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I am in Berlin - home of Checkpoint Charlie and the ex-Wall - at a Biodiversity networking meeting, talking with a totally new set of colleagues about how to connect the science we do with government policy in Europe and at home. Really interesting and has opened my eyes to a new world where nightshades are important (of course!), but where people and how they connect across cultures, languages and ways of working are even more important.

 

But while sitting in the talks and workshops, in the back of my mind I am thinking about Friday this week and the annual Science Uncovered event in London. Fortunately, I will be back in time.....  just.

 

This year, in addition to being part of the Food station with an array of potatoes, tomatoes, aubergines and their friends and relatives, I will be part of Science Fess Up - where a couple of us at a time will talk with people about what WE don't know about science. Challenging? You bet! Not because there is a lack of things to talk about, but just where to start, the depths of my ignorance about lots of things is so profound........ 

 

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An array of eggplants in Avignon - all but the red one in the centre are members of the same species, Solanum melongena - the aubergine.

 

This event has been a great opportunity for me to reflect on just why I love science so much - and why I feel so lucky to be doing it as a daily job - it is a constant adventure, something new around every corner. So come along and let's talk about why its good not to know everything, and why exploring what you don't know is so exciting...oh and of course there will be lots of nightshades - thanks to new colleague Xavier Aubriot, who has just joined the team to study the nightshades of Asia - a big area where we know very little.

 

Part of the Food station will be a pile of however many different sorts of edible nightshades we have been able to find in the markets of London - we hope lots!! These crops are so much a part of our daily lives we often forget about their wild relatives that harbour important genetic diversity that will be key to improving agriculture in the face of environmental change - including that of our climate - that we know lies ahead. The taxonomic work we do here at the Museum into these species is key to unlocking this treasure trove.... come and hear about our latest ideas and adventures, and share what you think we should be thinking about!

 

See you there!

 

Science Uncovered takes place tomorrow, Friday 27 September at the Natural History Museum, London. Join us from 4pm to midnight.

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As I mentioned in an earlier post on the Seeking Nightshades in South America blog, I am in North Carolina at Duke University to give a talk about Alfred Russel Wallace (whose centenary we celebrate this year with lots of exciting events at the Museum in London) at the opening of an exhibit featuring the Duke herbarium.

 

Collections associated with universities are under threat worldwide - they take up lots of space that could be given over to labs or teaching space, and are often not considered necessary for the research projects that attract funding. Larger collections like the ones we hold at the Natural History Museum in London, or those at Kew Gardens or the Royal Botanic Gardens Edinburgh sometimes have an easier time justifying themselves in the face of competing pressures, but not always!

 

The herbarium is thriving at Duke - with almost a million specimens, it is one of the largest plant collections associated with a university in the United States. There is new housing for the flowering plants, and the university administration values the herbarium as an integral part of the Department of Biology. This is a real success story.

 

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New compactors for the flowering plant specimens in the basement of the celebrated Duke Phytotron building; curator Layne Huiet bring me more Solanum specimens to identify!

 

I have spent the last couple of days working in the collection here, and it has come home to me how important these specimens are, and how important it is that they are held in institutions of higher learning and not just given away to big national museums.

 

The value of university collections

 

The Duke collection is a resource for a person like me - who comes in and wants to see as many solanums (or whatever else they might be working on!) as possible, but also a resource for the students, who can use the collection on-site to explore questions about the natural world.

 

These university collections are also unique in that they hold the materials that have been generated as part of PhD studies, or first year field courses - they are a part of the legacy of the institution in the same way as is a library. Unlike a library though, students can be part of building a museum or herbarium collection through their own contributions. The plants they collect on field trips or field courses become permanent records and can help other students.

 

The Duke collections are strong in plants of the region - making the herbarium locally relevant - and in plants from Costa Rica, where a long association with the Organization for Tropcial Studies brought projects and interest. So how did the botanists manage to make the herbarium seen as an asset and not a drain?

 

The power of positivity is at work here - the halls outside the herbarium are full of posters showing how herbarium specimens have been used to answer big questions in biology - climate change, invasive species, spread of disease - with big full page pdfs of articles in those high impact journals so beloved of those in charge. Kathleen Pryer, the director of the herbarium and fern systematist (and the person who, with her student and another colleague, rather famously named a fern genus for Lady Gaga!!), markets the collections tirelessly, with good effect.

 

Rather than giving ties or engraved glass bowls to visiting dignitaries Duke administrators now give away framed scans of beautiful herbarium specimens - and people love them! In fact, they are so in demand that the botanists are talking about going out and collecting some iconic local plants to make some new special prints - what a clever idea. Each scan comes with its biological relevance, driving home the message. The exhibit that opens today is entitled 'Botanical Treasures from Duke's Hidden Library' - a very good analogy.

 

 

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Framed scans of herbarium specimens from the Duke collections in a biology conference room

 

 

There is a lot of discussion worldwide about consolidation of collections and some universities at least are deciding they no longer wish to keep the herbaria and museums that formed part of their past academic offering. Perhaps they are seen as old-fashioned, a drain on resources or just not relevant anymore. This is a mistake I feel, as these collections are the starting place for many new questions - if they are made accessible and valued.

 

It is not necessarily easy, but university collections are special just because of where they are, in the thick of training the next generations not only of scientists, but of citizens.

 

Long may they last in their academic homes, inspiring students and being part of the fabric of universities everywhere......

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So, I arrived safely in Cordoba – was met at the airport by Gloria, went to the herbarium to check a few plant localities for the trip, and then crashed! Today we set off bright and early to drive due south from Cordoba to Bahia Blanca, a distance of some 1000 kilometres.

 

In Argentina, the most important thing to pack is the yerba mate equipment! Yerba mate, or mate as it is often called, is made from the leaves of a holly relative – Ilex paraguariensis – that grows in the forests of the northeast of the country (and in Paraguay). The leaves are dried and crumbled and look a bit like tea. In Argentina, mate is always drunk with hot water and through a silver straw.

 

So what happens is that the cup is packed with leaves, hot water poured over, it is given to one person, who drinks it up through the straw, and then the process is repeated for each person in the car. Very convivial and I do love mate! In Paraguay, mate is drunk with cold water and is called terere.

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Supplies for the long journey.

 

South from Cordoba we enter a huge agricultural region where fields of soybean, sorghum and maize cover the landscape. This region is one of the main soybean growing areas in Argentina – we saw various bits of graffiti saying (in essence) “Don’t let soybeans come and ruin our lives!” But soybean cultivation is there, and very extensive indeed. My colleagues say it is mostly exported to China.

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The landscape is flat, flat, flat – and was very hot! We got out a few times to look for a still elusive species of the genus Jaborosa (Jaborosa bergii) – but no luck yet…..  it is a tiny little annual growing in exposed sand dunes so might have just come and gone before we got there. Lots of the vegetation was drying up. A few things bloomed though – like this prickly poppy – Argemone subfusiformis.

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Argemone subfusiformis - a prickly poppy.

 

On and on we drove – until we reached what I thought of as real Argentine pampas – grassy habitat with cows and sheep. The road was absolutely straight, like a Roman road in England, but with lots of sun!!

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All road trips end up with some disaster, and today was no exception. We had a flat tyre out in the pampas, about 141 kilometres from our destination in the middle of nowhere. Amazingly, this was the first time any of my compañeros had experienced a flat during field work – incredible! The institute maintains their vehicles very well! So Juan and Franco set to work changing the tyre, while Gloria and I looked for Solanaceae.

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Flat tyre in the middle of rural Argentina - an apportunity for Solanaceae-hunting.

 

All’s well that ends well – and we arrived in Bahia Blanca (in the province of Buenos Aires and on the Atlantic) in time for supper at 11 pm or so. Tomorrow we will hug the coast looking for the elusive Jaborosa bergii again, plus a number of other treasures. I will not forget my first view of the pampas though, one can see forever, and if you imagine it right you can almost see the earth’s curvature, the horizon is so far away! Can’t wait for tomorrow’s excitement……..

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Human beings depend upon a handful of flowering plants for 80% of their caloric intake - this in spite of the estimated approximately 400,000 species of flowering plants! In the face of discussions and concerns about global food security, agriculture's attention is turning to the wild species that are related to these staple crops for ideas about how to face massive environmental change.

 

For the past few days, I have been at a meeting convened by the Global Crop Diversity Trust (http://www.croptrust.org/) and funded by a variety of organisations to discuss the challenges and opportunities wild relatives of crops represent. Now, my take on these plants is very firmly from the biodiversity end of the spectrum - and is pretty narrowly focused on Solanaceae, so these few days have been a real learning experience! The group includes people working on rice, maize and wheat, but also apples, barley, amaranthus, soybean, peanut - you name it, the crop is there!  The place is also fantastic - the Asilomar Conference Center on the Monterey peninsula in central California - what better place to come together and leave day-to-day cares behind to really talk about issues.

 

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The view of the Pacific Ocean (very cold!!) from Asilomar State Park

 

What has surprised me is the degree to which the world of germplasm banks (sort of museums for the seed and plant collections used by plant breeders to improve our crop plants) is parallel to, but rarely intersecting with, my more familiar museum world. Databases are an issue, the avalanche of data coming from genomic approaches .... we all have these same challenges! We could do a lot to help one another, and to see how the challenges we face are actually the same at their core, with subtle differences depending on the specific circumstances.

 

I feel incredibly privledged to have been invited to be a part of this group - and realise how relevant the data we hold in our rich and global collections can be used to help other communities ....  however distant those might be.

 

Solanaceae - my nightshades - have as members many important vegetable crops - tomato, potato, pepper, eggplant (aubergine).... vegetables are often left out of the equation in terms of food security, where focus is on the big grain crops that provide our carbohydrates. But vegetables are key to a balanced diet - vitamins and nutrients are key to human health.  Vegetablse are also locally adapted and consumed, providing a unique opportunity for linking local and global issues, and for linking food prduction to biodiversity issues.

 

My brain is buzzing with new ideas and possible new projects for the future....  at museums we often get bogged down in the enormity of our task, describing wild diversity and enablign its conservation, such that the sheer massive usefulness of the informationfrom our collections we hold and curate for future generations to biology beyond the museum walls can slip into the background. Getting out into communities very different from our own can be scary (lots of words I don't know were bandied about these few days!!) but it is critical for realising the role the Museum can play - its big, and a bit frightening, and very different - but oh so exciting!.

 

Getting out is GOOD!!

 

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Sunset over the Pacific.....

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So it seems that everybody just duplicates everything… As Sandy wrote from Étape Eggplant in Montfavet, our last week’s focus on eggplants has revealed that duplicates are an issues not only in our database but in any collections such as world’s seed bank collections. So what is it with duplicates that make them an issue?

 

My role last week included gathering data on eggplant wild relatives, including both records of their natural distribution and currently available germplasm collections in seed banks. The idea of the gap analysis is to see whether eggplant crop wild relative (CWR) diversity is conserved in seed bank collections, and to identify where new collections should be made. It is a fascinating job – not only does it surprise you that such basic questions have not been looked into before, but the job also turns out to be more complex than you would expect at first.

 

It is easy to assume we (or somebody high up in one of the United Nations offices) know what is currently conserved in seed bank collections around the world. Seed banks are, after all, cornerstones of food security, banking seeds for the future if something would to happen. So somebody is counting what is being conserved across the globe, right? The answer is not that simple. For the ten or so most important food crops, specialised research institutes have been established to secure conservation and management of these important crops. For others, such as eggplant, the story is different.

 

World’s major seed banks, or genebanks as they are often called, all have their focus groups or focal areas. The bulk of these genebanks belong to CGIAR, the Consultative Group on International Agricultural Research, which is an informal network of 16 international agricultural research centres. Together, these 16 institutions manage c. 600,000 agricultural seed samples – that is quite a lot! On top of these international giants, there are national or more regional genebanks, such as the United States Department of Agriculture’s National Plant Germplasm Service (NPGS), and the Dutch national seed bank at Wageningen University, the Centre for Genetic Resources, the Netherlands (CGR). Despite their different sizes and slightly different mandates, these seed banks all share the aim of preserving crop diversity.

 

Svalbard.jpgPicture of the Svalbard Global Seed Vault: located in Spitsbergen, an island north of Norway, the Vault is storing seeds for the future.

 

The idea behind seed banking is to conserved diversity for future, short or long term, needs. These needs change through time. Currently, focus is being given to breeding crops to prepare them for the changing climates, as well as increased disease and environmental stress resistance. What needs to be analysed, however, is whether the currently conserved accessions in seed banks have potential in breeding efforts for these priority traits. Gap analysis, such as our project on eggplants and their wild relatives, have been developed to answer these questions and play an important role in understanding the potential of currently banked accessions for these priority breeding targets.

 

How does this all relate to duplications? Well from my short experience in this field, I have learnt that many of our global seed collections are actually duplicates. I have now worked on both tomato and eggplant CWR collections, downloading germplasm data from individual genebanks and then merging them to a single file to prepare them for the gap analysis. Seed banks exchange material, not only for diplomatic reasons but for the very important reason of securing their collections. Such duplications are called safety duplications, and are mandatory for large genebanks. This assures that if something would to happen due to political (wars do happen unfortunately) or environmental reasons (e.g. earthquakes), not all eggs were put in one basket.

 

What does this mean for food security? Well firstly it is great that if something would to happen, duplicates are safe somewhere around the world. But the other side of the coin is that although seemingly looking large at first sight, the actual number of seed collections conserved around the world is not that big after all. Conserving and preserving seeds in long term storage is costly, and this reduces the amount that can be kept in the banks.

 

My job this week continues to focus on pruning some of these duplicates out. For the sake of our gap analysis, we want to make sure we represent the global collections realistically. Some argue that duplicates can be viewed as unique collections because seeds have to be regenerated at regular time intervals and this process leads to slight differences between the duplicate collections. From the point of view of unique genetic resources that could be used for adapting our crops to climate change, we need truly unique collections that represent extreme environmental adaptations. Complex traits such as drought resistance or salt tolerance do not vary between duplicates – they evolve over hundreds if not thousands or even millions of years.

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Sandy and Tiina, in Montfavet, near Avignon, France 

 

We had a small diversion in our sporting calendar to the south of France; we were invited to participate in a meeting convened by the Global Crop Diversity Trust (http://www.croptrust.org/) to discuss how the diversity of eggplant wild relatives could be conserved. The eggplant or aubergine is a species of SolanumSolanum melongena, and although not very physically similar to potato (Solanum tuberosum) or tomato (Solanum lycopersicum) it does have genetic similarities.

 

We worked hard, our days were not quite as physically demanding as those in the Tour de France ascent of the nearby Mont Ventoux (left out of the 2012 Tour), but we made a lot of progress! One fascinating fact is that in English, French biologists refer to our vegetable aubergine as the eggplant – just goes to show how language exchange can be pretty random!

 

Christine Daunay of INRA (http://www.international.inra.fr/), Jaime Prohens of the Universitat Politècnica de València (http://www.upv.es), Hannes Dempewolf of the Trust along with Tiina and I talked about the taxonomy of wild eggplants (based on the work of Maria Vorontsova), the state of seed collections of wild eggplants and what eggplant breeders need to improve the crop, especially in the face of climate change.

 

Despite its importance as a world crop, the community of plant breeders working on eggplant are few and far between – it is clear from the meeting that future collaboration with colleagues in India and China – the home of eggplant domestication – will be critical. The wild relatives of the crop are from Africa and future collecting to understand their ranges and environmental tolerances will be important for eggplant improvement. This is where the world of taxonomy intersects with the world of plant breeding and agriculture – knowledge from wild relatives can really help with problems faced by those in agriculture, not just in terms of genes that can be introduced into crops from wild relatives, but in understanding adaptation to different environments and habitats.

 

Our colleague Christine keeps a collection of seeds of wild relatives of eggplants, and we toured her fields and greenhouses – reminding us that Solanum species are more amazing than imaginable – truly paradoxical plants!

 

We returned to London and Edinburgh via TGV (Train à Grand Vitesse – and it is really fast!) through the French countryside and came back to an excited Britain – lots had happened while we were deep in discussing food. Time to catch up with all the other action!

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Day 1 and 2 from Edinburgh

 

Similar to Sandy I was impressed by the plant inspired ending of Friday night’s ceremony! Whilst watching the inspiring event, I was looking through our database and seeing how big my part of the task ahead really is going to be…

 

As Sandy explained, simple differences in typing collectors names can result in two names being allocated to a single person – like the example of A. Fernandez and A. Fernández. The accent makes all the difference to the computer! The implications of such typo’s or spelling differences are what I’ll be focusing on this week.

 

Let me give an exaxmple of job as the “duplicate hunter” as I have named myself. If, for example, specimen “Fernandez 212” is being entered to our database, the database performs an automated check if other specimens (also known as duplicates) of the collection event already have been entered or not. If another duplicate of the collection event has been entered as “Fernández 212” with the accent on the a, whilst the one being entered is missing it, these two specimens will become part of two separate collection events… Again we can’t blame the computer, as the names are not exactly identical!

 

So I went into our database and checked how many collection events are identical based on collection number (for example 212) and collection date (day, month and year). As collection number and dates are numerical, typo’s caused by alternative spellings do not generally cause issues (although see below), meaning that identical entries can be identified easily.

 

Using the above ever-so-clever but simple technique, I identified 1839 records that are potentially duplicated. Of course there is a large list of collections that are not true duplicates although they appear on our suspected list. These are collections that have, just by chance, same number and collection dates. A mere 1549 of the 1839 suspected are collections that lack number, which are all labelled with number “s.n.” according to old tradition as “s.n.” means “without number” in latin. What the letters s.n. truly stand for escapes me now – s. = sin, but n. = numero or numerus? Latin speakers will be able to help me out here…

 

Prior to our Plant Challenge, I did a spur of duplicate spotting in our database over one quiet day. I found out that there are several errors leading to duplications. Spelling mistakes or alternative spellings of collectors’ names is one reason, but alternative spellings of numbers is another reason, although small I grant you. There is a set of numbers which have been entered with an unnecessary 0, such as “012” which appears simply as “12” in another duplicate entry. I plan to tackle these duplicates by filtering all collection numbers with “0” and then sorting in numerical order. There seems to be an additional 100 or so records to check there.

 

And lastly there are ones where duplicates appear simply as identical duplicates. These are ones where collectors name and collection number appear perfectly identical, and truly are. Although we try to elimanate entering duplicate records, it always happens, somehow

 

Quite impressively, I have now tagged myself a list of 11 388 collection events to check and go through!!! By no means will all of these records represent true duplicate entries – our data set is relatively clean we believe – but one never knows …

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Plant Challenge Day 1 from North London

 

After the wowser event on Friday night (http://www.bbc.co.uk/news/in-pictures-19020830) that even had a botanical motif at the end - data cleaning began early on Saturday morning.......

 

My task is to check names of people in the database, eliminate duplicates and correct spellings, and to fill in fields like first name and full name. Sounds easy.......

 

I made it through the letter A, well almost. Checking the identity of collectors of plants involves seeing where they were when - for example two Stephen Allens - one from the 1890s and one from the 1970s, could exist, so just assuming they are the same is dangerous. Once I had determined people were indeed different, I cross-checked with numerous external web databases ( like that at Harvard http://kiki.huh.harvard.edu/databases/publication_index.html, or the one in JStor Plant Science http://plants.jstor.org/) to double check first names, initials and dates.

 

Along the way I correct diacritical marks (accents) in non-English surnames - it is easy when entering data to leave off the accent in a name like Fernández - the computer thinks A. Fernandez and A. Fernández are different people - it is only a machine after all - when in fact they are one and the same. So the collections attributed to each need to be merged.

 

All this takes time, but in the end is worth it. I also managed to find a few plant name mysteries while dealing with people - all tiny little things that once solved put another puzzle piece in place for our eventual documentation of the diversity of Solanum. Even though my eyes go squiffy from staring at the screen it is great to feel like things are getting cleaned up - and it just reminds me how much I really do like these plants - they are great!

 

We are also getting ready to go to a meeting in France with some eggplant (aubergines for we Brits) breeders - so I have also been thinking about how to present our results on the taxonomy of African Solanum (done by Maria Vorontsova - see her previous blogs on collecting in Africa http://www.nhm.ac.uk/natureplus/blogs/wildspiny/tags/africa?fromGateway=true) in the most user-friendly way - a different sort of challenge!

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Plant Challenge - Let's begin!

Posted by Tiina Jul 23, 2012

A certain major sporting event will get under way this Friday and we'll be having our own celebration by launching our own Plant Challenge!

 

Here at the Solanaceae team we will be writing daily blogs about our activities. We have set ourselves a goal – a challenging goal we hope to achieve but in order to do so we might need a bit of luck and lots of hard work! The great big goal is to clean and update our ever growing BRAHMS database which holds the data needed for running the great Solanaceae Source website soon to be updated to Scratch pad 2. This is not a small task by any means: the database currently includes 60,005 collection events, 72,301 individual specimen entries, 16,759 collectors names, 13,565 species names, 19,318 gazetteer entries, and 71,345 species determination records!

 

Between Friday 27 July and Friday 10 August you can follow up on our progress and hear how our efforts are going. Our Team consists of three people: Mamen (Maria Peña Chocarro), Sandy, and Tiina. Mamen will be in charge of geography, Sandy is focusing on cleaning collectors, nomenclature, and literature, and Tiina is taking on data entry and unifying data records. Despite months of hard and strenuous training, the contestants are feeling nervous yet incredibly excited! One thing is for sure - the journey will be full of surprises, as you never know what one finds inside the big matrix!!!

 

The team will use “divide and conquer” strategy to tackle the mammoth task. Whilst Mamen and Sandy will stay at the project headquarters in London, Tiina will be sent to Edinburgh to the Royal Botanic Gardens Edinburgh to establish a remote base for the operations. The equipment for the task will include three laptops, three internet connections, and three desks. Coordination of research will be done through email and phones.

 

Whether you are a scientist or a keen natural historian, join us in your efforts in Plant Challenge! Send your comments to our blog, with links to your own planty challenge feat!

 

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