revised catalogue can contribute to integrating older and newer resources: we have ensured that book and report titles are given more fully and precisely, helping you to spot the potentially useful item. Whilst course teaching and focused research inevitably lead to purposive literature searching, there is still a role for browsing catalogues and along library shelves. Thanks to Dewey, material on quite specific subjects from over a hundred years of publishing is brought together to inspire and compare. Centre staff and users need to find the time to explore the shelves. You can of course borrow items to read at leisure.

We followed up our work at Preston Montford by spending two weeks in March cataloguing the library collections at Malham Tarn Centre. The Centre had no useable previous catalogue, so we were able to create a clean and clear new one, that incorporated the library, serial and education office collections. We used the Preston Montford catalogue as a base, to ease our task within the tight time schedule. There was some common material, but more than a half of the 1,137 titles were unique to Malham Tarn. This hints that networking FSC library catalogues could prove valuable, making staff aware of items across the whole organisation.

The view from the library windows over the Tarn was seductive, as light played across the water and surrounding limestone hillsides. Our visit coincided with the mini-Beast-from-the-East, bringing more than two days of continuous blizzards, forcing snow between window frames and making the fireplace howl. The serials are kept in the Paul Holmes Room (think exclusive London club). The finely bound volumes dating back to 1837 share the glass-fronted shelves with the bar supplies, leading to a unique conjunction of real ale and the Yorkshire bird report.

The prize item was a copy of Darwin’s final book, The formation of vegetable mould through the action of worms, and observations on their habits (1881). Maybe this book was justification for the retention of some older FSC library items. Even though Darwin was tired and in pain whilst writing it, the prose is clear and surprisingly modern. Earthworms are fascinating and biologically important, and he is really keen to convey this to a general, as well as a scientific audience.

Editor's note: the spreadsheet cataloguing the libraries resources can be browsed below or downloaded here.

Book review: Britain's Spiders - a field guide

rich burkmar — Thu, 29 Jun 2017 14:31:44 +0000

Britain’s Spiders – A field guide by Lawrence Bee, Geoff Oxford and Helen Smith is a new book from the excellent WILDGuides stable, published in association with the British Arachnological Society. This book will likely fuel a revolution in spider identification in the UK that I believe is already underway. In this blog I will review the new book, but more than that I want to describe what it offers within the context of how people are learning spider identification and recording skills today.

Like many before me, I started to learn spider identification by attending a couple of Field Studies Council courses back in 2006. They were excellent courses and really kick-started the development of my spider ID skills. In common with most spider identification courses running at that time, we dived straight into microscopic identification and our field visits concentrated on collecting adult spiders for preservation and identification back at the ‘lab’; we hardly did any field ID.

A few years later I was confident that I could identify the vast majority of specimens that came my way with the aid of my microscope and the excellent literature available (mainly the three volume Spiders of Great Britain and Ireland by Michael Roberts). But while helping out at a couple of BioBlitzes, I became painfully aware of a considerable gap in my identification skills; some species whose genitalia I knew intimately remained a mystery to me in the field! It was a real barrier to illustrating the diversity of form, biology and ecology of living animals and inspiring budding spider enthusiasts.

I felt sure that I should be able to go progress further with identification in the field and that even where spiders couldn’t be identified to species – as I knew would most often be the case – it should nearly always be possible to identify them to family level and frequently to genus too.

I addressed the gap in my knowledge by making a deliberate effort to go as far with ID in the field as I could and reinforced this by looking at lots of images, particularly on iSpot and the Facebook group now known as the British Spider Identification Group created by Jenni Louise Cox. I obtained a copy of the out-of-print Country Life guide to spiders of Britain and northern Europe by Dick Jones and read it from cover to cover. The latter gave really useful ID tips for living spiders, but the really transformative feature of all of these resources was the photography.

I’m a big fan of artwork in field-guides, e.g. for groups like birds, moths and dragonflies, where I think well-executed paintings frequently capture the essence of the living animals and encompass a degree of natural variation that is harder to illustrate with photographs. But the superb spider illustrations by Roberts never attempted to capture the essence of a living spider – indeed they deliberately illustrate preserved specimens since they were designed to facilitate identification of such – and for my money photographs of spiders are a much better tool for illustrating these animals as they appear in the field.

Today I manage the Field Studies Council’s Tomorrow’s Biodiversity Project and one of our ‘exemplar projects’ within this involves working with Nigel Cane-Honeysett of the Shropshire Spider Group to develop a suite of integrated spider ID courses that cater for different levels and requirements. We differentiate four different types of training:

Engagement (we badge these day courses as ‘Learn to Love Spiders’) where we concentrate on discovering the wonder of spiders and try to avoid too much technical talk and ID per se.
Field ID of Spiders (and harvestmen) where we tackle ID in earnest but strictly with living spiders both in the field (using spi-pots and hand lenses) and in the classroom (using digital microscopes and captured live spiders). Upcoming course: Aug 9th, Bishops Wood, Worcs
Spider ID with Microscopes which is more like the ‘traditional’ ID course where we work with preserved specimens in the classroom and introduce the idea of definitive ID by examination of reproductive organs and other microscopic features. Upcoming course: Sept 6th, Preston Montford, Shropshire
A variety of events/courses for ‘experts’.

These courses link together well and, for those that want it, they provide a path to progress ID skills from zero to the highest level at their own pace. But equally we recognise that different people like to take their learning in different directions – whilst some want to develop the skills to be able to identify any preserved specimen, others prefer to go as far as they can with the living animals only.

In our experience, more and more people count themselves in the latter category and our field ID courses are amongst our most popular. I believe that this is fuelled by a number of factors including:

Incredible advances in the quality and accessibility of digital macro photography equipment.
The popularity of social media platforms that have helped leverage the power of digital photography as an ID tool.
A growing recognition amongst the established natural history and recording community that quality macro photography is opening up some taxa to reliable field ID where previously microscopic examination of preserved specimens was the norm.
A growing trend to record across several taxonomic groups in the field.
A cultural shift resulting in fewer new naturalists being willing to collect specimens for ID.

Some worry that this change may represent a threat to the ongoing development of a vital pool of people with skills in microscopic ID and the collection and curation of spiders. I don’t see it that way; I believe that in the past many people were alienated from spider recording and ID because even introductory courses started at the level of collection, curation and microscopic ID. With a more structured development path and opportunities to make a valuable contribution to spider recording at different levels, including field ID only, we stand to retain more of that early interest. Some of those who start with the intention of only recording spiders in the field may become sufficiently absorbed to move on to collection, curation and microscopic ID. Those who don’t can continue to make a valuable contribution with field ID alone.

All of which brings me to the new WILDGuide – Britain’s Spiders. For a couple of years at our field ID courses Nigel and I have introduced participants to the available literature including Roberts’ Collins field guide, the FSC fold-out chart and Dick Jones’ Country Life guide, but we’ve always concluded by whetting everyone’s appetite for the upcoming WILDGuide! We’ve waited for several years with such great anticipation that it would have been easy for the final product to fall short of our expectations, but I can happily report that it does the opposite!

First impressions are those of size and quality. It is a surprisingly large book, but it just about manages to stay small enough to be convenient for a keen learner to take into the field. It is not a hardback, but neither is it a ‘flimsy’ paperback – the cover is something in-between with folded edges (both front and back) that can be used to mark pages if required. The binding is that of a high-quality hardcover (case bound), which makes it surprisingly easy to open any page in this thick book (480 pages) and have it lay pretty flat. The production values scream quality and it is a real credit to the WILDGuides series and attention to detail by the authors and whole publishing team.

There are excellent introductory sections on anatomy, biology & ecology, spiders & people, finding spiders – all well worth careful reading. An excellent section called a ‘Guide to spider families based on appearance’ does what it says on the tin. This is a really useful section for teaching field ID to beginners since a newcomer really feels that they have started to make progress when they can start to recognise broad groups of spiders (i.e. families) based on some features of their appearance and other clues like web structure and behaviour. (Though identification based on web structure is largely covered in separate sections in the book – see below.)

Next there are a couple of really useful sections - a ‘Guide to webs’ and a ‘Guide to egg-sacs’. When one really starts to look at spiders in the field, their webs and egg sacs become central to your observations. During both our engagement and field ID courses, we talk a lot about silk and, in particular, webs (or absence thereof); not only as useful identification features but also for what they tell us about the fascinating biology and ecology of the different groups. So I was really pleased to see these dedicated sections.

A minor criticism is that I feel the excellent information on web ‘taxonomy’ is unnecessarily split between a sub-section of spider biology (‘Webs’) and the ‘Guide to webs’ section. I think I understand why this has been done – webs can hardly be ignored in the ‘Spider biology’ section but they also deserve a section of their own. However I would prefer to see a much more cursory treatment in the ‘Spider biology’ section with a reference to an enhanced ‘Guide to webs’ section with all the important information in one place. The real problem is that both these sections (well-separated in the book) include a taxonomy of web types, but they are not entirely consistent. The ‘Webs’ sub-section (of the ‘Spider biology’ section) states that ‘webs can be classified approximately into eight broad types’ but only describes six plus ‘other web types’. The ‘Guide to webs’ section covers nine types. Regardless of these criticisms, the two sections are excellently produced with first class information and illustrations.

The central piece of the book is, of course, the species accounts. They are first class and the attention to detail is amazing. Somehow squeezed into each account, yet without appearing cramped, is information on scientific name, common name, observation tips, habitat, size, appearance, similar species, distribution, phenology, status and ease of identification. Furthermore each family, and within that each genus, is introduced separately with useful identification features (covering appearance, behaviour, webs etc). The species accounts (and the rest of the book) are superbly illustrated with hundreds of high-quality images, contributed for the most part by hundreds of amateur photographers, which are intelligently and attractively laid out.

There is a very clear double-page spread explaining how to use and interpret the information accounts. This is compulsory reading – no one should expect to be able to interpret the species accounts correctly without reading this first (and probably continually referring to it until it all becomes second-nature). For example, following the phenology chart for each sex of each species is a coloured dot which indicates the number of records from which the information is drawn (and hence it’s reliability), but unless the reader has referred to the explanation of the species accounts, it will mean nothing. It is this very careful planning and thoughtful layout of the species accounts that has enabled so much information to be presented so succinctly. Given the importance of information on interpreting the species accounts and the frequency with which it will need to be referred to by new users of the book, it would benefit from some way of making it easier to find, for example reproducing it on the front or back endpapers.

One of the most eagerly anticipated features of the book is the information on how far it is possible to identify a species (or genus) in the field. Three symbols are consistently used throughout the book: an eye – meaning the spider ‘can be identified in the field (with experience), usually without capture’; a hand lens – meaning the spider ‘can be identified in the field but needs careful, close examination requiring temporary capture, usually a spi-pot and hand lens’; and a microscope – meaning the spider ‘requires examination and high magnification in good light of features that are beyond the scope of this book’.

Traditionally, the British Arachnological Society’s (BAS) Spider Recording Scheme (SRS) has been rather conservative, only routinely accepting records for twenty or so species identified in the field. This conservatism is an effective defence against too many poorly determined records, not backed up with sufficient evidence, finding their way into the SRS, but it has also been a barrier for participation in spider recording for many people.

The so called ‘Chinery Effect’ – whereby users of field guides merely picture-match specimens against illustrations in the book and submit records of the best match without critical regard to whether or not there are similar species which cannot be determined by eye – was a real danger with the spider field ID resources we’ve had at our disposal to date. But this new WILDGuide, when used correctly, allows the diligent user to avoid the Chinery Effect – effectively informing them just how far, with experience, they can go with reliable identification without collecting and preserving a specimen. I hope that this might now encourage the SRS to open up for more species that can be recorded with care in the field. (An online recording sheet could require recorders to indicate how they determined the spider and discounted similar species. This information could be used for verification purposes.)

Which of the three levels (eye, lens, microscope) to assign to each species was a critical task for the authors: being too conservative risked disappointing recorders who know that it is possible to securely identify more species in the field than has been openly acknowledged to date, but being too permissive risked encouraging recording of species without sufficiently critical determination. I think that the authors got the balance right. If anything, they have erred on the conservative side; for example it is possible to determine male Metellina spp. in the field with lens and spi-pot (using palps and hairs on tarsus/metatarsus I), but the book indicates that the three Metellina species require microscopic examination (irrespective of sex). In truth space considerations probably prevented the inclusion of these kinds of finer points of field identification and given this, it was right to err on the conservative side.

All-told, the book indicates that 34 species are identifiable in the field, with practice, without capture and a further 92 are identifiable in the field, with practice, if captured and examined carefully in a spi-pot. I stress the words ‘with practice’ since, just like bird or moth ID, beginners should not expect to be able to identify all of these as soon as they start; it may take years of practice to sharpen the eye and appreciate the subtle, but very real, differences between some species.

Where the hand-lens symbol is used, it would be useful to have an explicit indication of what should be looked for with the lens. I suspect that it may currently often be used to indicate that more caution and circumspection is required when looking at all the morphological features described, but this should be made clear.

The book keeps on giving! After the species accounts come additional useful sections on working in the field, recording spiders, legislation & conservation, further reading and the BAS. There is a large table listing all British species (including the small money spiders – Linyphiids – which aren’t included in the species accounts), with full details on common and scientific name (including the ‘authority’ and synonyms), the ID difficulty symbol, conservation status, relevant legislation and the percentage of 10 km squares in Britain where the species has been recorded. There is also a page reference to the species account where applicable. It’s handy to have this information together in a single reference table.

The WILDGuide, Britains Spiders – a field guide, is a masterful example of a modern field guide for an invertebrate group. It is set to become a central resource for our field ID courses in Shropshire; I have already purchased three classroom copies for the Tomorrow’s Biodiversity/Shropshire Spider Group courses as well as the Kindle version for a laptop which we intend to use by projection in the classroom. This book will equip spider recorders to learn both the possibilities and the limitations of identifying British spiders in the field. It stands to enrich the way we learn about spider identification and provide a useful staging point for those that want to move on to the identification of preserved specimens. I commend this book to all those interested in recording British spiders in the field.

QGIS tips - building a map background

rich burkmar — Thu, 10 Nov 2016 10:04:23 +0000

I had a query today from someone who wants to use QGIS to show distribution maps of butterflies and moths for the Dordogne in France. His question was about presenting a detailed background. Sourcing and creating map layers to build good looking backgrounds for distribution maps is probably one of the major hurdles for biological recorders wishing to use GIS to create distribution maps. To help answer his question I had a go at it myself and I thought it worth sharing what I found.

For an area like the Dordogne, some of the freely available maps built on the OpenStreetMap (OSM) data would probably be suitable for static maps (i.e. non-interactive maps). Several nicely themed OSM maps can be very easily viewed within QGIS where they are accessible as Web Mapping Services (WMS) via a number of plugins - the one I use is QuickMapServices (with the 'contributed pack' installed).

Using one of these themes I had a quick look at the Dordogne area (after finding out where it was!) and, as you can see, that there is sufficient detail to provide useful context as background to a distribution atlas map. One of the great things about these OSM maps is that the licensing is very open (https://opendatacommons.org/licenses/odbl/summary/) meaning that you can freely publish any maps you create from them, virtually without restriction. The OSM map shown above is from the 'OSM TF Landscape' theme available from QuickMapServices.

The most difficult task would to source a vector layer that described the boundary of the Dordogne region - what they call a 'department' in France (Dordogne is department 24). Being unfamiliar with French geospatial data and sources for it (as well as the language) I had to do a bit of trawling around, but I eventually found a vector dataset, downloadable as a Shapefile, that described all the small administrative areas of France known as 'communes' - all 35,000 plus of them.

And the great thing about this vector layer is its attributes - there are a good number including one, 'NOM_DEPT' which had the name of the department to which each commune belonged. So I was able to use QGIS' 'Select features using an expression' feature to select all the regions that belonged to the Dordogne (see map above). Then I saved the selected features to a new layer and used the vector processing tool 'Dissolve' on this layer to create a new layer representing then region of Dordogne. This is shown on the map below, styled to remove the 'fill' removed and showing a slightly thicker black line for the boundary.

Now I could see the OSM background in relation to the boundary of the Dordogne, I tried one or two other OSM map themes from the QuickMap tool and I decided that I preferred the OSM theme 'Wikimedia map' which is shown below.

There are a couple of final touches I wanted to make to this atlas map background. The first is to 'fade out' the map background surrounding the Dordogne. I did this by creating a new vector layer of polygon topology, setting my 'advanced snapping options' to 'avoid intersections' for both the Dordogne layer and this new mask layer. Then I zoomed the map out a bit and digitised a very large rectangle over a wide area around the Dordogne. When I completed the capture with a right-click of the mouse, QGIS 'cookie-cut' a Dordogne-shaped hole from the middle of my mask layer (because I had specified 'avoid intersections'). Note that for this to work, both layers have to use the same CRS. My Dordogne layer had the CRS 'RGF93 / Lambert-93' since that is what the original Commune shapefile used. So I needed to make sure that when I created the mask layer, I specified this as the CRS.

By styling the mask layer so that it has a white, semi-transparent background I'm able to 'fade out' the background map outside of the immediate area of interest. By adjusting the transparency, I can have this as strong or as faded as I like.

Finally I wanted to put a coarse 10 km grid over the map. This is where some careful thought is required. It's easy in the UK since we almost always work to the British National Grid, but in other parts of the world there may be more than one option. Despite the fact that the vector maps have the internal CRS of 'RGF93 / Lambert-93' I actually chose to re-project the maps shown above with 'WGS 84 / Pseudo Mercator' in the QGIS map view since the OSM raster data displays best with this projection.

But the grid needs to be created using the same projection as the atlas project is using in order to give the correct frame of reference for the atlas maps. Assuming the atlas project is to be created for the CRS 'RGF93 / Lambert-93', we first need to set the map view CRS to the same value if we want to create the grid using the Tom.bio OSGR tools. Then we can set the precision drop-down to 'user specified' and set the grid size to '10000' (see illustration on the right). Note that the grid size is in map units and the map units for both 'RGF93 / Lambert-93' and 'WGS 84 / Pseudo Mercator' is metres. Then all that remains is to select the Dordogne polygon and click the button to automatically generate grid squares overlapping the selected feature. The resulting grid is shown below (with the map projected with 'RGF93 / Lambert-93').

Note the slight loss of definition with the OSM backdrop when it is re-projected to a CRS other than 'WGS 84 / Pseudo Mercator'. There are two possible ways to overcome this if it is considered a problem - either source a version of the OSM mapping (or some other backdrop) that works better with this projection (for example you could get vector OSM shapefiles for this region here: http://download.geofabrik.de/europe/france/aquitaine.html) or, once the grid (and atlas maps) are created, project the QGIS map view at 'WGS 84 / Pseudo Mercator' again as shown below. Note how, once re-projected, the grid (and any atlas maps) will be 'bent' to match the map view projection.

Want to know more about QGIS?

Journeys through Inner Space

rich burkmar — Mon, 01 Feb 2016 18:24:10 +0000

Some of the most memorable media images of 2015 came from NASA's New Horizons mission to Pluto. Although the images of Pluto were spectacular, those that really stuck in my memory were those of the scientists themselves as they watched the images appear on their monitors, beamed back to earth by New Horizons over 3 billion miles of intervening space. The looks on their faces speak volumes. New Horizons launched in 2006 and I suppose that many of those scientists must have been anticipating these pictures for the intervening 9 years - wondering and imagining what they would see. But our imaginations can never do justice to the wonders of the universe; you can see it in their faces.

Just before Christmas I was corresponding by email with a couple of friends and former colleagues from my time in Merseyside; Ben Deed, who I worked with at Merseyside BioBank LERC, and Thom Dallimore, who I first met through the Lancashire Wildlife Trust. Our common interest, and the subject of our correspondence, was springtails - Collembola.

Ben now runs Merseyside BioBank and Thom is a PhD student at the Biosciences department at Edge Hill University and together they have been kicking ideas around for a while about invigorating Springtail recording in Lancashire. Meanwhile in Shropshire, Charlie and I have been working with Pete Boardman (formerly of FSC and now an invertebrate specialist with Natural England's Field Unit) to get a new Shropshire Springtail Atlas project off the ground. Thom, Ben and I all live in Lancashire and we agreed that it would be a great idea for the three of us to get together before Christmas for a bit of a social and a chat about Springtails and ways in which we might work together. Thom dropped this little nugget into one of his emails:

If you guys head over this way, I could show you the Scanning Electron Microscope in action. It gets the imagination going that’s for sure.

Well that was a done deal then. Neither Ben or I had ever seen a Scanning Electron Microscope (SEM) in action. On the day in question, Ben and I arrived at the Biosciences department at Edge Hill in the evening. Most of the staff had gone home but Thom was there to meet us. During our visit, he showed us around some of the facilities of the Biosciences department which were amazing; it's clear that Biosciences at Edge Hill is going places, but he wasted little time before taking us to see his pride and joy - the SEM!

I had imagined that preparing a sample to view under the SEM would be a time-consuming and fiddly job. I thought that Thom would say "here's one I prepared earlier". But instead he went to a cabinet where he stores some of his samples, whipped out a random springtail (which turned out to be Orchesella villosa) and in less than 5 minutes he had it ready to be viewed in the SEM. The preparation simply involved mounting it on a little stage and then using an amazing machine to coat it in gold which took only a couple of minutes. The resulting gold coating on our little Orchesella villosa was just a few nanometres thick and would enable the SEM to resolve the most minute topographic details.

Once in the SEM, the image of our springtail quickly materialised on the screen in front of us. For me and Ben, it was our Pluto moment; the first of many. As Ben and I looked at the springtail on our monitor, it was hard to shake the impression that we were looking at a static image rather than a live one; so that as Thom kept zooming in closer and closer still, our brains expected the image the pixelate - as it would if we were viewing a static image on a computer. But Thom zoomed in and the image didn't pixelate. He zoomed again - still no pixelation. And so it went on, crystal clear detail upon detail; hairs upon hairs upon hairs.

Thom - the intrepid pilot of the SEM, our inner space probe - took us on a roller-coaster ride around the springtail, over mountains that were, in fact, individual occelli, and into valleys that were no more than wrinkles in its cuticle. The surface of the cuticle of our springtail was as strange to my eyes as the surface of Pluto was to the NASA scientists (see the banner image). We saw minute structures, that we had struggled to see at all with the most powerful optical microscopes available to us, filling the whole monitor. And then we would zoom in again and see stuff that was beyond our imagining.

Thom was right, it did get the imagination going and over a pint in the pub we bounced around many ideas about recording springtails which fed and grew on the excitement that had been generated by that SEM.

When I was first getting into spiders, one of the things which I loved about them - particularly the tiny money spiders - was that people see them all the time and yet they never really see them. But if you put these tiny money spiders under a microscope they start to resolve into their 200+ species - sometimes in spectacular and fantastic fashion. Pete Boardman has said that despite many years studying invertebrates he has had to learn to look differently - at a different scale - to even see many of the species of springtail which now fascinate him.

I don't know what you call the space that resolves itself when you look extremely carefully at tiny things and when your imagination starts to operate at a different scale, filling your mind with universes that are microns across. I want to call it near space, but apparently that's reserved for the "stratosphere, mesosphere, and the lower thermosphere". Perhaps inner space will do and although one definition has this as "the region between the earth and outer space, or below the surface of the sea", another has it as "the part of the mind not normally accessible to consciousness". That'll do.

Further information

For more information on the Tom.bio project, visit the Tom.bio homepage. Details of Tom.bio invertebrate ID events can be found on our training calendar. For more information on other FSC natural history courses, check out our 2016 FSC field courses.

Embracing uncertainty: version 2 of the earthworm multi-access key

rich burkmar — Tue, 19 Jan 2016 14:39:46 +0000

When I identify earthworms (a hobby that I find increasingly compelling!) my main identification resource is the knowledge-base developed by Emma Sherlock for her excellent FSC ADIGAP publication - Key to the earthworms of UK and Ireland. But my first point of access to that knowledge-base isn't the book itself, it's the Tomorrow's Biodiversity multi-access key.

I like to use the multi-access key because it lets me home straight in on the features that grab my attention on any earthworm I'm trying to identify and puts me in charge of the identification process. I find it more empowering than using a dichotomous key and I think that it is speeding up the rate at which I am assimilating the knowledge of earthworm morphology. However, I always have the AIDGAP key close to hand - it's invaluable for confirming identifications or for trying to sort out identification when the observed features don't quite match the knowledge-base.

But after using version 1 of the key for a while, I noticed that it was weakest (like any key) when the features on the earthworm I was trying to identify didn't seem to match the knowledge-base that well. This could happen for a number of reasons. For example sometimes the segment before the segment on which the clitellum (saddle) starts can be intermediate in appearance between the segments that come before it and those on the clitellum itself. Depending on how similar it is to those on the clitellum, it can be hard to say whether or not such a segment should actually be counted as the first clitellum segment.

In the first version of the key, if I indicated that the the clitellum for a tanylobic earthworm started on segment 25, then all earthworms that were not tanylobic with their clitellum start range encompassing the value of 25 would be shifted to the 'excluded' column as shown in the picture below.

The trouble with version 1 of the key is that it considers all species not matching a particular character as 'equally wrong' for that character. But if we specify 25 for the clitellum start, is a species for which the minimum clitellum start character is 26 'equally wrong' as a species for which the minimum clitellum start character is 33? Clearly not: the first species is much more likely to be a match than the second when we account for the kinds of problems we've already discussed in interpreting characters like these (as well as other things like natural variation in morphology).

Version 2 of the key, which we have recently published, radically changes the matching algorithms used to decided whether or not an earthworm is moved to the 'excluded' column and also how the earthworms are ranked (arranged from top to bottom) to indicate how far they are from matching the specified taxa. The outward appearance of the key has changed very little, but the changes to matching and ranking have resulted in a much more useful and information-rich key.

The image below shows version 2 of the key with the same character specification as before, i.e. a tanylobic worm with the clitellum starting on segment 25, but you can see significant changes in the way the earthworms are arranged in the two columns.

The first difference you notice is that although Allolobophoridella eiseni is still at the top of the 'matching' column, the species Lumbricus rubellus and Lumbricus castaneus are now shown just below it instead of being pushed into the 'excluded' column. Eagle-eyed readers will also have noticed that the 'matching' and 'excluded' columns have also changed their names from 'candidate taxa' to 'possible species' and 'excluded taxa' to 'unlikely species' respectively - partly to reflect the idea that the new matching and ranking methods embrace uncertainty. This alerts us to the possibility that Lumbricus rubellus and Lumbricus castaneus might be possible matches if we are not sure of the clitellum start character. For the specified user input, these are the next most likely matches according to the knowledge-base. But if you look for these species in the figure showing version 1 of the key, it is not obvious that these two species are quite close matches. This is why version 2 is such an improvement over version 1.

That the species Lumbricus rubellus and Lumbricus castaneus are not relegated to the 'possible species' column reflects the fact that a 'tolerance' of two segments difference has been specified for any of the segment-based characters (accessed from the new 'Options' button which you can see in the image above). The bold number to the right of the species names indicates the total disagreement between all specified segment characters and the numbers in the knowledge-base for each species. 'Possible species' are always ranked, from top to bottom, in descending order for this number. 'Unlikely species' are ranked first according to how well they match the two categorical characters - 'head type' and 'setae spacing' - since these characters are considered to be the least variable. After that, they are ranked according to the total disagreement between the segment characters.

Another change in version two of the key is that no earthworm is ever moved to the 'unlikely species' on the basis of either the 'length' or 'diameter' characters - which reflects their extreme variability. The image below is from version 1 of the key where the only characters specified is 'length' at 10 mm. On the basis of this, all the earthworms except two species have been discounted.

An image from version 2 of the key is shown below. The arrangement of the species is radically different. None of the earthworms have been excluded based on the character, but the difference between their length ranges in the knowledge-based and the specified length of 10 mm has been used to rank them.

In version 1 of the key, the coloured indicators for specified characters were coloured either blue for species that matched or red for species that didn't. In version 2 of the key, the colours for segment and size characters show variations between blue and red depending on how different they are from the specified values. Colours for the two categorical characters - 'head shape' and 'setae spacing' - are still either blue or red.

Because the two categorical characters are considered to be the most reliable, they are positioned first in the list of characters (this has meant moving 'setae spacing' higher up the list of characters compared to version 1). Any earthworm that isn't a match for either of these categorical characters, if they are specified, are moved into the 'unlikely species' - no half measures. So if there's any doubt about either one of these characters, it's best not to specify a value for it.

In summary, the sorting and ranking for version 2 can be summarised thus:

A disagreement between a specified categorical character and any earthworm results in the earthworm being moved to the 'unlikely species' column.
A disagreement between a specified segment character and any earthworm will only result in the earthworm being moved to the 'unlikely species' column if the difference exceeds the 'tolerance' value specified in the options (default value is 2).
Earthworms are never moved to the 'unlikely species' column based on values of either of the size characters.
Earthworms in the 'possible species' column are firstly ranked on the basis of the total disagreement between all specified segment characters and the values in the knowledge-base and secondly on the basis of the difference between any specified size characters values and their values in the knowledge-base.
Earthworms in the 'unlikely species' column are firstly ranked on the basis of the number of matches with categorical characters, secondly on the total disagreement between all specified segment characters and the values in the knowledge-base and thirdly on the basis of the difference between any specified size characters values and their values in the knowledge-base.

Give the new version a go. See what you think.

Further information

For more information on the Tom.bio project, visit the Tom.bio homepage. Check out upcoming FSC field courses. For upcoming earthworm ID events in 2016 run by the Earthworm Socieity of Britain (including two run jointly with FSC Tomorrow's Biodiversity) goto the ESB events page.

On microscopy and the joy of SX

rich burkmar — Fri, 31 Jul 2015 10:23:38 +0000

Ever noticed how so many microscopes seem to be called SX something or other? No? Maybe it's just the really sexy ones. Yes, I expect that's the technical reason for the SX moniker.

Anyway, now that you're here and I've explained my rather poor joke, I'll move on to the real subject of this blog post: microscopy. According to the excellent website History of the Microscope, it is widely held that Dutch spectacle makers Hans & Zacharias Jansen (a father and son team) made the first optical microscope. But ask any biologist and they will tell you that it was the publication of Robert Hooke's Micrographia that made microscopy really sexy.

If you can recall peering down a microscope at a small organism - such as a housefly - for the first time and being completely blown away by the intricacy and beauty of its structure, you can begin to appreciate how Hooke must have felt in those pioneering days knowing, as he must have, that he was beholding visions not only new to him but new to mankind. The joy and excitement of astronomers watching as the spacecraft New Horizons beams back images of Pluto must come close to what Hooke felt.

But whereas Pluto, until a few weeks ago, was not much more than a faint smudge of abstract ideas - even to 'Pluto experts' - the things that Hooke examined under his microscope were everyday organisms; creatures and plants familiar to us; things that occupied the same space as us. Things that we thought we knew intimately. Hooke must have been completely astonished - giddy with excitement. His whole understanding of every organism around him, even the very stuff he was made of, would have been thrown up in the air.

And we can still capture some of that excitement whenever we look down a microscope at something we think we know. Last year I attended an event called Merefest which celebrates the landscape, culture and wildlife of the Mere's & Mosses in North Shropshire & Cheshire. Together with fellow Shropshire Spider Group member Nigel Cane-Honeysett, I manned a stall where we introduced people to the wonders of spiders! The most memorable thing for me was the reaction of children looking down our microscopes - many of whom had never used one before. I didn't have to talk to them to know when they managed to focus on a spider - I only had to watch their faces or, in many cases, listen to their cries of astonishment! Their joy was palpable - no spider morphology pun intended! (Nigel and Tom.bio's own Charlie Bell will be bringing some spidery delights to this year's Merefest.)

Unlike Hooke, but like the rest of us, children are constantly bombarded with amazing images on TV, social media, websites, etc and we might wonder at how, amidst all of this, first-hand experience of using a microscope can still be so enthralling. But no matter how amazing images are, you can only look at so many before you cease to be amazed; you are looking at images of someone else's experience. When those children (and many adults too) approached our microscopes at Merefest, they could see the spider on the microscope's stage with their own eyes and it was familiar to them. But as they looked down the microscope it dawned on them that something they thought they knew was actually so much more wonderful than they had imagined. That vivid experience of a changing perception was intensely personal to each of them as individuals and that's what so excited them - not the image itself.

Some biological recorders use microscopes out of necessity; others are drawn to them. Back in 2006 I was a student on the MSc in Biological Recording and I knew that I wanted to specialise in an invertebrate group, but I wasn't sure which one. I eventually settled on spiders for a number of reasons and one of them was the fact that it requires an element of microscope work. There's something about the discipline of microscope work that appeals to me but, above all, I understood that microscopes would reveal the diversity and beauty of spiders to me in a way that my naked eyes could not. I remember the thrill I got the first time I identified, to species, a tiny money spider - distinguishing it from upwards of 200 other species of tiny money spiders to be found in Britain. As a kid I thought a money spider was a money spider and I liked them. Thanks, in large part, to microscopes, I now know better and I love them.

I'm very pleased to be involved now in teaching other people to identify spiders through the Tomorrow's Biodiversity project. We've run a number of courses in 2014 and 2015 - so far largely confined to teaching people how far they can go in identifying species in the field without a microscope (which is further than most people imagine). But I am particularly excited about a one-day course we are running at Preston Montford on October 28th which will concentrate on using microscopes for spider identification. This will gently take people to the next level of spider identification and reveal some of the otherwise hidden wonder of this fascinating group of animals.

For reasons not hard to fathom, autumn and winter seem to be the seasons for microscope work and Tomorrow's Biodiversity is supporting a number of other courses that make use of microscopes after the field season. On November 14th we are supporting a one-day Sphagnum microscopy workshop run by Martin Godfrey of the British Bryological Society. Back in the mid 1980's I spent three field seasons in the beautiful uplands of Mid-Wales studying Meadow Pipits and Skylarks for my PhD. When one spends long days in the field miles from any civilised facilities, sphagnum has practical applications that are best not discussed on polite blogs; suffice it to say, I have a soft spot for them. They are also undeniably beautiful organisms, often serving as ecological keystones upon which much of our special wildlife depends (including a good-many spiders!).

Of all the beautiful things you can imagine beholding under a microscope, the genitalia of a moth might not be foremost in your mind. But when you look at them under a microscope they are unexpectedly beguiling! Most of our moths can be identified in the field from external morphological characters but there are some cryptic groups where the only way to identify them to species is by examining genitalia. For one reason or another - a discussion for another day - the skills required to prepare moth genitalia for examination and identification under a microscope are becoming scarce. It is very important to nurture a core of people with these skills in the mothing community so that we can retain some sort of handle on the relative distributions and abundances of species that are otherwise recorded as aggregates by most moth-ers. To this end, Tomorrow's Biodiversity is very pleased to be working with Dave Grundy to provide a two-day course on dissection techniques for moth ID verification.

As Charlie mentioned in her recent blog on peer support and mentoring, a legacy of successive biodiversity projects run at FSC Preston Montford, including Tomorrow's Biodiversity and Invertebrate Challenge, is that we have microscopy equipment and space for people to use it outside of formal courses. We weclome attendees of our courses back to use these facilities (there is no charge). Should anyone wish to do so, contact either Charlie or me to discuss your requirements.

Further Information

You can find descriptions and links to all of the courses mentioned in this blog, and others, on the Tommorow's Biodiversity training page. The Field Studies Council run a plethora of courses every year involving microscopy including those that concentrate on lichens, bryophytes, fungi and invertebrates of many different kind. Our publications unit produces a host of relevant ID guides.

Bashing the squares: the BBS and NPMS

rich burkmar — Mon, 22 Jun 2015 15:16:57 +0000

Like many UK naturalists at this time of year, last weekend I was busy playing my part as a volunteer - a citizen scientist if you like - monitoring the UK's biodiversity. Mid to late June can be a slightly anxious time for me as I study the weather forecasts hoping for a weekend morning with good conditions on the West Pennine Moors - the window of opportunity I need to complete the 'late' visit for my Breeding Bird Survey (BBS) square. (The BBS is partnership project between BTO, RSPB and JNCC.) On Sunday I was lucky and a leaden sky stayed its hand just enough for me to squeeze in my two-hour visit on the 1 km² of moorland allocated to me for the BBS.

I've been monitoring that square for more than 20 years now - since the BBS started in 1994 in fact - and I've got the badge to prove it! I've only missed one year - 2001 when Foot and Mouth prevented access. Many times, when rousing myself at 6 a.m. on a Saturday or Sunday after a hard week at work, my motivation to stick at it has been sorely tested. The low points have come when I've done the hardest part - dragging my sorry butt out of bed and up onto the moor - only to find the cloud base too low to conduct the survey.

But oh, the high points! I wish I had the words to describe how these have made me feel; still May mornings with Snipe drumming, Curlews and Cuckoos announcing themselves, the near-constant chorus of Skylarks vying over airspace, squadrons of parachuting Meadow Pipits each adding, as Edward Grey, 1^st Viscount Grey of Fallodon put it, their own “minute but perceptible contribution to the happiness of the day”. Moments of sublime stillness. They don't come every year and sometimes, like buses, several may come at once. That's what gets me out of bed. (That and knowing I'm doing my bit to monitor our biodiversity, obv!)

I've done my two BBS transect counts on that square, year in, year out, for 20 years (did I mention that?!) - about 40% of my life. It's part of me now; a sort of annual marker every bit as significant to me as my birthday. But I adhere to the axiom that it's never too late in life to start something new and this year was the first year - I hope the first of many - of my association with another national biodiversity monitoring scheme: the NPMS.

The NPMS is the National Plant Monitoring Scheme. I grant you, it doesn't exactly roll off the tongue to begin with, but say it often enough - N-P-M-S, enpee-emess, NpeaEmess - and your laughing gear soon starts to find its way around it. This is the first full year of the NPMS - a new habitat-based monitoring programme for flowering plants - run under the auspices of Plantlife, BSBI, CEH, BRC and JNCC.

I'm one of the lucky naturalists who earns a crust doing what I love - working in natural history - and I am tremendously proud that FSC's Tomorrow's Biodiversity project has facilitated a number of training courses in 2105, led by Plantlife's Hayley New, to introduce NPMS volunteers to the new monitoring protocol. But I'm also an NPMS volunteer in my own time.

In 2014 I piloted the emerging NPMS protocol on the 1 km square I surveyed in previous years for Wildflowers Count. Like my BBS square, this was on the West Pennine Moors. But selection of survey squares for NPMS 'proper', as with BBS, has followed a scientifically rigorous procedure and my old 1 km square was not on the final list: the square I was allocated was in the lowlands to the west on the Lancashire Plain in an area I know vaguely but not well.

So my first task, a fortnight ago, was to recce my allocated square and select locations for five sampling plots from a number of suggested locations marked on a map of my square sent to me by the NPMS organisers. This was quite a time-consuming and tricky task involving navigating to all the suggested plots and assessing the accessibility and quality of each. I found my smart-phone's GPS, used in conjunction with the map, a great help in locating the suggested plots. Maybe I was lucky, but I could not have hoped for better or more accessible sampling plots than those I found in my square. The plots I settled on were:

a 10 x 10 metre woodland quadrat in a local authority-owned park;
a 1 x 25 metre linear quadrat along a roadside hedgerow;
two 5 x 5 metre quadrats in some beautiful meadowland within a publicly accessible Woodland Trust reserve; and
a 1 x 25 metre quadrat along the margin of a gorgeous well-vegetated pond in the same WT reserve.

Part of the NPMS protocol is to identify which of the scheme's target habitats each of your plots belong to. The guidance for identifying the habitats is clearly and concisely written and I found this easy to do (though admittedly, my habitats are not the hardest to identify). The habitat associated with my plots are Dry Deciduous Woodland, Hedgerows of Native Species, Neutral Pastures & Meadows and Nutrient-rich Lakes & Ponds respectively. Although all this reconnaissance and set-up work is time-consuming, this is essentially a one-off task. Next year I will know where my plots are and how to access them from the get go.

On Sunday, after the dull morning in which I completed my BBS square, the afternoon brightened considerably and I set out to conduct my first ever NPMS survey. One thing to recommend the NPMS survey is that it doesn't require an early start! I had an extremely enjoyable and satisfying afternoon surveying my NPMS plots. Considering I was taking time to decide on the exact positioning of my plots, photographing them and drawing sketch-maps - all one-off tasks that I will not have to repeat for my second visit later in the year or in subsequent years - I got through the survey remarkably quickly. It took just a few hours.

This is my hedgerow plot. In the fortnight between the recce and the survey, the verge was mown as you can see! But the survey was relatively unaffected since the the width of the plot is 1 metre from the centre of the hedge and includes relatively little verge. Despite the mowing, it was my richest plot.
One of the grassland 5 x 5 metre plots marked out with canes and string. This one contained Southern Marsh Orchid.
Typical view of one of the grassland plots with, amongst other things, Red Clover, Yorkshire Fog, Red Fescue, Meadow Vetchling and Meadow Buttercup.
A very unexpected pleasure in one of the grassland plots was this Quaking Grass. I would have missed this if I had not been surveying the plot carefully. It's the first time I've found it anywhere close to where I live!
I could not believe my luck when I found this lovely pond with rich marginal vegetation during the recce. I surveyed a 1 x 25 metre plot along the margin on the far side.
A view into the pond margin plot. The Southern Marsh Orchid is actually just outside the plot, but the Yellow Flag is in along with Meadowsweet, Soft Rush and much more.
Branched Bur Reed with some Greater Reedmace in the background.

I'm no expert botanist, but I know my local flora well enough to survey my plots at the 'inventory level' which means that I recorded every flowering plant (including grasses etc) that I encountered within them. But another great thing to recommend the NPMS, particularly for beginners, is that you don't have to survey at this level. You can also choose to survey at 'indicator level' or 'wildflower level' - both of which involve recording a restricted set of the species present. These key species are listed in the survey guidance for each NPMS habitat. The 'wildflower level' is the easiest level and is great for those just starting to record flowering plants. But because the full list of species for any set of plots in an NPMS square will be reasonably short (I had around 30 species in my richest plot), beginners will rapidly find themselves getting to grips with most of the plants present in their plots over the first few years, so people are likely to progress rapidly from wildflower to indicator level (the NPMS 'target' level) and beyond.

Unlike many taxa that the Tomorrow's Biodiversity project focuses on, flowering plants do not want for people skilled in their identification and survey. However, as the the research and consultation phase of the project highlighted, there is a glaring gap in UK biodiversity monitoring when it comes to these incredibly important taxa. Other monitoring projects, such as the infrequent Countryside Survey, are neither regular or secure enough to provide the fine-scale monitoring that the NPMS could give us if it is supported by enough botanists - existing and new.

One thing I've learned during the years I've contributed to the BBS (20 if you recall) is this: two decades in the life of a man or a woman can just evapourate like dew. You look over your shoulder and, when you look back, your babies are grown. You drift into a springtime reverie and when you rouse yourself it is autumn. But 20 years in the life of the BBS or, let us hope, the NPMS is hard data; real currency. It never disappears - its relevance and value only grows as it ages. I very much hope that in 20 years time I am still involved as an active participant in the NPMS and that it becomes as much a part of my life, and of my annual calendar, as the BBS has.

(And just an early heads-up to the NPMS organisers: when I make that 20 year milestone, I'll be wanting a badge.)

Further Information

Botanical identification training has been a mainstay of the Field Studies Council natural history offering for some 70 years and we offer a full range of courses on botany every year. We also offers a full suite of bird identification courses, some of them run in association with the BTO.