Thursday 30 April 2020

Apps for plant identification: interview with Hamlyn Jones

Lyn Jones botanising on Jersey
Image courtesy of H. Jones
Over the past few years, Hamlyn Jones, Emeritus Professor of Plant Ecology at the University of Dundee, has been developing his Visual-flora, a visually-based key to the plants of Britain and Ireland. Recently he has been impressed by the power of Artificial Intelligence as a supplement to, or even a replacement for, conventional keys and approached John Norton, Editor of BSBI News with the offer of a review of this developing new technology. 

This was readily taken up and Lyn's review has just been published in the April issue of BSBI News. You may have read it, if you are a BSBI member and have received your copy of BSBI News. Or, if you are not yet a member, you may have spotted the review in the sampler issue of BSBI News which we issued yesterday. 

The homepage of Lyn's Visual-flora app
We are always being asked on the BSBI’s social media accounts if there are any plant ID apps that we recommend, or if they are a good idea in the first place, so I thought I’d take this opportunity to pick Lyn’s brains on this tricky subject. And at the end of the interview, there’s a nice surprise for you all!

LM: Hi Lyn, before we start on apps, could you tell us a bit more about yourself please: when did you first become involved in botany and how?

HJ: I have been interested in plants from at least my early teens, and recently came across a hard-back notebook where I (neatly!) recorded every plant that I saw over most of a year. At one stage we even had two geese named after a plant (Psophocarpus and Tetragonolobus)! Then, at A level I was inspired by my Botany teacher, Mr Pickering, to the extent that I ended up studying Botany at University. This ultimately led to a career as a physiological ecologist studying how plants work and how they tolerate environmental stresses. It is only since I officially retired that I started to use my extensive collection of plant photographs to develop a visual key suitable for the newly-developing smartphones.

LM: So how did you come to launch the Visual Flora and could you tell us a bit more about it please?

Lyn on Jersey with fellow botanists
including County Recorder Anne Haden (on left)
Image courtesy of H. Jones 
HJ: The origins of my Visual-flora lay in my early recognition that an important way in which I and many others get to an initial plant identification is by scanning the pictures in Floras, rather than following the often frustrating dichotomy of traditional keys. We all know the adage "a picture is worth a thousand words". The initial iteration of the key used the power of hyperlinks in Powerpoint to develop a simple key to the flora of Jersey, but as I extended this to cover the UK flora and especially that of the Scottish mountains, it became clear that the language of the internet (html) provided a much more powerful basis for the key. This allowed the key to be operated as a website or downloaded to a smartphone/tablet.

LM: So the Visual Flora still requires the user to work through a key of some kind. What about other apps that work in a similar way? Did you review any of those for the review in the latest issue of BSBI News? And what method did you use in order to test them?

Screenshot of the
front page of the
Flora Incognita app
HJ: Early on I had been making much use of use of image sets such as British Wild Flowers to help with identification but could not find any really good plant identification apps that could be downloaded to one's phone. Most that I could find were too limited with only a few species covered, or else they required a subscription. The best was the ETI Flora of the British Isles (sadly no longer available), though the pictures were often at too low a resolution to be much practical use. I have not reviewed any of these apps at this stage, though I might in the future. For the review in BSBI News, I just concentrated on Artificial-Intelligence based apps.

LM: Ok, so you just looked at the apps that claim to be able to identify plants via Artificial Intelligence and Automated Image Recognition? What did you think of their performance?

HJ: Although I had been involved over ten years ago in a proposal to develop a plant ID app based on automated image analysis (together with a colleague from the Computing Department at the University of Dundee), it was only last year that I was introduced to the current automatic AI-based apps by my 10-year old grandson, who was staying in Switzerland. He was able to demonstrate very convincingly the power of Seek. I was so impressed that I started to investigate the wider range of readily available AI apps, eventually finding ten different apps to test. These were the ones that I reviewed in the article in BSBI News.

LM: So, what’s your verdict on plant ID apps: when, and to whom, might they be useful? And are there any apps available yet that can replace a trained botanist?

Screenshot of
pot marigold seen on the
Seek app. 
HJ: The various Artificial Intelligence-based plant ID apps are an increasingly powerful tool that are particularly valuable for beginners and less experienced botanists. The best ones can frequently provide very good clues as to the identity of an unknown plant, though the IDs still usually need checking against a traditional ID book, or a good dichotomous or multi-access ID app. Examples of the latter include MAKAQueS, Quentin Groom’s BotanicalKeys and, of course, my Visual-flora. I do, however, believe that AI apps still have some way to go before they can fully, if ever, replace traditional botanical skills. Nevertheless, I am hopeful that their ready availability might benefit botany and actually widen interest in plant identification and lead beginners into further use of more conventional floras and ID apps (including my own!).

LM: Many thanks Lyn for talking to us today, for reviewing these plant ID apps and – here’s the surprise we are delighted to announce today! -  for kindly offering to make your review available to everyone, not just BSBI members reading the latest issue of BSBI News. The review is now available to view or download here - we hope that you find it useful!

For anyone looking to get started with plant identification, the apps Lyn mentions are certainly worth a look but as he has explained, you will still need to check your identifications. To help you do that, we would suggest that you visit this page which has some helpful tips to get you started, including support available via social media, and there is an impartial review of the ID books currently available. You will also find more ID resources on our Plant Identification pages, especially this page aimed at anyone just starting out – it has links to some useful websites and free ID sheets. If you know of any ID resources that don’t appear on our pages, please let us know and we’ll add them! 

Wednesday 29 April 2020

BSBI News: sampler issue for April 2020

On Monday we told you about the latest issue of BSBI News, our thrice-yearly membership newsletter, and listed some of the articles that members can look forward to. 

We also mentioned that there was some exciting news in the pipeline - so now here's the first bit of exciting news...

I was talking to BSBI News Editor John Norton and it occurred to us that any non-members who only know BSBI News from the back issues available in the BSBI publications archive, where everyone can access any issue from 1972 up to 2014, may not know about some of the changes that have taken place in recent years. Since 2017, BSBI News has been in full colour throughout and looks quite different to that first issue from 1972, although the quality of the articles hasn't declined. 

So John and I have selected a few of the pages and put together a sampler issue for you. It's only five pages long but it gives you a good idea of what BSBI News looks like these days. We think it looks pretty good! 

Marsh willow-herb: photograph illustrating
an article by Bob Leaney on
identifying willow-herbs
Image: J. Norton 
You can view or download the sampler issue here or by following the link on the BSBI News page on the website. If you are already a BSBI member, why not send the pdf to a non-member who might like a glimpse inside the pages?

Huge thanks to John for all his hard work on this latest issue and for producing the sampler! 

John said "It was a lot of work to pull everything together for this 84 page issue and for the five page sampler: I hope members will find the varied mix of articles interesting and stimulating. Do contact me if you would like to submit an article - the next issue is due out in September, but submissions should reach me by 25 July please."

We actually have a second piece of exciting news for you this week, again connected with BSBI News - watch this space and all will be revealed before the weekend!

Tuesday 28 April 2020

Wild Flower of the Month: April: Snake's-head Fritillary

For the Wild Flower of the Month feature in March, Kevin Walker (BSBI Head of Science) told us about Purple Saxifrage and the various treks he's undertaken over the years to see this montane plant. 

This month Kevin tells us about a wild flower growing in a very different habitat: floodplain meadows. 

Over to Kevin to tell us about Snake's-head Fritillary:

"One of my favourite botanical paintings is Charles Rennie Mackintosh’s exquisite watercolour (on right) of Snake’s-head Fritillary Fritillaria meleagris that he completed whilst recuperating from illness in Walberswick, Suffolk in 1915. Due to the war-time restrictions his activities, which included painting in the open-air and frequent evening walks with a forbidden lantern, were treated with great suspicion by the locals and in the end he was accused of spying, placed under house arrest and banished from East Anglia for the duration of the war.

Stand of Snake's-head Fritillary
Image: Pete Stroh
"Along with the Upper Thames basin, Suffolk has long been seen as a stronghold of ‘native’ populations of Snake’s-head Fritillary. Although Mackintosh’s plant is likely to be garden in origin, there are three large Suffolk populations that have long been considered native, including the magnificent Fox Fritillary Meadow near to Framsden, where it puts on a spectacular display each April (Trist, 1981).

"More has probably been written about the status of Snake’s-head Fritillary than any other British plant. Those who believe it to be native see British populations as the western outpost of a ‘Greater Rhineland’ range that was gradually cut-off from mainland Europe by rising sea-levels, isostatic adjustments and possibly finally by tsunamis created by the Storegga submarine landslip around 8,200 years ago (Oswald, 1994). Furthermore, its main British habitat, flood meadow grassland, is very similar to those in parts of Europe where it is accepted unquestionably as a native species. 

Snake's-head Fritillaries at Kungsängen
"Those who favour non-native status point to its remarkably late year of discovery in the wild (1736) and the lack of cultural references to it in art, literature, architecture, folklore and place names; to them both are inconceivable for such an attractive plant growing so abundantly close to a major seat of learning such as Oxford (Harvey, 1986). Indeed, one of the largest British populations occurs within the grounds of Oxford University’s Magdalen College.

"One of the key arguments supporting it being native is its association with ancient flood meadows, such as North Meadow in Wiltshire where numbers regularly exceed half a million individuals (Wolstenholme, 2011). However, the history of Snake’s-head Fritillary at Sweden’s most famous Fritillary site provides a salutary tale. Kungsängen (King’s Meadow) is a flood meadow near to Uppsala in Southern Sweden where Snake’s-head Fritillary first appeared in the 1740s having escaped from a nearby Botanic Garden. Since then it has spread prodigiously throughout the meadow and numbers are now approach the hundreds of thousands (Zhang, 1983). This shows that large populations in Britain, such as North Meadow, could have originated from garden escapes since it was first recorded. More recent introductions to ancient flood meadows in both Huntingdonshire (Portholme Meadow SSSI) and Yorkshire (Aubert Ings SSSI) are showing just how quickly the size of populations can increase under a traditional hay-cutting regime.

Snake's-head fritillaries in a
Warrington garden
Image R. Wheeler
"Although a recent genetic study has shown that British populations are most closely related to populations in Fance (Day, 2017) it fails to provide conclusive proof one way or the other. The historical (documentary) evidence seems to provide a more convincing picture, suggesting a seventeenth century introduction to monastic gardens from whence it escaped along watercourses to meadows downstream (Pearman, 2013). As a consequence, British botanists now accept that it is most likely to be a neophyte.

"Away from meadows, Snake’s-head Fritillary is without doubt a neophyte, introduced into a variety of habitats for ornamental reasons. Of the 500 hundred odd occurrences in the BSBI’s Distribution Database around 90% are deliberate introductions, mainly in urban areas (21%), gardens and parkland (15%), churchyards and other religious buildings (14%), and roadsides (7%). In recent years it has also been widely planted in grasslands as part of conservation and restoration schemes.

"Seduced by its beauty, many generations of botanists have wished for Snake’s-head Fritillary to be native (Harvey, 1986). Its relegation to neophyte status has therefore caused consternation in some quarters but has opened-up a lively debate as to whether we should be conserving non-natives of ‘cultural importance’. Either way its delicate chequerboard flowers, captured so beautifully by the Mackintosh’s transparent watercolours and architectural lines, is likely to remain one of our most cherished wildflowers."

Many thanks to Kevin for telling us about one of his favourite plants. I think that in order to appreciate the Snake's-head Fritillary at its best, you really need to see it nodding in the breeze, with birds singing in the background. We can't travel to see them during lock-down but thanks to the wonderful Joshua Ajowele, who is studying for a MSc in Plant Diversity at Univ Reading, we can enjoy a 5 second video clip of on-campus snake's-head fritillaries + breeze + birdsong by clicking here. Thanks Joshua!

Day, P.D. 2017. Studies in the genus Fritillaria L. (Liliaceae). Phd thesis
Harvey, J.H. 1996. Fritillary and martagon – wild or garden? Garden History 24, 30-38.
Oswald, P. 1994. The fritillary in Britain – a historical perspective. British Wildlife 3, 200-210.
Pearman, D.A. 2013. Late-discovered petaloid monocotyledons: separating the native and alien flora. New Journal of Botany 3, 24-32.
Trist, P.J.O. 1981. Fritillaria meleagris L.: its survival and habitats in Suffolk, England. Biological Conservation 20, 5-14.
Wolstenholme, R.S. 2011. The history of North Meadow, Cricklade. Fritillary 5, 35-40.
Zhang, L. 1983. Vegetation ecology and population biology of Fritillaria meleagris L. at the Kungsängen Nature Reserve, Eastern Sweden. Acta Phytogeographica Suecica 73, 1-96.

Monday 27 April 2020

BSBI News: April issue published

The latest issue of BSBI News, our thrice-yearly membership newsletter, has just been published and Editor John Norton has once again allowed us a sneak peek inside the covers. 

If you are one of BSBI's c3,000 members and don't want anything to spoil the surprise of opening up your full-colour copy and casting your eye over the Table of Contents... well, you'd better look away right now!

Still here and keen to find out what's in this latest issue? It's a corker, another triumph for Editor John Norton, and here are just a few of the highlights that members will be able to enjoy:

If you are just starting out with plant identification, you'll appreciate both Hazel Metherell's 'Beginner's Corner: Starting with buttercups' article and also a seven-page review by Hamlyn Jones of the various apps on the market which claim to be able to identify wild plants: are those claims justified? More on this subject in the next few days so for now, let's look at what else is in the latest issue. 

Ailsa Craig seen from Ayrshire
Image: C. Crawford
A new BSBI member reports on his first year of membership and what he got out of it. Very useful if you aren't yet a member but are considering joining

The regular 'Introducing my vice-county' feature returns and this time the focus is on Ayrshire, its plants and habitats. 

The spotlight also falls on Teesdale with an article by Margaret Bradshaw MBE and John O'Reilly about the area's distinctive wild flowers. 

Margaret Bradshaw passes on some of her
ID skills to the next generation of botanists
Image: John O'Reilly
BSBI News has long catered for botanists at all skill levels and in this issue, some trickier plant groups and species are discussed and de-mystified. There's a note about recording elms, there's an article about lesser meadow-rue, and John Poland gives an introduction to stipules as an aid to vegetative plant identification.  
Willow-herbs: a nightmare to identify but a nine-page feature by Bob Leaney, complete with his superb line drawings, sets out some of the common problems and how to tackle them. This is the sort of article BSBI News does so well and I think we'll all be referring to it for years to come. 

Rosy Evening-primrose: one of the
'Aliens & Adventives' reported
in Surrey in 2019.
Image: G. Hounsome
 Also in this issue:
  • 15 pages of reports on adventives and aliens (plants recorded for the first time in Britain and Ireland) including Cardamine occulta 'nursery bitter-cress' and Pilea microphylla 'artillery weed'. 
  • Reports on projects and activities from BSBI and partners, such as the New Year Plant Hunt (what was different about this year's results); Plant Alert (which species are being flagged as invasion risks, with the potential to cause problems in the years to come); and the National Plant Monitoring Scheme (what's in it for BSBI members?). 
  • Six pages of book reviews, edited by Clive Stace.
  • Round-ups and latest news from across the countries.
  • A note from Lynne Farrell, BSBI President.
  • Plans for post-Atlas projects.
  • Information about BSBI grants.
So, a fabulous issue and... this is the point where I usually remind you that in order to receive three copies each year of BSBI News, you need to join the society. And that is still the case. But we also have some exciting news about BSBI News to share with you later this week. Mum's the word for now but - watch this space!

Friday 24 April 2020

Notes from lockdown 1: Paul finds solace in his local woods

Lesser celandine by the stream
Image: P. A. Ashton
Regular News & Views readers will have encountered the name Paul Ashton before. Paul  is Head of Biology (and Professor of Botany) at Edge Hill University, who very kindly hosted  BSBI's Annual Exhibition Meeting in 2018. Paul is also a long-standing member of two of  BSBI’s standing committees - Publications and Training & Education. Paul was a co-author on this influential paper about field ID skills for the prestigious Times Higher Education and has also published in New Journal of Botany and contributed to Botanical University Challenge

Paul researches into aspects of plant ecology, with recent work including studies on grassland restoration and meadow connectivity and earlier work including research into sedge taxonomy and describing a sedge species new to the British Isles. Research notwithstanding, Paul views his primary role in life as being to inspire the next generation of botanists. Recent blooms from the Edge Hill hothouse include Dr. Elizabeth Sullivan, Jennifer Clayton-Brown and Josh Styles. This TV programme shows some of the devious methods used in the education work.

Dog's mercury flowersImage: P. A. Ashton
So, how is Paul coping under lockdown? We asked him to tell us what he's been up to and of course he started by reassuring us that no animals or plants were harmed in the writing of this guest blogpost! Paul also assured us that he has followed the government guidelines on COVID-19 to the letter and is fully behind BSBI's response to the crisis. The site visit Paul describes below was made during his daily one hour release period for permitted exercise.

Over to Paul: 

"Spring is a season to look forward to. The warmer temperatures and longer days mean that plant life starts to emerge. With this comes the emergence of the botanists, renewing acquaintances with favourite locations and exploring new ones. Or rather, it does in a typical year. However, 2020 is far from typical and if we aren’t going to feel that this spring is taken from us then we are going to have to explore our local patches more deeply than previously and to appreciate the common more fully than before. This is my attempt to do that.

Path, stream, Lesser celandine & Wood Anemone
Image: P. A. Ashton
"Within a short walk of where I live in south west Lancashire I am fortunate to have an ancient woodland. It isn’t a particularly remarkable woodland, it doesn’t house any rare vascular plant species nor any unusual communities and it is unlikely to ever be a candidate for SSSI status. It is my local woodland though and it is going to be the site I will come to know better than any other during these strange times.

"It has the rough shape of a triangle barely 2km long north to south and with the base at the south about 500m wide. It occupies a steep sided valley with a stream at the base. On the west it is bordered by houses and fields, to the east and north by farmland and to the south by rough grassland. It is typical of the ancient woodlands in this part of Britain. The valleys, or cloughs as they are known locally, probably escaped the plough due to the sheer steepness of their sides. 

Common dog-violet
Image: P. A. Ashton
"However, it hasn’t escaped other human influence. The north end once held a dam to power a mill, the eastern side merged into a park that surrounded the now long-gone stately pile and the south end contained a pit until 1961. While the current use is not so commercially exploited as in the past it does function as a site for recreation; whether that be as a child’s playground, for coming of age activities, dog-walking, or in 2020, as a local botanist’s paradise.

"The trees largely retain their winter skeletal form, but the ground flora has emerged. A significant sign that winter is finally receding and that collective hunching of the shoulders that typifies that season is being gently relaxed. The white and yellow stars provided by Anemone nemorosa (Wood Anemone) and Ficaria verna (Lesser Celandine) respectively occupy large swathes of the valley. I’m not the first to be struck by these plants, John Clare praised the former in his ‘Wood-Anemonie‘ poem,

Great wood-rush
Image: P. A. Ashton
‘How beautiful through april time and may
The woods look, filled with wild anemonie’

while Wordsworth was so enamoured of his Lesser Celandine that it was the focus of three of his poems, in the last the plant features as a reflection of the vicissitudes of human life.

‘There is a Flower, the lesser Celandine,
That shrinks, like many more, from cold an rain;
And the first moment that the sun may shine,
Bright as the sun himself, 't is out again!’

"Much more understated in its display and consequently less celebrated in poetry is Chrysosplenium oppositifolium (Opposite-leaved Golden-saxifrage) is abundant in the damper parts of the valley. The edge of an old mine sough that emerges in the wood hosts a few flowers of Viola riviniana (Common Dog-violet) while elsewhere there are localised patches of flowering Mercurialis perennis (Dog’s Mercury) and Luzula sylvatica (Great Wood-rush). The presence of these two, albeit in different locations, reveal the variety in soil characteristics within the wood.

Colony of Dog's Mercury
Image: P. A. Ashton
"Almost imperceptibly the wood is shifting as the days progress. The trees are beginning to come into leaf and the ground flora is changing. This is my field location this year. I hope my time here will engender a deeper understanding of its flora. This account will hopefully help share some of this understanding".

Many thanks to Paul for telling us how he's coping with life under lockdown as spring unfolds. If you are also managing to find solace in nature during your one hour per day permitted exercise, we'd like to hear from you, but please do ensure that you follow the guidelines on social distancing and minimal time spent away from home. Alternatively, you can explore the wild plants in your garden and record them for BSBI's Garden Wildflower Hunt or check out  the other activities on this list