All posts tagged with taxonomy

In the last decades of the 19th century, a monumental publication on the biodiversity of Mexico and Central America began publication—Biologia Centrali-Americana. Published in 215 parts from 1879 to 1915 by the editors Frederick DuCane Godman and Osbert Salvin, the work describes over 50,000 species and is illustrated with over 1,600 lithographic plates depicting over 18,000 species. Remarkable for its time, the title is still vitally important for the study of Neotropical biodiversity today, as it contained virtually all known information at the time about Mexican and Central American flora and fauna.

Biologia Centrali-Americana is a particularly important resource for entomologist Samanta Orellana, a PhD student in evolutionary biology at the Dr. Nico Franz Lab of Arizona State University (ASU) and a research assistant in the ASU Biocollections of the Biodiversity Knowledge Integration Center. Orellana began studying insects and working with entomological collections more than a decade ago, during her undergraduate studies in her home country of Guatemala.

“For many insect groups in Guatemala and the rest of Central America, Biologia Centrali-Americana still represents the only source of information available for the region,” states Orellana.

On 5 June 1834, avid amateur botanist Hardy Bryan Croom wrote a letter to botanist John Torrey describing a gymnosperm tree in northern Florida that he was struggling to identify. In this letter, he postulated—with some degree of confidence—that the tree was Taxus baccata, the common yew, and he hoped to acquire some specimens to send to Torrey for investigation.

Torrey was one of the most important 19th century botanists in America. He corresponded with hundreds of scientists in North America and Europe, many of whom sent him specimens from their various explorations for study and identification. As such a well-respected expert and advisor on botanical science, it comes as no surprise that Croom sought Torrey’s expertise regarding this mysterious Florida tree.

The next year, in a letter dated 18 November 1835, Croom wrote again to Torrey, stating:

“The letter which I wrote last summer has had the effect to procure me some perfect fruit of that remarkable Taxoid tree at Aspalaga. The result surprises me. It is an ovate one celled nut entirely enclosed in fleshy covering! as large as a pigeon’s egg! Calix imbricated; thus agreeing neither with Taxus nor with Podocarpus. Besides, the tree, I think, is dioecious, but of this I am not yet certain. What will you do with it? Will it make a new genus?”

The following year, Croom again wrote to Torrey in a letter dated 18 May 1836 that he had determined that the tree represented a new genus. He proposed the genus name Torreya and provided a description and habitat details for “this fine tree,” for which he remarked:

“It is so abundant about Aspalaga (especially on Flat Creek) as to have been sawed into plank and lumber. It is an elegant tree with dark green foliage.”

With this letter, Croom provided the first recorded description of the habitat and abundance of the Florida nutmeg, Torreya taxifolia.

Sadly, Croom and his family drowned in a shipwreck in the Atlantic Ocean near Cape Hatteras on 8 October 1837. As such, Torrey arranged that the new genus and species were formally named and described by botanist George Arnott Walker-Arnott in 1838.

While Croom characterized Torreya taxifolia as abundant in 1836, today the species is critically endangered. With a distribution restricted to the limestone ravines and bluffs along the Apalachicola River in northern Florida and southern Georgia, fewer than a thousand individual trees persist in their native habitat. The most significant threat to the species is continued reproductive failure resulting from fungal pathogens—a threat which is continuing but not well-understood.

In 1780, French naturalist François Le Vaillant traveled to the Cape of Good Hope and subsequently spent several years studying the region’s biodiversity. During his three journeys—the first around Cape Town and Saldanha Bay (April to August 1781), the second eastwards from the Cape (December 1781 to May 1783), and the third to the Orange River and into Great Namaqualand (June 1783 to c. May 1784)—Le Vaillant amassed a collection of thousands of specimens. Upon returning to Europe, he published accounts of his travels within Voyage dans l’intérieur de l’Afrique (1790, 2 vols.) and Second voyage dans l’intérieur de l’Afrique (1796, 3 vols.)—both of which were best sellers and were translated into several languages.

Within these narratives, Le Vaillant writes repeatedly of his Khoikhoi guide, whom he called Klaas (but whose name in Klaas’s own Khoe language seems to be unrecorded). Le Vaillant’s respect and affection for Klaas is evident. In the first volume of his Voyage dans l’intérieur de l’Afrique, Le Vaillant writes:

“…le bon Klaas fut déclaré mon égal, mon frère, le confident de tous mes plaisirs, de mes disgrâces, de toutes mes pensées ; il a plus d’une fois calmé mes ennuis, & ranimé mon courage abattu.” [“…the good Klaas is declared my equal, my brother, the confidant of all my pleasures, of my disgraces, of all my thoughts; he has more than once calmed my troubles, & revived my shattered courage.”]

Klaas, of whom Le Vaillant wrote “by long practice [he] had become a naturalist”, also collected specimens for the French naturalist, which Le Vaillant later described within publications such as Histoire naturelle des oiseaux d’Afrique (1796–1808, 6 vols.). One such specimen was that of Klaas’s cuckoo, a species native to the wooded regions of sub-Saharan Africa. According to Le Vaillant, Klaas collected the specimen “près de la rivière Platte” (“near the Platte river”). It was the only individual of this species that the company encountered during their expedition.

BHL has deployed a new taxonomic name finding tool to improve the speed and accuracy of identifying names throughout its 58+ million pages.

BHL is now usingGlobal Names Architecture’s (GNA) gnfinder tool to locate taxonomic names in the BHL corpus. Prior to this deployment, BHL’s name finding services were based on an index of scientific names created by GNA developers six years ago by parsing every page in BHL one by one. This took 45 days to accomplish, and the cost of repeating this process made updating or improving the index infeasible.

The gnfinder tool uses fast, scalable programming languages to significantly reduce computational time. Using Open Source applications in Go and Scala, the tool detects candidate scientific names and compares them to millions of scientific name-strings aggregated by GNA for verification. The new process decreases the time needed for name detection and name verification from 35 days to 5 hours and from 7 days to 12 hours, respectively. As a result, the entire BHL corpus can now be indexed in less than a day, compared to the 45 days needed for the previous index. Additionally, by significantly reducing computational time, implementing iterative improvements to the index is now achievable.

At the end of the twentieth century, the The Royal Botanic Gardens, Kew, The Harvard University Herbaria, and The Australian National Herbarium began collaboration on an ambitious project—to create an online index of names for all of the world’s vascular plants [1].

By combining the data in the nomenclatural indices of these three institutions—namely Index Kewensis, the Gray Card Index, and the Australian Plant Names Index—the collaboration created the International Plant Names Index (IPNI). Hosted by the Royal Botanic Gardens, Kew, today the database includes over 1.6 million records. As part of the provided nomenclatural information, IPNI includes bibliographic details linked to scanned literature in the Biodiversity Heritage Library (BHL) and links to taxonomic data through the Plants of the World Online.

Not surprisingly, given its role as a source of scanned literature for the Index, BHL is a vital resource for those working to build and maintain the IPNI database.

“I started working for the International Plant Names Index in 2013,” says Heather Lindon, Plant and Fungal Names Editor at the Royal Botanic Gardens, Kew . “I need to be able to look up protologues—the original place of publication of plant names and their descriptions. If the earliest place of publication isn’t known, we can use the name search in BHL to try to find it. Since our modern naming system dates to 1753, BHL has a lot of relevant literature for my work. Also, the rules of the International Code of Nomenclature that govern plant names apply to names published in the past, so consulting older works is still relevant for names being published today.”

The Consortium of European Taxonomic Facilities (CETAF) is launching a new initiative to reward early-career researchers, within the fields of taxonomy, biodiversity and geodiversity science, who base their research on natural science collections. E-SCORE – Excellence in Scientific Collections-based Research, is a celebration of the new generation of scientists who have shown dedication to the use of collections that help document, describe and understand life on earth, and the processes that have shaped it. The award also celebrates the United Nations endorsed International Day for Biological Diversity, which falls annually on the 22nd of May to commemorate the 1992 adoption of the Convention on Biological Diversity. CETAF will award E-SCORE for the first time in 2020 to mark the end of the UN International Decade of Biodiversity.

Two new fossil fly species have been named in honor of the Smithsonian Libraries and the Biodiversity Heritage Library. Sylvicola silibrarius Greenwalt, 2019 and Kishenehnoasilus bhl Dikow, 2019 have been described from specimens collected from the 46-million-year-old Kishenehn Formation of northwestern Montana. The species were published last week in the open access journal Palaeontologia Electronica.