Thursday, March 31, 2016


Tadpoles of the monotypic Indian dancing frog family Micrixalidae have remained obscure for over 125 years. Here we report the discovery of the elusive tadpoles of Micrixalus herrei from the sand beds of a forested stream in southern Western Ghats, and confirm their identity through DNA barcoding.

A group of Indian scientists discovered the tadpoles in the Western Ghats, a mountain range in southern India known as a biodiversity hotspot. They found them by digging in the sandy bottoms of streams. These tadpoles spend all their time underground consuming sand and bits of organic matter. After several months, they develop into adult Kallar dancing frogs (Micrixalus herrei), colorful frogs well known for waving their legs during mating displays.

The adult frog bears almost no resemblance to the tadpole form. Actually, the morphological differences were so great that the researchers had to use DNA barcoding to demonstrate that tadpoles and adults were one and the same species.

The tadpoles show some very interesting adaptation to life in the sand such as skin-covered eyes, a powerful tail for propelling them through sediment, and ribs, which haven’t been observed in other burrowing frogs. They also possess specialized mouthparts that act as a filter to prevent large sand particles from entering the mouth.

The documentation of Micrixalus herrei larval habitat informs decisions relating to their conservation and management. For instance, their association with forest cover, perennial streams, and sandy banks reveals specific habitat requirements for this species and potentially other threatened Micrixalus (e.g., M. gadgili and M. kottigeharensis). These tadpoles are also likely obligate burrowers that breed during low-water periods. This habitat and breeding information provides a basis for comparison with other Micrixalus species, most of which were only recently described.

Wednesday, March 30, 2016

New software on the block

Today a few new developments from the biodiversity informatics field. Of course they have something to do with DNA barcoding.

The introduction of high throughput sequencing technologies has triggered an increase of the number of studies in which the microbiota of environmental and human samples is characterized through the sequencing of selected marker genes. While experimental protocols have undergone a process of standardization that makes them accessible to a large community of scientist, standard and robust data analysis pipelines are still lacking. Here we introduce MICCA, a software pipeline for the processing of amplicon metagenomic datasets that efficiently combines quality filtering, clustering of Operational Taxonomic Units (OTUs), taxonomy assignment and phylogenetic tree inference. MICCA provides accurate results reaching a good compromise among modularity and usability. Moreover, we introduce a de-novo clustering algorithm specifically designed for the inference of Operational Taxonomic Units (OTUs). Tests on real and synthetic datasets shows that thanks to the optimized reads filtering process and to the new clustering algorithm, MICCA provides estimates of the number of OTUs and of other common ecological indices that are more accurate and robust than currently available pipelines. Analysis of public metagenomic datasets shows that the higher consistency of results improves our understanding of the structure of environmental and human associated microbial communities. MICCA is an open source project.

Taxonomic identification of biological specimens based on DNA sequence information (a.k.a. DNA barcoding) is becoming increasingly common in biodiversity science. Although several methods have been proposed, many of them are not universally applicable due to the need for prerequisite phylogenetic/machine-learning analyses, the need for huge computational resources, or the lack of a firm theoretical background. Here, we propose two new computational methods of DNA barcoding and show a benchmark for bacterial/archeal 16S, animal COX1, fungal internal transcribed spacer, and three plant chloroplast (rbcL, matK, and trnH-psbA) barcode loci that can be used to compare the performance of existing and new methods. The benchmark was performed under two alternative situations: query sequences were available in the corresponding reference sequence databases in one, but were not available in the other. In the former situation, the commonly used “1-nearest-neighbor” (1-NN) method, which assigns the taxonomic information of the most similar sequences in a reference database (i.e., BLAST-top-hit reference sequence) to a query, displays the highest rate and highest precision of successful taxonomic identification. However, in the latter situation, the 1-NN method produced extremely high rates of misidentification for all the barcode loci examined. In contrast, one of our new methods, the query-centric auto-k-nearest-neighbor (QCauto) method, consistently produced low rates of misidentification for all the loci examined in both situations. These results indicate that the 1-NN method is most suitable if the reference sequences of all potentially observable species are available in databases; otherwise, the QCauto method returns the most reliable identification results. The benchmark results also indicated that the taxon coverage of reference sequences is far from complete for genus or species level identification in all the barcode loci examined. Therefore, we need to accelerate the registration of reference barcode sequences to apply high-throughput DNA barcoding to genus or species level identification in biodiversity research.
The two new methods (NNCauto and QCauto) described above were implemented in the software package Claident.

DNA metabarcoding offers new perspectives in biodiversity research. This recently developed approach to ecosystem study relies heavily on the use of next-generation sequencing (NGS) and thus calls upon the ability to deal with huge sequence data sets. The obitools package satisfies this requirement thanks to a set of programs specifically designed for analysing NGS data in a DNA metabarcoding context. Their capacity to filter and edit sequences while taking into account taxonomic annotation helps to set up tailor-made analysis pipelines for a broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses. The obitools package is distributed as an open source software available on the following website: A Galaxy wrapper is available on the GenOuest core facility toolshed:

Tuesday, March 29, 2016

A tribute

Today's post is on a very sad occasion. March 18th, a very dear colleague and long-time collaborator, Allan Connell, died during a diving accident. 

Even though he did his PhD in Entomology, he had always been interested in fishing from a very young age and after his retirement he started a culture of collecting and studying fish eggs. He collected, catalogued, reared, and identified fish eggs at the KwaZulu- Natal coast off Park Rynie. Of course he often came across eggs and larvae he couldn't identify. Allan describes what happened next:

I searched the internet and came across an article in New Scientist about a researcher at the University of Guelph in Canada, who was barcoding cryptic butterflies, to unravel the mystery of very distinguishable larvae on specific host plants giving rise to cryptic adults that few experts could tell apart by traditional taxonomy. I made contact with the scientist (Paul Hebert) and asked whether it was possible to barcode some of my unknown species. He replied that they were in the process of sourcing funding for the launch of an international effort to barcode the fishes of the world. They asked if I was willing to collect fish from South Africa and in exchange they would barcode my hatched larvae.

I met Allan more than 10 years ago at the inaugural FishBOL meeting and we started a collaboration that went on until his untimely death. Countless emails went back and forth and it was great to see how it progressed. I am glad I kept most of those emails as some are wonderful examples of his enthusiasm. He often likened the arrival of new lab results to the opening of Christmas presents because some mysterious larva finally revealed its identity. Allan was a very friendly and patient person, always willing to help out colleagues by putting in an extra effort to obtain information or samples for them. He will be missed by many but my thoughts go out to his family.

A few weeks ago we got a paper accepted that summarized the first 10 years of this work. Little did we know that this would become Allan's legacy. This study delivered DNA barcodes for over 5000 individuals representing more than 1000 species of South African fishes. The fact that these specimens represent about 3% of all known fish species and 10% of the fish species barcoded to date is startling as they derive from the efforts of a single researcher, Allan. This effort took essentially 10 years, but it clearly shows his dedication and ardour. 

Farewell Allan. A number of people that knew you much better say that there is no other way you would rather have gone from this world than doing what you love most. I am thankful for the fact that I was able to join you for a small part of your journey over the last years. 

Monday, March 28, 2016

Rotational manipulation of cells and microorganisms

And now for something completely different:

Acoustic waves have been used to move and position biological specimens along the x, y and z axes, but for the first time researchers have used them to gently and safely rotate samples, a crucial capability in single-cell analysis, drug discovery and organism studies.

To achieve this, researchers from Penn State University trapped microbubbles within predefined sidewall microcavities inside a microchannel. They describe the acoustofluidic rotational manipulation (ARM) method that traps bubbles in a series of small cavities inside a microfluidic device. Acoustic transducers similar to ultrasound imaging transducers create an acoustic wave in the fluid, causing the bubbles to vibrate. The vibrating bubbles create microvortexes in the flowing liquid that can be tuned to cause the sample to rotate in any direction and at any desired speed.

Currently, confocal microscopes are required in many biological, biochemical and biomedical studies, but many labs do not have access to a confocal microscope, which costs more than $200,000. Our ARM method is a very inexpensive platform. And it is compatible with all the optical characterization tools. You can literally use a cell phone to do three-dimensional imaging.

To demonstrate the device's capabilities, the researchers rotated the famous model organism Caenorhabditis elegans, that is about a millimeter in length. They also acoustically rotated and imaged a HeLa cancer cell, also for the first time. Existing methods of manipulating small objects either depend on the optical, magnetic or electrical properties of the specimen, and/or damage the specimen due to laser heating. The ARM method, on the other hand, uses a gentle acoustic wave generated by a similar power as ultrasound imaging and at a lower frequency. The device is also compact and simple to use.

Wednesday, March 23, 2016

A portable lab for Biohackers, Educators and Researchers

How about a multiple-component DNA lab, complete with thermocycler, centrifuge and DNA electrophoresis box, all together in a device the size of a lunchbox? In addition the price is just a fraction of what the typical lab instrumentation would cost.

BentoLab just started a Kickstarter campaign to produce a first batch of instruments. And it is, with the prototype being set at £549 (€695, $740) for the ‘super early bird’ price and £699 (€885, $940) for the regular. Certainly better than the average cost of a standard laboratory PCR machine plus all the other components. The hope is that in the future, with a higher volume order this price could be set even lower.

Here is their Kickstarter video:

Tuesday, March 22, 2016

The 50 most wanted fungi

Environmental sequencing regularly recovers fungi that cannot be classified to any meaningful taxonomic level beyond “Fungi”. There are several examples where evidence of such lineages has been sitting in public sequence databases for up to ten years before receiving scientific attention and formal recognition.

No doubt, there are many not yet described fungi, and public DNA databases contain thousands of fungal sequences that cannot be assigned to any known fungal group with confidence. Very often these fungi can't be cultured in order to establish some taxonomic baseline. As a result many of these sequences have defied robust taxonomic assignment for more than 10 years. Some 100,000 species of fungi have been described formally, although current estimates put the number of extant fungal species to at least 6 million. The vast dark fungal diversity unraveled by molecular techniques hints that the interaction between fungal taxonomy and DNA sequencing of environmental substrates such as soil and water is not necessarily optimal.

There is no taxonomic feedback loop in place to highlight the presence of these enigmatic lineages to the mycological community, and they often end up in sequence databases for years without attracting significant research interest.

Frustrated about this situation, an international group of researchers took the matter into their hands and now presents a search function in the UNITE database for molecular identification of fungi. Its aim is to highlight the fungi we know the least about, and invite the scientific community to resolve their taxonomic affiliation. The effort seeks to bridge the substantial knowledge gap between fungal taxonomy and molecular ecology through a list, the authors refer to as the "50 Most Wanted Fungi." The list is recomputed on a monthly basis, accounting for any updates and additions contributed by the scientific community between each iteration. Community participation is strongly encouraged, and the UNITE database has extensive support for third-party annotation. 

By highlighting these fungal lineages, the colleagues hope to speed up the study and formal description of these species. 

Indeed, nothing can be said of the way they make a living. It is simply not known. We make no claim as to the importance of these fungi from whatever point of view -- ecological, economic, or otherwise. We do make claim to their uniqueness, though, because it is frustrating, in the year 2016, not to be able to assign a name to a fungal sequence even at the phylum level.

Monday, March 21, 2016

Biological field stations

Northern Studies Centre, Churchill, Manitoba
Biological field stations are essential to managing the rapid environmental change taking place globally. We need a sustainable vision to ensure their success -- one that includes political support, increased public awareness, modernized cyber infrastructure, and improved data sharing. At the same time, we need to expand stations in areas that are underrepresented ecologically and geopolitically.

Biological field stations are under continuous risk of closure due to financial insecurity, lack of public support, and weak governance. Some 38% are administratively tied to colleges and universities, with the remainder overseen by museums, governmental organizations, and not-for-profits. We badly need a sustainable framework for biological field stations that recognizes their regional, national, and global importance. In addition they need to be integrated with larger initiatives, such as the Global Lakes Environmental Observatory Network and the Intergovernmental Platform on Biodiversity and Ecosystem Services

A recent BioScience paper provides the first comprehensive inventory of the world's biological field stations. Its authors report 1,268 stations are operating in 120 countries - from the tropics to the tundra, monitoring terrestrial, freshwater, and marine ecosystems.

The global distribution of 1268 biological field stations (BFS). a: terrestrial BFS; b: marine BFS; c: freshwater BFS; d: BFS with multiple research domains.

Most biological field stations are located in pristine or remote areas, like the Tundra Ecosystem Research Station situated in Canada's Southern Arctic Ecozone. Far fewer are in urbanized areas, like the Ecological Rhine Station situated on a former ship in Cologne, Germany. There is a vital need to record more environmental data in human-dominated systems, such as cities, and in sensitive areas such as deserts, savannas, mountainous regions, and offshore locations.

Undergraduate and graduate training is another benefit provided by biological field stations. These 'living laboratories' play a key role in educating the next generation of environmental scientists, and offer collaborative, hands-on research opportunities.

Given the myriad of problems facing our forests, freshwaters, and oceans -- networked, sustainable biological field stations are essential. The information they collect is relevant to addressing most of today's pressing environmental problems -- from air and water pollution to the movement of invasive pests and pathogens. They deserve our strong support and protection.

Wednesday, March 16, 2016

Social media and trade of rare plants

Orchids make up 70% of species listed by the Convention on the International Trade in Endangered Species (CITES) and some can sell on the black market for large five-digit sums, thus providing the motivation for traders to bypass the rules aimed at preventing species from becoming extinct. Illegal traders are keen to find new ways to advertise and sell their plants on the black market, with social media emerging as the new way to do so.

New research found wild orchids were being traded from all over the world, and recorded trade in rare and threatened species including one assessed as Critically Endangered. At least two others are listed as protected in the country from which they were being sold. Although total numbers of trade posts are relatively small, the high proportion of wild collected orchids for sale supports calls for better monitoring of social media for trade in wild collected plants and other traded wildlife.

If you think it is difficult to find such sites with obviously at partially illegal trade or people that are willing to buy endangered species, well how about this little quote I found by just entering the words Paphiopedilum kolopakingii and Price into Google: If these were more widely available and cost not so much as an arm and a leg, I wouldn’t hesitate to get one in a wink. What this person neglects to state is the fact that this species (see image) has been assessed as critically endangered by the IUCN and I bet most of the ones in the trade are sourced from the wild.

A previous study by some of the authors of this publication shows that orchid hobbyists who buy on the internet have a preference for rare species. The sale of wild orchids on social media, if left unchecked, is likely to contribute to pressure on vulnerable wild populations.

In addition to research, our findings highlight the potential benefit that monitoring these websites could have for law-enforcement and conservation.  Previous monitoring of online trade resulted in eBay banning the sale of ivory products.  Even if this ban has not been completely successful, it demonstrates that monitoring can provide information to underpin action.  In addition to bans, this information could be used to provide intelligence to law-enforcement agencies on the key people involved in trade, or to conservationists and policy makers on the species being traded that may need further protection.Currently, large-scale monitoring by law-enforcement agencies would be difficult to achieve, primarily due to limitations of time to dedicate to this work, and problems that non-experts face in the identification of the species and origin of products for sale.  One solution to this could be the development of automated tools to detect potentially illegal trade on different platforms. Currently, work is on-going to develop such tools to detect illegal online trade via auction websites. Whilst structured commerce websites facilitate this kind of detection, social-media websites with free-form text present more of a challenge. However, developing similar tools in collaboration with social media companies may overcome these problems and improve our understanding of the nature and extent of the trade, and inform efforts to tackle it.  

Monday, March 14, 2016

Open Access: Biodiversity Conservation and Phylogenetic Systematics

Biological conservation has oft been hampered by those who have maintained that priorities for action should only be established using approaches that are easily understood by the general public. The same demand has not been made in many other arenas of human endeavor (e.g. medicine, nuclear power), and neither should it constrain biological conservation. That said, there does remain a substantial challenge of encouraging an informed citizenry around the justification and goals of
using a phylogenetic diversity approach, and gaining their support. Only by so doing will there be a genuine chance of aligning the multitude of biodiversity-critical decisions being made each and every day across the continents and oceans.

This is an excerpt from the introduction to a new book in the Springer Series Topics in Biodiversity and Conservation. The good news - the entire book is open access available either as full pdf or even as epub (which I just uploaded on my iPad). Of course you can also just download individual chapters: 

Roseli Pellens, Philippe Grandcolas

Christopher Lean, James Maclaurin

Daniel P. Faith

Kowiyou Yessoufou, T. Jonathan Davies

Steven A. Trewick, Mary Morgan-Richards

Philippe Grandcolas, Steven A. Trewick

Daniel P. Faith

Anne Chao, Chun-Huo Chiu, Lou Jost

Olga Chernomor, Steffen Klaere, Arndt von Haeseler, Bui Quang Minh

David A. Nipperess

Daniel Rafael Miranda-Esquivel

Roseli Pellens, Antje Ahrends, Peter M. Hollingsworth, Philippe Grandcolas

Anni Arponen, Laure Zupan

Débora Leite Silvano, Paula Hanna Valdujo, Guarino Rinaldi Colli

Laura J. May-Collado, Carlos Zambrana-Torrelio, Ingi Agnarsson

Jessica K. Schnell, Kamran Safi

Nicolas Chazot, Keith R. Willmott, André V. L. Freitas, Donna Lisa de Silva…

Anaëlle Soulebeau, Roseli Pellens, Porter P. Lowry II, Xavier Aubriot…

Roseli Pellens, Daniel P. Faith, Philippe Grandcolas

Friday, March 11, 2016

New Barcode Bulletin Issue

Another issue of the Barcode Bulletin just came out. Great reading for your weekend.

Thursday, March 10, 2016

Turning Up the Heat on a Hotspot

Changing patterns in plant and animal communities along elevational gradients have interested biogeographers and macroecologists since Humboldt’s pioneering studies in the Andes 200 years ago. It was long assumed that species richness would decline monotonically with elevation, reflecting decreases in temperature and primary productivity. However, species richness has actually been shown to peak at intermediate elevations in 70% of past investigations. Only 20% of prior studies have shown the predicted monotonic richness declines with increasing elevation or otherwise divergent patterns.

One of the problems is that the analysis of tropical species-rich assemblages are often confounded by an insufficient amount of properly identified species. No one is to blame for this. We simply don't have the necessary number of experienced taxonomists and especially for arthropod groups we are facing a rather large amount of cryptic species. I might start sounding like a broken record but I maintain my statement that DNA Barcoding could be the tool needed to overcome these limitations, and I have a new study to back this up.

Colleagues have conducted a study with the largest number of species from one order (Lepidoptera) from a rather small geographic region. They sampled and analysed over 14000 geometrid moths which turned out to represent more than 1850 species. The area was a forested elevational gradient from 1020 – 3021 m in the southern Ecuadorian Andes. The authors state that all sampling sites were actually undersampled which is inevitable in such species-rich areas. Consequently they did some extrapolation and concluded that the total number of geometrid species is likely closer to 2350. The study was comparative as the area was sampled twice. The first time only morphology was used to identify species and the second time DNA Barcoding was included. The result - species richness at sites rose by 32–43%, and the beta diversity component increased by 43–51%.

To put these numbers in context - this small area of the Ecuadorian Andes is home to more than twice as many Geometrids moths as in all of Europe (<1000 species) or even Borneo (~1100 species). In addition, the study focused on the presumably most diverse intermediate elevation range. There will be more (maybe not as many) species awaiting discovery below and above the studied range.

Wednesday, March 9, 2016

Fast DNA extraction

Whenever we want to work with DNA the very first step in any laboratory procedure is DNA extraction. Most procedures of DNA extraction exploit the fact that membranes of cells and of their organelles are composed of lipid walls that can be broken down using a detergent or an organic compound. The first step in most procedures is to break-up a tissue sample so that the cells are separated from each other as much as possible thereby exposing them to a detergent that dissolves the membranes. It is necessary to filter and wash the resulting mixture in a subsequent step to separate DNA from the remains of the cellular membranes and other cellular material. Finally, the DNA is precipitated in water for further use.

In the literature one can find literally hundreds of different protocols developed for different taxonomic groups, utilization, and budget. Very many are simple modifications of basic approaches. For instance, most DNA Barcoding protocols include long incubation steps with proteinase K, detergents, chaotropic chemicals, resins or organic extractions. Many of those take about a day, some are pretty toxic, or if you happen to use commercial extraction kits expenses are considerable.

A group of Italian researchers now developed a fast DNA extraction method without any purification step for both fresh and processed seafood, suitable for any PCR analysis. Their protocol allows the cheap and fast DNA amplification (as short as 30 min total)from any sample, including fresh, stored and processed seafood and from any waste of industrial fish processing, independently of the sample preservation method. 

There are other fast methods out there but what makes this one compelling is the fact that the tests conducted were not only one with vertebrates, which is usually relatively simple, but also mollusks, which very often are challenging due to the presence of mucopolysaccharides and polyphenolic proteins which can interfere with subsequent PCR analysis. Worth a try I'd think. 

Tuesday, March 8, 2016

The sixth DNA metabarcoding Spring School

The sixth DNA metabarcoding Spring School at Kunming
Eric Coissac, YU Douglas, ZHOU Xin

DNA metabarcoding is a rapidly evolving method for assessing biodiversity from environmental DNA and bulk samples. It has a wide range of applications: biodiversity monitoring, animal diet assessment, reconstruction of paleo communities, among others. DNA metabarcoding uses molecular techniques such as PCR and next generation sequencing, and integrates skills in bioinformatics and biostatistics with classical ecological knowledge.

The DNA metabarcoding spring school is now in its sixth edition, and this year it is co-organized by the team and the Kunming Institute of Zoology, with support from the Chinese Academy of Sciences, Yunnan.

The school will be divided in two parts:

Two days of lectures (22nd, 23rd)
Three days of practicals

All the lectures and the practicals will be taught in English

The number of participants in the lecture portion is not limited, but registration is mandatory.

The number of participants in the practical portion is limited to 24, with at least 6 places reserved for students from outside China.

Candidates can apply for the school by sending an email to the following address :
The email must contain a brief curriculum vitae and a short letter of motivation. For applicants wishing to participate in the practical sessions, we request a more complete letter indicating how your research will benefit from DNA metabarcoding and what you are hoping to learn from this school. As part of the course, each participant in the practical portion will give a flash talk (5 minutes) about your research and how it is related to DNA metabarcoding.

Registration deadline is 15 May 2016

Monday, March 7, 2016

Cryptic diversity in Colombian illegally traded bird species

Colombia became a member of the iBOL family at the end of 2011. It is the the second most biodiverse country in the world only topped by Brazil. It is estimated that Colombia might be the home to 150,000 to 200,000 species. Colombia is the country with the most bird species in the world. 

However, human induced deforestation has already substantially changed the Andean landscape in Colombia. It is also linked to the conversion of lowland tropical forests to palm oil plantations. However, compared to neighboring countries rates of deforestation in Colombia are still relatively low. Other challenges are caused by natural factors such as the geological instability related to Colombia's position along the Pacific Ring of Fire. Colombia has 15 major volcanoes, the eruptions of which have on occasion resulted in substantial loss of life. Geological faults that have caused numerous devastating earthquakes. Heavy floods both in mountainous areas and in low-lying watersheds and coastal regions regularly occur during the rainy seasons with varying rainfall intensities due to the El Niño-Southern Oscillation

Unfortunately, Colombia's avifauna is not only threatened by habitat degradation but also by poaching. This was reason enough for a group of Colombian researchers to start building a DNA barcode library for all the Nation's birds starting with the ones that are listed in the CITES appendices. Half of those (151 species) are now done and among them are many hummingbirds endemic of the Northern Andes region.

Even in this rather small subset (~8%) of all the birds described from Colombia (~1800 species), the colleagues identified eleven cases of high intraspecific divergence (up to 14.61%) that could reflect cryptic diversity. Although bird species have been well studied and we think we have a good idea of the number of species that occur globally, such high rates of potentially overlooked species (>7%) are still surprising and unsettling given that the discovery was made among birds that are subject of illegal wildlife trade.

Friday, March 4, 2016

From the inbox: PhD position at German Barcode of Life (GBOL)

The Center for Molecular Biodiversity Research at the Zoological Research Museum Alexander Koenig in Bonn (ZFMK, Germany) invites applications for a PhD studentship. The studentship will be part of a project within the German Barcode of Life (GBOL).
Starting date: not later than 1st May 2016, preferentially earlier. 
Duration: until 31st December 2018
Salary: German salary scale (TV-L E13, 55 %).

We seek an enthusiastic and highly motivated candidate to work on a project on metabarcoding and biodiversity at ZFMK in Bonn. The main objective of the studentship is to create a biodiversity map of invertebrate communities using environmental DNA samples derived from the Eifel National Park and to monitor species/ ecosystems over time. This will be a timely project since there is no comprehensive biodiversity study German National Parks, such as the Eifel NP, using HTP (high-throughput) sequencing approaches. This will move towards establishing an efficient biodiversity-monitoring approach providing critical insights into biodiversity assessment on a temporal scale.The project will involve handling environmental samples (Malaise insect traps and soil samples) in the lab and in the field, as well as using next generation metagenetics/ metabarcoding approaches to tracking mainly meio- and macrofauna communities. There will be opportunity to develop a preliminary pipeline as a tool for biomonitoring and best-practice guidelines for environmental barcoding (sampling protocols, preservation and downstream data analysis). The student will join a multi-disciplinary supervisory team led by Dr Vera Fonseca (biodiversity and metabarcoding) and Dr Jonas Astrin (Biobank and DNA barcoding), together with an external collaborator, Dr Christopher Quince from Warwick University (food web, meta-analysis), offering the student to gain knowledge and training in Bioinformatics, Ecology, Genomics, Conservation and Biodiversity.

The PhD candidate should be highly motivated, with good computer command line skills and with a strong enthusiasm for environmental molecular biodiversity. The candidate will have to spend some time in the Eifel NP (driving license not necessary, but helpful). Desirable skills are molecular biology (e.g., DNA/RNA extraction, PCR) and bioinformatic environmental meta-analyses experience (HTP). Students are expected to acquire and develop new skills but candidates with prior expertise in HTP meta-analysis will be given preference. The candidate should have a 
Master s degree, or be close to completing a Master s degree in Biology or related discipline. Fluent spoken and written English is essential. The Center for Molecular Biodiversity Research at the Zoological Research Museum Alexander Koenig offers a pleasant and stimulating research environment with a modern molecular laboratory and a state-of-the-art high-performance computing cluster. Current research projects in the department deal with DNA barcoding and metabarcoding 
terrestrial biodiversity (German Barcode of Life, GBOL) and Environmental barcoding of aquatic invertebrates (EBAI, Norway University Museum), as well as other exciting research lines such as the phylogeny of insects (e.g., and other groups of organisms and the organization and evolution of insect genomes (e.g., i5K).

Applications should include:
(1) Letter of motivation (relevant skills, experience and research interests)
(2) Curriculum vitae
(3) Official BSc and/ or MSc certificates
(4) Contact details of two (ideally academic) references

Closing date for Applications: 1st April 2016. Applications should be submitted in English and electronically as a single PDF to Dr Vera Fonseca,  with MetaEIFEL application in the subject line. Any enquiries, please also contact

The ZFMK values equality of opportunity, human dignity, and racial/ethnic and cultural diversity. According to German law, applications by women and by persons with a disability will be given priority in case of superior or equal qualifications. Women are especially encouraged to apply. The position is remunerated according to TV-L E13 (55 %).

Wednesday, March 2, 2016

Twitter to expose illegal release of alien fish

Some alien fishes, such as the bluegill (Lepomis macrochirus macrochirus) pose a significant threat to the native biodiversity in Japan. Therefore they have become strictly prohibited across the nation. All activities related to the possible introduction of the species into the wild are currently punishable by a fine of up to $30,000 for a person ($900,000 for corporations), or even a prison sentence of up to 3 years.

In June 2015, Akinori Teramura tweeted two photographs of the invasive bluegill, both adults and juveniles, along with two young goldfish, which do not belong to the local fauna, either. In his post he identified the species and shared his surprise at the irresponsibility of the people who had released the fish. When a researcher saw the tweet, he decided together with a colleague and the discoverer to publish this information as a scientific report.

The student found all fish in an outdoor public pool in Yokohama City, Japan, while it was being cleaned before opening for the summer. Usually, these facilities are closed to the public during the colder seasons and it is then when native aquatic insect species, such as dragonflies and diving beetles, use them as spawning and nursery habitats. Curiously enough, though, the pool had been isolated from natural waters since its construction.

Therefore, the researchers conclude that the alien fishes have most likely been released from an aquarium from a local shop or an aquarist who no longer wanted them. However,  keeping bluegill fish in a home aquarium is illegal as well.

Such aquarium releases are not uncommon and invasive snakeheads in the US and the invasion of lionfish in the Caribbean are well documented examples on what can go wrong if people act irresponsibly. This study is a nice example of applied citizen science and how social media can help to quickly disseminate information.