Creating country checklists using GBIF and rgbif

I wrote this function in order to create simple summaries of GBIF data per country (i.e. checklists based on the available GBIF information) to supply to other people without R expertise. I suspect there is a lot that could be improved (and perhaps I have even missed something obvious within the rgbif package that would have made it easier). Anyhow, this is where it is at. I have been using the function 'lapply-ed' across a vector of country ISO 2 character codes. Occasionally it fails (particularly with countries where there is a lot of data), hence the try...catch approach for when applying over such lists.

Of course, I realise that GBIF is not comprehensive in its coverage, and that there are often issues that need addressing with occurrence data and taxonomic precision; this code was written for a quick first assessment useful for comparing the presence/absence of potentially invasive species in countries in the context of horizon scanning. Use this code at your own risk!

Feedback/improvements welcome!

An update on Sheffield's urban trees

Just a small post to say that I've updated some of the trees on my map of the Urban Trees of Sheffield. Despite no longer living in Sheffield, I'm still a member of the most excellent Sorby Natural History Society, and in August of this year the annual tree walk took place, resulting in some extra identifications which I've tried to include on the map. Thanks to Joan Egan for writing her 'Report of the trees in the city centre meeting. Sunday 10 August' in the November 2014 Sorby Newsletter.

View The Trees of Sheffield -- An Interactive Map in a larger map

See here for the original post: http://sacrevert.blogspot.co.uk/2013/06/urban-trees-of-sheffield-interactive.html

England's new Red List of Vascular Plants

It seems to be an incredibly productive season for botanical publishing. A new bryophyte atlas on the way; fliers for a reprint of the BSBI handbook Docks & Knotweeds with BSBI News, and for books on Yorkshire's Hawkweeds and Bedfordshire's Orchids; but one of the most exciting publications has been that of the new Vascular Plant Red List for England

New #EnglandRedList shows that ~5th of wildflower species now threatened @BSBIbotany pic.twitter.com/e93DxbLbXS
— BRC (@___BRC___) September 17, 2014

The launch of the Red List was also a celebration of the contribution of David Pearman to British botany. His name might ring the loudest bell to many as co-editor of the 2002 New Atlas (now rather expensive, apparently because Defra pulped all of the left over copies -- the less said about that the better). However, David has also contributed a huge amount to many other areas of botany, including several interesting pieces encouraging a more critical perspective on the impacts of alien plants. For example, see this article for a stimulating read! His views on the native statuses of British plants have also been very influencial: see this paper for a host of fascinating examples.

David Roy of BRC and David Pearman at his eponymous celebration and Red List launch

The Pearman celebration segued into the launch of the England Vascular Plant Red List launch very nicely. This exciting publication has used new interesting methods, and of course plant distribution data collected over more than 80 years by BSBI members and others, to reveal a rather worrying picture of England's native floral diversity. The new analysis has found that around a fifth of our wildflowers are now under threat. Many plants were found to have undergone worse declines in England than in Great Britain as a whole, highlighting the importance of this new England-level analysis.

Of course, we have known for a long time that particular habitats have been under a lot of pressure in England, but it is fantastic to have the broad, volunteer-led distribution data revealing the same thing as smaller, habitat-focused studies. It all helps to form a compelling picture of ecological change that should convince politicians and funding bodies that plant conservation is both necessary and really worthwhile.

Oh, and whilst you can purchase the Red List (a fascinating read with lots of nice photos) at Summerfield Books, you can also take home a nice shiny pdf immediately! I have to admit to not having read mine probably yet, but this is far more than just a list, there are around 60 pages of text, analysis and photos, with the list (covering all native plants in England as far as I can tell) covering another ~110 pages. GB Red List designations are also included. I'm looking forward to settling down with it and learning a lot more about the British flora!

Atlas 2020 recording with the Oxfordshire Flora Group

It's been a while since I've blogged, but, a lot has been happening (no excuse really when I look at Louise's efforts at http://bsbipublicity.blogspot.co.uk !) Anyway, last week I went out with the Oxfordshire Flora Group, a group affiliated with the BSBI and the Ashmolean Natural History Society; seeing as this was only the second, in what will hopefully be a long-running series of Atlas 2020 recording meetings, I felt that it was a good time to do some blogging and promote the OFG meetings. In conjunction with this rebirth, vice-county 23 (or the old-fashioned county of Oxfordshire for those who don't habitually think in terms of Victorian vice-counties) also has a recently appointed new vice-county recorder, Sue Helm, and a new page on the BSBI website to boot. The page explains the myriad opportunities to get involved in plant monitoring and recording in Oxfordshire, and also assists with understanding the rather complex web of botanical societies and mailing lists extant in Oxon.!

But, back to the recording: Seven of us met up just south of Sibford Ferris in north Oxfordshire to accumulate records for a 2 x 2 km square (tetrad) in a region with precious few modern botanical records -- so just recording the car park would have a been a good achievement! Luckily we did get a bit further than that, and did a good circumnavigation of the tetrad, even gaining access to some private land, allowing us to add some extra stream-dwelling species to our list (just over 200 in the end since you ask).

The OFG inspect a verge. I think this was the Schedonorus pratensis v. arundinacea debate!

Needless to say, we all learnt a lot from each other, and an excellent day was had by all. We also had a good few conundrums to keep us on our toes. 

The mystery willowherb.

 This willowherb was a case in point. The general conclusion seemed to be that it was a hybrid -- but between which species? The jizz didn't seem quite right for E. parviflorum, but perhaps we shouldn't be doing willowherbs on jizz anyway. Although Crawley says that E. parviflorum is more-or-less unmistakable on jizz... anyway, one for the bag in the end. At home under the microscope I convinced myself that it might be E. hirsutum x parviflorum, but really it needs sending off to the referee. Another one for the to-do list! No doubt it will come back as parviflorum and I'll feel a fool!


But it wasn't all hybrid willowherbs, much of the trip was far more palatable. We found a ungrazed corner of pasture that must have been on the Cotswolds oolitic limestone. Here was Burnet Saxifrage, Chalk Knapweed, Rough Hawkbit and other denizens of high pH soils; a wondeful respite from the typical intensely managed pasture we are used to seeing in the countryside today. We then passed by an arable field, picking up a number of typical plants of such situations, including the Black Bindweed below.

Fallopia convolvulus

Not a rare plant at all, but one which I find strangely charming. The slightly manufactured perfection of the Polygonaceae in handy pocket size; the fearsome knotweed becalmed: who could fail to be charmed? By now it was raining, and a bit of a drudge was needed to circle around the bottom of the tetrad and re-enter it from the south. By good luck, the final habitat was a really special one: an abandoned quarry. The ground of the quarry was quite disturbed, presumably from rabbit grazing rather than recent use. Clearly an interesting habitat in which to look for new species. We were quickly rewarded with Basil Thyme (Clinopodium acinos), a plant which is relatively rare in Oxfordshire, with only around 20 sites or so. I had only seen it before around the entrances to rabbit burrows at Watlington Hill; here it was in abundance on every bit of bare ground, and even on some of the bare rock faces of the quarry. A wonderful end to a enjoyable day. Thanks OFG! And see you all next time (all welcome, regardless of ability!)

Clinopodium acinos

Local distribution maps for biological records in R

I thought it worth sharing this map that I created for a poster that Ambroise Baker and myself have prepared for the upcoming BSBI Annual Exhibition Meeting. It shows the occurrences of the non-native grass Polypogon viridis in Sheffield, based on records made by Ambroise and myself this year (2013). The map took a fair bit of fiddling around; working out how to correctly specify the manual scaling of the points seemed to cause me particular trouble!

Of course, R could also be used to create more traditional atlas dot maps; coastal outlines of Britain are freely available in more than one R package, and occurrence data relating to the UK grid could be manipulated in R to centre on monads, tetrads or hectads. External tools could also be used to do this before loading the data into R, e.g. see here.


The result is below. I'd be grateful to hear from anyone who can suggest any refinements to my code, or the general way in which I've gone about this.

Polypogon viridis in Sheffield, UK, 2013

Water Bent new to Sheffield and South Yorkshire

Several studies of urban areas have found that the composition of the flora can change considerably between survey periods. For example, a survey of the street flora of Aberystwyth between the 1970s and 1998-9 found a large turnover of species (Chater et al. 2000), with species associated with drier, warmer conditions becoming more prevalent. In this way it can be of interest to monitor the urban flora, because the rapid changes in the plants that make their homes there may provide an insight into how our urban environment is changing. In this spirit, Ambroise Baker and myself were excited to independently discover the alien grass Water Bent (Polypogon viridis) new to the streets of Sheffield and South Yorkshire. Whilst some records of this plant do exist for vice-county 63 (e.g., from wool shoddy, Halifax, 1960, F. Houseman), this appears to be the first find of Water Bent for the modern county of South Yorkshire (GTD Wilmore, pers. comm., 2013).

Surprisingly, Ambroise and myself have not just discovered one new colony, but 6, in 5 different 1 km squares (monads) in Sheffield, with some populations of considerable size, suggesting that this species has been amongst us for at least a few years. This is a species that appears to be spreading throughout the British Isles; its principal habitat is pavement edges and waste ground, although some records from canals have also been made. It is not clear that this species negatively affects any of our native flora, although, with a warming climate, it will be interesting to monitor for any habitat changes that might occur in the future. So far, our records of this alien grass are:

Eastwood Rd, Sharrow, SK335858, 11.06.2013, a few plants (AB)

Robertson Rd, Walkley, SK324884, 16.06.2013, one large plant (OP)

Stewart Rd, Sharrow, SK333857, 19.06.2013, thousands of plants (AB)

Truswell Rd, Crookes, SK324874, 12.07.2013, over 20 plants (OP)

Armthrop Rd, Nether Green, SK315855, July 2013, one large plant (AB)

Clumber Rd, SK313864, July 2013, over 20 plants (AB).

It seems likely that Water Bent is lurking in other parts of Sheffield’s suburbia, and, given that it has also just been recorded for the first time in Derbyshire (Willmot & Moyes, 2012/13, Derbyshire Flora Group Newsletter No. 22), this is a great opportunity to get some good baseline data to monitor the spread of an alien plant in an urban area. The above photo demonstrates how it is most likely to look at this time of year. Water Bent is, unsurprisingly, most similar to a bent grass (Agrostis spp.); indeed, it was previously classified in that genus; however, one key difference is that the glumes (very small leaves at the base of the flower spikes) fall with the flowers. In our other common bents, and in meadow grasses (Poa spp.), parts of the flower remain on the stalks as the plant dies. The fact that the glumes fall with the seeds in Water Bent gradually creates a skeletal flower-head. This is demonstrated as a progression from the flower-head on the right to the one on the left in the photo.

Urban Trees of Sheffield -- An interactive tour

"But let it be remembered, that the principles of a science are to be taught as truly with

 reference to the commonest forms as to the rarest.  And have we not the fields and the rivers?

But besides this, is not the whole suburb of this metropolis one magnificient botanic garden?"

 John Lindley, in his Inaugural Address as Professor of Botany in London University, 1827

(Quoted in Walters, 1993, Wild & Garden Plants)

View The Trees of Sheffield -- An Interactive Map in a larger map

This is something that I have had at the back of my mind for a few years, and have been, very slowly, mentally collecting notes on. I've finally decided to get on with it and put it out there. The idea was basically to provide a guide to the more interesting or unusual of Sheffield's urban trees, perhaps for a walking tour, or for those who would like to see a certain species.

Google Maps also allows collaborations on these types of maps, so, if you would like to get involved, and edit the map in some way, please let me know. I know there are lots of relatively common, interesting trees, in Sheffield's streets and gardens that are not on here. So, if you know of one that is easily viewable, and is not too far from the city centre, please let me know. I particularly need to add the trees of Weston Park; outside of the botanic garden, this probably has the best collection of trees in a location near to the city centre. 

The other place close to the city centre with a great collection of trees would be Tapton Experimental Gardens; unfortunately this is still closed as the University of Sheffield decides its fate. If I am not mistaken, Weston Park has, amongst others, Hungarian Oak, two varieties of Tulip Tree, the Tree-of-heaven, and Cappadocian Maple. The only tree I can remember seeing in Tapton is Bronvaux Medlar (+Craetaegomespilus dardarii), one of the very few trees that is a chimera of two species, rather than a hybrid; however, I am sure there are many more interesting species in there!

Another nice thing about Google Maps is that it allows data layers such as the one above to be exported as KML files. This should allow one to generate the corresponding biological records of the trees by opening the file in a GIS software like QGIS, reprojecting the layer to the OS National Grid, and exporting the points. Another exciting software for analysing the environmental importance of trees is the USDA Forest Service's application iTree. If one has enough information on the locations and sizes of trees in an area, this free piece of software will calculate all sorts of interesting metrics: the trees' cooling effects; their contribution to the reduction of urban pollution; and carbon storage to name a few! These 'urban ecosystem services' are discussed in many places, but I have found the relatively short, but very readable book, by William G. Wilson called 'Constructed Climates' to be a great introduction to this fascinating topic.

Coppiced Hornbeam in Hedges

I was out surveying around Watton in Norfolk recently, and found these wonderful coppice Hornbeams in a field hedge.

According to Edward Milner's Trees of Britain and Ireland (2011), the prime use of Hornbeam was as firewood, and he cites the 17th century arborist and gardener John Evelyn as reporting that it burns "like a candle". I don't know if the poles resulting from cutting these specimens would have been used in such a way. The coppice effect may just be the outcome of the hedge having been laid many times in its past, and then being neglected at some point; presumably if the main function of a hedge is to be stockproof, the poles would have been laid rather than harvested. Alternatively, some hedges were managed by coppicing, especially if their primary function was not for containing animals; so perhaps this hedge was essentially only a boundary marker, and so has been managed by coppicing for a long time.

It seems from Oliver Rackham's Ancient Woodland (2003, 2nd Ed.) that Hornbeam is relatively rare in hedges. He states in Chapter 14 that "in a few places hornbeam grows in ancient hedges, particularly in the Harleston [Norfolk] hornbeam area". Interestingly, in the recent Flora of Suffolk (Sanford & Fisk, 2010), the authors suggest that in that county, hedges with Hornbeam are often the remaining "ghostly" edges of long grubbed out woods. Suggestively, this hedge was accompanied by a ditch, a common boundary marker of ancient woodlands.

Hornbeam was only occasional to rare in the hedges of this site near Watton, but the glorious, fresh, colours of the leaves, coupled with the twisted, degrading bases, was a real treat.

Creating masked vice-county rasters in Quantum GIS

I was inspired by Teresa Frost to have a go at making a good base-map for South Yorkshire (well, the Watsonian vice-county 63 to be precise) in Quantum GIS (v. 1.8.0). I thought it would be relatively straight-forward, but, I soon came up against an irritating problem, that of successfully trimming a raster of elevations using a vector of vc63. I overview the process below, because by the look of the many mentions of this topic on many forums and mailing lists, there is a need for more examples! There are no doubt easier ways of achieving what follows, but this is what worked for me.

Firstly, I retrieved the Land-Form PANORAMA^® data from the Ordnance Survey's new(ish) OpenData website, and the Watsonian vice-county boundaries from the NBN. The Land-Form download contains, amongst other things, Digital Terrain Models (DTM) in ASCII format, by 10 km grid squares.

In order to merge all of the necessary 10km DTM square into one raster, it was first necessary to get a list of all the 10 km squares overlapping vc63: this Biological Records Centre website was handy for that.

1) In Quantum GIS, the Raster --> Miscellaneous --> Merge option allows the import of multiple rasters and merges them to one raster layer in your project. I chose OSGB 1936 (EPSG:4277) (the Ordnance Survey National Grid) as the Spatial Ref. System for this work.

2) Visualising the DTM data is also a minor challenge, and can be overcome by right-clicking the raster layer, and choosing 'Properties'. Under 'Style', change the color band option to 'pseudocolor' and you should now see the DTM data, albeit in fairly lurid colours.

3) Import the vc63 shapefile via the normal route (Layer --> Import Vector Layer). (If you get it from NBN, it should already be georeferenced to the OS National Grid, but you can check that the bottom right box in the QGIS window says EPSG:4277).

4) As far as I know, it is necessary to polygonise the vice-county boundary in order to use it to "mask" (i.e. clip) the raster image. Luckily, there is a handy plugin for this (Plugins --> Fetch Python Plugins... --> search and install 'Polygonize'). Whilst you are there, it is also worth installing the plugins "Value Table", and, by adding a new repository, the "1-Band Raster Colour Table" (see this stackexchange question for advice on this).

5) Polygonize your shapefile using the new plugin. (Vector --> Polygonizer --> Polygonizer). As it says, try the "old" method if the new one doesn't seem to work.

6) The mask step was the most complex, and, despite trying numerous routes, it was this method that worked in the end: Raster Masks in QGIS/FOSSGIS. The result is below (don't let the change in colour put you off!):

7) Actually, this didn't quite work, because the clipped raster was still showing the "null data" outside the clipping boundary as coloured. Luckily I could get around this by reprojecting the clipped raster to a new file (using the same Spatial Ref. System) using a Raster --> Warp (Reproject).

8) Then I applied a b/w DTM colour scheme using the 1-Band Raster Colour Table plugin (under Raster menu) mentioned earlier. This generates a text file style, that can subsequently be imported and applied via right-clicking on the raster layer, and choosing 'Properties', then the 'Style' tab, also mentioned earlier.

Now I just need to add rivers and urban areas! Think I'll save that for another day : ) All in all, this did take a fair bit of messing around to accomplish, and occasional quirks of QGIS did slow me down (for example, layers sometimes need to be exported (right click and "Save as..." for vectors; Raster --> Warp (Reproject) for rasters) and re-imported, before they can be selected as layers for masking or other transformations). Additionally, very few of the methods suggested out on the web seemed to work, until I found the method used above. But, once you know the pitfalls, work-arounds seem to be possible. Also, more background knowledge on my part wouldn't go amiss...

Rustyback in Sheffield

After recently noticing a single clump of the rare wall-inhabiting fern Rustyback (Asplenium ceterach) by the entrance to Walkley Library, I was alerted to the fact that the nearby gennel connecting Walkley Road to Parsonage Street held a very sizeable population, estimated to hold more than 80 plants. Since then I have found two more very small populations of Rustyback in Walkley, one at the corner of Greenhow and Camm Streets, and one plant in another gennel connecting Fern Road to Walkley Bank Road. It seems likely that the large 80+ population is acting as a source for these three more recent colonisations.

Rustyback is only known from a handful of sites in the Sheffield conurbation, including a good population on the wall next to the entrance of Norfolk Park on Norfolk Park Road, so its pleasing to see that it is apparently spreading, and highlights the especial importance of protecting sites with large populations that can act as sources for the colonisation of new territory. Ferns on walls are great for winter identification, and a good key is available freely at http://www.wildlifebcnp.org/ecology-resources.htm.

Don’t forget that photos of wall ferns uploaded to the Sorby Flora flickr group (http://www.flickr.com/groups/sorbyflora) will also contribute to an updated Sheffield Flora.

Rustyback (Asplenium ceterach) at Walkley Library, Sheffield

Sheffield's Ancient Woodland and SSSIs: Open data

Here are some data I retrieved a couple of years ago from the UK government's MAGIC site. Unfortunately, this site only provides downloads in proprietary GIS formats, ArcGIS and MapInfo I think. Given that the government's recent open data initiative is encouraging people to use public data in new ways, I guess it's ok to change the data into formats that make it more usable for the average person.

The files from MAGIC were edited in QGIS (a miracle of open source programming) to restrict the data to the Sheffield area. (EDIT: I should point out that this means the data are arbitrarily cropped to particular OS gridlines. This was done to reduce the file size for posting to the internet. If your local wood is not shown as 'ancient', it may simply be outside of the area that I cropped to. As I say above, the full national dataset is available through the MAGIC link above).

Then I followed the protocol that I posted earlier to turn them into KMZ files. So, the first map is Ancient Woodland, the second is Sites of Special Scientific Interest. The data can be downloaded for home use in Google Earth here and here, for the moment at least. Clicking the 'View larger map' link below each map will link-out to Google Maps, where, at least for the woodland dataset, the names of each land parcel are shown. [Also, choose the 'View larger map' link if the sites (which should be in red) do not appear automatically -- sometimes the site outlines do not seem to be retrieved from the hosting website.] Alternatively, if you zoom in on the map below and click on a woodland boundary, the name will be displayed. Obviously the original data are from MAGIC, and users should take heed of the license agreements imposed by the government, which restricts usage to non-commercial activities.

Ancient Woodland in the Sheffield Area

View Larger Map

SSSIs in the Sheffield Area

View Larger Map

Sorby Botanical Outing to Derwent Reservoir

Four members met at the Fairholmes car-park on one of the few sunny days in September to enjoy a mild ramble across the Derwent Reservoir towards Dovestones Clough and Mill Brook on the eastern side of the water. As well as appreciating the botanical bounty of the many Raspberry and Blackberry plants lining our path, we also took the time to identify many plants, many of which had finishing flowering and so were tackled vegetatively. 

Several plant groups were looked at in detail, including the Vetches (Vicia species). In particular, we compared the presence of extra-floral nectaries on the stipules of Bush Vetch with their absence on Tufted Vetch. Nectaries outside of flowers are not uncommon amongst plants, in fact, they seem to have evolved on numerous occasions; for example, the common fern Bracken also has them. Their function is seemingly to attract ants that, in turn, will attack insect herbivores, providing a benefit to the plant. Interestingly, some research has found this effect to be weak, and scientists have suggested that some plant herbivores may have themselves evolved to overcome this ant-protection system! 

After this overlap between plant identification and plant-animal mutualisms, we progressed up a sunken lane with a typical acid grassland flora at head-height, for easy inspection. We were able to pick out all of the common acid grassland grasses, including Heath-grass (Danthonia decumbens), a handsome grass with large florets that make it relatively easy to spot, even though it is often at low abundance within the sward. This is also one of only three native British grasses with a ring of hairs at the junction of the leaf-sheath and blade, making confirmation relatively straightforward (for a grass!) Finally, we arrived at the junction of Mill Brook and Dovestones Clough, where a number of typical plants of upland streams and acid-neutral flushes were found and enjoyed. Lemon-scented Fern, Star Sedge, and Creeping Forget-me-not were all identified and enjoyed.

 Botanists wanting to find out more about the cloughs around the Derwent Reservoirs are strongly recommended to purchase a copy of Sorby Record No. 40 (see the Sorby website), featuring John and Valerie Middleton's thorough survey of these splendid and exciting landscapes.

Sorby Botanical Meeting to Leash Fen, Derbyshire

Six wellie-clad members braved the ominous black clouds of the weather forecasts to explore the northern corner of Leash Fen. Leash Fen is a mosaic of acid grassland, heath and mire, and most of the hard work at this meeting was navigating the treacherous and tussocky mires around the Bar Brook, and not in finding the plants, of which there were a huge variety. I am happy to report that, apart from cranberry, all of the targeted mire plants were found. 

We were particularly lucky to see the locally Red-Listed Marsh Cinquefoil in flower; blooming Bog Bean escaped us, but we at least saw its large trifoliate leaves, somewhat reminiscent of an overgrown clover. In no particular order, Marsh Violet, Marsh Pennywort, Southern Marsh Orchid, Bottle Sedge, Greater Tussock Sedge, Common Sedge, Ragged Robin, Water Mint, Bugle and Narrow-leaved Buckler Fern were all seen and appreciated. We were also able to compare Marsh and Heath Bedstraw, discovering that the latter could do a good impression of the former in marginal wetter areas, quite different from its typical, prostrate acid grassland habit. Short-fruited Willowherb was also tentatively identified using the Vegetative Flora of the British Isles (Poland & Clement, 2009).

If you fancy tagging along next time, see www.sorby.org.uk for membership details. 

Marsh Cinquefoil (Comarum palustre)

Sorby Botanical Meeting to Greno and Hall Woods, Sheffield

Six Sorby members gathered to explore these ancient woodlands near Grenoside. We were lucky to have a member of the Grenoside Conservation Society to fill us in on the history of the site and on recent management implemented by the new owners, Sheffield Wildlife Trust. This large site is quite varied, consisting of conifer plantation, heathland, open Oak-Birch woodland and Beech plantation, allowing us to note the differences in the plant communities found in the different areas.

After observing the differences between the Lodgepole, Corsican and Scotch Pines that make up the majority of the conifer cover, and appreciating the sunken pathways that put the Bilberry at head height and allowed a particularly effortless view of the flowers, we proceeded to the old quarry area, where we were informed of the recent history of Cowberry at the site. Apparently one patch had emerged after the fires of the long, hot summer of 1976, and had spread to some size, before subsequently declining. Our group could only find one remaining Cowberry plant, leaving some doubt over its future at the site. The book Comparative Plant Ecology (Grime et al., 2007) suggests that germination of Cowberry seed requires high temperatures, which, with its apparent reappearance after the 1976 fire, suggests that burning may be a management tool to be experimented with.

We also enjoyed the spectacle of several teeming Wood Ant nests, and recalled that at least two plant species that we had seen in the woods (Common Cow-wheat and Hairy Wood-rush) had ant-dispersed seeds with special oil-bodies (“elaiosomes”) that ants find particularly nutritious.

After lunch we headed to Hall Wood, and investigated the stream running close to the wood boundary: we were amply rewarded for our trouble with an excellent suite of woodland plants in flower (or spore!), including Wood Anemone, Wood Sorrel, Dog’s Mercury, Three-nerved Sandwort, Lesser Celandine, Sweet Woodruff and Lady Fern. A flushed area at the bottom of a slope also yielded two Sphagna for the bryophyte enthusiasts, these being fallax and palustre, two bog-mosses typical of moderately nutrient rich woods. Other interesting finds included Blinks (Montia fontana), in a wet depression, and seedlings of Buddleia and a Tree Cotoneaster (Cotoneaster cf. xwatereri), which we hoped were not about to establish a novel role as colonisers of heathland and woodland. Overall, everybody was glad that they had ignored the widespread mis-forecasting of rain, and so been able to enjoy the immense pleasure of the spring-flowering of the woods.

Future invasive trees in the Sheffield area?

Academic ecologists these days spend a lot of time thinking about invasive species: How fast are they likely to spread? What traits allow a certain species to succeed where others fail? What is the impact on native plant and animal communities? With our warming climate, alien species, previously innocuous, might escape from ‘captivity’. Garden plants are of course one of the most common sources. The charity Plantlife recently compiled a list of the plant species most likely to become invasive in the UK in the near future.

Particularly high risk were two tree species, the Tree-of-heaven (Ailanthus altissima) and the False-acacia (Robinia pseudoacacia). The Tree-of-heaven has already spread itself all over London, and seems a good bet to do the same thing in other UK cities in the near future. Both these trees can be found occasionally in Sheffield’s gardens, parks and streets; unfortunately, both produce fertile seed in Britain, and also sucker. Indeed, one of the main problems with these trees in other countries has been their ability to sucker into native woods, potentially transforming them into monocultures. False-acacia suckers particularly can travel considerable distances: the next time you walk past the University Arms pub, up Brook Hill, have a look at the trees at the corner with Hounsfield Rd and you might be able to spot False-acacia shoots popping up at some distance from the main tree. The Tree-of-heaven suckers profusely when the main bole is cut down; the resulting thickets can be seen in some gardens around Sheffield, at the corner of Carr Rd and South Rd in Walkley, for example.

For naturalists keen to monitor potentially harmful changes to our region's flora, the seedlings of these species will be particularly important to keep one's eyes open for.

Bean Broomrape? (Orobanche crenata)

I spent the weekend in the Cotswolds with my wife and a friend, and this was one of the botanical highlights, Bean Broomrape (Orobanche crenata). It's not native to Britain, and is currently thought to be naturalised only a one site in north Essex. It does turn up in other southern counties however, as here in Gloucestershire. As you might guess from the name, it parasitises legumes (plants related to peas). This specimen, and the hundreds of other plants in the field, was parasitising White Clover (Trifolium repens). No doubt it was a seed contaminant that arrived with the Clover when it was sown.

The corolla with its five flared lobes (2 up, 3 down), each at almost 90 degrees to the main corolla tube, is a key feature apparently. Although on older flowers this was not so obvious.

Unfortunately this Orobanche is not included in a lot of the popular picture guides to Britain's plants, so hopefully it won't increase too much in Britain: if it does we may not notice! (And it might become an agricultural pest of other cultivated legumes, as it is in North Africa and other warmer climes).

Red Bartsia

This is Red Bartsia, or Odontites vernus, growing at the edge of a path in Crookes Recreation Ground, Sheffield. It's not unusual to find it on waste ground or trampled path edges, but it is easily overlooked. Like all members of the Orobanchaceae it is parasitic; in this case on the roots of grasses I believe. It's green, so obviously it can still photosynthesize, so we might suspect it is only using its hosts for mineral nutrients and water. However, the line between hemi-parasitism (as here) and holo- or complete parasitism seems to be fairly thin in an evolutionary sense, so it's possible that some sugars are received from the host as well.

A nice plant to look out for in urban situations; I used to see it a lot in Birmingham along the canal in the Edgbaston area.

Remarkable Creatures: Epic Adventures in the Search for the Origins of Species

A Review

With Remarkable Creatures Sean Carroll, the evolutionary-developmental biologist, expands his already impressive popular science oeuvre. His latest book features 13 sketches of some of the greatest discoveries in evolutionary biology, but also an inspirational appreciation of the creative, smart, often lucky, but always supremely dedicated scientists behind the textbook facts.

Starting, as a prelude, with the great polymath Alexander von Humboldt’s achievements, and his influence on Darwin, Wallace, and Bates, Carroll divides the rest of the book into 3 sections dealing with different aspects of evolutionary origins: the theory of species’ origins; the actual origins of various animal taxa; and the origins of humans. Chances are you will have met some of the scientists, and their discoveries, before; the trinity mentioned above, of course; Louis Leakey, quite possibly; others might ring vague bells, but due to the breadth of the discoveries covered, revelations are guaranteed. The tenacity and daring of Eugene Dubois, discoverer of Homo erectus, and the part played by Linus Pauling in the development of molecular clock theory, were two such revelations for me.

           

This anthology, of biography melded with discovery, succeeds in finding a wonderful balance between human drama and scientific fact. The excellent referencing and clear scientific content also make it a great introduction to the evolutionary topics covered. Give this book to young scientists whom you wish to inspire; it’s just the antidote for a textbook!

Pre-nuptial botany

Don’t get too excited folks, I just mean before the flowers come out! Incidentally, the word gamete (sex-cell) actually comes from the Ancient Greek for husband and wife.

Identifying plants without flowers is known as vegetative identification and is extremely useful if you want to identify all the plants (above-ground!) at a site in one visit. The wonderful thing about learning vegetative identification is that it makes one look very closely at a plant. One may start botany by identifying the showier herbs and most obvious trees, but, for an intimate knowledge of plants and how to identify them using keys, training your hand-lens on cilia or hydathodes is where it’s at. Luckily a Vegetative Key to the British Flora  (J. Poland & E. Clement; known as ’Poland’) has recently been published, and is available on Amazon.

As an example of the benefits of such knowledge, a recent walk in the Rivelin Valley (Sheffield) to see that “loveliest of trees”, the cherry, yielded the flouncy white flowering spikes of the Bird Cherry (Prunus padus). Even without flowers this can be quickly separated from almost every other Prunus except Rum Cherry (Prunus serotina) by the strongly smelling pith of the twigs (a useful winter ID trick). The heart-shaped (cordate) leaf bases allow us to decide between these two on Bird Cherry: few other books besides the Vegetative Key give you this information. 

However, vegetative characters may not solve all of our problems, elsewhere in the valley I encountered a sapling of a Whitebeam (Sorbus spp.) and a large Cotoneaster shrub. Whitebeams and Cotoneasters are both members of that prudish coterie of plants that often go without sex; one of the upshots of this is that clonal reproduction may result in numerous ‘micro’-species with few obvious differences to help the field botanist. This is where we will want to confirm our identifications by taking so-called ‘voucher’ specimens. Understandably, an identification in a database of a difficult plant species that is not backed up by a voucher will likely be discarded by future botanists as unreliable. 

The Botanical Society of the British Isles (www.bsbi.org.uk) is there to help botanists in this respect: their network of referees (including a ‘Beginner’s referee’) will check member’s specimens, confirming or questioning their identity. The wonderful thing about botany today is the amount of excellent material and support that is available to the enthusiastic. So, to paraphrase (or butcher!) Housman: since fifty springs are little room, to learn about the things in bloom, I’ll go with Poland and a press, so next year I won’t have to guess.