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

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SSSIs in the Sheffield Area

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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)