Mudhand » research

Another day

Johannes — Thu, 09 Jul 2009 10:56:21 +0000

Sitting at work, going through some 8000 records in our Scanning Database. When I started working with the API-project (no, not API but API or African Plants Initiative, a truely international project that has now expanded to “Latin American Plants (and Global Types) Initiative(s)”, with more than 100 collaborating herbaria and institutions) we already had a Collection Database that was in use and, so I was told, already had all our Type Specimens entered. So all I had to do was to unpack the scanners and start scanning our 4500 African Types.

Urtica lobata (S-G-6253), scannad at NRM

Or so I thought. After my training week at Kew it was obvious that our Collection Database, thought a very good Collection Database, was not up to the task when it had to communicate with the rest of the world, as it had to do now. So I created a separate Scanning Database, where I transfered all relevant information from the Collection Database, and modified and added what was needed before submitting the metadata to the Aluka Production Team. So at the end of the API-project I had a database with detailed information on more than 8000 African Types (yes, we found a few overlooked specimens in the meantime) that only partly matched the information in our Collection Database. Meanwhile the Collection Database had evolved and, with only some minor modifications, it was now also useful for both presenenting our collections on the webb (Krypto-S), but also for the metadata to Aluka. So now we have decided, rightly so, to phase out the Scanning Database. And thus I’m sitting here, going through all the 8000+ records by hand so not to overwrite any unique information in the Collection Database. Outside the window the rain is pouring down. And M is in Austria, right now out trekking.

OK, I know…

Johannes — Mon, 02 Mar 2009 14:44:32 +0000

…that I’m a lousy blog writer… Right now I’m a lousy researcher too. Trying to come back to my small African plants, after a few weeks without them when I tried to get Krypto-S for FBO up working again. But right now I think I can leave it for a while, and do whatever I’m supposed to do. Try to remember what it was. Biogeography? Or character evolution? Oh well, think I’ll go for biogeography for the time being. Interesting distribution, these small plants, with basal nodes apparently distributed in south-western Africa, and a later dispersal east and north? Must try to understand the distribution so I can code it, and then analyse it. And at the same time try to find somewhere to stay (practically homeless in Stockholm since December). Not until then I will be able to update the layout of my webbpage and the blog. But until then I’ll try to write more! So see you soon, and I’ll might be able to tell more about distributions and dispersals over southern Africa!

Drafts

Johannes — Wed, 27 Aug 2008 13:18:49 +0000

Yesterday I got an e-mail from the Production Editor of Taxon with my contribution to the forthcoming book on the plant family Compositae (Asteraceae). It was a terrible reading! I was invited to give a talk on its nearest relatives on the 2006 years Compositae Conference in Barcelona, and this was thought to form the basis for a book chapter that was supposed to be submitted shortly after the conference. Unfortunately other things came in between and I never started writing on the chapter, and as time passed I thought (with some relief!) that it was too late for my contribution – when one day Vicki Funk sent me an e-mail telling me that I still had some time for finishing my contribution! With much too little time and many other obligations, I made a not very inspired attempt to write, something that shine through in the text I noticed today. I had a terrific chance to write an initiated and inspiring text about a fascinating part of the Angiosperm Tree of Life, with many interesting and curious members, but instead I only produced a worse-than-average, boring and quite uninteresting contribution… I clearly must write more and more often, to improve my scientific writing. Perhaps starting here at my web-page?

Research update

Johannes — Tue, 17 Jun 2008 13:15:59 +0000

Yesterday I finally finished determining the Geigeria vouchers for the DNA samples sequenced for my new research project! Geigeria of family Compositae is a small genus of some 20+ species, mostly in the deserts of southern Africa. In the next nine months or so, I will try to investigate the evolution of its pappus (modified calyx, aiding in the dispersal, and present on all members of Compositae, in one form or another), and perhaps also other structures like life form, presence/absence of spines, winged stems, etc. I also want to take a deeper look into the biogeography of the genus; its member are desert living and might tell something about the evolution of the deserts in that part of Africa over the last 5 million years or so. To my help I have sequences from six DNA markers from some 20 specimens. Today I aligned the sequences, and right now I’m running a phylogenetic analysis that will finish tomorrow. Then I will know if I need to sequence more representatives from the genus… The best would be if I have to go to Angola and Namibia and collect more material, but I don’t think there will be time for that…

Internet i Afrika

Johannes — Mon, 09 Jun 2008 06:01:40 +0000

En av de globala skandalerna just nu är (avsaknaden av) internetaccess i Afrika söder om Sahara, rapporterat i senaste numret av Science (6 juni 2008, s. 1261). Till Västafrika går en (1) fiberoptisk kabel, Östafrika får förlita sig på satellitlänk. Vad det gör för möjligheten för de få botanister verksamma i Afrika att koppla upp sig mot tillgänglithetsprojekt som Aluka eller JSTOR är inte svårt att se, inte heller hur denna begränsning i internettillgång sätter stopp för effektiv utvecking såväl vetenskapligt som ekonomiskt (dessa hänger ju dessutom tätt ihop). Trots detta är det viktigt att projekt som är riktade mot att tillgängliggöra information åt Afrika får fortsätta och uppmuntras. Om inte annat så visar det hur mycket information och kunskap vi har hämtat (några skulle säga stulit) från Afrika och som det är något av vår skyldighet att dela med oss, och när väl Afrika och dess universitet blir uppkopplad mot resten av världen kommer de att ha en rik källa att ösa ur och behöver inte bli ytterligare fördröjda.

En solig torsdagsmorgon

Johannes — Thu, 05 Jun 2008 06:55:50 +0000

Jag sitter och försöker koncentrera mig på att läsa ett manuskript som jag har fått för review… Funderar nästan på att ta med den ut i skuggan under en ek men då kommer jag bara att somna… Annars hade det varit perfekt idag, att sitta under en ek, dricka kall saft och reviewa manuskript. Obetalt jobb som måste göras, reviewa. Som man dessutom inte vet hur viktigt och betydelsefullt det egentligen är. Men förhoppningsvis så höjer det ändå kvaliteten på det som sedan publiceras. Eller så stoppar det bara nya oprövade vilda idéer och gör att det som skrivs alltid följer samma mall. Inget ont i det, i sig själv, en viss återhållsamhet är ibland bra, men reviewprocessen kan döda kreativitet. Samtidigt som man, förhoppningsvis, slipper stå där efteråt och skämmas över att man har publicerat dålig forskning, ogenomtänkta tankar eller missat andras forskning… Så därför fortsätter vi läsa varandras manuskript åt tidskrifterna, på arbetstid som borde ägnas åt annat eller obetald fritid.

Long overdue

Johannes — Tue, 03 Jun 2008 20:14:47 +0000

I felt very honoured when, in March 2006, I was asked by Alfonso Susanna if I could present an overview of the phylogeny of Asterales for The International Compositae Alliance TICA meeting in Barcelona later the same year. Of course my first — and probably wisest — reaction was to say Thank you very much I’m flattered, but no thanks, I can’t this time, and try to come up with some in all likelihood quite transparent excuse (like my new job at the museum…). But in the end I throw away all my concerns and decided to at least make a try (after all, I was asked after Kåre Bremer and Michael Donoghue who both had to decline). Or, try and try… it is not very much a try when you are up there in front of many of the world leading botanists and senior experts on many of these very plants I was going to present. It’s akin to present a person to her childhood friend. And not only doing it good, but also making people learning new things about their old friend. I think I failed miserably, but I tried, and I enjoyed it. And kind of completely forgot (or ignored perhaps) the second part, writing all up into a short chapter for congress volume, that was due a few months later… I did the only possible thing to do: I blamed the working situation, as I naturally had all my focus on the API scanning project, but in reality it was a writer’s cramp coupled with a feeling bordering to certainty that I didn’t had anything new or interesting to write, and that I really didn’t know anything about the plants (other than how they related to each other).

No, not really. I did an early attempt to write an interesting piece. Inspired by Richard Dawkins‘ The Ancestor’s Tale, I started with Asteraceae and tried to, almost literally, travel backwards in time, meeting the different clades, branches, at the nodes where they connected to the Asterales (part of the) Tree of Life. But I tried in vain, being way too stuck in the Dawksonian way of writing. I was not good enough (and nobody should be surprised about that). And I quit and tried to forgot. Or ignore.

But funnily enough, when I was sure I was “safe”, and started to blame myself for missing this great opportunity to ponder on my favourite subject, a subject off which I know so much (or so I now could think), an e-mail from Vicki Funck reached my mail-box at the museum, desperately trying to get some kind of response from me (only an hour later, Bertil Nordenstam came and told me that Vicki tried really hard to get into touch with me). Now I really couldn’t hide more, and I responded at once. She gave me a few weeks (a month or two) to finish my contribution, and this was exactly the stress level I needed to get started! Somehow, I managed to write a chapter (that unintentionally ended up somewhat Dawksonian!) that’s perhaps not the best thing I ever will publish (I’m sorry ’bout that, but my writing skills in English are not good enough yet!), but is a personal meditation upon what I, right now, think is the most likely relationships and evolutionary scenarios on the Asterales branch of the Tree of Life. And not only that, but thanks to the Association Endemia Faune et Flore de Nouvelle Calédonie (Endemia), Flickr, the International Carnivorous Plant Society’s forum, and Google Images search – and most importantly, the generosity of several photographers around the globe, I even (in the very last seconds) could submit a beautiful two page colour plate with photos of representatives of all the families of Asterales!

Now I’m only eager to see the chapter (and colour plate!) in print! As soon as I have a pdf (which I hope I will receive), I will forward it to all the persons who contributed with photographs to the colour plate. I will also try to make my contribution available through my homepage in one format or another.

In conclusion, I only want to say many thanks to Vicki for pushing me to write the chapter, to Alfonso for asking me to present my view of the phylogeny of Asterales, and to the photographers who helped me complete my chapter! In the end, it was great fun writing, and very inspiring! A lot of new ideas took shape during the process… hopefully I will be able to follow up on one or two of them…

Basal uncertainties

Johannes — Mon, 05 May 2008 12:10:18 +0000

One of last years greatest surprises was the removal of Hydatellaceae from Poales to Nymphaeales. It might not sound grand, but since Poales is the group of monocots that the grasses, sedges, rushs (and pineapples!) are a part of, and the Nymphaeales are the water lilies, the magnitude of the transfer of this small family of minute, sedge-like aquatics is so more impressing. And even more interesting since the Nymphaeales is one of the prime suspects for the sistership to the rest of the flowering plants! The implication of all this is simply that Hydatellaceae migh be the one of the missing keys needed to solve Darwin’s “abominable mystery“, the grand origin of flowers and flowering plants themselves! When DNA sequences first was used in large scale to resolve evolutionary relationships among plants, the big surprise then was finding the hornwort family, Ceratophyllaceae, at the very base of the Angiosperm tree of life. Soon however, the hornworts lost their isolated position outside all the other Angiosperms, and was replaced by a virtually unknown and thoroughly neglected small shrub from New Caledonia, the now famous Amborella trichopoda. Amborella has since then as best as it can defended its position as sister to the rest of the flowering plants, but what can be ask for from a shrub? From time to time its sistership has been challenged, but no obvious candidate has turned up. One of the challengers have however been Nymphaeales, either alone or together with Amborella, but already small changes in parameters or data sets have restored Amborella as the sole sister. And we are still waiting for the definitive analysis that will show us with high confidence what the basal relationships are. In the meantime, we need to see what the traditional data sets can tell us about the evolution. One possible large step forward was presented in the last issue of Nature, in the paper “Hydatellaceae are water lilies with gymnospermous tendencies” by William Friedman of University of Colorado (Nature 1 May 2008, vol. 453: 94-97). Here Friedman describe the embryology of the female gametophyte (the structure harboring the egg cells and, after fertilization, forms the seed). Not surprisingly, now when we are pretty certain that Hydatellaceae are “water lilies” (albeit seemingly sedgy ones), much of the embryological features correspond to the other water lilies (the female gametophyte of the water lilies and the likewise early-branching Austrobaileyales have a development not found in most other angiosperms, including Amborella), but Hydatellaceae have an additional feature unique among flowering plants: the allocation of nutrients (starch) to the embryo-nourishing tissue prior to the fertilization! All other flowering plants allocate nutrients first after the fertilization, thus avoiding “wasting” valuable nutrients on unfertilized seeds, but the gymnosperms (conifers and allies) don’t. They allocate nutrients before the embryo is formed, and interestingly this is also the case in Hydatellaceae! What the implications of this finding are is not apparent yet, but one obvious possibility is that this is the plesiomorphic (primitive or original) condition among the flowering plants, later changed (lost) in all other flowering plants with the evolution of second fertilization (trigging the onset of the formation of the nutrition tissue), including Amborella, but still present in Hydatellaceae. And the easiest explanation for this pattern is that Nymphaeales is the sister to the rest of the flowering plants, with two “independent” origins of the second fertilization (one on the branch with the other members of the water lilies, one on the branch with all other flowering plants including Amborella). With Amborella as sister to the rest, three “independent” origins are needed, or we need to interpret the pre-fertilization nutrition tissue in Hydatellaceae as a truely unique feature, not really the same as in the gymnosperms (there are differences) but instead evolved from an ancestor with second fertilization, something that is not easily explained. The next logic step from here will be to describe and characterize the genetic system behind this feature, and compare it with the other early branching angiosperms as well as the gymnosperms. The evo-devo people are probably already working hard with it!

Finally at travels end

Johannes — Tue, 29 Apr 2008 11:05:16 +0000

Last week a two years journey finally reached its end. It started springtime 2006, with Aberia tristis (i.e., Dovyalis zeyheri, Flacourtiaceae), the first of the then estimated 4900 type specimens that was to be included in our part of the African Plants Initiative. It ended last Thursday, when I scanned the 7881:st specimen, a Zygophyllum uitenhagense (i.e., Roepera maritima, Zygophyllaceae). Both specimens were collected by Christian Friedrich Ecklon (1795-1868) and Carl Ludwig Philipp Zeyher (1799-1858) in the Cape province of South Africa, probably in the 1820’s. Ecklon, a poor Danish pharmacist, and Zeyher, a German plant collector, are among the most prolific collectors of South African plants, and we have a very rich collection of their specimens here at the Swedish Museum of Natural History (more than 1500 of the 7900 scanned specimens were collected by them). It is their collections together with the collections of the contemporary Johann Franz Drège (1794-1881) and the later Rudolf Schlechter (1872-1925), that make up the bulk of our South African type specimens, and indeed the majority of our African types. In my virtual travel through Africa, I have met many more collectors, spanning three centuries from Peter Forsskål (1732-1763) to contemporary botanists like Marie Källersjö and PO Karis, and I have visited almost every contry on the continent (and many, many of the old colonies). I will miss some of these old men (and a few women)! Apart from learning a lot of old African colony geography, I have been quite good in reading old German hand writings. Now I must admit that I’m not sure how often I will need that particular knowledge…

Savis klöver

Johannes — Fri, 04 Apr 2008 11:59:45 +0000

Det är de oväntade detektivarbetena som gör jobbet med African Plants Initiative roligt. Idag kom jag över ett ark med med en pressad Trifolium elegans, en klöverart beskriven av den italienska botanisten Gaetano Savi (1769-1844) i hans Flora pisani (publicerad 1798). Arket, eller i alla fall växten som är monterad på det, var skickat av Savi själv, men till vem vet jag inte. Man kan misstänka att Olof Swartz (1760-1818), som var den förste professor Bergianus, fick den i sin hand och att växten därefter har hamnat på Riksmuseet. Men det finns inga noteringar om detta på arket, och inte heller har Swartzs efterträdare Johan Emanuel Wikström (1789-1856), som annars var annoterade alla ark han kom över, skrivit något på det. Det står inte heller var växten var insamlad, den enda ledtråden är det lilla “Prof. Savi misit” – “Professor Savi skickade mig den”. Eftersom han publicerade arten i Flora pisani, som är en förteckning över växter som växte i Provincia di Pisa (Italien) i slutet av 1700-talet, så kan man misstänka att den också är insamlad därifrån. I databasen har jag nu i alla fall angett Italien, Toscana, Provincia di Pisa som urpsrungsområde, om än med ett litet litet frågetecken. Namnet Trifolium elegens används för övrigt inte längre, utan arten har slagits ihop med samma art som vår alsikeklöver, Trifolium hybridum, men som en egen underart (den heter alltså numera Trifolium hybridum subsp. elegans).