Wednesday, August 27, 2014

From the inbox - Seafood fraud

Dear Colleague;

I am writing because you have undertaken research in illegal fishing or seafood species substitution in the market place or seafood supply chain.  The U.S. government is currently soliciting comments on how to combat illegal, unreported, and unregulated fishing and seafood fraud and trying to document the extent of the problem. Please consider signing the attached comment letter in support of full seafood supply chain traceability and respond by August 29, 2014 with your name, title and organization/institution (if applicable). Please forgive cross postings and forward to your colleagues.

Background: On June 17, 2014, the White House released a Presidential Memorandum entitled, “Establishing a Comprehensive Framework to Combat Illegal, Unreported, and Unregulated Fishing and Seafood Fraud.” Among other actions, the Memorandum established a Presidential Task Force on Combating Illegal, Unreported, and Unregulated Fishing and Seafood Fraud (Task Force), co-chaired by the Departments of State and Commerce. The Task Force must report to the President within 180 days with recommendations to combat IUU fishing and seafood fraud that emphasizes areas of greatest need. 

On July 31, 2014 Department of Commerce published a notice for public meetings and a request for comments (due September 2, 2014) in the Federal Register aimed at gaining broad input and expertise from key stakeholders and interest groups to inform and advise the Task Force. The attached letter with scientist’s signatures would be submitted to Federal Register under this notice. You may also wish to submit your own comments directly to the Federal Register.

As you are likely aware, seafood mislabeling and species substitution is a global problem which has been documented in all continents except Antarctica. Oceana has compiled an interactive Google map of seafood fraud and mislabeling found around the world which cites your or your colleague’s research, in addition to the recent work that Oceana has undertaken in this area. While the weighted level of species substitution of over 100 studies is 22%, these levels range higher for many popular seafood species.

As a researcher who has demonstrated evidence of the extent of this problem, you can join your colleagues by signing on to the attached letter in support of seafood traceability in the U.S. If you would like to sign onto the letter, please provide us with your name, title and organization/institution by August 29, 2014.  And please do not hesitate to contact us with any questions.

Thanks and Best Regards,

Kimberly Warner, Ph.D. | Senior Scientist
OCEANA | Protecting the World's Oceans
1350 Connecticut Ave. NW, 5th Floor | Washington, DC 20036 USA
D +1.202.467-1932 | T +1.202.833.3900 | F +1.202.833.2070

Robert Hanner, Ph.D. | Associate Professor
Biodiversity Institute of Ontario | Centre for Biodiversity Genomics
Department of Integrative Biology, University of Guelph
50 Stone Road East, Guelph, ON N1G 2W1 Canada
T +1 (519) 824-4120 x.53479

Monday, August 25, 2014

Blog for kids

Only intermittent posting these days as I have a few day off - well deserved vacation.

Today just an announcement - Last week I started a new blog. One bug a day is made for kids. Every weekday a new bug, starting with the ones I find in my backyard, on walks or hikes, or simply at home. The idea is certainly not new and that's why added a little twist to it. Every post has about 150-200 words which is equivalent to about one minute of reading. The idea is to engage kids in their natural environment but accommodate for the little time they usually have in times of instant all-accessible information.

So, if you have kids or know some, please let them know about this new blog :-)

Friday, August 22, 2014

Novel Ecosystems - a really bad idea?

Novel ecosystems arise when human activities change biological communities e.g. through species invasions or environmental change. Many policymakers and ecologists consider them acceptable or even see them as new normal ecosystem because they appear ubiquitous. 

Some proponents of the concept assert that because of the global nature of climate change, all ecosystems are at risk of transformation by extinctions and invasions. Moreover, the pervasiveness of the human footprint suggests to some that no corner of the earth can escape transformation. Consequently, all systems previously considered ‘wild’ or ‘natural’, and the abandoned remnants of previously managed systems (particularly agricultural lands), are likely to become so profoundly transformed that no effort will suffice to return them to their historic state. In this scenario, conserving and restoring ecosystems is a futile endeavor, driven by sentimentality (R.J. Hobbs, cited in Science article) and psychological impairment. Instead, efforts should focus on steering ecosystems towards a desirable state or away from an undesirable state, none of which involves an historical pre-disturbance condition (hence its difference from restoration).

Meanwhile, the concepts of ecological restoration are making their way to the top of the agenda worldwide. Thirty years of research and development show it is possible to rehabilitate and restore degraded landscapes. Importantly, restoration makes scientific and political good sense as an investment whose benefits far outweigh its costs. Consequently, an international scientific team heavily criticizes the adoption of concepts such as novel ecosystems by colleagues and policymakers.

The authors warn that the concept is not only an empty shell; it is also a real threat in terms of policy direction. It would be tantamount to opening the floodgates to invasive species and abandoning ecosystems and their communities that have evolved over a long period of time.

Instead, they call for applying the precautionary principles of conservation and restoration to re-establish or try to emulate the historical trajectories of ecosystems, to allow restored systems to adapt to environmental changes while providing essential services to human populations.

The authors acknowledge barriers to restoration and conservation but note that they are sociological, political and economic, not ecological.  "Novel ecosystems yield unintended and perverse outcomes, and the concept provides 'license to trash' or 'get-out-of-jail card' for companies seeking to fast-track environmental licenses or to avoid front-end investment in research and restoration," says Dan Simberloff, co-author of the study. "The concept may even provide incentives to governments to continue to ignore the long-term environmental and ecological negative impacts of business as usual with respect to sustainable development and natural resources management."

According to the paper the concept of novel ecosystems is largely based on faulty, data-deficient assumptions and conclusions drawn at an inappropriate scale. It does not rest on robust and empirically tested science. The discussions in the ecological community will continue but it is my hope that especially decision makers understand that there is no easy way out and that accepting novel ecosystems as the new normal comes with a very high price:

What is at stake is whether we decide to protect, maintain, and restore ecosystems wherever possible or else adopt a different overall strategy, driven by a vision of a ‘domesticated’ Earth, and use a hubristic, managerial mindset. Scientists should exercise caution when making recommendations that might undermine initiatives and diminish investments intended to protect or restore natural ecosystems.

Thursday, August 21, 2014


Unpacked and ready to go.
Do you want to know which bug just ate all the tomato plants in your backyard? 
Do you want to know what fish species you just had for dinner? 
Do you want to know what mysterious animal roams around in the nearby park but all you have is a couple of hairs it left behind?

As announced via twitter yesterday - I have received my LifeScanner kit and as promised here is my blog post about the first encounter. Actually it wasn't the first, as my wife got a kit earlier and she and the kids tested it out last weekend but that's a different story for maybe another post.

I knew about the development of the LifeScanner app and the collecting kit already for a while. That's not surprising as both have been, at least partially, developed at our institute. The BOLD group teamed up with SAP to develop this new approach to citizen science.

So what is LifeScanner?
LifeScanner is an app for iPhone and iPad devices designed to help people discover the diversity of living organisms around them and to help them contribute to a global knowledge-base on biological diversity. 

The app actually does a bit more. It connects the user to the wealth of BOLD's public data in a creative and very intuitive fashion. If the GPS function of your device is switched on it will provide you with a map of the surrounding region and all sampling locations that are recorded on BOLD. You can swipe between the species of a particular location, many come with images that are also retrieved from the database. The system allows you to search for particular species and whether you can find them in close proximity. Overall handling is very simple and user-friendly. The only caveat is that it is not available for other platforms outside the Apple world, which means at this point it won't be used by the other half of mobile users that own e.g. Android devices. It is also not optimized for iPads which is an issue when it comes to the specimen photos as they appear pixelated on the larger screen.

The Lifescanner sampling kit can be used to submit any kind of animal sample one comes across. It contains everything needed to submit 4 samples for identification and contribution to BOLD. Thanks to DNA Barcoding a sample can be many things. A citizen scientist can submit a hair found in the backyard, an insect, a feather, but also animal products from the store or the restaurant. No plant material at this point but that will change in the future. Lets not forget that for plants we need at least two DNA sequences for a good ID. That is probably not the best thing to start with during a trial phase.

The app is designed to help with the collecting work. Each vial has QR code, which can be scanned using the app. You can make a photo of the specimen and add it to the data record together with some details about the specimen. The data are transferred to BOLD through the app which ensures that all required data are in place when the specimen arrives. The sampling tubes are pre-filled with a non-toxic DNA preservation liquid. Once all four tubes are filled. they are packed in specimen bag and send off via return envelope. The app includes a detailed tracking system and the DNA Barcoding results are delivered to it as well.

Here is a video that shows all the described functionality in a bit more detail.

At this point you (if you reside in Canada or the US) can request a trial species identification kit but the number of free kits is understandably limited. In the future it will be available for purchase everywhere but the price is not yet known. I would imagine that it won't be overly expensive and lets face it, there aren't many labs that accept such a mixed-bag of samples from public sources without charging an arm and a leg. Their service has been designed for professional use and not for a family that took some samples on the last weekend hike.

To me this combination of educational app and collecting kit is a big step forward  in making DNA-based species identification available to everyone. It is simple and fun to use, and it puts a form of curiosity driven science in the hands of the public.

Wednesday, August 20, 2014

Chilean sea bass and mercury

Despite the many health benefits of eating fish, most commercially harvested fish are contaminated with mercury. The most common form of mercury in fish is methylmercury, a neurotoxin that is especially dangerous to the developing nervous system. Although present in only small quantities in the environment, mercury accumulates in living organisms. Among fish, accumulation of mercury is prevalent but variable, primarily due to differences in trophic level and body size, such that mercury concentrations tend to be high in larger, longer-lived predatory fish. Therefore, the amount of fish and the particular species of fish consumed are considered the most important factors determining the health risk associated with eating seafood contaminated with mercury.

New measurements from fish purchased at retail seafood counters in 10 different US states show the extent to which mislabeling can expose consumers to unexpectedly high levels of mercury. The issue at hand are fishery stock substitutions which falsely present a fish of the same species, but from a different geographic origin.

A new study conducted at the University of Hawaii compared two kinds of fish sold at retailers: those labeled as Marine Stewardship Council-certified Chilean sea bass (Dissostichus eleginoides), and those labeled simply as Chilean sea bass (uncertified). The certified version is supposed to be sourced from the Southern Ocean waters of South Georgia, near Antarctica, far away from human-made sources of pollution. Certified fish is often favored by consumers seeking seafood harvested in a sustainable fashion but is also potentially attractive given its consistently low levels of mercury.

However, in a previous study, the scientists had determined that 20% of fish purchased as Chilean sea bass were not genetically identifiable as such. They used a mtDNA marker (control region flanked by tRNA proline and 12S rRNA) to determine both species and stock population. About 15% of the Chilean sea bass positively identified, were not sourced from the South Georgia fishery.

In the new study, the scientists used the same fish samples to determine their mercury content. When they compared the mercury in MSC-certified sea bass with the mercury levels of, non-certified sea bass, they found no significant difference in the levels. 

It turns out that the fish with unexpectedly high mercury originated from some fishery other than the certified fishery in South Georgia. Actually, the DNA analysis indicated they were from Chile. Thus, fishery stock substitutions are also contributing to the pattern by making certified fish appear to have more mercury than they really should have given their origin. Certain fish had very high mercury levels - up to 2 or 3 times higher than expected, and sometimes even greater than import limits to some countries.

Although on average, MSC-certified fish is a healthier option with respect to mercury contamination than compared to uncertified fish, our study showed that fishery-stock substitutions, can result in a larger proportional increase in mercury consumption than species substitutions for consumers, and that variation in mercury contamination among fishery stocks may be considered in future seafood consumption guidelines.

Tuesday, August 19, 2014

Discoveries of the week

It's Tuesday again - time for another round of new discoveries.

Jerzego corticicola
Jerzego corticicola (taken from paper)
A new genus and species of hisponine jumping spider from Sarawak, Jerzego corticicola Maddison sp. nov. are described, representing one of the few hisponine jumping spiders known from Asia, and the only whose male is known. Although similar to the primarily-Madagascan genus Hispo in having an elongate and flat body, sequences of 28s and 16sND1 genes indicate that Jerzego is most closely related to Massagris and Tomomingi, a result consistent with morphology. Females of Jerzego and other genera of Hisponinae were found to have an unusual double copulatory duct, which appears to be a synapomorphy of the subfamily. Two species are transferred from Hispo, Jerzego bipartitus (Simon) comb. nov. and Jerzego alboguttatus (Simon) comb. nov.

Not only a new species but also a new genus. The genus of this jumping spider was named after Prof. Dr. Jerzy Prószyński, whose works have provided the first comprehensive view of salticid diversity worldwide. The species epithet is Latin for “bark dweller". The paper also provides a new name combination: Jerzego alboguttatus (used to be Hispo alboguttata).
no DNA barcode (only 28S and 16SND1 were sequenced)

Salmoneus yoyo (taken from paper)
An unusual new species of the alpheid shrimp genus Salmoneus Holthuis, 1955 is described from Sekotong Bay, southwestern Lombok, Indonesia. The holotype and single known specimen of Salmoneus yoyo sp. nov. was collected with a suction pump from a burrow of unknown host, on a seagrass flat partly exposed at low tide. The new species presents three characters on the chelipeds that are unique within Salmoneus: a conspicuous, mesially curved, hook-like process on the distomesial margin of the merus, a row of blunt teeth on the ventromesial margin of the merus, and a series of blunt teeth on the ventromesial margin of the propodus. Salmoneus yoyo sp. nov. also has a characteristic colour pattern consisting of bright red chromatophores occupying most of the carapace surface, except for the frontal and post-frontal areas.

A new little alpheid shrimp named after Dr. Dwi Listyo Rahayu, aka Yoyo for friends and colleagues, to honour her important contributions to South-East Asian carcinology and for organising the seagrass and mangrove survey in Lombok, during which this discovery was made..
no DNA Barcode

Lamprologus markerti (taken from paper)
A new Lamprologus is described from the lower Congo River (LCR) in the Democratic Republic of Congo. Lamprologus markerti, new species, is readily distinguished from L. tigripictilis and L. werneri, the LCR endemic lamprologines with which it was once taxonomically conflated, in the possession of a reduced number of gill rakers on the first arch (9–11 versus 12–17), a longer head (32.1–34.7% SL versus 29.3–31.9 and 29.1–32.9% SL, respectively), and a longer predorsal length (33.0–35.9% SL versus 29.3–32.7 and 28.5–32.6% SL, respectively). Further, L. markerti lacks a second intestinal loop present in both L. tigripictilis and L. werneri, and has a highly reduced infraorbital series often consisting of a single first infraorbital (lachrymal) element.

I had to include this particular newcomer. For years I bred several Lamprologus and Neolamprologus species at home. Beautiful little fish with very interesting behaviour. In the last few years I was also fortunate enough the get some specimens of cichlid fish from around the world which were barcoded here. One of them we named Lamprologus cf. tigripictilis as it looked very much like L. tigripictilis but we were not entirely certain about its identity. I was looking forward to some barcode sequences that could have help me to put a reliable ID on my fish but the only data available for the new species are cytb and ND2. Given the geographic distribution shown in this new description my guess is that my samples are  Lamprologus tigripictilis. Too bad, I had hoped to use DNA Barcodes to close this case. 
The species was named for Named for Jeffrey Markert whose initial molecular analyses of cichlid population structure stimulated the subsequent morphological study.
no DNA Barcode

Tylopus corrugatus

Tylopus parahilaroides
Tylopus currently comprises 55 species, including three new from Thailand: T. corrugatus sp. n., T. trigonum sp. n. and T. parahilaroides sp. n. A new distribution map and an updated key to all 29 species of Tylopus presently known to occur in Thailand are given. Illustrated redescriptions of all four Indochinese Tylopus species described by Carl Attems are also provided, based on type material.

Three new members of the Southeast Asian millipede genus Tylopus. Intersting group of millipeds that appears to be confined to montane forest habitats living on elevations of 500 m and higher. 

Tylopus trigonum
All the names refer to some characteristic morphological features.
no DNA Barcode

In this contribution a new species of the land crab genus Gecarcinus Leach, 1814, from the Neotropical Pacific coast of South America is described and illustrated. In addition to its unique body color, Gecarcinus nobilii sp. n. is distinguished from congeners by a distinctly wider carapace front and differences in the shape of the infraorbital margin. The new species is not isolated from Gecarcinus populations from the Pacific coast of Central America by an insurmountable geographic barrier. Considering the closure of the Panamanian Isthmus as a calibration point for morphological divergence between the trans-isthmian mainland populations of Gecarcinus, the virtual lack of morphological differentiation (other than color) between them and the distinctness of G. nobilii sp. n. suggests that G. nobilii sp. n. evolved from a common ancestor before the Isthmus closed.

The species was named in honor of Giuseppe Nobili, who built the crustacean collection in the Museum of Turin thereby providing important contributions on the knowledge of crustaceans.
no DNA Barcode

A new, nickel-hyperaccumulating species of Rinorea (Violaceae), Rinorea niccolifera Fernando, from Luzon Island, Philippines, is described and illustrated. This species is most similar to the widespread Rinorea bengalensis by its fasciculate inflorescences and smooth subglobose fruits with 3 seeds, but it differs by its glabrous ovary with shorter style (5 mm long), the summit of the staminal tube sinuate to entire and the outer surface smooth, generally smaller leaves (3–8 cm long × 2–3 cm wide), and smaller fruits (0.6–0.8 cm diameter). Rinorea niccolifera accumulates to >18, 000 µg g-1 of nickel in its leaf tissues and is thus regarded as a Ni hyperaccumulator.

Not brand-new as the description came out in May but I picked it because of its unusual lifestyle. It eats nickel for a living, accumulating up to 18,000 ppm of the metal in its leaves without itself being poisoned. Such an amount is a hundred to a thousand times higher than in most other plants. This rare phenomenon is called Nickel hyperaccumulation and it is rather rare with only about 0.5-1% of plant species native to nickel-rich soils having been recorded to exhibit the ability.
no DNA Barcode (but pretty cool)

Monday, August 18, 2014

2 years blogging and European bees

Two years ago I started this blog with the intention to report as often as possible on news in the field of DNA Barcoding and biodiversity science. Who would have thought that this blog survives 2 years? The vast majority of bloggers give up within the first year of blogging but not this one. This is post number 416 and the audience is still growing, e.g. a few days ago the blog broke through the magic number of 100 000 unique all time visits. 

As long as people out there are interested in what I have to say I will certainly continue. However, I know exactly that I could not have done it without the support of all the people who read my posts, share my blog with others, and provide me with new ideas. So, a big THANK YOU to all readers for making this possible.

By the way, looking for an interesting read? How about bee diversity along a gradient of urbanization?

More than 900 species of wild bees are found in France alone, but many of them are in decline. French colleagues have carried out a comprehensive study to evaluate the impact of urbanization on wild bee communities. They studied 24 more or less urbanized sites in and around the city of Lyon and recorded a total of 291 different bee species. Although bee abundance decreased with the level of urbanization, most species were found in periurban areas, and about 60 species lived at the most urban site:

Overall, our results suggest that urbanized sites can provide forage and nesting resources for a large community of wild bee species, even if the landscapes with an intermediate proportion of impervious surface have a more diverse and abundant bee fauna. Flagship species are defined as ‘known charismatic species that serve as a symbol or focus point to raise environmental consciousness’. Although their individual species may be difficult to identify, bees can collectively be considered as a flagship group of species and used to raise the awareness of city-dwellers to biodiversity, as we observed in this study ( Indeed, the loss of a charismatic species can affect people more than the loss of habitat, even when the loss of habitat is the very threat to the species. Also, because bees are a key group of pollinators worldwide for both wild and cultivated entomophilous plants, bees can be readily used to illustrate the importance of ecosystem services, ecosystem functions and natural capital. Focusing public attention on city-dwelling species such as wild bees provides great opportunities to demonstrate the importance of conservation to society. The perception of wildlife by society is crucial for effective conservation of biodiversity, and, since today 74% of the Europe's population lives in cities, it is both essential and urgent to raise the awareness of urban citizens on the importance for biodiversity conservation.