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From Joseph Banks to big data, herbaria bring centuries-old science into the digital age



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Specimens in herbaria include “pickled” plants in pots (shown here), dried specimens and fruits or seeds preserved whole.
Ainsley Calladine, State Herbarium of South Australia , Author provided

Michelle Waycott, University of Adelaide

Last month, priceless botanical specimens were destroyed after an apparent miscommunication between scientists and Australian customs officials.

Although unfortunate, the incident has focused attention on the importance of being able to share scientific specimens around the world, and the vital role that herbaria play in modern science.

Despite being sometimes described as “museums for plants”, herbaria aren’t just natural history storage and displays. In this era of DNA barcoding, big data, biosecurity threats, bio-prospecting, and global information sharing, herbaria are complex and evolving institutions.

The modern herbarium is steeped in tradition and full of antiquities, but it also leads the application of modern approaches to understanding our past, present and future natural world.

The power of 8 million specimens

If you tell someone that you work at a herbarium, most will ask “what’s that?”, or perhaps “oh, what kind of herbs do you grow there?”.

Herbaria house historically important plant specimens with precise details of their collection. The card on this 247 year old example reads: Viitadinia scacbra, DC. Australia: Queensland. Bustard Bay 24°05’S 151°28’E. 23 May 1770. Collected by Joseph Banks and Daniel Solander, Captain Cook’s first voyage 1768-1771.
The State Herbarium of South Australia, Author provided

Conventionally, a herbarium is a collection of preserved plant specimens that are stored and managed in an organised and structured way by curators and botanists who specialise in plant taxonomy and systematics.

There are some 3,000 active herbaria worldwide. As a collective, they contain more than 380 million specimens, spanning collections dating back as far as 500 years ago.

In Australia there are nine state, territory or national herbaria that, along with some university collections, hold close to eight million specimens. Four major Australian herbaria hold over a million specimens:

Herbarium specimens exist in many forms, including “pickled” plants or plant parts such as flowers or other delicate structures, dried specimens still attached to the surface on which they grew (like tree bark and rocks), and fruits or seeds preserved whole. But the overwhelming majority are dried, pressed plant specimens attached to archival card. Alongside these specimens there are sometimes drawings, paintings or photographs of the species, which capture details that are not discernible in the preserved specimen.

The Australasian Virtual Herbarium

The plant specimens don’t just exist on their own inside herbaria. Along with the specimens, the accompanying information is vital, such as where and when they were collected, specific details of the environments where they were collected, and who collected them.

In Australia, the major herbaria have been actively adding this information into a digital repository, resulting in a world-leading dataset: the Australasian Virtual Herbarium.

Sites of collection of Australian and New Zealand herbarium samples of the weed ‘Salvation Jane’ as displayed on the Australian Virtual Herbarium website.
Australian Virtual Herbarium

The collation of these resources helped to inspire the development of the Atlas of Living Australia, and gives anyone with an internet connection access to specimen records from around Australia and the world.

Specimen-based, online data sets provide evidence of what species are found in a particular place at a particular time. They are a direct link from the presence of a species in the field, to collections of physical specimens held in herbaria, with the current name (that is, the latest changes in taxonomy) for that specimen.

There are many applications of such evidence including tracking changing species distributions such as ferals and weeds (an example of the weed “Salvation Jane” is shown in the figure above). Herbaria have been active in supporting detection of biosecurity threats. New introductions of species to Australia need careful determination of their identity and herbaria work with agencies to assist with this.

Sometimes, herbarium or museum specimens are the only evidence that a species existed at all. For example Gentianella clelandii, a species of native Gentian, is only known from the collection made of it in 1947 in the South East of South Australia. This species and others like it are likely to have been lost as a result of changing land use in the region at this time.

Samples from Cook, Flinders and Baudin

Australia’s banksia is a well loved plant. This specimen card reads: Banksia serrata L/F New Holland, Banks and Solander, Botany Bay, April 1770.
National Herbarium of Victoria, Author provided

Important historical, scientific or cultural plant specimens exist in herbarium collections.

Plants collected during the voyages of early European explorers – including Dampier, Cook, Flinders and Baudin – are still found in herbaria. Some of these plants were also shipped live back to Europe, and have been grown in gardens and in scientific collections all over the world.

Remarkably, due to the care in methods of preserving them, these specimens are often in excellent condition more than 200 years after their collection and still able to be used productively in scientific research.

Type specimen collected by Robert Brown, who circumnavigated Australia with Matthew Flinders. The card reads: Hakea rugosa R. Br. South Australia: Port Lincoln (Bay 10) March 1802.
State Herbarium of South Australia, Author provided

These historical specimens are often the first known collections of a previously undescribed species. If so, they will be designated as “type” specimens by the taxonomist naming the new species. Type specimens are very important as they allow the work of taxonomists to have a global frame of reference. This allows scientists to work out if two (or more) species have been assigned the same name.

Herbarium records enable resource managers to track distributions of both pest plants and endangered plants, providing a historical and current view of how widely spread and common the various species are across Australia.

You say River Red Gum, I say Yarrow

Taxonomy is the science of describing, classifying and naming plants, animals and microorganisms of the world. Taxonomists do the work of describing and arranging plant species into classifications based on their morphology (what they look like), their genes and sometimes other features.

While highly scientific by nature, taxonomy is also vital to society at large. For invasive plant control, for border control, for environmental management and for urban planning, there must be no ambiguity as to which plant species we are talking about. Common names of plants can be misleading, the same plant often having many different common names. For example, the Australian iconic tree species Eucalyptus camaldulensis is known as River Red Gum, Blue Gum, Murray Red Gum, Red Gum, River Gum and Yarrow. We know these are all the same species, because taxonomists can compare herbarium specimens and determine if they share the same characteristics.

Expansion of the search for new biological compounds for human use — including medicines, food, cosmetics and other applications — exemplifies the problem of misapplied taxonomic names. For example the search for bioactive compounds in marine algae yields very different results for different species.

But imagine if there wasn’t a way to apply the precision of taxonomy in the search for information on the characteristics of a species to be used for biological control? Not only would time and money be lost, but the incorrect species could be used and unforseen outcomes may occur.

An example from the insect world is the Southeast Asian termite. A potentially harmful species of the termite genus Coptotermes was known regionally by another name, affecting its management as a pest causing building damage in the Americas and Malaysia.

A botanist reviews a herbarium sample, in this case Helichrysum gatessi, or ‘the everlasting flower’
State Herbarium of South Australia, Author provided

Herbaria as a research resource

In addition to storing and organising specimens, larger or highly specialised herbaria usually have an associated research program. Focus scientific areas typically include taxonomy, systematics (how living things are classified and named), evolutionary biology, conservation biology and applied botany (using plants for economic benefit) .

Many herbaria have molecular genetics laboratories attached to them. DNA can be extracted from many specimens, even very old ones, and thus they can become a core part of ongoing DNA based scientific research. Today, DNA barcoding can provide a rapid tool for identifying species when flowers or fruits are not available, or if we have only fragments. Globally, DNA barcodes are now available for more than 265,448 species in the BOLD database. This aggregation of DNA sequences, which for plants are linked to herbarium vouchers, are a global resource that can be used in a “big data” context to explore ideas.

The value of herbaria samples extends beyond just the plants themselves. Herbarium specimens have been used to collate data for inferring changes in flowering times, leaf morphology and species ranges with climatic shifts.

Scientists also analyse chemicals that herbarium specimens have been exposed to, such as heavy metals associated with urban development, and different elements incorporated as leaves grow. Knowledge about waxes on leaf surfaces, as well as inhabitation by insects, fungi and bacteria are all possible through herbarium samples.

The global network of herbaria share specimens so that taxonomists and other researchers can benefit from their existence. With online resources making it known exactly what specimens are in which herbarium, there is an ever growing set of demands made on the use of specimens.

The ConversationCurators who look after collections must balance the requests for using specimens in the present with long term preservation. The ability to track the impact of climate change and other unforeseen influences on plant health may make our current herbaria collections even more priceless in years to come.

Michelle Waycott, Professor, School of Biological Sciences, University of Adelaide and Chief Botanist, State Herbarium of South Australia, University of Adelaide

This article was originally published on The Conversation. Read the original article.

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A digital archive of slave voyages details the largest forced migration in history



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A slave fortress in Cape Coast, Ghana.
AP Photo/Clement N’Taye

Philip Misevich, St. John’s University; Daniel Domingues, University of Missouri-Columbia; David Eltis, Emory University; Nafees M. Khan, Clemson University , and Nicholas Radburn, University of Southern California – Dornsife College of Letters, Arts and Sciences

Between 1500 and 1866, slave traders forced 12.5 million Africans aboard transatlantic slave vessels. Before 1820, four enslaved Africans crossed the Atlantic for every European, making Africa the demographic wellspring for the repopulation of the Americas after Columbus’ voyages. The slave trade pulled virtually every port that faced the Atlantic Ocean – from Copenhagen to Cape Town and Boston to Buenos Aires – into its orbit.

To document this enormous trade – the largest forced oceanic migration in human history – our team launched Voyages: The Trans-Atlantic Slave Trade Database, a freely available online resource that lets visitors search through and analyze information on nearly 36,000 slave voyages that occurred between 1514 and 1866.

Inspired by the remarkable public response, we recently developed an animation feature that helps bring into clearer focus the horrifying scale and duration of the trade. The site also recently implemented a system for visitors to contribute new data. In the last year alone we have added more than a thousand new voyages and revised details on many others.

The data have revolutionized scholarship on the slave trade and provided the foundation for new insights into how enslaved people experienced and resisted their captivity. They have also further underscored the distinctive transatlantic connections that the trade fostered.

https://giphy.com/embed/3o7bubi6p8AiWkeK52

Records of unique slave voyages lie at the heart of the project. Clicking on individual voyages listed in the site opens their profiles, which comprise more than 70 distinct fields that collectively help tell that voyage’s story.

From which port did the voyage begin? To which places in Africa did it go? How many enslaved people perished during the Middle Passage? And where did those enslaved Africans end the oceanic portion of their enslavement and begin their lives as slaves in the Americas?

Working with complex data

Given the size and complexity of the slave trade, combining the sources that document slave ships’ activities into a single database has presented numerous challenges. Records are written in numerous languages and maintained in archives, libraries and private collections located in dozens of countries. Many of these are developing nations that lack the financial resources to invest in sustained systems of document preservation.

Even when they are relatively easy to access, documents on slave voyages provide uneven information. Ship logs comprehensively describe places of travel and list the numbers of enslaved people purchased and the captain and crew. By contrast, port-entry records in newspapers might merely produce the name of the vessel and the number of captives who survived the Middle Passage.

These varied sources can be hard to reconcile. The numbers of slaves loaded or removed from a particular vessel might vary widely. Or perhaps a vessel carried registration papers that aimed to mask its actual origins, especially after the legal abolition of the trade in 1808.

Compiling these data in a way that does justice to their complexity, while still keeping the site user-friendly, has remained an ongoing concern.

Volume and direction of the transatlantic slave trade from all African to all American regions.
David Eltis and David Richardson, Atlas of the Transatlantic Slave Trade (New Haven, 2010), Author provided

Of course, not all slave voyages left surviving records. Gaps will consequently remain in coverage, even if they continue to narrow. Perhaps three out of every four slaving voyages are now documented in the database. Aiming to account for missing data, a separate assessment tool enables users to gain a clear understanding of the volume and structure of the slave trade and consider how it changed over time and across space.

Engagement with Voyages site

While gathering data on the slave trade is not new, using these data to compile comprehensive databases for the public has become feasible only in the internet age. Digital projects make it possible to reach a much larger audience with more diverse interests. We often hear from teachers and students who use the site in the classroom, from scholars whose research draws on material in the database and from individuals who consult the project to better understand their heritage.

Through a contribute function, site visitors can also submit new material on transatlantic slave voyages and help us identify errors in the data.

The real strength of the project – and of digital history more generally – is that it encourages visitors to interact with sources and materials that they might not otherwise be able to access. That turns users into historians, allowing them to contextualize a single slave voyage or analyze local, national and Atlantic-wide patterns. How did the survival rate among captives during the Middle Passage change over time? What was the typical ratio of male to female captives? How often did insurrections occur aboard slave ships? From which African port did most enslaved people sent to, say, Virginia originate?

H.M.S. ‘Rattler’ captures the slaver ‘Andorinha’ in August 1849.
The Illustrated London News (Dec. 29, 1849), vol. 15, p. 440, Author provided

Scholars have used Voyages to address these and many other questions and have in the process transformed our understanding of just about every aspect of the slave trade. We learned that shipboard revolts occurred most often among slaves who came from regions in Africa that supplied comparatively few slaves. Ports tended to send slave vessels to the same African regions in search of enslaved people and dispatch them to familiar places for sale in the Americas. Indeed, slave voyages followed a seasonal pattern that was conditioned at least in part by agricultural cycles on both sides of the Atlantic Ocean. The slave trade was both highly structured and carefully organized.

The website also continues to collect lesson plans that teachers have created for middle school, high school and college students. In one exercise, students must create a memorial to the captives who experienced the Middle Passage, using the site to inform their thinking. One recent college course situates students in late 18th-century Britain, turning them into collaborators in the abolition campaign who use Voyages to gather critical information on the slave trade’s operations.

Voyages has also provided a model for other projects, including a forthcoming database that documents slave ships that operated strictly within the Americas.

We also continue to work in parallel with the African Origins database. The project invites users to identify the likely backgrounds of nearly 100,000 Africans liberated from slave vessels based on their indigenous names. By combining those names with information from Voyages on liberated Africans’ ports of origin, the Origins website aims to better understand the homelands from which enslaved people came.

The ConversationThrough these endeavors, Voyages has become a digital memorial to the millions of enslaved Africans forcibly pulled into the slave trade and, until recently, nearly erased from the history of not only the trade itself, but also the history of the Atlantic world.

Philip Misevich, Assistant Professor of History, St. John’s University; Daniel Domingues, Assistant Professor of History, University of Missouri-Columbia; David Eltis, Professor Emeritus of History, Emory University; Nafees M. Khan, Lecturer in Social Studies Education, Clemson University , and Nicholas Radburn, Postdoctoral Fellow, University of Southern California – Dornsife College of Letters, Arts and Sciences

This article was originally published on The Conversation. Read the original article.


Infographic: The History of Digital Storage


The link below is to an article and infographic dealing with the history of digital storage.

For more visit:
http://mashable.com/2011/10/08/digital-storage-infographic/


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