Sunday, 17 August 2014

The problem of data discovery for invasive species

At a recent conference on invasive species someone from the audience requested that there should be fewer databases, to which there was a general muttering of agreement. Can you imagine if someone had said the same thing about books? Surely only an anti-intellectual would want fewer books. However, I perfectly understand the frustrations that lead to this request. All the time there are new launches of databases and websites on alien species, they never have precisely the same remit, but they will always have overlapping interests with other databases. For a time-pressed user, who is scouring the internet for a simple answer to a simple question, there is a bewildering array of data sources. Some are highly visible, others are hidden; some are nice looking, but superficial, while others are mines of information but hard to navigate. The same thing could be said of books, but people expect more of the internet where they were promised a bright future of connectedness and interoperability.

Yet we are not going to get fewer databases any time soon, current funding models and the missions of providers restrict us. Funders want to see clear results from their investment and providers want to create something new for their effort. It is currently hard to achieve those aims if they are tied to a single product. There are other problems, too. Single products don't handle differences of opinion well and local issues related to culture and language are not well suited to a monolithic approach. Furthermore, data is best managed by the people with most interest in it. They have the most incentive to gather new data and they are the experts in their specialisms.

We all want discoverable, accurate, up-to-date information on alien species that are sustainably managed, but for all the reasons I've mentioned we can't yet have fewer databases. Nevertheless, there are many things we can do to improve the situation, which include federation, openness and standardisation.


There is duplication of effort in our invasive species databases. Taxonomic names, common names, references, observation data and specimen data are repeatedly entered and curated by each database independently. This does not have to be the case. We can federate out some of our work to providers who specialise in those data. For example, all modern scientific publications have a Digital Object Identifier (DOI). This simple, but unique identifier is the key to all the bibliographic information on a publication. DOIs are maintained by the publishing industry who will do a better job of looking after this domain of data than we will. In our databases it is only necessary to store the DOI and derive other information from the DOI resolvers. ORCIDs are another example; they are an open, self administered system for uniquely identifying a scientist. They are administered by the scientists themselves who are best placed to do the job and we potentially only need to store the ORCID in our database.
Federation has the potential to reduce costs, while at the same time improving standards, improving sustainability and helping us to concentrate on our core interest of invasion biology.
Nevertheless, if we federate some services we need to trust those services to provide the information we need, at a price we can afford and for those services to be provided for the long term and reliably. DOIs and ORCIDs are supported by the publishing industry and by large academic institutions. Other infrastructures to which we could federate responsibilities might be the Global Names architecture and the GBIF. These infrastructures need communities such as ours to justify their existence, but similarly we might benefit considerably from their domain expertise and investment.


Working within a framework of standards for data quality can be frustrating, particularly in an emerging discipline where standards often seem to be unnecessarily constraining. There is a temptation for everyone to invent their own ‘standard’, yet the advantages of standardization are numerous. We should always be looking to other disciplines to reuse and build upon their standards. Standards that are extensible can provide a flexible approach.
The ability to combine digital resources is a fine goal of standardisation, but to do it we need to understand each other’s data. Wherever possible, we need to explain and annotate our data. Using common standards is a good first step, but we also need to ensure that the metadata is kept up-to-date and accurate. Many people will have noticed the problem of data aggregators where the meaning of data can subtly change as it is transferred from one database to another. The creation of domain ontologies can clarify the meaning of terms without necessarily constraining the development of new data sources. This is a comparatively new field within computer science, but one that should be explored for invasion biology.


Even if we don't want it, we get copyright automatically and are stuck with it for many years after our death, unless we ensure that each of our works is openly licensed. You can't deny the usefulness of open resources such as Wikipedia. And yet, it is perhaps most remarkable for its success in mobilizing data providers. However, scientists are often afraid of openness, thinking that others will ‘steal’ their work and not give them sufficient credit. However, often the reverse is true. Open licensing promotes data discovery and experts can use it to promote themselves through their expertise not the data they hold. Work still needs to be done on providing traceable citations for data, but scientists already have mechanisms for doing this, such as so-called data publications. Scientists also need to become more educated about copyright, as data per se can’t be copyrighted.

To conclude, making data more accessible and discoverable is not an easy task, yet the tools and practises to do it are available to us. What is needed is a change in culture, not necessarily towards having monolithic databases, but towards sharing, openness and connectivity. It will take some investment of resources and progress might seem slow at first, but eventually we can build a global infrastructure for invasive species that satisfies our needs and we don’t necessarily need to have fewer databases to do it.

This work by Quentin Groom is licensed under a Creative Commons Attribution 3.0 Unported License.

Wednesday, 25 June 2014

A third reason for the success of invasive species

A recent paper by Colautti et al. (2014) stated that the success of invasive species can be explained by two views.
  1. intrinsic factors make some species inherently good invaders
  2. species become invasive as a result of extrinsic ecological and genetic influences such as release from natural enemies, hybridization or other novel ecological and evolutionary interactions
This is not an unusual view of invasion biology, but one that is based on a static view of the world. This philosophy views habitats as fixed entities and the invaders being imposed upon them. There is a third reason for the success of invasive species, that new habitat has been create for them. Take for example the simple case of oak gall wasps Andricus aries, A. corruptrix, A. grossulariae, A. liginocolus, A. lucidus and A. quercuscalicis which have all invaded northern Europe in the past 60 years. They all have a complex alternating life cycle requiring two oak species Quercus cerris and Q. robur (Ozaki et al., 2006). However, only Q. robur is native to northern Europe. Q. cerris was introduced to northern Europe in the 18th century and was first found in the wild in the mid-19th century. It has, since then, continually been planted and has naturalised in many places. Thus, mankind created a habitat for these Andricus species where both oaks lived side-by-side and after a short lag the wasps came and occupied it. There is no reason to think these wasps are particularly good invaders, though some have spread quicker than others. Nor have they managed to escape their parasitoids (Ellis, 2005). It is not known if some evolutionary process aided their spread, but why invoke such a mechanism when a more parsimonious one exists?
Another, much less obscure, example is roadside halophytes. In recent years in the UK, roadside halophytes were amongst plants with the largest increase in range (Groom, 2013). Some plants such as Danish scurvy-grass (Cochlearia danica), reflexed saltmarsh grass (Puccinellia distans) and lesser sea-spurrey (Spergularia marina) have increased the quickest, but many different native saltmarsh plants can also be found by roadsides somewhere in Britain. There is no reason to think that halophytes are better invaders than other plants, nor is there any reason to believe that they have escaped natural enemies, as these are native plants. It is unlikely that all of them have undergone evolutionary changes or that there are “novel ecological and evolutionary interactions”. The main thing that has changed is the creation of large amounts of interconnected saline habitat at the side of roads.
Many other examples exist, C4 grasses are spreading in northern Europe due to changes in farming practises (Hoste & Verloove, 2001). Chasmophytes such as ivy-leaved toadflax (Cymbalaria muralis), buddleia (Buddleja davidii) and wall-rue (Asplenium ruta-muraria)  are increasing in cities because of the large number of walls on which they can grow. In numerous cases of invasion the creation of new habitat precedes the invasion. Climate change, atmospheric nitrogen deposition, pollution, forestry, agricultural and cultural changes all alter habitats, potentially priming these species for invasion. If a new habitat is being created one can be fairly sure that some organism will come along and occupy it. I do not discount the other two reasons for invasions, but if we ignore mankind's role in priming the environment for invasion we misunderstand the invasion process of many species.

Cited Literature

  1. Colautti, R.I., Parker, J.D., Cadotte, M.W., Pyšek, P., Brown, C.S., Sax, D.F. and Richardson, D.M. (2014) Quantifying the invasiveness of species. In: Capdevila-Argüelles L, Zilletti B (Eds) Proceedings of 7th NEOBIOTA conference, Pontevedra, Spain. NeoBiota 21: 7–27 doi:10.3897/neobiota.21.5310
  2. Ellis, H.A. (2005) Observations of the Agamic (Knopper Gall) of Andricus quercuscalicis and the associated inquilines and parasitoids in Northumberland. Cecidology 20: 12–27
  3. Groom Q.J. (2013) Some poleward movement of British native vascular plants is occurring, but the fingerprint of climate change is not evident. PeerJ 1:e77
  4. Hoste, I. & Verloove, F. (2001) De opgang van C4-grassen (Poaceae, Paniceae) in de snel evoluerende onkruidvegetaties in maïsakkers tussen Brugge en Gent (Vlaanderen, België). Dumortiera 78: 2–11
  5. Ozaki, K., Yukawa, J., Ohgushi, T. and Price, P.W. (2006) Galling Arthropods and Their Associates. Springer-Verlag, Tokyo
File:Knopper gall on oak (Quercus robur), induced by Andricus quercuscalicis (gall wasp), Arnhem, the Netherlands.jpg
Knopper gall on oak (Quercus robur) induced by Andricus quercuscalicis (gall wasp) by Bj.schoenmakers

This work by Quentin Groom is licensed under a Creative Commons Attribution 3.0 Unported License.

Sunday, 22 June 2014

A request for material of Oxalis corniculata

Oxalis corniculata has become an almost ubiquitous weed of plant pots and borders. Its explosive capsules and sticky seeds let it jump, like a vegetable flea, from pot to pot. This phenomena is not unique to Britain and Ireland. All across Europe O. corniculata can be found in similar situations.
Linnaeus first described the species from Europe, but it is not clear if it is native here. Close relatives exist in North America, Asia and Australasia. It has an extremely plastic phenotype depending on habitat. Characters such as hairiness, leaf size and habit all overlap between species in this group, even though these species do not hybridise readily. It is for this reason my colleagues and I at the Botanic Garden Meise (Belgium) are trying a molecular genetic approach to understanding the O. corniculata group. We are hoping to be able to unravel the phylogeny of these taxa and more precisely define the taxon boundaries. Perhaps we will even get indications of its geographic origins.
We are looking for specimens (fresh or rapidly dried) of plants in the O. corniculata group from as many places as possible. In addition to O. corniculata the corniculata group includes O. corniculata var. atropurpurea, O. dillenii, O. exilis and O. stricta. It doesn't matter if you can’t identify it with certainty, but it would help us match molecular and physical traits if you are able to provide a specimen with fruits and flowers. Nevertheless, even non-fruiting material will help.

Contact me at

This work by Quentin Groom is licensed under a Creative Commons Attribution 3.0 Unported License.

Saturday, 14 June 2014

The Bouchout Declaration for Open Biodiversity Knowledge Management

The Bouchout Declaration for Open Biodiversity Knowledge Management

On the 12th June 2014 the Bouchout Declaration was launched at Bouchout Castle in the grounds of the Botanical Garden Meise, Belgium. The declaration aims to promote openness of biodiversity data and encourage digital access to those data. The original signatories included more than 50 institutions from all over the world. Many were influential institutions such as Kew Gardens in the UK; Berlin Botanic Garden in Germany; Naturalis in the Netherlands and the Natural History Museum, Paris.

I encourage you to sign up to the declaration and support its values, either as an institution or an individual.

Below I've given five reasons why you should sign the declaration and five Dos and Don’ts of data openness… 

Five reasons to sign the The Bouchout Declaration

  1. Good scientists show the evidence for their assertions
  2. Modelling and protecting the biosphere is impossible without large amounts of high quality data
  3. We need evidence-based, not opinion-based, policies
  4. Small amounts of data have little value, but large amounts of pooled data are priceless
  5. These data should not be lost, they will have just as much value in the future

Five DOs of digital openness

  1. Publish your data, so that people can cite you
  2. Ensure your data is available in an agreed standard
  3. Make sure your data is well described so that it can be discovered and is useable
  4. Deposit your data in a long-term repository
  5. Promote the use of your data to others, who might not know how useful it is

Five DON'Ts of digital openness

  1. Don’t sit on your data for years because you think you might make use of it one day
  2. Don’t display your data, but make it difficult for people to download
  3. Don’t hold on to it because you think it has commercial value, unless you actually have a business plan for its exploitation
  4. Don’t restrict access of your data to the IT literate
  5. Don’t think your data is insignificant

Delegates of the pro-iBiosphere Final Event at Bouchout Castle

This work by Quentin Groom is licensed under a Creative Commons Attribution 3.0 Unported License.

Sunday, 6 April 2014

A report of a trip I took to Corsica in 2004

A Continent-like Geography

Corsica has a lot packed into a small area. It is 180 km long and 83 km wide. It covers an area only slightly larger than North Yorkshire, but with less than half its population. Its physical geography reads more like a continent than a small island. It has about 1000 miles of coastline and more than 100 peaks over 2000m. Unlike many islands in the Mediterranean, Corsica has rivers that flow all year round, fed by snow from the highest peaks. This makes Corsica the sparsest populated and the most mountainous island in the western Mediterranean. Habitats of interest to botanists abound. Around the coast are marshes, lagoons, cliffs, dunes, and beaches of sand and shingle. Cultivated land is typically Mediterranean, with meadows, olive groves, chestnut plantations and vineyards. While an impenetrable maquis covers uncultivated land at low elevations; at higher altitude are large forests of Oak and Pine and ascending further still, you can find a true alpine flora.

The mountains of Corsica are built predominantly of granite and rhyolite and though the island is geographically close to Italy, the mountains originate from a thirty million year old chain of mountains that stretched across northern Spain, through the Pyrenees and into the Alps.  Since then, the land mass that includes Corsica and Sardinia has moved south-eastwards and rotated anticlockwise to its present position. Though the topography is dominated by igneous and metamorphic rocks there are some sedimentary rocks, particularly along the east-coast. There are only three small outcrops of limestone rocks, but these are disproportionately important for a number of endemic plants.

More than 130 plant taxa are endemic Corsica and another 75 are only known from the Corsican-Sardinian archipelago. Amongst these are two endemic monospecific genera (Morisia monanthos and Nananthea perpusilla) and a number of other paleoendemics. Some of these endemics are widespread within the island, such as the Corsican Hellebore (Helleborus lividus subsp. corsicus) and the Corsican crocus (Crocus corsicus). Others, such as Brassica insularis and a number of Limonium and Ophrys species, are restricted to limited lengths of coastline and to outcrops of limestone, respectively.

History Has Aided the Conservation of Corsica

Corsica has frequently suffered as a pawn in the power struggles of stronger neighbors. The Pisans, then the Genoese ruled the island for a long time, but Corsica's strategic importance and its vulnerability to seaborne invasion kept the political position of the island unstable until the very end of the 18th century. Napoleon Bonaparte took control of the Island from the British in 1796 and, although he was born of a Corsican family and originally expressed ideas of Corsican nationalism, he did as much as anyone to Gallicise the island. Corsica's problems have not all been created by external powers. The code of the vendetta, which set family against family for generations, reached a peak at the turn of the 17th and 18th centuries. At this time, official records show that about 900 people were being murdered each year out of a population of about 120,000.

Fighting over the ownership of Corsica and under-investment by those rulers have encouraged emigration and has kept the population small. Between the 8th and 18th centuries raids from pirates and slavers forced people to inhabit villages away from the coast. Compounding the political difficulties the mountainous terrain makes communication and transportation difficult and restricts areas suitable for agriculture. Though potentially destructive activities such as overgrazing, charcoal production and timber extraction occur on Corsica they have been moderate, at least in comparison with other Mediterranean islands. Though these geographic and political factors have protected Corsican wildlife to some extent, they have done little to help the Corsican citizens, who have never been wealthy and often favoured their own leaders and system of justice over that of their overseas rulers.

A number of different organisations are involved in conservation on the island, but the largest is the organisation of the Parc Naturel Régional de Corse (PNRC). Founded in 1972 the PNRC covers almost a third of the island and protects an abundance of wildlife. It has a much broader mission than wildlife conservation. It also aims to protect the cultural heritage and the way of life of rural Corsica, while attempting to stimulate enterprise in the much-abandoned villages. While the PNRC oversees conservation in the mountainous centre of the island, many coastal sites are protected by the Conservatoire du Littoral. This is a national organisation dedicated to protecting coastal sites. Though there are many reserves and areas of botanical interest, two in particular deserve mention. Firstly, the Valley of the Fango River, which has been designated a biosphere reserve by UNESCO since 1977, and secondly, the neighboring reserve of Scandola, which is almost entirely inaccessible by land, but includes a large marine reserve. Together, these reserves contain some of the best preserved habitats in the Mediterranean basin. Not only are they important for their flora, but also for their populations of birds, reptiles, fish, amphibians and mammals.

Diverse Forests

Corsica has some extensive forests of native pines and oaks. Perhaps the most inspiring and emblematic are those of Corsican pine (Pinus nigra subsp. larico). These trees can grow to over 50m tall and can live for many hundreds of years. They form forests at altitudes between 900m and 1800m, which are important habitat not only for native plants, but also the endemic and elusive Corsican Nuthatch (Sitta whiteheadi). The variation in relief and rainfall around the island makes for varied forests. On the hills and mountains, in addition to Corsican Pine, are species such as Maritime Pine (Pinus pinaster); Yew (Taxus baccata); Flowering Ash (Fraxinus ornus); Holm Oak (Quercus ilex); Beech (Fagus sylvatica) and Silver Fir (Abies alba). While in wet areas there are Alders (Alnus glutinosa), Willows (Salix alba etc) and the Narrow-leaved Ash (Fraxinus angustifolia). There are also species one might not expect on a Mediterranean island for example Fragrant Alder (Alnus viridis subsp. suaveolens) is an endemic taxa of a species that is found in the mountains of central Europe, northern Asia and North America. It does not grow to much more than 3m, so cannot be called a forest tree, yet it does form dense stands in the sub-alpine zone (1600m-2100m), frequently together with the taller Mountain Ash (Sorbus aucuparia subsp. praemorsa).

Osumda regalis


Wetlands habitats do not instantly spring to mind when thinking of the environment of Mediterranean islands; yet they contribute greatly to the overall biodiversity of Corsica. These habitats include coastal lagoons, marshes, seasonal ponds, rivers, streams, alpine lakes and bogs. Along the east coast are the largest lagoons, such as the Étang de Biguglia.  A literal translation of the word "étang" is "pond", though this is no pond, being 11km long and 2.5 km wide. The Étang de Biguglia is an important reserve for all sorts of creeping, flying and swimming wildlife, but it is also home to a number of rare plant species, including Kosteletzkya pentacarpos, a beautiful member of the Malvaceae. This species is found around the Mediterranean basin, but only where suitable marshland habitat exists.

Site Naturel de la Vallée du Fango
The tides around Corsica do not amount to more than 40cm, so saltmarshes like those on oceanic coasts are not found. Nevertheless, there are a number of saline "wetland" habitats, known in French as sansouire. These are characterised by winter inundation with seawater and then drying in the summer.  A number of halophytes, particularly halophytic members of the Chenopodiaceae (Salicornia, Sarcocornia etc), populate these highly saline habitats. Also near the coast are a number of freshwater ponds, some of which dry out during the summer. Unusual plants such as Baldellia ranunculoides, Ranunculus ophioglossifolius and Pilularia minuta can be found in these uncommon habitats.

The Royal Fern (Osmunda regalis), which has declined across northern Europe, is still common along streams in Corsica as well as in inundated woodlands. It is a species of shady wet habitats on acidic soils and in much of Europe it has been lost where these habitats have been drained. Corsica's rivers, streams and torrents are also home for several endemic species including Doronicum corsicum, Hypericum corsicum and Narthecium reverchonii.
Narthecium reverchonii Celak

 One of the unique wetland habitats of Corsica are the pozzines, which are found between altitudes of 1600m and 2200m. The pozzines are bogs that are frequently traversed by serpentine streams and are pitted with circular pools. These pools give the bogs their name, as the name possine is derived from the Corsican word for pit (Pozzi). Some of the species found in these bogs are more common in Northern Europe than the Mediterranean, for example Drosera rotundifolia and Menyanthes trifoliata, while others are unique to Corsica such as Pinguicula corsica, Bellis bernardii and Juncus requienii.

It is interesting to note that although the species epithets corsicum, corsicus and corsica are used extensively for the islands endemic plants, a number of other names are frequently encountered, for example soleirolii, reverchonii, briquetii and conradii. These names commemorate the botanists Captain Joseph Francois Soleirol (1796-1863); Elisée Reverchon (1835-1914); John Briquet (1870-1931) and Marcelle Conrad (1897-1990). Notice that these botanists were working at a time when the flora of continental France was largely described. Yet whole habitats such as the pozzines were unknown to scientists until the latter half of the twentieth century.

Risks To The Flora

With large areas of forests and scrub, fires are a serious issue on Corsica. Fires are usually started for one of three reasons. They may be unintentionally started; they may be started maliciously, or they may be started intentionally to clear land. At one time the European Union grant system for breeders of nursing cows led to an increase in fires. Farmers were using fires to increase their grazing land to comply with the requirements for subsidies; fortunately, these grants have now been suspended. The EEC has actually made many positive contributions to the island's economy including significant funds for fire prevention and protection on the island. There is a small army of people involved in fire fighting and they possess an arsenal of modern equipment such as recognisance planes and water bombers. Still, on average about 8,200 hectares are burnt each year. While much of the vegetation of the Mediterranean can recover rapidly from fires, even these habitats do not respond well to frequent fires, which contribute significantly to soil erosion.

Opuntia ficus-indica
Alien plants have been introduced to Corsica since at least the Roman period and many of those species, such as the Olive, are as much part of the landscape as the native plants. Yet modern introductions, many from different continents, present a threat to native plants. About 140 species have naturalised on the island and many others are planted or are casual. Two of the most destructive are the South African succulents Carpobrotus edulis and C. acinaciformis. These species form mats over coastal rocks, eliminating all other plants. Another South African introduction, Cotula coronopifolia, poses a threat to wetlands. In places, this plant has become the dominant species, eliminating practically all other herbs. A number of other potentially damaging species have naturalised or are planted such as Prickly Pear (Opuntia ficus-indica); Bermuda buttercup (Oxalis per-caprae) and several Eucalyptus species.

Changes in farming practices have had both positive and negative impacts on native plants. Since world war two there has been continual migration out of villages and a decline in traditional farming. The cultivation of chestnuts and the maintenance of terraces have declined in the hills, whereas in the lowlands vineyards have increased as has the growing of non-traditional crops such as kiwi fruit. At one time, the annual movements of livestock, known as transhumance, were an important element of agriculture in the mountains. However, these days the ancient mountain trackways are more frequently used as hiking trails.

Improvements in the roads and increased ownership of four wheel drive vehicles have made once remote corners of the island accessible. Even high altitude has not protected the pozzines from damage and popular hiking routes to the high mountain lakes have been rerouted where damage was occurring. With jeeps and motorbikes, tourists can visit once deserted beaches that are only accessible by rough tracks and these days damage to dune systems by motor-sports is common. Other risks include the collection of wild plants for gardens or for their medicinal properties. Wetlands are particularly vulnerable as they can easily be drained or overgrazed.

One should not overplay the risks though. Corsicans, in general, are proud of their environmental heritage and one can hardly deny the Corsicans the improvements in lifestyle that decent roads and an adequate infrastructure bring. Here, I can only give a flavour of the flora of Corsica and hint at the conservation challenges. I encourage you to learn more about Corsica, even though you may need to learn some French to do so. Corsica's history has protected its wildlife to some extent, but in the future, it will be a challenge to balance the aspirations of the people with environmental protection. Still, in this respect, Corsica is not unique and it is fortunate to have a population and institutions friendly towards environmental protection.

This work by Quentin Groom is licensed under a Creative Commons Attribution 3.0 Unported License.

Tuesday, 18 March 2014

Help conservation and science by being more proactive in managing your copyright

Botanical floras are subject to copyright, In the UK you are prohibited from copying someone's text until 70 years after their death, although there are some limited exceptions.
Copyright is automatic and protects you from someone else profiting from your work without your permission. This concept works well for J.K. Rowling, but it is a disaster for science and conservation. Why? Well, I expect most people do not write floras for money, but to communicate to other interested people. Floras are usually printed in small volumes, often only in one edition. Once they are sold out, they can be very hard to obtain. If a person of 25 wrote a flora, then that volume could pass out of copyright more than 100 year from now.
What does this mean in practise? People who want to reuse floras for research and conservation can’t. Historical publications are essential for understanding change in our flora. They contain information about the present that will be an invaluable source of information in the future. Floras contains all sorts of useful information, keys, pictures, descriptions and observations. They only have scientific value, and no one will make money from them. Just look at how useful open resources such as Wikipedia and the Biodiversity Heritage Library are. If you are an author be more proactive in managing your copyrights. Think about publishing with the creative commons CC-BY licence or perhaps put an embargo period on your licencing, after which the work becomes open-access.

This work by Quentin Groom is licensed under a Creative Commons Attribution 3.0 Unported License.