The four-letter code: How DNA barcoding can accelerate biodiversity inventories

With unprecedented biodiversity loss occurring, we must determine how many species we share the planet with. This can start in our backyards, but speed is critical. A new study shows how biodiversity inventories can be accelerated with DNA barcoding and rapid publishing techniques, making it possible to survey a nature reserve in just four months. The final inventory of 3,500 species was written, released and published in the Biodiversity Data Journal in under one week.

To assess how quickly and effectively DNA barcoding could aid in quantifying biodiversity on a massive scale, the Biodiversity Institute of Ontario partnered with the rare Charitable Research Reserve, a 365+ hectare land reserve located in Ontario, Canada, in an attempt to expand the reserve’s existing species inventory list. To complement this speed in surveying, the two partners also used cutting edge tools and venues for data release and publishing to rapidly disseminate the results.

Surveys of different habitats on the reserve were conducted over four months and culminated in a bioblitz, at which point delegates of the 6th International Barcode of Life Conference joined the effort. “These experts possess invaluable skills that enabled us to identify so many species,” Angela Telfer, University of Guelph, comments in hindsight. “It was a great chance to marry barcoding data with taxonomic data and further our efforts to build a DNA barcode reference library.”

The use of DNA barcoding to conduct this inventory greatly improved the speed at which the results were made available to the public. For the 3,502 specimens barcoded from the bioblitz, the data were generated at an impressive time scale – samples went through lysis, DNA extraction and PCR, sequencing and validation within 72 hours of their collection. Using the BOLD barcode reference library, taxonomy was applied and these results were uploaded to the Global Biodiversity Information Facility (GBIF) via Canadensys within 96 hours of their collection.

Even the choice of journal for publication contributed to the rapid process. The manuscript preparation and submission took considerably less time due to the online writing platform and pre-submission peer-review offered by the Biodiversity Data Journal, used for the first time in this survey. This allowed the 100+ co-authors of this study to all provide input, and reviewers were able to discuss and comment on the paper during the authoring process. All data are now publicly accessible, through the journal article and the various repositories above, and all specimens have been deposited in the Biodiversity Institute of Ontario’s natural history collection and herbarium.

Over the span of four months, the two-staged survey produced a total of 28,916 specimens barcoded or observed across 14 phyla, 29 classes, 117 orders, and 531 families of animals, plants, fungi and lichens. A total of 1,102 species were recorded for the first time for the nature reserve, expanding its existing inventory by 49%.

The results from this mass data collection uncovered abundant biodiversity in taxa that were previously understudied. For example, there were no previous records of spiders at the reserve, but the team’s efforts added an impressive 181 species to the inventory list, three of which were new to the province.

“The survey at rare Charitable Research Reserve is unique to other studies in that within four months – plus a single day of a concentrated bioblitz – more than 25,000 specimens and 3,500 species were recovered, often by non-experts,” explains Connor Warne, a co-author on the paper and specialist in ants. “This model of assessment has the potential to revolutionize the way we uncover diversity in our world. With a coordinated effort, we could implement this model in parks, conservation areas and reserves across the world and take a much needed step in filling in the blank pages of the story of life on earth.”

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Original source:

Telfer A, Young M, Quinn J, Perez K, Sobel C, Sones J, Levesque-Beaudin V, Derbyshire R, Fernandez-Triana J, Rougerie R, Thevanayagam A, Boskovic A, Borisenko A, Cadel A, Brown A, Pages A, Castillo A, Nicolai A, Glenn Mockford B, Bukowski B, Wilson B, Trojahn B, Lacroix C, Brimblecombe C, Hay C, Ho C, Steinke C, Warne C, Garrido Cortes C, Engelking D, Wright D, Lijtmaer D, Gascoigne D, Hernandez Martich D, Morningstar D, Neumann D, Steinke D, Marco DeBruin D, Dobias D, Sears E, Richard E, Damstra E, Zakharov E, Laberge F, Collins G, Blagoev G, Grainge G, Ansell G, Meredith G, Hogg I, McKeown J, Topan J, Bracey J, Guenther J, Sills-Gilligan J, Addesi J, Persi J, Layton K, D’Souza K, Dorji K, Grundy K, Nghidinwa K, Ronnenberg K, Lee K, Xie L, Lu L, Penev L, Gonzalez M, Rosati M, Kekkonen M, Kuzmina M, Iskandar M, Mutanen M, Fatahi M, Pentinsaari M, Bauman M, Nikolova N, Ivanova N, Jones N, Weerasuriya N, Monkhouse N, Lavinia P, Jannetta P, Hanisch P, McMullin R, Ojeda Flores R, Mouttet R, Vender R, Labbee R, Forsyth R, Lauder R, Dickson R, Kroft R, Miller S, MacDonald S, Panthi S, Pedersen S, Sobek-Swant S, Naik S, Lipinskaya T, Eagalle T, Decaëns T, Kosuth T, Braukmann T, Woodcock T, Roslin T, Zammit T, Campbell V, Dinca V, Peneva V, Hebert P, deWaard J (2015) Biodiversity inventories in high gear: DNA barcoding facilitates a rapid biotic survey of a temperate nature reserve. Biodiversity Data Journal 3: e6313. doi: 10.3897/BDJ.3.e6313

New Indonesian crayfish species escapes the decor market to become a freedom fighter

With its orange to greenishly orange motley tip, the new crayfish species has been long-confused with its relatives by the tradesmen who have been collecting them for ornamental purposes. Being exported to countries in Europe, East Asia and America C. snowden specimens inevitably landed in the hands of the scientists from Lukhaup’s team who eventually recognised and proved them as a new crayfish species. Their research is available in the open-access journal ZooKeys.

Although the new crayfish species has probably been sold along with its motley relatives under another name for decades, the scientists figured that it is in fact easily distinguishable by its shape of body and colouration. In order to prove it as a separate species, the team used sequence divergence as well.

Having travelled across the world from its so far only known locality, West Papua, New Guinea, the new freshwater crustacean was given the name of the controversial former CIA employee and government contractor Edward Snowden. Its ‘godfather’ is famous for leaking secretive information from the U.S. National Security Agency, which later led him to a continuous search for political asylum. The authors speak of him as an “American freedom fighter” with “achievements in defence of justice, and freedom.”

In their conclusion the authors note that there could be potential threats to the new species. The freshwater crayfish is being collected in large numbers for both the ornamental fish global market and for food for the locals. Asked about the crustacean’s populations, the collectors spoke about a decline in the last few years.

“Clearly, the continued collection of these crayfish for the trade is not a sustainable practice, and if the popularity of the species continues, a conservation management plan will have to be developed, potentially including a captive breeding program,” the researchers comment.

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Original source:

Lukhaup C, Panteleit J, Schrimpf A (2015) Cherax snowden, a new species of crayfish (Crustacea, Decapoda, Parastacidae) from the Kepala Burung (Vogelkop) Peninsula in Irian Jaya (West Papua), Indonesia. ZooKeys 518: 1-14. doi: 10.3897/zookeys.518.6127

Under the wing of science: Two methods for aging nestling Carnaby’s cockatoo species

Multi-year research on two populations of the endangered endemic Carnaby’s cockatoo in southwestern Australia was conducted in order for two separate methods for nestlings aging to be assessed. If accurate enough, Dr. Denis Saunders and his team believe that the results could be vital in the threatened species’ preservation, as explained in the Carnaby’s cockatoo’s recovery plan.

One of the methods they have looked into is based on changes in the physical appearance of nestlings over the 10-11 week nestling period. The other relies on measurements of a nestling’s folded wing length and its comparison with growth curves from measurements of nestlings of known age. In their paper the Australian team also examines the timing and length of the egg-laying season. Their research is published in the open-access journal Nature Conservation.

The researchers point out that accurate nestling aging is essential for many ecological studies. The data could be used in investigating population dynamics, life histories, behaviour, longevity, conservation planning and management. It could also help in scheduling the visits of breeding areas so that the disturbance for the populations is minimised without compromising the results.

The scientists found out that observing the changes in a nestling’s size and feathers is less accurate than measuring the folded wing length. Its main disadvantage turned out to be the lack of distinguishable physical changes once the birds become about nine-week-old. However, “with experience it may be useful for gaining an approximation of the commencement and end of the breeding season without having to handle nestlings to take measurements,” the team says.

Their research on the egg-laying dates concluded that the most effective approach for examining nestlings is to conduct two visits per breeding season. Curiously, their findings showed that in wetter autumns the egg-laying begins earlier.

The team also suggests that their methods could be adopted for aging the currently under-researched closely related Baudin’s cockatoo until more species-specific technique is found.

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Original source:

 

Saunders DA, Dawson R, Nicholls AO (2015) Aging nestling Carnaby’s cockatoo, Calyptorhynchus latirostris, and estimating the timing and length of the breeding season.Nature Conservation 12: 27-42. doi: 10.3897/natureconservation.12.4863

Cave snail from South Korea suggests ancient subterranean diversity across Eurasia

As tiny as 1.7 mm, a snail whose relatives live exclusively in the deep recesses of caves, provided a sensational discovery from the depths of Nodong cave, South Korea, back in 2000 for its collector, J. S. Lee. It is the only cave-dwelling representative of the family of hollow-shelled snails in the whole of Asia with its closest relatives known from as far as Croatia and Northern Spain. The scientists, Adrienne Jochum, Bern University and Natural History Museum Bern, Larisa Prozorova and Mariana Sharyiool from the Far Eastern Russian Academy of Sciences and Barna Páll-Gergely from Shinshu University, published its description in the open-access journalZooKeys.

The Asian species has awaited 15 years to come out of the dark for a name and into the limelight of subterranean biodiversity and conservation awareness. This barely visible snail suggests a former pan-Eurasian distribution of cave-dwelling, hollow-spired snails.

The tiny-shelled treasure, called Koreozospeum nodongense, belongs to a larger group of ancient cosmopolitan air-breathing relatives known to have been amongst the first snail colonisers of land via mangroves about 65 million years ago. Similar to its European relatives from the genus Zospeum, the South Korean snail was also found on muddy cave walls.

Although more than 1,000 caves have been explored in South Korea, Nodong is so far the only one to harbour these beautiful denizens of the dark. Hypotheses made by Culver et. al. in 2006 about the existence of a very narrow, mid-latitudinal ridge of subterranean biodiversity (ca. 42-46°N in Europe and 33-35°N in North America) might clarify this unique find.

A high amount of caves known to exist within these latitudes provide ample habitats for colonisation of life. If this hypothetical ridge were to be extended further East away from Europe, then Koreozopseum‘s gliding along walls in a South Korean cave (33-35°N) makes a strong call for further investigations and discovery of rare biodiversity.

Jochum and her international team described K. nodongense using computer tomographic scans (Nano-CT) in a video film to view and compare the contours and architecture of the very fragile shell. Chemical trace elements, such as aluminum (Al) and silicon (Si) were detected in other scans of the thin diaphanous shell using mineralogical analysis techniques (SEM-EDX). These elements may play a role in the biomineralization (hardness) of the shell or may be contaminants absorbed by the snail from sediment consisting of volcanic ash from former eruptions in the region.

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Original Source:

Jochum A, Prozorova L, Sharyi-ool M, Páll-Gergely B (2015) A new member of troglobitic Carychiidae, Koreozospeum nodongense gen. et sp. n. (Gastropoda, Eupulmonata, Ellobioidea) is described from Korea. ZooKeys 517: 39-57. doi: 10.3897/zookeys.517.10154

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Additional information:

The Naturhistorisches Museum der Burgergemeinde Bern, Switzerland and the Far Eastern Branch of the Russian Academy of Sciences supported this work.