Barcoding local - Contributions by course participants (1)

The Introduction to DNA Barcoding course I am teaching is in its final week but we have already lined up another one running from June 1 to July 24, 2015. One of the weekly assignments of the course is an essay that combines what participants learned in the first 7 weeks and what they are doing at their home institution. This is one of the highlights of the course for me as it provides me with some unique insights into the work of colleagues world wide but it also shows me how well I did with teaching to that point. 

There are usually so many very interesting contributions that I always thought it would be a loss to the community at large if not shared more broadly. Therefore, I asked the participants of this course if they would give me permission to share their work through this blog. 

This is what I ask the participants in the respective unit:

Consider what you have learned so far about the application of DNA barcoding in several socio-economic fields. Try to come up with an application of the method in your professional or social environment. Your main motivation to take this course might be related to such an issue. Describe the issue at hand and how DNA barcoding could help. Assess how difficult or easy it might be to implement the new technology.

The first one who agreed to share his answer is Charuwat Taekul, head of the insect collection at the Insect Museum Thailand which is part of the Federal Department of Agriculture located in Bangkok. 

The development of a DNA barcoding knowledge base can help alleviate the situation of current trade negotiation. The International Plant Protection Convention (IPPC) currently plays a vital role in trade negotiations after non-tariff barriers have been established by the WTO. This means all members of the WTO not only are free to trade but also cannot limit the import/export of commodities unless there are scientifically proven health concerns or other reasons. The IPPC calls this subject "Sanitary and Phytosanitary (SPS)." However, this issues results in several issues when it comes to trade between countries. For example, EU countries claim that certain species of insects contaminate agricultural products and because these species do not occur in the EU member states, those products are banned from import into the EU. However, we are currently not sure these claims stem from actual research or trade barriers. To resolve such issues, the IPPC established experimental procedures, which all member countries can uniformly employ, the International Standard Phytosanitary Measures (ISPMs).

A number of protocols using DNA Barcoding are applied into ISPMs, e.g., ISPM No.27: Diagnostic Protocols for Regulated Pests. This protocol deals with the detection of Thrips palmi using real-time PCR since this species represents a trade barrier for import into the EU as it is a recognized invasive species. My research focuses on establishing ideal conditions for real-time PCR to detect Thrips palmi in Thailand to support the ISPM. 

DNA barcoding may help in pest control strategies as well as save the governmental money. A couple years ago, Thailand had critical pest problems with the coconut black-headed caterpillar, Opisina arenosella and the Pink sugarcane mealybug Saccharicoccus sacchari. These two species play an important role as invasive alien species and had a huge impact on the federal budget due to the large scale import of their natural enemies to control them. This classical control was applied without investigating the species richness of native natural enemies since the damage is quite widespread and uncontrollable. Nevertheless we might have saved a lot of money by investigating if suitable biocontrol agents are already available from native sources before importing them from elsewhere. Obtaining the information for both native pests and their natural enemies is important.

The formation of the ASEAN Economic Community (AEC) and ASEAN+3 (China, South Korea, and Japan) in late 2015 will bring the major changes to the economy, businesses, the workforce and society. The AEC is not only establishing free trade zones within Asia but also generating a single market and production zone to boost the competitiveness, thereby unequivocally creating free mobility of goods, services, investments, and skilled labors. DNA barcoding could help develop national capacities in detection and management of invasive alien species and plant pests as well as utilize the knowledge base to other research areas. After all, Thailand provides suitable conditions for many  alien species which might allow them to establish quite well. 

Despite the fact that DNA barcoding could play a significant role in trade facilitation as well as pest control and invasive species management, only little financial support has been provided for the program. A taxonomic proposal for pest and natural enemies has been suspended. The national science foundation claims that it is not a pressing issue and that the results cannot be applied at this moment. The main problems here are the lack of financial support from the government and the lack of recognition from the other fields of the scientific community.

Discoveries of the week #35

Hisonotus vespuccii

A new species of Hisonotus is described from the rio São Francisco basin. The new species can be distinguished from congeners by having (1) a unique coloration pattern of caudal fin with one black spot extending from its origin to the ventral lobe and two dark spots at the end of the lobe’s rays; (2) odontodes forming longitudinally aligned rows on head and trunk; (3) a functional V-shaped spinelet; (4) a single rostral plate at the tip of the snout; (5) by lacking contrasting dark geometric spots on the anterodorsal region of the body; (6) a lower caudal-peduncle depth; and (7) lower counts of the lateral median plates and (8) higher premaxillary and dentary teeth. The new species is the second described species of the genus Hisonotus in the rio São Francisco basin. It was found inhabiting the marginal vegetation of the rio São Francisco and three of its tributary, rio das Velhas, rio Paraopeba and rio Formoso.

And yet another new loricariid species. This one was named after Amerigo Vespucci, navigator and explorer who discovered the Rio São Francisco in 1501, which is the type locality of the species.

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Taxidiotisoma portabile

Taxidiotisoma portabile gen. n., sp. n. is described from scattered populations in New South Wales, Victoria and Tasmania, Australia. Populations of T. portabile in Victoria, Tasmania and parts of New South Wales occur in urban, suburban and agricultural areas, with no collections of the species in natural habitats in the same district. Taxidiotisoma portabile is likely to be a native exotic species whose home range is in eastern New South Wales.

Not only a new millipede species but also a new genus. The genus name means travelling body and refers to the fact that the only species of this genus is perhaps a species that moved into new areas. The species name has a similar meaning referring to the fact that this species is almost certainly being transported to new areas in Australia by cars or trucks.

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Savarna kraburiensis

The small genus Savarna Huber, 2005 only contains three species: Savarna baso (Roewer, 1963) from Sumatra, Indonesia, S. tesselata (Simon, 1901) from Malaysia, and S. thaleban Huber, 2005 from Thailand (World Spider Catalog 2014). In this paper, we describe one more, a new species from Ranong, Thailand.

A new spider species from Thailand named after the type locality district.

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Cyphastrea kausti

A new scleractinian coral species, Cyphastrea kausti sp. n., is described from 13 specimens from the Red Sea. It is characterised by the presence of eight primary septa, unlike the other species of the genus, which have six, ten or 12 primary septa. The new species has morphological affinities with Cyphastrea microphthalma, from which it can be distinguished by the lower number of septa (on average eight instead of ten), and smaller calices and corallites. This species was observed in the northern and central Red Sea and appears to be absent from the southern Red Sea.

This new scleractinian coral species was discocvered at the coast of Saudi Arabia. This species is named after the King Abdullah University of Science and Technology (KAUST).

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Sarothrias sinicus

The family Jacobsoniidae Heller (短跗甲科) is newly recorded from China upon the discovery of Sarothrias sinicus Bi & Chen, sp. n. (中华短跗甲) from Motuo, Southeast Xizang. Description and illustrations of the habitus and major diagnostic features of the new taxon are provided. A key to the species of Sarothrias and some ecological notes on the new species are presented.

This new species is named after the country of the type locality, China.

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Critoniopsis narinoensis, Critoniopsis tausae

Critoniopsis bogotana is more precisely delimited, and two related Colombian species are described as new. The form of trichomes on the abaxial surfaces of the leaves is found to be of major importance. A short key to the C. bogotana group is provided.

Two new species from the Northern Andes. One has been named after a department of Columbia, Nariño, and the other one is named after the type locality, Municipality de Tausa.

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School Malaise Trap Program - Spring 2015

Today was the day. All participants of the School Malaise Trap Program deployed and 'armed' their traps. The weather hasn't been optimal this year to say the least but over the last few weeks things started to get better and most importantly warmer. We pitched a trap here at our institute and there are already quite a few insects trapped in it. My guess is that the majority of them are the infamous Chironomids as those always seem to be the first ones out after the Winter.

As last Fall we encouraged students and their teacher to let us know via Blog and Twitter what they are up to and how their traps are doing. Here is a selection of some pretty cool entries to our program blog and Facebook page.

Here a video from Blair Outdoor Education Centre not far from here:

Set up at M.C. Knoll Elementary School:

big excitement at the Chedabucto Education Centre:

and even a cheer from John Polanyi Collegiate Institute:

DOPA Explorer

The Digital Observatory for Protected Areas (DOPA) has been developed to support the European Union’s efforts to substantially strengthen the effectiveness of international governance for biodiversity and ecosystem services and more generally for strengthening the capacity to mobilize and use biodiversity data, information and forecasts so that they are readily accessible to policymakers, managers, experts and other users. DOPA is conceived as a set of web based services to provide a large variety of end users with means to assess, monitor and possibly forecast the state of, and pressures on protected areas at local, regional and global scale.

I have to admit that until very recently I didn't know much about this very interesting biodiversity information system which was developed over the last five years at the Joint Research Centre of the European Commission in collaboration with other international organizations, such as GBIF, UNEP-WCMC, Birdlife International and RSPB. DOPA is not only designed to assess the state and pressure on protected areas and to prioritize them accordingly, in order to support decision making and fund allocation processes, but it is also conceived as a monitoring and ecological forecasting service, through e-Habitat, its core web processing service. The use of open standards and of open source programming languages for the development of the core functionalities of the system were expected to encourage the participation of the scientific community beyond existing partnerships and to favor the sharing of such an observatory which could be installed anywhere.

The first of the proposed tools, DOPA Explorer  has been released in early April:

The main purpose of the DOPA Explorer is to provide simple means to explore, analyse and compare the existing reference information on species and ecosystems that is available on protected areas at the country and ecoregion levels. End-users can use DOPA Explorer to identify the protected areas with the most unique ecosystems and species or assess the level of pressure coming from agriculture or population.

The web interface provides users with simple means to explore nearly 16 000 of the world's protected areas. Although the system is currently frequently overloaded it provides some very interesting mapping tools and one can certainly see its value for a lot of applications. 

In a recent letter of the United Nations Convention on Biological Diversity (CBD), the Executive Secretary encourages all the Parties to the CBD to make use of the DOPA Explorer in their actions towards achieving Aichi Biodiversity Target 11:

By 2020, at least 17 per cent of terrestrial and inland water, and 10 per cent of coastal and marine areas, especially areas of particular importance for biodiversity and ecosystem services, are conserved through effectively and equitably managed, ecologically representative and well connected systems of protected areas and other effective area-based conservation measures, and integrated into the wider landscapes and seascapes.

Niche partitioning in diatoms

Life on Earth is diverse and abundant, and there's no need to look any farther than the ocean's surface for proof. There are over 200,000 species of phytoplankton alone, and all of those species of microscopic marine plants that form the base of the marine food web need the same basic resources to grow--light and nutrients. This diversity of phytoplankton has puzzled researchers for a long time. The many different species coexist in this relatively stable environment, competing for the same resources but no species seems to out-compete others.

A study by a team of researchers from the Woods Hole Oceanographic Institution (WHOI), University of Rhode Island (URI), and Columbia University, reveals how diatom species - one of the several major types of marine phytoplankton - use resources in different ways to coexist in the same community. The colleagues used a novel approach combining new molecular and analytic tools to investigate how similar species utilize resources differently - known as niche partitioning - in Narragansett Bay, R.I.  In conjunction with the sequencing analysis, the research team developed a new bioinformatic approach that uses data from nutrient amendment experiments to help interpret signals from the environment.

Here, we use quantitative metatranscriptome analyses to examine pathways of nitrogen (N) and phosphorus (P) metabolism in diatoms that co-occur regularly in an estuary on the east coast of the United States (Narragansett Bay).

Using these data the researchers e.g. observed two species of chain-forming diatoms--Skeletonema spp. and Thalassiosira rotula--coexisting in the same subset of water, but doing fundamentally different things with available nutrients, specifically nitrogen and phosphorus. Skeletonema is the more dominant species of the two and has specialized on inorganic nitrogen sources, like nitrate and nitrite. The less dominant species, Thalassiosira, is bringing in nitrogen from organic sources, such as amino acids.

We have long suspected that even closely related phytoplankton must have ways of distinguishing their needs from that of their neighbors, for example using different forms phosphorus or nitrogen, but this has been hard to track in the environment, as most approaches are not species-specific...Part of the challenge is that you would need to track species-specific patterns in resource utilization to compare one diatom to another.

The annotation of RNA sequences via "pattern matching" was facilitated by the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP), which has sequenced the genetic material of more than 300 marine species. In this study, a new database that is part of the MMETSP was leveraged to identify species-specific signals. In addition the team developed a way to normalize those signals to be able to compare quantitatively between species.

Finalists for GBIF Ebbe Nielsen Challenge

The Global Biodiversity Information Facility (GBIF) officially established in 2001 is an international open data infrastructure, funded by various governments. It allows anyone, anywhere to access data about all forms of life on Earth, shared globally and openly.

Last year GBIF launched the GBIF Ebbe Nielsen Challenge, an open incentive competition seeking for the best and most innovative applications of open-access biodiversity data by scientists, informaticians, data modelers, cartographers and other experts. GBIF wanted to encourage use of the more than half a billion species occurrences and other data mobilized through and related to GBIF’s international network.

The competition goes through two rounds. Round one has just been finished and the jury selected six finalists from among 23 submissions received, inviting their creators to compete for €25,000 during the innovation prize’s second and final round. 

Here they are and it will be a tough choice for the jury as all are pretty cool and innovative ideas. 

#myGBIF

Developed by Tom August

This service leverages location information from Twitter users who use the the hashtag #myGBIF—“One hashtag, infinite possibilities”, as August suggests. Functioning as a hyper-local personalized biodiversity assessment, the call to #myGBIF retrieves species occurrence data from the user’s area, mashes them up with common names and IUCN extinction risks via the Encyclopedia of Life, and promptly tweets a resulting infographic back to the user.

BioGUID.org

Developed by Richard Pyle

Biodiversity informatics needs reliable, persistent and actionable digital identifiers, but the community has made little progress toward resolving its glut of multiple identifiers and sources for any given data object. BioGUID.org provides a common service for indexing and cross-linking a wide range of identifiers, making it easier to cross-link biodiversity datasets, and making them more powerful by harnessing identifiers.

ecoSpace

Developed by Miguel Porto

Promising “a new way of looking at species occurrence datasets”, this dynamic web application lets users navigate the relationships within regional species groups that are displayed as an ecologically meaningful network. Its interactive interface shows species’ ecological or biogeographical affinities based on user-selected bioclimatic variables and expands at each step to reveal the network’s complexity.

GBIF dataset metrics

Developed by Peter Desmet, Bart Aelterman & Nicolas Noé

This team has created a ready-to-use browser extension for Google Chrome, offering quick insights about the datasets available through GBIF.org. Its chart-based visual approach provides at-a-glance assessments of the occurrences contained in a dataset, enabling a user to assess its fitness for his or her use without having to download, filter and clean the data.

GBIF Soundscape

Developed by Ben Raymond & Peter Neish

This application taps the rich if unconventional stream of information available in sound recordings associated with some occurrence records. Drawing on the GBIF API, it reconstructs the natural "soundscapes" using audio files associated with bird and frog occurrences in selected regions.

Wallace (beta v0.1): Harnessing Digital Biodiversity Data for Predictive Modeling, Fueled by R

Developed by Robert P. Anderson, Matthew Aiello-Lammens, Bob Muscarella, Bruno Vilela & Jamie Kass

This submission combines data from the GBIF network with two recently developed tools developed in R, a high-powered programming language for statistical computing and graphics, allowing users to generate predictive distribution models. The web application enables researchers working online or offline to map, filter and remove occurrence records and build, evaluate and visualize complex predictions.

Here is what Rod Page, member of the jury had to say about the winners. He calls this quote rather cheesy but I let you be the judge of that. 

The creativity and ambition displayed by the finalists is inspiring. My biggest hope for the challenge was that the biodiversity community would respond with innovative - even unexpected - entries. My expectations have been exceeded, and the jury is eager to see what the finalists can achieve between now and the final round of judging.

I really like to encourage everyone to play around with these new tools. Most of them are in working condition and what will take place next is refinement. 

Discoveries of the week #34

Chaerilus pseudoconchiformus

A new species, C. pseudoconchiformus sp. n., is described from Xizang, China. The present new species is distinguished from its congeners by a body length of 32−40 mm, carapace with the anterior margin straight, chela with length/width ratio average of 3.3 in males (3.2−3.4, two adults), and 2.5 in females (2.3−2.6, nine adults), eight or nine (eight usually) rows of denticles on fixed and movable fingers of pedipalp chelae, five pectinal teeth in males and three or four in females. To date, the chaerilid species fauna of China consists of nine species. An updated identification key to Chaerilus from China is presented.

The first of two newly described scorpion species. The species name of this new member of a small monotypic family refers to the geographically and morphologically most closely related species Chaerilus conchiformus, by adding the Greek prefix “pseudo".

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Scorpiops ingens

A new species, Scorpiops ingens sp. n., from Xizang, is described and illustrated. Scorpiops ingens sp. n. is characterized by yellow-brown color, large size (length of adults above 70.0 mm), small and dense granules on tegument, a pair of small median eyes, 17 external trichobothria (5 eb, 2 esb, 2 em, 4 est, 4 et), and 7 or 8 (usually 7) ventral trichobothria in the pedipalp patella, chela with a length/width ratio average of 2.2 in males and females, pedipalp chela fingers on adult females and males scalloped, pectinal teeth count 6–8, pectinal fulcra absent. With the description of this new species, the number of known species of Scorpiops from China is raised to 12. An updated identification key to Scorpiops from China is presented.

This is the second new scorpion from China. The species name refers to its size. The Latin word "ingens' means huge.

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Neomida diminuta

Neomida diminuta sp. n. is described, based on a single male specimen from Colombia, and a redescription of N. suilla (Champion) is given. Data on the morphology of the aedeagus for both species, and on the female abdominal terminalia for N. suilla are provided. New records of N. suilla from Atlantic Forest remnants in the states of Espírito Santo and Minas Gerais, Brazil are given.

This new species of darkling beetle belongs to genus of strict fungivorous beetles that live in hard conks of wood decomposing fungi. The species name “diminuta” means small, referring to its minute size (1.7 mm total length).

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Stephos geojinensis, Stephos projectus

Stephos geojinensis

Two new species of benthopelagic copepods of the genus Stephos T. Scott, 1892, belonging to the family Stephidae G.O. Sars, 1902, are described based on specimens collected in the stagnant water flooding the burrows excavated by ocypodid crabs in two intertidal mud-flats, and from near-bottom shallow waters in Korea, respectively. They can be easily diagnosed based on the ornamentation of both the female genital double-somite and genital operculum; the morphology of the distal segment of the male right P5; the presence/absence of a tiny pointed process on the distomedial angle of second segment of female P5; and the condition (seta or spine) of the lateral armature element on the distal segment of female fifth legs, among other features. This is one of the few cases reported of calanoid copepods living as commensals of other invertebrates, and raises to six the number of members of the genus reported from Asia. This is also the first record of the family Stephidae in Korea.

These two new species are first records of the calanoid family Stephos in Korean waters. One was named after the type locality Geojin Port, Gosung-gun, Gangwon-do, Korea. The second species go tits name from some dorsolateral spiniform projections present on the female genital apparatus.

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Paepalanthus serpens

We describe and illustrate Paepalanthus serpens, a microendemic species of Eriocaulaceae from the Espinhaço Range. The species is known from a single population growing in rocky areas of the Serra do Cipó, Minas Gerais. It is placed in Paepalanthus ser. Paepalanthus, and is easily distinguished from its congeneric species by its elongated, lignescent stem, thickened by the marcescent sheaths of the linear leaves, which are arranged in a rosette at the stem apex, scapes equalling the leaf height, and capitulae with straw-coloured involucral bracts. Comparisons with the morphologically similar species are provided, as well as comments on distribution, ecology, phenology and conservation status.

This new perennial species is known only from one population at the western slopes of the Serra do Cipó in Brazil. The name "serpens" refers to the serpent-like growth, with an unbranched, thick woody stem that slowly elongates and becomes creeping, with an erect apex.
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Indigofera magnifica, Indigofera asantasanensis

Indigofera magnifica

Two new species of Indigofera L. (Leguminosae) are described from the Sneeuberg Centre of Floristic Endemism on the southern Great Escarpment, Eastern and Western Cape Provinces, South Africa. Both species are localised high-altitude endemics. Indigofera magnifica Schrire & V.R. Clark is confined to the summit plateau of the Toorberg–Koudeveldberg–Meelberg west of Graaff-Reinet, and complements other western Sneeuberg endemics such as Erica passerinoides (Bolus) E.G.H. Oliv. and Faurea recondita Rourke & V.R. Clark. Indigofera asantasanensis Schrire & V.R. Clark is confined to a small area east of Graaff-Reinet, and complements several other eastern Sneeuberg endemics such as Euryops exsudans B. Nord & V.R. Clark and E. proteoides B. Nord. & V.R. Clark. Based on morphology, both new species belong to the Cape Clade of Indigofera, supporting a biogeographical link between the Cape Floristic Region and the Sneeuberg, as well as with the rest of the eastern Great Escarpment.

The first of these two new high altitude species is named for its magnificent, showy, vivid fuchsia-pink flowers and the second for the Asante Sana Private Game Reserve, the owners and managers of which have been generous and instrumental in facilitating biodiversity research in the Sneeuberg region. The known range of this species is almost entirely confined to this property.
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