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.

Friday, August 15, 2014

Biological Control Agents

Aulacidea pilosellae galls on Pilosella officinarum
(Credit: Jean-Yves Baugnée)
Two papers, two stories about insects that humans recruited for a specific mission - biological pest control. In an attempt to reduce the pestizide use we team up with predators and parasites (or parasitoids) of pest species. Some insects pests serve as prey for other arthropods (particularly spiders and mites), and several groups of vertebrates. Others are parasitized by various types of wasps and roundworms (nematodes) and are also attacked by a diverse group of pathogens including fungi, protozoa, rickettsiae, bacteria, and viruses. In addition a variety if arthropod species feed on plants and are used to control the spread of invasive flora. The biocontrol arsenal grows rapidly but every new introduction requires a series of tests before it is officially approved for use. The occurrence of such a candidate species in the region of proposed use can certainly expedite the approval process as there is no apparent risk of releasing another non-native and potential harmful species. 

The first story reports on such a case. The European gall wasp species Aulacidea pilosellae is a promising candidate that is supposed to help with a North American problem - invasive hawkweeds of the genus Pilosella. Two Canadian researchers apparently found this species in Canada:

Here we report the first North American detection of the gall wasp Aulacidea pilosellae Kieffer (Hymenoptera: Cynipidae), native to Central Europe and a promising candidate biological control agent for invasive hawkweeds (Pilosella Vaillant, Asteraceae) in North America. This occurrence was discovered through the intersection of (i) publically available DNA barcode data and (ii) DNA sequencing of a biocontrol agent before its release. COI DNA sequences of A. pilosellae collected in Central Europe were compared with publically available DNA sequence records.

As part of the host range assessment for the proposed biocontrol programme, DNA Barcode sequences of the European Aulacidea pilosellae were compared to all publicly available sequences on GenBank. The researchers found a COI sequence belonging to a specimen identified only to order, which differed by only one base pair. Surprisingly, this specimen was collected in eastern Ontario, Canada. Interestingly, it was this discovery that started communication between the two scientists, and once identity and origin of the specimen were verified, they decided to sequence a nuclear marker (28S-D2) to further substantiate their find. They found very little sequence variation between the specimen and its European counterparts(<0.2%). 

By detecting the presence of A. pilosellae in Canada, the process for approving this candidate biocontrol agent for release in North America may potentially be expedited. Regardless of the outcome of this particular case, there is clear potential significance of both (i) the DNA barcoding of candidate biocontrol agents and (ii) making publically available standardised DNA sequences even from un-identified specimens. 

Case closed.

United States National Collection
of Scale Insects Photographs Archive,
USDA Agricultural Research Service,
Invasive cactus species are certainly not a problem here in Canada but they have been causing problems in Australia since they escaped from early settlements. A number of species had became established as weeds, spreading considerable distances from the original point of introduction. 

Cochineals are scale insects of the genus Dactylopius which feed on a variety of cactus species. One species of scales (Dactylopius coccus) is the source for the crimson-colored natural dye carmine and it was this fact that brought the cacti to Australia as early settlers tried to start a cochineal dye industry in the late 1700s. Some Dactylopius species have been used successfully to control invasive cactus species. On of them is Dactylopius tomentosus which has a restricted host range within the Cactaceae, being associated only with species of the genus Cylindropuntia and according to story number two of today's post it consists of more specialized groups:

Recent studies have demonstrated that this scale is composed of host-affiliated biotypes with differential host specificity and fitness on particular host species. We investigated genetic variation and phylogenetic relationships among D. tomentosus biotypes and provenances to examine the possibility that genetic diversity may be related to their host-use pattern, and whether their phylogenetic relationships would give insights into taxonomic relatedness of their host plants.

The researchers used DNA Barcoding to investigate the genetic variation and phylogenetic relationships between Dactylopius tomentosus specimens from different localities and host plants. Their results were meant to improve the selection for biological control agents for invasive cacti.

Sequences of individuals from the same host plant within a region were identical and characterized by a unique haplotype. Individuals belonging to the same biotype but from different regions had similar haplotypes. However, haplotypes were not shared between different biotypes. Phylogenetic analysis grouped the monophyletic D. tomentosus into 3 well-resolved clades of biotypes. The phylogenetic relationships and clustering of biotypes corresponded with known taxonomic relatedness of their hosts.

In fact some of the observed intraspecific genetic divergences suggest that currently described Dactylopius species may be species complexes composed of cryptic or sibling species. Biological pest control is by no means a simple business.


Alex Smith (Aulacidea pilosellae story)
Scott Miller (Dactylopius tomentosus story)

Thursday, August 14, 2014

Virtual Barcodes

This weeks literature screen revealed a very interesting proof-of-principle study published by some colleagues from Brandeis University in Waltham, USA. They thought of utilizing a PCR method that was developed about ten years ago.

Linear-After-The-Exponential-PCR (LATE-PCR) is an asymmetric PCR method in which one DNA strand in a double-stranded DNA template is preferentially amplified. It is used in sequencing and hybridization probing where amplification of only one of the two strands is required. The colleagues used LATE-PCR to amplify a portion of the CO1 gene for each of five commercially available, beneficial species of soil nematodes. A set of ten low temperature Lights-On/Lights-Off consensus probes were included in the reaction mixture and were used at end-point to coat the accumulated single-stranded amplicon by dropping the temperature. Because each of the probes is mis-match tolerant, the temperature at which it hybridizes to its complementary region within the target is sequence dependent. As anticipated, each species had its own unique fluorescent signature in either three different colors, or a single color depending on which fluorophores were used to label the Lights-On probes. Each fluorescent signature was then mathematically converted to a species-specific Virtual Barcode.

This is yet another pretty cool non-sequencing method (like High Resolution Melting) which could be used in cases where rapid, low cost species identification is needed. What makes such non-sequencing methods so attractive are not only the highly reduced costs but also the flexibility of the system. One needs much less equipment and all of a sudden it becomes possible to work remotely (in the field, point-of-sale, border control etc.). 

It is great to see all these applications seeing the light of the day even more so when they hold the promise to bring us closer to the dream of every DNA Barcode aficionado - the handheld DNA Barcode gadget. Granted, this idea has a lot of potential for a variety of applications but I think at some point the authors start to overstate. 

One reason for development of this new method lies in the fact that the current approach to barcoding the tens of millions of eukaryotes on earth is slow, labor intensive and expensive. 

I am afraid that building the DNA Barcode library for all species will always be slow, labor intensive and expensive because collecting, obtaining and preparing specimens won't change much no matter what molecular high-tech we throw at the problem. If the only issue is the rate at which we can assemble DNA sequences, filter out duplicates and store everything in our databases, the job could be done by metabarcoding of entire ecosystems. But what would be the knowledge gained by such approaches? No sequence could be tied to a specimen (voucher) and all the information that comes with knowing the actual source of DNA. It is a feasible way to explore the diversity of all those unculturable micro-organisms but for most eukaryotes we should do more.

Don't get me wrong, I do like the approach using LATE-PCR but I am a bit puzzled by some of the motivation expressed in the paper. Should we consider iBOL's progress as slow? I really hope that there will be a day in the coming year were we lean back for a moment realizing that 500,000 species have indeed been assigned a DNA Barcode in just a little over a decade. A decade of which at least the first third was wasted in a battle against egos instead of engaging in proper scientific reasoning. The more all the 'barcoders' can be proud of what they accomplished in short time and against all odds. I will. Even more so because most of these DNA Barcodes won't be just naked sequences. They come with lots of valuable information attached to them.

Of course we all wish we could be faster in what we are doing. Reality is that we are still outpaced by extinction and hampered by human ignorance but I don't think limits to technology are holding us back any longer. The bottleneck is what some call the front-end of the barcoding enterprise. It is about collecting all the specimens, finding them, surveying the planet in a systematic way to ensure we didn't miss entire groups of organisms. Here is where we could save time by thinking more strategically. This is not another on of those calls for 'more collecting' or 'more money'. No doubt, more money would help, especially given that the current investments are rather modest but it is more about getting creative, making the most of the opportunities we have. Yes, we do need more collecting but perhaps we better look at new ways to accomplish that. I am talking about 'citizen scientists' and in my head this encompasses everyone from the hobby naturalist to the one who's livelihood depends on biodiversity. Not only would that increase the collecting workforce but perhaps more importantly the life that surrounds us becomes more meaningful to everyone directly involved. 

I'd like to ensure the authors of the paper (in case they ever read this post) that I didn't mean to downgrade their accomplishment by going off on a tangent. I do share they hopes that the new Virtual Barcode along with its nucleotide sequence can be added to an ever expanding Barcode of Life library of information - perhaps alongside with HMR melting curves and all future derivatives.

Wednesday, August 13, 2014

We shall overcome

Over the past year it has become a morning ritual. Once settled in the office, which means that I have ensured sufficient coffee intake, I start browsing through various email, RSS feeds, and newsletters always on the look out for topics worth a blog post, a bulletin article, or simply a good read that might be useful in teaching. It doesn't happen very often, maybe once a month, that I come across a publication were my first reaction is an outcry of bewilderment. Today was such a day. It was just a title at first but that was enough to cause uneasiness: 

Really? Isn't that the kind of title one would expect from early DNA Barcoding studies? You know, the good old days were we had to convince everybody (public and peers alike) of the fact that the use of one standard gene region can provide reliable species discrimination. Maybe I am too naive, but I thought the marker discussion for animals ended a long time ago with the result that COI  is now agreed-upon standard for all animals and that in fact it actually works well for almost all of them including the phylum mollusca. We know that sponges and some cnidarians are problematic and require either extended COI sequences or alternative markers but overall one of the, for some colleagues surprising, messages of the first decade of DNA Barcoding is that COI works extremely well across the board. So, why did these authors went back to the drawing board? A closer look at the paper revealed their rationale:

However, along with the increase in the number of investigated species, the COI barcode has failed to deliver the reliable DNA barcode in some animal groups. For example, in insects, gastropods and amphibians, intraspecific variation in COI is high and usually overlaps with interspecific variation. In addition, the universal primers often failed to amplify the fragment of COI barcode and other primers were needed. Therefore, it is necessary to search for alternative DNA barcodes to avoid an exclusive reliance on COI.

Indeed, in some taxonomic groups intraspecific variation in COI is high and sometimes it might even overlap with interspecific variation but the word 'usual' is really misleading. There aren't that many examples in the animal kingdom and it is by no means a phenomenon that occurs across entire groups. In fact, in a number of cases were people find no real 'barcode gap' it turns out that the taxonomy was simply wrong or specimens had been misidentified. This so called 'weakness' of DNA Barcoding has led to quite a few species discoveries, taxonomic revisions, and improvements to insufficiently documented collections. Mollusks are no exception to this.

Surprise, surprise, some universal primers aren't that universal after all. Time to find a different gene region. I've come across this attitude before. Some colleagues can't get universal or other published primers to work and as a consequence they switch to a different marker that is easier to retrieve. Who said that PCR is easy? Primer design, chemistry composition, and thermal regime require some thinking and series of experiments. Initial failure should stimulate further experimentation and not abandonment of the original concept. Instead of simply testing the discriminatory ability of mitochondrial protein coding genes the authors could have used the wealth of data they downloaded from GenBank to design a suite of experimental primers for subsequent testing.

I don't want to go into much of the technical details of this paper. The authors used three different ways (distance, monophyly and character-based methods) to determine the discriminatory power of a chosen gene. From what I can tell from the methods section all analyses were carried out using full length genes only. The standard animal DNA Barcode however, is just a fragment (a little more than a third of the total length) of  COI and therein lies one of the strengths of this choice. It is a compromise between sufficient resolution at species level and the ability to retrieve it in an economic fashion. In order to avoid comparing apples and pears the authors should have aimed for comparisons between shorter fragments (in the DNA Barcode size range). And in order to raise the bar a little more those fragments should be flanked by potential universal primer sites. 

Mollusk DNA Barcodes do have some specialties in stock for us, e.g. sex specific COI versions in a number of mussel species due to limited biparental inheritance, but when it comes to their overall applicability they deserve good marks. The mitochondrial genome of mollusks is very interesting for many other reasons, e.g. gene order variation between species or the lack of genes such as ATP8 in many mussel species. Maybe the authors should have used the opportunity to investigate more into that direction as the results of this study must have been quite disappointing:

In another word, any one of the 12 PCGs (mt Protein Coding Genes) can be potentially used as a molecular diagnostic for species identification in mollusks.

So what they are saying is that the result of their study, conducted because COI is allegedly not a good choice for DNA Barcoding, is that after all COI is suitable for species identification in mollusks (as are all other PCGs).

Hmm. Why did they do this study in the first place?

Tuesday, August 12, 2014

Discoveries of the week

And another weekly dose of new discoveries. Readers have started to send me copies of their publications including new descriptions. I am happy to post them here in this weekly column as well.

Turcinoemacheilus bahaii
Turcinoemacheilus minimus
Three new species of Turcinoemacheilus are described from Iran and Turkey raising the number of species in this genus to six, five of them in the Middle East. Turcinoemacheilus bahaii, new species, from the Zayandeh River in Iran is distinguished by having the anus situated in a posterior position and a dark brown blotch on each side of the anal-fin base in both sexes. Turcinoemacheilus minimus, new species, from the upper Euphrates drainage in Turkey is distinguished by having the anus situated in an anterior position, a slender and long caudal peduncle and a very small maximum size (up to 38 mm SL). Turcinoemacheilus saadii, new species, from the Karoun drainage in Iran is distinguished by having the anus situated in an anterior position and an unique colour pattern of large dark brown saddles. In the Middle East, all Turcinoemacheilus species are well distinguished by molecular characters and show between 5.3 and 8.5 % K2P sequence divergence in their COI barcode region.
Turcinoemacheilus saadii

Not one but three new species of dwarf loaches were described recently as a result of an German-Iranian-Turkish collaboration. All descriptions are the result of combined analysis of morphological and molecular data.

Valencia robertae
Valencia robertae, new species, from the lower Pinios in northern Peloponnese and Mornos Rivers in southern mainland of Greece is distinguished from V. letourneuxi and V. hispanica by having short lateral bars or vertically elongated small blotches along the midlateral body and an almost triangular anal fin in females, prominent lateral bars between the axial blotch and the caudal-fin base and a long anal fin reaching almost or to the first caudal-fin rays in males larger than 27 mm SL. It is also distinguished by 32 fixed, diagnostic nucleotide substitutions in the mtDNA COI barcode region.

I have to admit that killifish belong to the list of my favorite freshwater fish. Aside from my professional interest in fishes I am a freshwater aquarium enthusiast. This passion grew during my childhood when my dad and I filled the entire house with a number of tanks in which we kept and bred a plethora of freshwater fishes. We never kept killifish for some reason although they are beautiful little creatures, and nowadays so many of them are endangered that I would not dare to keep some in a tank at my home.

The new species is named for Roberta Barbieri, who studied the Greek Valencia species for many years and is engaged in the conservation of the two species.
DNA Barcodes available (there are also some sequences on BOLD but unfortunately not publicly available)

Hylarana centropeninsularis
We describe a new species of ranid frog from the Hylarana signata complex in Peninsular Malaysia based on morphological and genetic differentiation. The new species can be distinguished from its congeners by the following combination of characters: (1) adult males reaching 37.4–37.6 mm snout–vent length; (2) nuptial pads absent in males; (3) humeral glands in males large; (4) webbing on toes reduced, one phalanx free of web on postaxial side of Toe II and pre-axial side of Toe V; (5) dorsolateral stripe straight, continuous, red to orange in color; (6) middorsal region black, unmarked; (7) flanks black, coloration unstratified; (8) flanks, dorsal surfaces of limbs, and upper lip with large, round, yellow spots; (9) venter grayish-brown, with light spots on throat and light reticulations on ventrum. The new species is phenotypically most similar to Hylarana siberu but differs by having larger, more-dense, and more-rounded spots on the flanks and dorsal side of limbs, larger spots along the entire upper lip, and having light, distinct spots on the throat and light reticulations on the ventrum. We use mitochondrial data to estimate genealogical relationships and genetic divergences between the new species, H. siberu, a related and undescribed Sumatran population, and other members of the H. signata complex. These data unequivocally support the specific recognition of the new taxon and provide insights into its evolutionary relationships.

The name was chose to reflect that the species is currently only known from the Central Peninsular Malaysia. Older records show that a comparable frog had been collected in the area 10 years earlier, but it was written off then as a species from an Indonesian island about 450 miles to the west. 
no DNA Barcode (there should be molecular data for this study but I couldn't find anything in GenBank or BOLD)

Metaphire tengjhihensis
The Metaphire formosae species group is a member of the Pheretima complex of the family Megascolecidae. It is composed of 12 nominal taxa, Metaphire bununa Tsai et al., 2000, Metaphire feijani Chang & Chen, 2004, Metaphire formosae (Michaelsen, 1922), Metaphire glareosa Tsai et al., 2000, Metaphire nanaoensis Chang & Chen, 2005, Metaphire paiwanna paiwanna Tsai et al., 2000, Metaphire paiwanna hengchunensis (James et al., 2005), Metaphire paiwanna liliumfordi Tsai et al., 2000, Metaphire tahanmonta Chang & Chen, 2005, Metaphire taiwanensis Tsai et al., 2004, Metaphire trutina Tsai et al., 2003, and Metaphire yuhsi (Tsai, 1964). In this study, we describe a new species, Metaphire tengjhihensis sp. nov., and two new subspecies, Metaphire nanaoensis truku ssp. nov. and Metaphire taiwanensis tsaii ssp. nov., belonging to this species group. DNA barcodes (partial sequences of the mitochondrial cytochrome c oxidase subunit 1, COI) from type specimens of M. feijani, M. tengjhihensis sp. nov., M. nanaoensis truku ssp. nov., M. tahanmonta and M. taiwanensis tsaii ssp. nov. have been deposited in GenBank in previous studies and are explicitly linked to the type specimens for the first time, enabling unambiguous identification using both morphology and DNA barcodes. Finally, we comment on the systematics of the M. formosae species group and suggest an integrative taxonomic approach that combines morphology and DNA barcodes for future descriptions of new species of Amynthas and Metaphire.

This species was named after its type locality Tengjhih, a National Forest Recreation Area in Taiwan.
DNA Barcodes available

During several days of entomological expedition, as part of a thesis on the phylogeny of Phaegopterina, the first author collected in Northwestern Argentina (provinces of Jujuy and Salta) a series of Mazaeras species previously treated as Mazaeras janeira (Schaus, 1892). The second author, after an expedition in the southern Bolivia (departments of Chuquisaca and Santa Cruz), had a series of specimens of the same taxon also identified as M. janeira (Schaus, 1892).  Examination of the male genitalia of the Argentinean specimens showed several differences with the male genitalia of  the lectotype of M. janeira. Molecular analysis with specimens of the two taxa confirmed the discrimination. The new  species is described and a comparison based both on morphological characters and DNA barcodes with closely related  species is provided. The new species can be found in northwestern Argentina (Salta and Jujuy provinces) and southern Bolivia (Santa Cruz, Chuquisaca and Tarija departments) in Yungas montane forest. 

The name of this species is derived from the meridional Yungas area on the western slopes of the Andes stretching from northern Peru to northwestern Argentina. 
no DNA Barcode (there might be some data on BOLD but they are not publicly available)

Hieracium sinoaestivum
Hieracium sinoaestivum Sennikov sp. nov. is described as new to science and illustrated. This presumably apomictic species is solely known from two old collections made in a single locality in the Shanxi Province of China. It belongs to the hybridogenous group Hieracium sect. Aestiva (Hieracium sect. Prenanthoidea × Hieracium sect. Umbellata) and is most similar to Hieracium veresczaginii from southern Siberia. The new species occurs at low altitudes in the forest belt of Lülian Mts. and belongs to taiga forest elements.

Today's newcomer post ends with a new hawkweed species. Its name is derived from Sino, a prefix meaning 'from China', and aestivum, which refers to the sectional placement of the species. Hieracium is a large genus with a pretty messy taxonomy. The International Plant Names Index holds more than 12,000 named taxa, including subspecies and synonyms.
no DNA Barcode

Monday, August 11, 2014

2 x Bemisia tabaci

The silverleaf whitefly (Bemisia tabaci) is one of several whiteflies that are currently important agricultural pests.Their nymphs use their mouth parts to stab into the plant and consume the plant’s juices. The honeydew they leave behind can induce the growth of sooty molds, which can then reduce the plants ability to absorb light. This results in less growth, lower yield, and poor quality plants. It is thought that the United States alone has suffered crop and ornamental plant damages in excess of $1 billion through this pest. All over North America, Bemisia tabaci is a particularly important pest of greenhouse poinsettia (Euphorbia pulcherrima) .

Actually, Bemisia tabaci is a cryptic species complex consisting of at least 24 morphologically indistinguishable yet behaviorally and physiologically distinct species. The currently accepted classification represents the presumed phylogeographic origins of the proposed cryptic species and is based on a partial COI sequence derived from the 3′ region of the gene. This is not the accepted DNA Barcode region which is derived from the 5' region from the same gene. The authors of the first of two papers I am presenting in this post comment on this problem:

Given the widespread adoption of DNA barcoding as a tool for species identification, we would encourage researchers generating COI sequence data for B. tabaci to consider including both the 5′ and 3′ regions, and to follow DNA barcoding metadata standards. This will ensure that data collected with one marker can be unambiguously linked to data collected from the other and that the data will be useful to the largest community possible.

Two papers on Bemisia tabaci within a fairly short time frame are proof on how important the issue is. Interestingly both studies were done at our institute but they are completely independent from each other focusing on different regions of the planet. 

Paper number one looks at the situation in Canadian Greenhouses and more specifically at the poinsettia cultures therein. In local poinsettia production, two species from the Bemisia tabaci complex, Mediterranean and Middle East Minor 1, often infest crops simultaneously. Differences in pesticide susceptibility between these two cryptic species have the potential to influence growers' management decisions, including the use of biological control or insecticides, and the choice of insecticide active ingredient.

The colleagues did a survey of populations in commercial greenhouses here in Ontario, Canada, and they were able to show that under biological control, the species Middle East Minor 1 can displace the species Mediterranean within one growing season (5-6 fly generations), whereas under insecticide treatment Mediterranean numbers stay stable because this species is more resistant to, and likely has a greater capacity to develop resistance to, a range of insecticides. These results have important implications, e.g. the ability of Middle East Minor 1 Bemisia tabaci to naturally displace Mediterranean under biological control-based management may increase the efficacy of “clean-up” insecticide applications when necessary, which can be important for ornamental crops. These data also support the use of biological control-based Bemisia tabaci management, as it can effectively reduce Bemisia tabaci populations below economic levels while allowing Middle East Minor 1 to displace Mediterranean.

For study number two we have to travel to the other side of the planet. In Pakistan three species (Asia 1, Asia II 1, and again Middle East Minor 1) are associated with the transmission of cotton leaf curl disease which causes a significant reduction in yield. This disease is caused by a virus which devastated the Pakistan cotton industry in the early 1990s where it led to an estimated yield reduction of 30-35%. The severity of cotton leaf curl disease varies across Pakistan with higher losses in central (Punjab) than southern (Sindh) Pakistan. There has been a continuing debate as to the identity of the whitefly lineages in these regions and whether differences in the vector pool account for the differing levels of infection on cotton plants from these provinces. Because Asia II 1 was associated with a higher incidence of cotton leaf curl disease in both Punjab and northeastern India , it is thought to play an important role in the transmission of this disease.

This study used DNA Barcodes and the COI 3′ region and showed that six species of the Bemisia tabaci complex were present in Pakistan. The COI-3′ sequences were used to map five of them to known species but the authors also found a new species which they named “Pakistan”. Concerning is the fact that the species Asia II 1, previously restricted to Punjab, is now the dominant lineage in southern Sindh. This expansion to the south may have serious implications for cotton plantations in this region. 

Both studies tackle the problem of COI-3' vs. COI-5' (DNA Barcode) by sequencing both gene regions (either independently or by sequencing the entire COI gene) and thereby help to establish a translation matrix from COI-3′ to DNA Barcodes which will in turn help to build a much needed DNA Barcode reference library for this agglomerate of pest species.

From the inbox

Sounds like a great learning opportunity and Innsbruck is a wonderful city:

Course module on Molecular Analysis of Trophic Interactions held at the University of Innsbruck, Austria.

This course welcomes anyone interested in the analysis of food web interactions using DNA-based approaches. The module includes a lecture and seminar series as well as a practical lab course and runs from 29 September to 10 October 2014.

Friday, August 8, 2014

A mysterious butterfly

Credit: Chihuahuan Desert
Research Institute
About three years ago in spring 2011 the undergrad student Jon Spero found a dead butterfly beside a road next to our institute. The street cuts right through the campus of the University of Guelph and a large number of students need to cross it sometimes several times to get to their classes.

Admitted, finding a dead bug beside a road isn't something special worth a blog post but as it turns out this find is extremely unusual. Actually it was so unusual that it led to a paper that was published yesterday in the journal The Canadian Entomologist.

At first the find must have looked rather exotic and that spurred further interest. Thanks to the curiosity of Spero and his then supervisor, Alex Smith, the find was identified as lyside sulphur (Kricogonia lyside). The colleagues used DNA Barcoding to determine the species and its likely origin.

Kricogonia lyside adults winter in southern Texas, United States of America and typically disperse northward into the Great Plains in mid to late summer, but not in April. In the spring of 2011, lyside sulphurs were relatively scarce in southern Texas and were not reported further north until later in the year. Historically they have been recorded in summer as far north as Nebraska, Missouri, and Kentucky, and possibly Illinois, but never in Canada.

Kricogonia lyside is a small tropical butterfly colored pale yellow to white with few distinctive markings. It's caterpillars hide in bark crevices during the day, and come out to feed at night on their favorite plants of the Zygophyllaceae family (e.g. Guaiacum coulteri and Porliera angustifolia). Adults periodically make huge migrations - here a video of a mass emergence at the Rio Grande (or Rio Bravo) in Texas.

But the question is - how did this small butterfly got all the way up to Southern Ontario? The authors discuss several options in their paper and as you can see nothing was deemed impossible in the first place:

1. Natural dispersal of the butterfly from southern Texas to Ontario
2. Weather system transport of the adult butterfly
3. Transportation of butterfly specimen on or in a vehicle
4. Importation of a pupa on imported produce
5. Specimen dropped by an insect collector
6. April Fool’s Day joke
7. Escapee from a live butterfly exhibit

However, they provide compelling arguments to rule out all possible explanations for the find of the lyside sulphur although personally I wouldn't exclude number 2 just yet. Storms and strong climatic fronts often transport butterflies outside of their normal range and according to the authors a very strong weather system extending from southern Texas into eastern Canada was recorded around the time of the find.

In summary, it is highly likely that the lyside sulfur individual found in Ontario originated in southern Texas or northern Mexico[...]the way in which this unusual specimen reached Ontario remains a mystery.

h/t Alex Smith