Scottish Rock Garden Club Forum
General Subjects => Blogs and Diaries => Topic started by: alanelliott on February 20, 2014, 05:31:50 PM
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What I do when not swanning about taking pictures in the Alpine house here in the Garden.
I've been a member of the SRGC since 2006 [I think]. I was press ganged by Boyd Barr, Ed Stone and Steve McNamara when I was a Horticulture student getting some work experience at Branklyn Garden. I have been lucky enough to be supported by the SRGC on a number of occassions to get me to where I am today. So I am going to share with you what I do here at Royal Botanic Garden Edinbrugh (RBGE).
I am in what I see as the enviable position of not only being able to cultivate alpines at home for the sheer enjoyment and frustration of it, but I also get to do research on the influence of the Himalaya has had on mega-diversity of plant life (with a focus broadly on alpines) found there. This also comes with plenty of enjoyment and frustration.
I am currently in year three of a four year studentship funded by the Biotechnology and Biological Sciences Research Council (BBSRC) with the University of Edinburgh, but as many of you will know I am based at RBGE. My project has the grandiose title of Phylogeography and the dynamics of speciation in the Himalaya. Hopefully by the end of this series of posts we'll have a fair idea what its all about.
I am also lucky in that I’ve had the opportunity to participate in fieldwork in the Nepal Himalaya - supported by the SRGC. In 2012 I took part in the Japanese Society of Himalayan Botany led expedition to the Api Himal in Far West Nepal. www.srgc.net/forum/index.php?topic=9543.0 (http://www.srgc.net/forum/index.php?topic=9543.0) - plenty of pretty pictures there.
This year I am hoping to join the RBGE led expedition starting in Baglung District then through Jajarakot and into Dolpa district. We are specifically aiming for the type localities of several Nepalese endemic species, including Clematis phlebantha and Primula ramzanae - Phoksundo Tal visited by Polunin Sykes and Williams. These collection trips gather plant material to create herbarium specimens and also bits of leaf that we store in silica gel for later molecular analysis. We are no longer able to collect living material as there is a blanket ban on the export of all living material and seed from Nepal. Even buying chilli seed at a market in Kathmandu will end up confiscated at the airport. As frustrating as that is we have to respect the laws of the country as we would expect visitors to respect ours.
My project has three distinct threads.
- Some alpha taxonomy - describing the diversity of Clematis found in Nepal.
- The phylogeography of Clematis in the Himalaya - using the genetic relationships of the species and analysing the geographic distributions
- and a Meta-Analysis of existing published phylogenies - this will hopefully give a bigger picture of how evolution has happened in the Himalaya
I'll go through each of these bits in turn over the next wee while.
But here some images from 2012 in Darchula. Mountains and international scientific collaboration in action.
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Looking forward to more Alan. Yet another attempt (probably doomed to failure as a result of the lack of intellect from the student rather than from the lecturer) to give me even a basic understanding of the scientific world.
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Very interesting. You say "We are no longer able to collect living material as there is a blanket ban on the export of all living material and seed from Nepal". I have just received a flyer inviting me to buy shares in a seed collecting expedition to Nepal in September and October. Participants are Dr Paul Bygrave of Forde Abbey, David Howard, former Head Gardener at Highgrove, and Ray Brown of Plant World in Devon. So how does that work? Could it be the Highgrove connection - HRH pulling a few strings?
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I have just received a flyer inviting me to buy shares in a seed collecting expedition to Nepal in September and October. Participants are Dr Paul Bygrave of Forde Abbey, David Howard, former Head Gardener at Highgrove, and Ray Brown of Plant World in Devon. So how does that work? Could it be the Highgrove connection - HRH pulling a few strings?
John
Interesting.
It will be 100% illegal and it has been that way for a several years now. Law categorically states that no living material including seed can be collected or removed from the country, no ifs no buts. I know that collectors have been selling seed from Nepal in recent years, I'm not naming any names but I'm sure people are well aware of who they are.
However the recent uptdate to the legislation in Nepal has tightened the law further. The legislation now covers Nepalese nationals too. They are now no longer allowed to collect plants and seed without a permit - one way people were side stepping the legislation by getting people in-country to collect on their behalf.
I know some folk are still in the mindset that its ok to collect plants saying what hard would it do to collect a few plants? Looking at it on the flipside I'm sure there would be an outcry here if collectors came to the UK and helped themselves to some of the remaining populations of Primula scotica in Sutherland and Primula farinosa in Teesdale. As sad as it is the world has change and people have to accept it.
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Looking forward to more Alan. Yet another attempt (probably doomed to failure as a result of the lack of intellect from the student rather than from the lecturer) to give me even a basic understanding of the scientific world.
David. You and me both.
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Alan - as a 'philosophical point' does this imply that an interest in wild species will in the future only be open to Botanic Gardens and Nationals of particular countries? The specialist plant societies, and in particular the AGS and SRGC are rooted in this individual interest in wild species, and introducing new material from the wild, so will this intellectual curiousity become more stifled in the future? Will gardeners with that fundamental interest in natural species find this no longer possible to satisfy? After all many are not well enough off to travel widely. (I am taking a slightly extreme stance because at the moment seed is available from many sources, and I suppose may well continue to be). I am not sure there is a flipside because how many people in other countries would be especially interested in the British flora? (though I take your underlying point). Seeds of many plants are produced to huge excess in Nature, whereas of course plants themselves should be properly protected.
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As Alan's earlier comment shows, and as has been mentioned in earlier threads, NOT EVEN Botanic Gardens can legally collect seeds in many countries nowadays.
With some joint expeditions with RBGE and Chinese Botanic Gardens, as I understand it, the only collecting has been for herbarium specimens for the Chinese Botanic Garden involved, the RBGE members have not been allowed anything.
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Apologies for all the text.
Yes I would say there is a general stiffling at the moment for everyone. Botanic gardens find it increasing difficult to work in certain countries. US institutes find if difficult because many countries see their Botanic gardens as commercial enterprises. A recent UK example I know of is RBG-Kew were unable to collect Araucaria from New Caledonia because the perception was that they would release the material into the UK trade.
We only work in countries where we can collaborate because it is the only way to get through the bureaucracy. What Maggie said is true RBGE despite our historic links and continuing working relationship with Kunming, running the joint field station, have found increasingly difficult to get herbarium material from China. One reason China are now reluctant to "give" material away is the sheer volume of money being thrown at science out there and the hope that what they find might generate income in new products. There is a growing body of work on the biochemistry of Meconopsis all produced in China because of its medicinal uses. So unsurprisingly countries see the income of large pharmaceutical companies and to an extent "how much" horticulture generates may well play a role in the protection of their plantlife.
Its not just China.
The Flora of Nepal team a couple of years ago were on their way to Nepal and the law was changed while they were in the air. Arriving to find the permits to collect herbarium material were no longer valid - two week sitting around in kathmandhu trying to get them reissued. Some latin American countries have sold their entire biodiversity "rights" to pharmaceutical companies and unsurprisingly they are now guarding it fiercely.
Tim what you say about seeds being produced in large quantities is often true but relative to any quantitiy of seed produced only small percentages will survive to maturity and by taking any it will deplete the potentail genepool.
Woodsia illvensis (not a seed producer) does not regenerate in the UK anymore - the climate is no longer suitable. This species in its few remaining populations produce thousands of viable spores but they do not grow but they are there in the soil "seed" bank. We know they are viable because of harvesting soil from around exisiting plants and giving controlled conditions have generated hundreds of plants for reintroduction to the sites.
If you are somewhere and you see a population of mature plants how do you know if its ok to take seed? It might be like Woodsia , the seed needed in the seed bank to wait for their day or then again with if it never comes? It is a difficult problem.
There is at least some cause for hope. India is impossible to collaborate botanically and they also prohibit the removal of any plant matieral. However, I hope you are aware of this nursery, http://himalayangardens.com/index.html (http://himalayangardens.com/index.html) . They have been growing material from India in India and shipping it to a nursery in Scotland for sale in the UK. The government there only agreed to it because the parent company is in India and therefore tha cash flows back. This model is probably the way forward - if you are a species snob like me.
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Thanks Alan that is very valuable to know. I think also it highlights the importance of those specialist nurseries in the UK that do grow and keep plants (especially species) in cultivation, rather than being entirely at the whims of the horticultural trade and public (relatively uneducated) demand.
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I hadn't expected the discussion aspect of the previous post but keep it coming. Happy to field questions, and (try to) take things into more detail if requested. So...
The first aspect of the project is writing the taxonomic account of Clematis for the Flora of Nepal project. This is very much a traditional alpha taxonomy exercise: finding, naming, describing diversity.
I’ve been doing this using the time honoured tradition of looking at dry, dead bits of plants also known as herbarium specimens. Most of the work has been done here in the herbarium in Edinburgh but I’ve also spent time in the Natural History Museum London, RBG-Kew and the National Herbarium in Kathmandu.
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RBGE's herbarium - it is as glamorous as it looks.
So how do you go about describing the diversity of a group of plants?
The first step is to layout all your specimens. You then start making piles of specimens that look similar. You then look at one of your piles and see if they are all similar or if you can split them up some more. Perhaps after a cup of tea you come back look at your two piles and think nonsense, clearly the same thing. So you put the piles back together again. Then after a good hearty RBGE canteen curry you split the pile up again because, you know, you can’t really have too many Clematis.
Once you are happy with your piles (is anybody ever?) you can start describing what you see. This often involves using a hand lens or looking down microscopes because the “important” characters are often not clear to the naked eye.Then there is the measuring, the endless measuring and most importantly trying to remember the proper word for that feathery bit or the correct term for that green thing - oh yes a leaf.
As part of the Flora of Nepal project and others based out of the garden we take field images of the specimens to create records of the plants as they looked before they were pressed, dried and mounted. This is because characters don’t always survive the process - colour is the classic one. These often end up being incredibly useful.
Like this Clematis alternata
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Habitat shot
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Flowering Stem
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Close-up of flowers.
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The specimen the unfortunate plant became
Often it isn’t enough to delimit a species based on what it looks like, lord knows people have tried and it turns out we are all the same. In this revision it has been done in the light of the genetic relationships and any other relevant data that can help with the decision of what is a "distinct" entity. But more on that another day.
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An important part of the taxonomic side to the project is checking nomenclatural rules associated with plant names. IT can range from tedious when it’s all been done correctly to quite engaging when it hasn’t and you are doing your best paper trail detective work.
You should check every single name you are working with. For Clematis in Nepal i have about 25 species and subspecies to work with but when you take synonomy into account its almost 100 names to check.
When looking into a plant name you have to check it has been validly, effectively and legitimately published. There is too much to go into here but as a synopsis
Effective Publication refers to the body of work not the name.
- It has to be printed in a text book or journal, although a recent change to the rules no allows the publishing of names online. Since 1953 exsiccata (bound books of specimens) labels, trade catalogues are not acceptable.
- It has to be printed. Before 1953 mechanically reproduced handwriting was acceptable. Nathanial Wallich's catalogue of plants from India is an example of this and has caused a massive headache ever since.
- It also has to be accessible to botanists in libraries etc.
Valid Publication affects the individual name.
- Must be in the correct form. So for a species must be a botanical latin binomial = Genus + specific epithet.
- Must accepted. The author decided that it was definately something new worth describing - no sense filling up an already cluttered universe with names you aren’t sure about.
For New taxa
- Must have a description or diagnosis
- A full description of what the plant looks like had to be in botanical Latin after 1935 until 2011. Now English is acceptable.
- A diagnosis is when you say your new species is clearly related to species B but is different in these characters…
- After 1958 you had to cite a Type specimen. I’ll talk about them in another post.
Legitimate Names
Flipping it on its head. An illegitimate name is one that is validly published but not usable. There are two types.
- Superfluous names where the author of the species should have taken up an earlier name. This could be because they didn’t know about a publication that dealt with what they were naming. Or if they have mistakenly included as a synonym a perfectly valid existing name.
- Later homonyms are when an author uses a name for a new species but it is already in use for a completely different species. The older name is the legitimate one.
Sorry this is dry but that's botanical nomencalture for you!
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Today, Alan is : Presenting 2yrs worth of BBSRC funded PhD work to University of Edinburgh Institute of Molecular Plant Sciences symposium today
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Cor blimey, I might manage to understand one word in 50. Hope you get jelly and cheese-cake after it Alan
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I know some folk are still in the mindset that its ok to collect plants saying what hard would it do to collect a few plants? Looking at it on the flipside I'm sure there would be an outcry here if collectors came to the UK and helped themselves to some of the remaining populations of Primula scotica in Sutherland and Primula farinosa in Teesdale. As sad as it is the world has change and people have to accept it.
Unfortunately, many do not & carry on regardless. A bit like "our oil under their sand".
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Cor blimey, I might manage to understand one word in 50. Hope you get jelly and cheese-cake after it Alan
Close I am currently enjoying some Stewart's Radical Road triple hopped pale ale. Good it is too and compared to some of the other talks mine was science light.
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Today, Alan is : Presenting 2yrs worth of BBSRC funded PhD work to University of Edinburgh Institute of Molecular Plant Sciences symposium today
(Attachment Link)
Thanks for that Maggie. The whole day was bonkers. Should have stayed a gardener merrily weeding at Branklyn.
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Alan,
Whats become of the odd Thalictrum-esque plant you reported on from Nepal? New species, different genus, or new genus? While I may be working on the treatment of Polygonatum for Nepal I doubt I'll get to go before I finish that work.
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tentatively Thalictrum rostellatum but I'm not quite convinced.
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Out of interest :Thalictrum rostellatum herbarium specimen from 1971 .... http://www.iiim.res.in/herbarium/ranunculaceae/images/thalictrum_rostellatum.jpg (http://www.iiim.res.in/herbarium/ranunculaceae/images/thalictrum_rostellatum.jpg)
photo: http://plantsoftibet.lifedesks.org/pages/46197 (http://plantsoftibet.lifedesks.org/pages/46197)
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Part of what I do [badly] is molecular lab work. This is another dark art of plant science.
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I’ll take you through the basics steps over a couple of posts.
First you need a sacrificial plant, or more accurately a leaf. I work from material that is stored and dried in silica gel, same stuff your new shoes come with.
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Now I know what you are thinking a small bag of white powder. Just cause I lived in Dundee don’t go tarnishing me with that brush thank you very much! Incidentally if you ever want an interesting conversation with good people at an airport take a couple of kilos with you on fieldwork.
You do not need much leaf about the size of your wee finger nail. This get put in a tube with a steel grinding ball. The sample then gets literally put through the mill and the end result is a fine powder in the tube.
I use a cheap and cheerful method of extracting the DNA from the ground up powder using a “homemade” mixture of chemicals called CTAB, brace yourselves, Hexadecyltrimethylammonium bromide.
The CTAB is mixed with beta-mercaptoethanol (which is toxic, reeks and is the most dangerous thing in the whole process) and heated to 65°C. 1ml of the heated CTAB/ mercaptoethanol buffer is added to your tube of powdered leaf. This is then incubated for 30min on a heated block.
The CTAB buffer is nothing more than a detergent that helps break down lipids in the cells to release the DNA and “wash way the rest”
0.5ml of Chloroform-IAA is added to the tube then it is placed on an orbital shaker to gently mix it all together. After about 20min the tube is centrifuged at 13,000rpm and this creates a two layered mixture, an upper layer which you want and a murky-green sludgy layer below which is discarded.
The upper layer is removed and 0.6ml of ice cold isopropanol (alcohol) is added. This helps the DNA to precipitate out of the solution. At this stage it is left in the freezer overnight if the leaf material is fresh but can be left for weeks if you are working with old herbarium material.
I find lab work a bit tedious and massively frustrating; just like weeding but at least you get some fresh air with that.
As a reward for getting this far this is the plant that was in the bag of suspect white powder.
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Clematis gracilifolia from the ACE expedition collection number 1834 for anyone interested.
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Yesterday I presented a modified version of the talk I gave at the University of Edinburgh last month at the “Inter-institute postgraduate symposium” this year held at the James Hutton Institute (latest incarnation of the SCRI) at Invergowrie.
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There were students from SRUC (Scottish Rural University Colleges), The Rowett Institute of Nutrition and Health, Moredun, BioSS, the James Hutton Institute and me representing RBGE postgraduate science. The common defining feature of these institutes is that their primary funding body is the Scottish Government.
It was a mixed bag of talk ranging from the use of novel techniques for in-situ measurement of root-reinforcement of mountain slopes to humane mechanical methods for killing poultry to nanomedicines in the treatment of Tuberculosis. There was also a mix of nationalities represented: Scots, English, Swedish, French and Dutch.
It was very heartening to see the breadth and quality of science being produced by early career scientists at Scottish research institutes. I felt quite proud to be there part of it.
The three, well deserved, talks that were judged to be best to go forward to the annual Science for Life Lecture at the Royal Society of Edinburgh later this month were:
- The role of the gut microbiota in inflammatory disease states - Catherine MacDonald.
- In virto fermentation of oats (Avena sativa) and barley (Hordeum vulgare) by faecal gut microbiota -Andrew Chappell
- Computational identification and functional characterisation of DNA binding effector in Phytophthora - Graham Motion.
You'll be glad to know I held my own and actually enjoyed presenting a full on science talk for a change.
As just a brief summary of some fo the things I talked about in my half hour slot.
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The checklist diversity of Clematis in Nepal.
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What my revision has done.
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Looked at the genetic relationships of different groups and the timing that we believe that they began to diverge to become the "species" we know.
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And of course acknowledge those who have supported and help me to this point.
Best question I received from a statistician was “Just what is the Scottish Rock Garden Club?”
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Very well done Alan we are proud of you and your efforts, cheers Ian the Christie kind
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Very well done Alan we are proud of you and your efforts, cheers Ian the Christie kind
Cheers Ian. Its been a busy stressful wee while lately.
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Alan, on your chart of clematis above third one along on the bottom line, is it C. koreana?
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It's Clematis tibetana subsp. brevipes an geographic and morphological intermediate between ssp. tibetana and ssp. vernayi. Only occurs in central Nepal in the Transhimalaya the dry area behind the tops of the main Himalayan range. The name covers Grey-Wilson's names from his monography that were used for ssp. vernayi and its various forms in Nepal but only in Nepal.
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Thanks very much. I have a clematis with flowers that look similar but I got the seed as C koreana.
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Thanks very much. I have a clematis with flowers that look similar but I got the seed as C koreana.
Nice always curious to know what people are growing. This isnt the taxa from Nepal - foliage from what I can see in your pic is different. Would need to see other characters to pass judgement as to what it is. :)
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It can take a while to pin an ID to some things - but eventually someone like Al, beavering away in a herbarium, will make a breakthrough ;
"New taxa for TheBotanics herbarium. 1889 Clematis collection from SE India sitting unidentified is Clematis heynei "
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Alan is just about to set off on another field trip in pursuit of Clematis knowledge and we wish him all the very best for the expedition.
Meanwhile, take a look at this : Botanical Selfies - eXtreme botany at 3600m with Alan Elliott
http://drmgoeswild.com/extreme-botany-at-3600-m-alan-elliott/#comment-34449 (http://drmgoeswild.com/extreme-botany-at-3600-m-alan-elliott/#comment-34449)
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Alan is safely returned from his recent expedition: we look forward to reading more here in the fullness of time - the fellow is very busy, you know!
On the 28th September Alan will be giving a talk for Plant Heritage Scotland (www.plantheritage.com (http://www.plantheritage.com))
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Julia Corden is also involved in this event -
The Royal Botanic Garden Edinburgh will be hosting Plant Heritage's All Scotland Meeting, to which non-members are most welcome. The focus of this year's event will be a celebration of the achievements of Scottish plant hunters past and present, exploring some of the less obvious ways used at RBGE to conserve their findings. Speakers include Julia Corden of the Plant Hunters Garden, Pitlochry and Alan Elliott of RBGE.
see full programme of the day and booking details below
[attachurl=2] - when booking, you might like to mention you read about this event here. :)
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Alan's blog post "Into the Flora of megadiverse Himalayas" http://researchhimalaya.wordpress.com/2014/12/19/the-flora-of-nepal-project/ (http://researchhimalaya.wordpress.com/2014/12/19/the-flora-of-nepal-project/)
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Well, time has passed- for Alan it has been an action-packed spell of great research and effort - he submitted his doctoral thesis and now we are able to send warmest congratulations to Alan Elliott on the successful completion of the viva voce for that thesis.
Congratulations, Dr. Alan Elliott!
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Congrats Doc 8)
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Well done, Dr. Elliott!
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Thank you all.
If I can be half as (in)competent as 'Dr Nick' from the Simpson's i'll be happy enough.
Al
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Hearty congratulations Dr Al!!! and welcome to the club. When's the operation? :D
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Very Well done Dr Alan hope to catch up with you at RBGE soon, cheers Ian the Christie kind
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Congratulations Alan - wish I'd known on Saturday we could have celebrated with you! Now I need to change your title in the Year Book! ;D
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Thanks all (sorry Carol)