Feb 122017
 
Charles Darwin, aged 51
Charles Darwin, aged 51

Charles Darwin, aged 51

Charles Darwin

Charles Darwin was born on 12 February 1809 (208 years ago this week), and died on 19 April 1882. Although he studied for a short time in Edinburgh, it was through his close friend and botany professor in Cambridge John Stevens Henslow that he was invited to join Captain Robert FitzRoy as naturalist on HMS Beagle for a round-the-world voyage which began on 27 December 1831 and lasted almost five years until 1836. On the voyage Darwin spent as much time as possible on land investigating geology and making natural history collections including dried plant specimens, while the Beagle surveyed and charted coasts. As is well-known, the voyage took Darwin first to the east coast of South America, round Cape Horn and north to the Galapagos Islands, then to New Zealand, Australia, South Africa, Brazil and home.

Darwin’s Beagle Plants

In studies of the ‘top set’ of Darwin’s plant specimens in the Cambridge University herbarium, Duncan Porter has catalogued the 248 vascular plants which include 16 species of ferns, 35 of monocotyledons and 166 of dicotyledons. These specimens had been entrusted to Henslow to deal with, but the latter’s lack of time and expertise caused him to turn to William Hooker in Glasgow for help. Henslow numbered all the specimens before sending as complete a set as possible to Glasgow, where Hooker in turn enlisted the help of George Walker Arnott. Together they published many vascular plants new to science in the following years. Amongst these were some important novelties such as Berberis darwinii collected by Darwin on Chiloe Island in Chile in 1834 and now a familiar garden plant in Britain.

Darwin’s Bryophytes

Darwin apparently collected relatively few bryophytes, and very little has been published on them. A short list of eight from the Galapagos Islands was published by Hooker’s son Joseph in 1847 following study by the English bryologist William Wilson and these specimens are now in Hooker’s bryophyte herbarium in the Natural History Museum in London. Few of those from other parts of South America have been documented except for Dendroligotrichum dendroides (collected as Polytrichum dendroides) from Tierra del Fuego illustrated and described by William Hooker in his Icones Plantarum in 1836. Duplicates of this specimen, and two other Darwin bryophytes, were found in Arnott’s herbarium in Edinburgh several years ago.

Newly-found Darwin mosses in Edinburgh

In an important new discovery, made in the course of searching for specimens collected by Alexander von Humboldt in Arnott’s herbarium, two unexpected new discoveries have been made of Darwin bryophytes, bearing Henslow’s numbers 436 and 464.

436. Polytrichum magellanicum Hedw., now Polytrichadelphus magellanicus (Hedw.) Mitt., labelled ‘Straits of Terra del Fuego, Darwin per Henslow No. 436’. (E00826655, herb. Arnott). This specimen was collected by Darwin probably in January or February 1833. However, it had been first described by Johannes Hedwig in his Species Muscorum in 1801, based on a collection from the Straits of Magellan made by the French explorer Philibert Commerson in 1767. Remarkably, a duplicate of Commerson’s original specimen is also present in Arnott’s herbarium in E.

Polytrichadelphus magellanicus

Polytrichadelphus magellanicus

Polytrichadelphus magellanicus, Tierra del Fuego(Photo David Long)

Polytrichadelphus magellanicus, Tierra del Fuego(Photo David Long)

 

 

 

 

 

 

 

 

 

464. Hypnum arbuscula Brid., now Dendrohypopterygium arbuscula (Brid.) Kruijer, labelled ‘Chonos archipelago, Darwin per Revd. J.S. Henslow, No. 464.’ (E00826690, herb. Arnott). This specimen was collected by Darwin when he visited the Chonos Archipelago in Chile in December 1834. As with Darwin’s Polytrichum, this species was also first discovered by Commerson on the Straits of Magellan in 1767, and a duplicate of his specimen is also present in Arnott’s herbarium in E.

Dendrohypopterygium arbuscula is something of a controversial moss as it has recently been moved to a brand new genus Arbusculohypopterygium distinguished primarily on DNA sequences, perhaps the first example of such a genus. It remains to be seen if this will become generally accepted.

Dendrohypopterygium arbuscula

Dendrohypopterygium arbuscula

Hypopterygium arbuscula in Chile (photo Oliver Whaley)

Dendrohypopterygium arbuscula in Chile (photo Oliver Whaley)

 

 

 

 

 

 

 

 

 

How did some of Darwin’s mosses get to Edinburgh?

At the time of the Beagle voyage in the early 1830’s Scotland was one of the world’s leading centres of cryptogamic botany. This was brought about by the appointment of William Jackson Hooker (later Sir William Hooker, Director of Kew) to the Chair of Botany in Glasgow University in 1820 where for 21 years he led the study of mosses, liverworts, ferns and algae, along with his Scottish colleagues Robert Kaye Greville in Edinburgh and George Walker Arnott based in Edinburgh, Fife and Paris. They published extensively and formed a formidable cryptogamic team. All three acquired large herbaria, both from their own field work in Britain and France, and more importantly through gifts and exchange of specimens with botanists and plant collectors worldwide. When Hooker left Glasgow in 1840 he took his very large herbarium with him to Kew, but Greville’s herbarium remained in Edinburgh, and Arnott’s in Glasgow. Fortunately, Hooker was extremely generous with his specimens and gave many duplicates to his friends Arnott and Greville. At later dates Arnott’s herbarium (except for his British collections which went to the Kelvingrove Museum) came to the Royal Botanic Garden, Edinburgh. Through their efforts, and also through the very important acquisition of the herbarium of the Scottish botanist/ explorer Archibald Menzies, Edinburgh now has one of the world’s best historic cryptogamic collections from the late eighteenth and early nineteenth centuries.

Arnott in particular seems to have been especially well-connected with other botanists through his work in Paris where he obtained large numbers of specimens from leading contemporary continental botanists and explorers such as Jean Baptiste Bory de Saint-Vincent, Adolphe-Théodore Brongniart, Jules Paul Benjamin Delessert, Alexander von Humboldt, Adrien-Henri de Jussieu and Carl Sigismund Kunth. It was through Hooker and Arnott’s contact with Henslow in Cambridge that a set of Darwin’s Beagle plants came to Glasgow and later some of these moved to Edinburgh. The Edinburgh collections are still being catalogued, and though much fewer in number than the approximately 250 collections housed in Cambridge, nevertheless duplicates of around one third of the Beagle vascular plants are present in Edinburgh. The two new ‘finds’ of mosses show that this cataloguing may not be complete and more Darwin specimens may yet come to light at RBGE.

David Long

Feb 012017
 

On 1st February 2017 an exhibition opens in the Library Foyer at RBGE displaying work which was produced through association between RBGE and Edinburgh College of Art and inspired by our research collections.  This exhibition will run until the first week of March. 

Context

In October 2016, the Edinburgh College of Art 2nd year Illustration course, were assigned a 5 week project based on the Herbarium, Library, Archives and Living Collections here at Edinburgh.  This collaboration is part of a concerted effort by RBGE in seeking new audiences for our collections, in addition to the traditional taxonomic researchers and was valuable for strengthening the relationship between organisations.

Assignment

As we curate such a potentially overwhelming amount of material to choose from, we decided on a geographical focus, based on some of the scientific projects that are currently active at RBGE.   The students were divided into groups and allocated one of the countries highlighted on the map.

Each student group was given a tour of our research collections and a session with one of our taxonomists who specialises in the flora of their designated country.  These experts gave the students an overview of their current research, including anecdotes from their fieldwork emphasising the need for habitat conservation and showed them herbarium specimens and living material to be inspired by.

Artwork

The work displayed was chosen from all the material submitted by the students.  We have included the sketchbooks to illustrate the research that is such a significant part of the artistic process and to give the viewer an insight into how each student created the final artwork.  The herbarium specimen and living collection images seek to put the work into the context of the RBGE collections.

You can view a small selection in our archive cabinet in The John Hope Gateway at the West Gate of the Botanics and the main exhibition is in the Library Foyer of the Balfour Building (10am-4pm).  There is directional signage in the Garden.

Directions map

@rbge_herbarium                                                                  #rbge_eca

Oct 182016
 
Harry Powell

The RBGE Herbarium is frequently gifted plant specimens from individual collectors. In recent years we have received material from

  • T. Powell (seaweeds)
  • F. Dobremez (flora of Nepal)
  • C. Townsend (mosses)
  • C.R. Fraser-Jenkins (ferns)

Often the culmination of a lifetime’s collecting and botanical expertise, these gifts are of enormous importance to the Herbarium.

However, some specimens require a considerable amount of preparatory work before they can be incorporated into the collection. Following an initial condition assessment, tasks may include:

  • Cataloguing ancillary material eg photos, drawings, collecting books
  • Sending duplicate specimens to other Herbaria
  • Producing or photocopying labels
  • Databasing & imaging
  • Mounting or remounting
  • Laying away [filing specimens in herbarium cabinets]

This preparation is vital if the specimens are to be maintained in the best possible condition and made fully accessible to future researchers. It may take weeks, months or years.

Volunteers play a vital and much appreciated role in assisting Herbarium staff with this work. Some are featured here, but to all we would like to say a huge Thank You!

 

The gifted herbaria and the volunteers who work on them:

Harry Powell

Harry Powell

Collector: Harry T. Powell (1925-2016)

Background: Henry Powell (known as Harry) had a lifelong career with the Scottish Marine Biological Association (SMBA), later the Scottish Association for Marine Science (SAMS).  He carried out seaweed surveys all around the Scottish coast, publishing several significant papers, and conducted important studies on Fucus species (wracks). He was an active member of his workplace union branch and a chairman of Connel Community Council.

Collection: Over 500 hundred dried pressed seaweed specimens, and papers, photographs, films and collecting equipment. He also rescued a variety of items when the SMBA relocated from Millport to Oban in 1967. These included 19th century pressed specimens and nature prints.

 

Clare Scanlan

Clare Scanlan

Volunteer:  Clare Scanlan

Background: Recently retired from the Scottish Environmental Protection Agency (SEPA) – Senior Marine Specialist (marine plants). Long-term interest in seaweeds.

Project: Sorting and cataloguing the collection bequeathed by the late Harry T. Powell.

Likes: Working with seaweeds, and on a collection that is both interesting and useful.

 

 

Professor Jean Francois Dobremez

Professor Jean Francois Dobremez

Collector: Jean Francois Dobremez (1941-2009)

Background: A professor at the University of Grenoble, Dobremez was the ecologist who mapped Nepal. His vegetation types are still used in official documents in Nepal.

Collection: Over 9000 herbarium sheets, mainly specimens collected by Dobremez and his colleagues in the 1960s and 70s, but supplemented by other botanists collecting in Nepal around the same time. They are a valuable resource for RBGEs Flora of Nepal research.

Jean Keeling

Jean Keeling

Volunteer:  Jean Keeling

Background: Consultant pathologist, former allotment holder, always into walking and cooking.

Project:  Preparing pressed specimens from the Dobremez collection for remounting by herbarium technicians.

Likes: Stepping into the Herbarium, a haven of tranquillity. Meeting people from a variety of backgrounds, both staff and other volunteers is a bonus.

Dislikes: Visitors who don’t replace the microscope covers and haven’t discovered how to turn off their mobiles!

 

 

C.C.Townsend

Clifford Charles Townsend

Collector: Clifford Charles Townsend (b.1926)

Background: Townsend was a member of staff at Kew Botanical Gardens, where his main area of research was the production of the Flora of Iraq. Collecting bryophytes [mosses] was just a very prolific hobby.

Collection: He gifted around 11 000 specimens to RBGE in 2001 and a further 14 000 in 2012! The gift of 2012 had to be collected at very short notice, as he gave an ultimatum that the Natural History Museum, London, could have them unless we collected them within a week or so!

 

 

 

Margaret Johnson

Margaret Johnson

Volunteer:  Margaret Johnson

Background: Worked in drawing offices producing geographical/architectural plans, and records of utilities. Has always been interested in plants, gardens and plant collectors, and loves travelling.

Project:  Preparing C. C. Townsend specimens for mounting (mosses are stored in paper packets glued on to herbarium sheets). Checking for duplicates to send to other Herbaria.

Likes: The staff, Friends and volunteers are very friendly which makes an enjoyable atmosphere in which to be able to help out in the Garden.

 

Christopher Fraser Jenkins

Christopher Fraser Jenkins

Collector: Christopher R. Fraser-Jenkins (b.1948)

Background: He began collecting in April 1957 at the age of 9, and went on to make thousands of wild fern collections from Europe, Russia, the Middle East, Southern Asia, North (incl. USA, Hawaii and Mexico) and Central America, Jamaica, Réunion and Africa.

Collection: His collection came to us from the Welsh National Herbarium in 2011, and includes over 32 300 accessions as well as correspondence, field books and hard drives of photographs. Further collections are held at the Natural History Museum, London.

 

 

Sheila Rennie

Sheila Rennie

Volunteer:  Sheila Rennie

Background: Administrative/managerial position with Scottish Certification Authority (SQA). Interests include cinema, books, tennis, golf, skiing and travel.

Project:  Preparing archival quality labels for specimen collections. Previously worked on transcribing information from C. R. Fraser-Jenkins collection books into the RBGE Herbarium database.

Likes: The stress-free working environment and interacting with other volunteers – tea breaks and lunchtimes are pleasant social occasions.

 

Bridget Laue

Bridget Laue

Volunteer:  Bridget Laue

Background: An active member of the British Pteridological Society (BPS), I have a very strong fondness for ferns.  So when the RBGE needed someone to help with ferns in the herbarium, it seemed an ideal project to pursue in my retirement.

Project: Processing the unmounted specimens, preparing them for mounting, and then barcoding and laying away the mounted specimens.

Likes: The fern specimens are lovely and I have learned so much from dealing with them.  But besides this, I have really enjoyed getting to know other members of the herbarium team, as well as visiting researchers.  Everyone has their own peculiar area of interest and expertise.  I also like the flexibility; I can work away on my own at the times that work well for me.  My supervisor, Sally King, is great about giving me clear instructions and having material ready for me.

Dislikes: Okay, really the only downside of working in the herbarium is finding myself working indoors on the occasional dry, sunny, Scottish day.

Aug 252016
 
Jul 142016
 

This Blog post was written by Olivia Nippe, a PhD intern who spent three months working in the RBGE Herbarium:

The RBGE herbarium contains over 3 million pressed plant specimens that are systematically filed according to evolutionary relationships. Such an establishment enables researchers to access vast amounts of material that could not possibly be studied in the field at any one time and place. Comparative studies are thus made possible over not only large geographical areas, but ecological time spans of up to 200-300 years, and even with now-extinct species. The collection is added to every year by field expeditions carried out by botanists worldwide.

When an expedition comes to an end the discoveries need not. So what happens to the plant specimens that a botanist collects in the wild, over the course of a lifetime, and just how important is it that we preserve these specimens for the years to come?

The answer to this question is of course synonymous with that of another: How do we process newly collected specimens that are sent to the Herbarium in order to make them accessible to our researchers, and how can such specimens be used in the future? There are many steps to be taken before the specimens that we receive at the Royal Botanic Gardens here in Edinburgh make it to the herbarium cabinets. As a volunteer at RBGE I have spent my time working through the extensive collection of renowned plant taxonomist Brian ‘Bill’ Burtt, obtained during his expeditions to Sarawak on the island of Borneo. The samples have been carefully dried and preserved between pages of newspaper by their collector and possess a wealth of information both about the physical characteristics of the plant, and in its DNA which will remain intact for many years to come.

 

DSC_9554_1

Olivia looking at a Bill Burtt specimen and collection information on the collectors label. To the right is a bundle of specimens in newspaper waiting to be processed.

 

When collecting in the field, a collector will make several duplicate specimens for each plant and these will be distributed to different institutes, including a herbarium in the country of collection. It can sometimes take some time for this to happen and this project worked through one such collection. From the plant material available we select a specimen to mount to show the diagnostic characters, and where possible save extra leaf material, flowers and/or fruit in an accompanying paper envelope, or ‘capsule’.

 

DSC_9546_1

Selecting material for the capsule which will be mounted alongside the specimen.

 

This ensures that not only are researchers able to get the best possible impression of the plant’s morphological features, but that they have access to sufficient material to extract and analyse its DNA for use in studies of plant phylogeny, the study of evolutionary relationships between species. Intact fruit may be dissected and flowers can be rehydrated from a sample in the capsule to provide further indication of plant structure, as such characteristics can prove to be essential when determining species identity. When mounted it will be securely taped, glued and/or stitched to a durable card backing (to learn more about mounting herbarium specimens click here) and placed into the herbarium cabinets.All of the material we use to affix the specimens is of archival quality and will enable the preservation of our specimens for hundreds of years.

While the herbarium serves as a historical reference library, the increasing ease of whole-genome sequencing means that these specimens also have the potential to offer new insight to evolutionary branching patterns. With even textbook examples of interspecies phylogeny such as those of Darwin’s finches being revised in light of new sequencing data, these plant specimens have much more to tell us long after they have been discovered.

Whilst working on this project Olivia processed 852 specimens from 101 different plant families. The specimens were collected in Sarawak, Bolivia, Namibia and South Africa. 374 of the specimens will be mounted and incorporated into the RBGE herbarium . 478 will be distributed to the following organisations: Sarawak Forest Department (SAR), Research Centre for Biology, Indonesia (BO), Brunei Forestry Centre (BRUN), Naturalis, Netherlands (L), Royal Botanic Gardens, Kew (K), Singapore Botanic Gardens (SING), Forest Research Institute, Malaysia (KEP) and the South African National Biodiversity Institute (PRE).

Jul 042016
 
Inga umbellifera Matthews

Fig. 1. Inga umbellifera, Mathews 1593, collected in Peru, Departamento San Martin: Provincia San Martin, Tarapoto, in 1835.

As part of our hybrid capture project, we sampled from an Inga umbellifera specimen that was collected about 180 years ago, by Andrew Mathews, in Peru in 1835. We made our Qiagen Plant DNeasy DNA extractions from the piece of plant tissue shown in Fig. 1. The DNA was very degraded, and present in quite low quantities (Tapestation fragment size distribution 46 to 306 bp; Qubit concentration 1.23 ng/μl; Fig. 2); from this we were still able to generate both Illumina Tru-Seq and NEB-Next DNA libraries (#13) that we sent to Edinburgh Genomics sequencing facility at the University of Edinburgh for Illumina Mi-Seq sequencing.

Inga umbellifera DNA from 1835 herbarium sheet

Fig. 2. Tapestation trace for Inga umbellifera DNA from Mathews’ 1835 herbarium sheet

We analysed the sequence data from the Tru-Seq and NEB-Next libraries separately, as our study aimed to compare different DNA extraction and library preparation techniques; from each library, we obtained over 300 thousand bases of Inga DNA sequence data that matched to our hybrid bait set. For the two libraries combined, we obtained over 1.6 million reads that passed quality controls, over 85% of which matched the hybrid baits that we’d used, and another c. 5% of which matched the Inga plastid genome. However, that still leaves around 10% of the reads that were not from the legume hybrid baits that we’d used, and we were interested to see what else might be present in that data set.

Library No. of trimmed reads % reads aligned to baits % reads aligned to Inga plastid Average quality score of variant positions (AQV) Number of variant bases Loci recovered (max 276) Conservatively called sequence (CCS), bp
H1835_NEB13+ 1,013,414 87.40% 4.30% 139.18 7,186 249 317,244
H1835_Tru13+ 659,161 84.20% 5.20% 132.97 7,045 247 310,949

 

We compared the DNA sequences of the reads from one of these libraries, H1835_NEB13+, to a publically available database (using a blast analysis run using Galaxy). This gave us a metagenomic analysis of the H1835_NEB13+ library reads, so that we could tell if anything other than Inga DNA had been in the extractions. Of 12,754,803 untrimmed reads, a huge number, over 8.3 million, were matches to legume sequences, exactly as we would expect from an Inga specimen (65%, with 1,211,319 Ingeae tribe reads, 2,015,461 Mimosioid legume reads, and 5,088,509 Fabaceae reads).

But not all the sequence reads were matches to plant DNA…

There were also:

3,047 reads that matched Homo sapiens (0.02%, which may or may not come from our intrepid plant collector, Mr Andrew Mathews, from his Peruvian wife, from the herbarium worker who stuck the pressed plant onto the card sheet, from taxonomists who have handled the specimen over the years, or indeed from anyone in the laboratory when the DNA extractions were being made…),

88,216 reads that matched Mediterannean mussels (0.7%),

and 346,820 reads that matched Streptococcus (2.7%; always wash your hands after touching herbarium specimens!).

Humans and bacteria are pretty easy to explain – people have been handing this plant material ever since it was collected, and there are bugs everywhere. But what about the mussels? The city of Tarapota in Peru is a long way from the coast, but after the plant was collected, it was squashed and dried in a plant press, and transported across the country, and eventually over to Europe. When we first got these results, we imagined working dinners in the Mathews household, with the botanist splitting his attention between his plant collections and a towering plateful of shellfish, dripping mollusc juices across the specimens. It does, however, seem unlikely that a professional plant collector would be quite that careless.

An alternative explanation is that we’ve also extracted DNA from glue. The leaf material we are working with has been removed from a herbarium sheet, to which it had been stuck. Animal-based glues were common in the 19th century, and although the classic glues were from mammal hides and fish, mussels certainly have a lot of sticky potential.

 

 

References:

Hart, M.L., L.L. Forrest, J.A. Nicholls & C.A. Kidner. In press. Retrival of hundreds of nuclear loci from herbarium specimens. Taxon.

James A. Nicholls, R. Toby Pennington, Erik J.M. Koenen, Colin E. Hughes, Jack Hearn, Lynsey Bunnefeld, Kyle G. Dexter, Graham N. Stone & Catherine A. Kidner. 2015. Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae). Frontiers in Plant Science 6: 710. doi: 10.3389/fpls.2015.00710

 

Capturing Genes from Herbaria. I. What it’s all about. http://stories.rbge.org.uk/archives/16411

Capturing Genes from Herbaria. II. Inga. http://stories.rbge.org.uk/archives/16427

Capturing Genes from Herbaria. III. The samples. http://stories.rbge.org.uk/archives/16441

Capturing Genes from Herbaria. IV. DNA. http://stories.rbge.org.uk/archives/16470

Capturing Genes from Herbaria. V. Fragmenting the DNA. http://stories.rbge.org.uk/archives/16525

Capturing Genes from Herbaria. VI. Size Selection. http://stories.rbge.org.uk/archives/16645

Capturing Genes from Herbaria. VII. Comparisons. http://stories.rbge.org.uk/archives/16737

Capturing Genes from Herbaria. VIII. Amplification. http://stories.rbge.org.uk/archives/16788

Capturing Genes from Herbaria. IX. Hybrid capture. http://stories.rbge.org.uk/archives/17298

Capturing Genes from Herbaria. X. An update. http://stories.rbge.org.uk/archives/20751

Capturing Genes from Herbaria. XI. Some metagenomics of a herbarium specimen. http://stories.rbge.org.uk/archives/20817

Jun 302016
 

Last May (the 15th, to be precise), we sent three eppendorf tubes containing Illumina Tru-Seq and NEB-Next libraries constructed from Inga DNAs, most of which had been extracted from herbarium specimens, to the Edinburgh Genomics sequencing facility at the University of Edinburgh. A series of Botanics Stories blogs (listed below) described the rationale for the project, and the methodology that we followed in order to fill these tubes with libraries. Then followed a bit of a hiatus, so it seems that a quick update is in order.

In short: We got the data back on the 1st of June 2015, analysed it – it worked – and wrote a brief paper that was submitted to the journal Taxon on the 4th of February 2016, and accepted on the 19th of May. This was followed by a pleasant celebratory lunch in one of the local bars, the Orchard, on Wednesday the 25th… but back to the data:

Data from Hart et al. (Taxon, in press 2016): The results of the MiSeq runs, by library, are given in the following table. The final row is the silica-dried material from Dexter 401 (E) sequenced by Nicholls & al. (2015), for comparison with libraries from H2004. The library names start with H or S, depending on whether the DNA was extracted from herbarium specimens or silica-preserved tissue samples, followed by the collection year for each accession; the second part of each name reflects the library preparation kit (Tru-Seq or NEB-Next) and whether or not the DNA was repaired (+ or -), with a number that links back to previous blogs on DNA extraction, fragmentation, size selection and library preparation methods.

 

Library No. of trimmed reads % reads aligned to baits % reads aligned to Inga plastid Average quality score of variant positions (AQV) Number of variant bases Loci recovered (max 276) Conservatively called sequence (CCS), bp
H1835_NEB13+ 1013414 87.4% 4.3% 139.18 7186 249 317244
H1841_NEB07+ 214315 53.9% 0.7% 101.80 883 137 46045
H1841_NEB08+ 365550 73.2% 0.8% 73.44 2773 226 120148
H1932_NEB11+a 1226043 89.0% 4.7% 157.83 6377 248 322337
H1932_NEB11+b 862599 89.1% 4.1% 141.89 6253 246 310470
H1932_NEB11+bv2 1152606 90.0% 2.3% 133.15 5930 248 301994
H1932_NEB12+ 1919229 87.4% 6.4% 173.56 6463 249 331326
H1948_NEB05+ 583010 87.4% 1.6% 94.94 5028 239 241758
H1948_NEB06+ 704977 87.1% 3.7% 136.32 6132 247 298809
H2004_NEB09+ 1787314 74.3% 9.2% 168.53 7018 248 328618
H2004_NEB10+ 1595602 80.3% 10.4% 174.46 7135 250 334242
H2009_NEB01- 1711918 75.0% 8.6% 169.24 6482 248 326187
H2009_NEB01+ 1658799 76.6% 8.2% 169.21 6484 250 324340
H2009_NEB02- 1355984 75.2% 8.3% 163.79 6525 247 322957
H2009_NEB02+ 1668026 76.2% 8.5% 171.90 6516 250 326466
H2009_NEB03- 1513515 73.8% 8.3% 162.85 6463 246 319683
H2009_NEB03+ 1504758 74.0% 8.4% 161.80 6419 245 320273
H1835_Tru13+ 659161 84.2% 5.2% 132.97 7045 247 310949
H1932_Tru11+a 1584437 87.7% 3.8% 155.89 6246 248 322199
H1932_Tru11+b 1015706 87.5% 3.8% 144.88 6194 248 314862
H1932_Tru11+b2 1416246 87.0% 4.6% 159.42 6448 249 324910
H1932_Tru12+ 1774508 84.4% 6.3% 169.72 6503 248 330462
H1948_Tru05+ 1042441 83.9% 2.6% 136.01 5941 248 296844
H1948_Tru06+ 892927 84.6% 3.9% 145.22 6211 247 308853
H2004_Tru09+ 1958838 77.9% 9.2% 173.90 7041 249 333904
H2004_Tru10+ 1576572 77.4% 9.5% 170.05 7066 248 330278
H2009_Tru01- 1338317 77.6% 9.1% 167.51 6601 249 324201
H2009_Tru01+ 1536759 77.2% 8.4% 167.03 6594 248 325184
H2009_Tru02- 1476338 76.6% 8.4% 166.63 6569 249 323881
H2009_Tru02+ 1226123 75.6% 8.5% 161.46 6572 249 319045
H2009_Tru03- 1630041 75.4% 8.6% 168.09 6509 250 324451
H2009_Tru03+ 1753019 75.0% 8.4% 167.90 6512 249 323951
S2004_TruKD401 689439 74.4% 9.2% 156.29 5809 245 330396

 

References:

Hart, M.L., L.L. Forrest, J.A. Nicholls & C.A. Kidner. In press. Retrival of hundreds of nuclear loci from herbarium specimens. Taxon.

James A. Nicholls, R. Toby Pennington, Erik J.M. Koenen, Colin E. Hughes, Jack Hearn, Lynsey Bunnefeld, Kyle G. Dexter, Graham N. Stone & Catherine A. Kidner. 2015. Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae). Frontiers in Plant Science 6: 710. doi: 10.3389/fpls.2015.00710

 

Capturing Genes from Herbaria. I. What it’s all about. http://stories.rbge.org.uk/archives/16411

Capturing Genes from Herbaria. II. Inga. http://stories.rbge.org.uk/archives/16427

Capturing Genes from Herbaria. III. The samples. http://stories.rbge.org.uk/archives/16441

Capturing Genes from Herbaria. IV. DNA. http://stories.rbge.org.uk/archives/16470

Capturing Genes from Herbaria. V. Fragmenting the DNA. http://stories.rbge.org.uk/archives/16525

Capturing Genes from Herbaria. VI. Size Selection. http://stories.rbge.org.uk/archives/16645

Capturing Genes from Herbaria. VII. Comparisons. http://stories.rbge.org.uk/archives/16737

Capturing Genes from Herbaria. VIII. Amplification. http://stories.rbge.org.uk/archives/16788

Capturing Genes from Herbaria. IX. Hybrid capture. http://stories.rbge.org.uk/archives/17298

Capturing Genes from Herbaria. X. An update. http://stories.rbge.org.uk/archives/20751

Capturing Genes from Herbaria. XI. Some metagenomics of a herbarium specimen. http://stories.rbge.org.uk/archives/20817

Apr 262016
 
David Harris

Herbarium Curator

DavidMy favourite thing in the Herbarium is the labels on the cabinets. They tell us what is in the cabinet and where we are in the taxonomic sequence. When visiting other herbaria I always look at the labels – they are never, ever, as clear, as consistent or as informative, as they are back home in Edinburgh. It is just another example of the amount of careful thought that went into the design of this herbarium in the years leading up to its opening in 1964.

 

 

 

 

Erzsebet Gyongy

Herbarium Assistant

LizzieMy favourite object in the Herbarium is the tablet. I do loads of laying away [putting specimens away in correct taxonomic order in the cabinets], and the tablet helps me do this more efficiently. I can carry it with me and use it to check specimen details right at the cabinet: I don’t have to go back and forth to another computer. I can see on the tablet if a specimen needs to be imaged or not and can also catch mistakes and avoid mislaying specimens. It is a handy little tool for my job!

 

 

 

 

Jenny McCutcheon

Herbarium Technician – Plant Specimen Preparation

Jenny

My favourite thing in the Herbarium is my sponge stippler. This fantastic little tool is perfect for applying archival glue to fragile specimens and for getting good glue coverage on the larger ones without getting messy, gluey fingers!

With the stippler you can control the pressure applied to each specimen and also use a rolling technique to release the glue which really helps to preserve the vast number of varied specimens which arrive in the mounting room.

 

 

 

Kate Eden

Herbarium Technician – Plant Specimen Preparation

Kate

My favourite thing in the Herbarium is this photo of a woman mounting plant specimens while her cat sleeps! I have it on the wall behind my desk. I think it captures the quiet, methodical nature of the job, not to mention the sheer volume of work (all those piles of specimens …) At RBGE we aim to mount plant specimens for the Herbarium as soon as possible; those that have to go into a backlog are safely and systematically stored, in boxes recorded in a spreadsheet.

 

 

 

 

Lesley Scott

Assistant Herbarium Curator Loans

LesleyMy favourite thing in the Herbarium is the large spirit bottle containing the Camomile specimen which has suffered from fasciation (it has a swollen stem due to abnormal growth activity).  It is suspended in a beautiful old jar and has turned the spirit solution a lovely warm yellow colour and we use it for tours of the Herbarium.  It is recognisable as Camomile showing all the flower heads, but most of all I love the fact that it looks like a mutant plant from another world.

 

 

 

 

Lorna Glancy

Herbarium Technician – Plant Specimen Preparation

LornaMy favourite thing in the Herbarium is my tweezers. I would be lost without them. My job is to mount dried plant material onto archival board to make herbarium specimens. The tweezers are a versatile mounting tool:  they are useful for picking up fragile and brittle plant material, and both the pointed and flat ends are perfect for manipulating the fine paper tapes used to secure the plant material to the sheet.  A lot of effort has gone into collecting these plant specimens from around the globe, and my tweezers help me to handle them with the care they deserve!

 

 

 

Robyn Drinkwater

Digitisation Officer/Technical Developer

RobynMy favourite things in the Herbarium are the barcodes, in particular the long empty strip you get when doing minimal data entry. It’s satisfying to see (and rip off) at the end of a day’s databasing. Each long empty strip shows that several hundred more specimens are ready to be imaged and made available online. Currently around 750,000 (25%) of specimens have been databased.

 

 

 

 

Sally King

Digitisation Officer/Herbarium Volunteer Coordinator

SallyK

Choosing a favourite thing from the Herbarium was impossible because it’s such a treasure trove! I chose a sentimental object, my wee Mexican tortoise, a gift from a digitisation team member at Kew Herbarium, where I used to work. He puts a smile on my face and reminds me of where I’ve come from. Without my time at Kew I wouldn’t be working here. I’m so happy to be working at the best Botanic Garden in the UK ;) The world map in the photo is marked out into the geographical regions the herbarium specimens are filed under: Mexico is in Area 14.

 

 

 

Sally Rae

Assistant Curator Bryophytes

SallyRMy favourite thing in the Herbarium is my glue spatula. Rather than being mounted like other plant specimens the small, fragile bryophytes [mosses] are stored in archival paper packets which I glue to the appropriate herbarium sheet at the cabinets. I have used the same spatula for the last 30 odd years. If I find someone using it I will always ask if I can change it for the spare on my trolley which is much stiffer and does not feel right to me. I only have 2 spares and as they are not made any more; when they are gone I will have to retire! (A fact I tell visitors and volunteers when I let them use the spare.)I am very possessive about my spatula!!

 

 

 

Suzanne Cubey

Deputy Herbarium Curator

SuzanneMy favourite thing the Herbarium is my ‘box of tricks’.  It contains all the essentials I need to prepare a specimen for mounting or to annotate a specimen that has been used for research purposes.  I can’t remember where the box came from, I’ve had it so long but it contains secateurs, dissection kit, capsules, and my precious 10 very old, different sized black and white carpological boxes with glass lids to keep all my important labels in.  The Cultivated labels are for the specimens made from plants growing in our truly amazing Living Collection. I like the function of labels  – labels on the herbarium specimen are as equally as important as the plant material itself.

 

 

Terry Gilmour

Herbarium Cleaning Operative

TerryMy favourite thing in the Herbarium is the job of cleaning and buffing the floors. It’s a calm, almost meditative job, but an important one. Without regular cleaning dust and plant debris from specimens can build up and provide a hiding place for herbarium beetles which damage the specimens. I report any beetles or larvae I find to Herbarium staff so they can record them and take action if necessary.

 

 

 

 

Elspeth Haston

Deputy Herbarium Curator

ElspethMy favourite thing in the Herbarium is Grumpy, a herbarium trolley that saw a lot of service in 2006 when we reorganised the three million specimens in the collection. It took us nine weeks, thanks to a team of people and a set of seven trolleys. When moving specimens from one cabinet to another between two floors, the characters of the trolleys became evident and so we named them. Happy was the favourite – running smoothly and turning nicely. Grumpy needed more effort to manoeuvre, but I grew very fond of it! The RGBE Herbarium was the first large herbarium to be organised according to the Angiosperm Phylogeny Group classification, a system now adopted by many other large herbaria. Grumpy is still in the herbarium, helping us to recurate some of the larger families.

Jan 202016
 
the team meets with the Head of Kebun Raya Bogor (l-r Hannah Atkins, Helen Yeats, Dr.Didik Widyatmoko, Dr.Mark Hughes, Sadie Barber, Prima Hutabarat, Dr.Peter Wilkie)

the team meets with the Head of Kebun Raya Bogor (l-r Hannah Atkins, Helen Yeats, Dr.Didik Widyatmoko, Dr.Mark Hughes, Sadie Barber, Prima Hutabarat, Dr.Peter Wilkie)

A team of five staff from RBGE (three scientists and two horticulturists) have set out on an expedition to Indonesia; Phase 1 of a project which aims to discover the biodiversity and promote the conservation of the Indonesian flora. The group are particularly interested in key research groups Begoniaceae, Gesneriaceae, Sapotaceae and Zingiberaceae.

Here is the first report from the team…

We arrived on the 10th of January to one of the world’s hottest, busiest, noisiest cities – Jakarta. Before any expedition in Indonesia can start, first there is a huge amount of paperwork to complete. Many teams from Edinburgh have had experience of this over the years, but it does not make the process any faster or easier.

the team looks around the Begonia collection with Wisnu Ardi

the team looks around the Begonia collection with Wisnu Ardi

We spent the first few days in Jakarta, our hotel close to the offices to process research permits, letters of permission and police travelling permits. On Thursday morning we got news of bombs and shootings going off near to our hotel, and we are reminded that on these travels the most important thing always is to stay safe. Early on the Friday morning the team moved to the city of Bogor, home to a magnificent Botanic Garden, and where we feel safe amongst the people and plants!

We are now waiting for paperwork from the Immigration office and the Ministry of Forestry, which will allow us to collect plants with our counterpart scientists in the forests of Sumatra, Sulawesi and Kalimantan (Borneo). While we wait, it is a good opportunity to work in the Herbarium, photographing specimens, and meeting with our counterparts to plan for the fieldwork. With all going well, we will be setting off for the jungles of Sumatra at the weekend. We will send another report from there.

Lanterns made from banana leaves in Bogor

Lanterns made from banana leaves in Bogor

 

Working in the Herbarium