Citizen Science in Malaysia

Over the past 50 years, Southeast Asia has suffered the greatest losses of biodiversity of any tropical region in the world. Malaysia is a biodiversity hotspot in the heart of Southeast Asia with roughly the same number of mammal species, three times the number of butterfly species, but only 4% of the land area of Australia. Consequently, in Malaysia, there is an urgent need for biodiversity monitoring and also public engagement with wildlife to raise awareness of biodiversity loss. Citizen science is “on the rise” globally and can make valuable contributions to long-term biodiversity monitoring, but perhaps more importantly, involving the general public in science projects can raise public awareness and promote engagement. Butterflies are often the focus of citizen science projects due to their charisma and familiarity and are particularly valuable “ambassadors” of biodiversity conservation for public outreach.

The Peninsular Malaysia Butterfly Count is a great example for citizen science involving school children. We were following their work through Facebook already for a while and it is wonderful that all this work and its results now made it into the scientific literature through an article just published in Pensofts Biodiversity Data Journal.

Congrats to John Wilson and his team - keep up the good work. Here's their summary:

1) The level of participation in the first Peninsular Malaysia Butterfly Count was encouraging, but reaching and engaging rural communities remains a challenge.

2) The non-lethal DNA barcoding approach for species identification worked effectively, however, protocols could be improved to limit the number of returned samples which could not be identified. The family-level identification guide could use some improvement but provides an important educational tool for the participants.

3) The sampled butterflies revealed that widely distributed, cosmopolitan species, often recently arrived to the peninsula or with documented "invasive" potential, dominate the habitats sampled by the participants. Data from the first Butterfly Count helps establish a baseline from which we can monitor changes in butterfly communities in Peninsular Malaysia.

Complementary and alternative medicines

Globally, there has been an increase in the use of herbal remedies including traditional Chinese medicine (TCM). There is a perception that products are natural, safe and effectively regulated, however, regulatory agencies are hampered by a lack of a toolkit to audit ingredient lists, adulterants and constituent active compounds.

A new study just published in Nature Scientific Reports does just that (including metabarcoding) and the results are - perhaps not surprising - pretty alarming. Researchers of Curtin University, Murdoch University and the University of Adelaide found that 90 % of 26 widely available medicines (in Australia) tested were not fit for human consumption. Half contained illegal substances, including toxic metals, prescription medications, stimulants and animal DNA, none of which were listed on the product's label.

Arsenic, cadmium and lead were found in some of the Chinese medicine. One of the herbal concoctions contained over 10 times the recommended daily limit for arsenic exposure. Another contained strychnine, which is used as a rat poison and at lower levels as a performance-enhancing drug. The researchers also found one of the herbal medicines for sale had trace amounts of snow leopard DNA in it. In addition they found DNA from pit vipers, frogs and trace amounts of cat and dog DNA. Whether the animal products were primary ingredients or the result of a poor manufacturing processes is yet to be determined.

The researchers were especially concerned about contamination with undisclosed pharmaceuticals. Over-the-counter drugs like paracetamol and ibuprofen were found but also steroids, blood thinner warfarin and even sildenafil, the active ingredient in Viagra.

Here the summary of the paper:

This study presents genetic, toxicological, and heavy metal data that should be of serious concern to regulatory agencies, medical professionals and the public who choose to adopt TCM as a treatment option. Of the 26 TCMs investigated, all but two can be classified as non-compliant on the grounds of DNA, toxicology and heavy metals, or a combination thereof. In total, 92% were deemed non-compliant with some medicines posing a serious health risk. The multi-tiered approach outlined in this study provides a much-needed auditing toolkit that should swiftly form the basis of best-practice pharmacovigilance across the CAM  [complementary and alternative medicines] sector.

Lots of marine species actually unprotected

The increase in the number MPAs in recent years is encouraging, but most of this increase has come from a few very large MPAs. Those very large MPAs provide important value, but they can be misleading in thinking that biodiversity is being well protected because of them. Species all around the planet need protection, not just those in some locations. 

The first comprehensive assessment of protected areas coverage on marine life says that more than 17,000 marine species worldwide remain largely unprotected

The authors of the study looked at the ranges of some 17,348 species of marine life, including whales, sharks rays and fish, and found that 97.4 percent have less than 10 percent of their range represented in marine protected areas. Nations with the largest number of "gap species" or species whose range lie entirely outside of protected areas include the U.S., Canada, and Brazil. 

Despite these dismal and somewhat shameful results, the authors say the study underscores opportunities to achieve goals set by the Convention on Biological Diversity to protect 10 percent of marine biodiversity by 2020. For example, the majority of species that were considered very poorly represented (less than two percent of their range found in marine protected areas) are found in exclusive economic zones. This suggests an important role for particular nations (see above) to better protect biodiversity.

As most marine biodiversity remains extremely poorly represented, the task of implementing an effective network of MPAs is urgent. Achieving this goal is imperative for not just for nature but for humanity, as millions of people depend on marine biodiversity for important and valuable services.

Combat fish food fraud

Over the years I have presented several studies that showed ongoing food fraud in the seafood trade and how DNA Barcoding helped to unravel these cases. Now a large multi-species survey of fish labeling accuracy indicates a marked reduction of seafood mislabeling in supermarkets, markets and fishmongers in the EU.

Scientists in six European countries tracked samples of the mostly commonly consumed fish, including cod, tuna, hake and plaice, after a series of studies going back 5 years had shown mislabeling in up to 40% of cases.

Of the 1 563 DNA sequence samples examined, just 77 (4.9%) proved to be mislabeled. Most commonly mislabeled was anchovy (15.5%), hake (11.1%) and tuna (6.8%). By contrast only 3.5% of cod and 3% of haddock was  wrongly labeled. 

The study argues that this positive trend is due to a combination of transnational legislation, governance and public outreach, which has forced new regulation and self-regulation, and it contrasts the European 'turn-around' with the experience of the United States, where improvements appear more sluggish.

Genetic identification methods have progressively exposed the inadequacies of the seafood supply chain, raising awareness among the public, and serving as a warning to industry that malpractice will be detected. This evidence indicates we are now on the road to greater transparency, which should help the management of exploited stocks worldwide, but further standardised studies on a greater range of food provision channels, such as restaurants and auctions, are warranted, in order to have a complete understanding of the current state of the trade.

Topical Issue on DNA Barcoding of Fishes

A new special issue dedicated to FishBOL work has been published in the journal DNA Barcodes. Quite a few articles on recent research of the global fish barcoding community. Have a look:

Cods for sale. Do we know what we are buying? 

DNA barcoding increases resolution and changes structure in Canadian boreal shield lake food webs 

DNA Barcoding, species delineation and taxonomy: a historical perspective 

Extending DNA barcoding coverage for Lake Whitefish (Coregonus clupeaformis) across the three major basins of Lake Huron 

An exploration of sufficient sampling effort to describe intraspecific DNA barcode haplotype diversity: examples from the ray-finned fishes (Chordata: Actinopterygii) 

Community engagement in seafood identification using DNA barcoding reveals market substitution in Canadian seafood 

Standards for Conducting a DNA Barcoding Market Survey: Minimum Information and Best Practices 

Status of DNA Barcoding Coverage for the Tropical Western Atlantic Shorefishes and Reef Fishes 

A case study of the forensic application of DNA Barcoding to sharkfin identification in the Mexican Pacific 

Molecular identification of Leporinus from the south portion of South America 

Species delimitation in Neoplecostomus (Siluriformes: Loricariidae) using morphologic and genetic approaches 

Use of DNA barcode in the identification of fish species from Ribeira de Iguape Basin and coastal rivers from São Paulo State (Brazil)

Knodus moenkhausii (Characiformes: Characidae): one fish species, three hydrographic basinsa natural or anthropogenic phenomenon? 

A record of the Porbeagle, Lamna nasus, in coastal waters of Buenos Aires (Argentina) confirmed by DNA barcoding 

DNA barcoding Indonesian freshwater fishes: challenges and prospects 

Fishing for barcodes in the Torrent: from COI to complete mitogenomes on NGS platforms 

Adding nuclear rhodopsin data where mitochondrial COI indicates discrepancies – can this marker help to explain conflicts in cyprinids? 

Quantitative metabarcoding

It is a bit of a holy grail for metabarcoding and a dream of many: Using it not only to determine species identities but also for quantifying relative species abundances. It is widely accepted that metabarcoding has its limits and is biased both biologically and technically. For example, chimeric sequences, contaminants and clustering algorithms can bias even the most basic outputs of DNA metabarcoding studies such as species richness. This becomes very problematic if one tries to infer abundance from the proportions of species DNA. Attempts have been made to extrapolate differences in mass or abundance of species through differences in sequence read abundance but biases have been repeatedly reported.

Previous attempts to control biasing factors in DNA metabarcoding studies have primarily focused on correcting for a single source of bias, or altering protocol steps that are known to introduce bias...An alternative approach to correcting for individual biases is to create control materials for target organisms, which when sequenced alongside environmental samples can be used to create correction factors that account for multiple sources of bias simultaneously.

A new study that just showed up in the accepted article section of Molecular Ecology Resources went the latter route and used sequencing of 50/50 mixtures (target species/control species) to establish relative correction factors (RCF) that account for multiple sources of bias and are applicable to field studies.

The colleagues focused on a rather small model system containing a few fish and a small prey library for Pacific harbour seals. However, they also applied the prey library derived correction factors to some wild seal scat samples to determine the impact of the correction method on a real world scenario. Their results show that the 50/50 RCF approach represents an effective tool for evaluating and correcting biases for the model chosen and likely for other studies as well. The authors also clearly state that their new method will not solve the problem for all possible scenarios and that there will be lots of cases where it is simply unrealistic to expect accurate estimates of species proportion based on DNA sequence read abundances.

However, in study systems focused on a limited number of species which have conserved barcode priming regions, 50/50 RCFs offer potential to improve proportional estimates by accounting for multiple sources of bias. The 50/50 RCF approach will be particularly useful when biases to sequence read abundance are substantial and the resulting species correction factor magnitudes are large. Even when it is not possible to generate a complete tissue library, a 50/50 RCF library consisting of a subset of key species could be used to screen for large species-specific biases and aid in the interpretation of sequencing results.

We're crowdfunding!

Dear Colleagues,   Today is Giving Tuesday, the global day of giving, and we are excited to announce that this year the School Malaise Trap Program will be hosting a crowdfunding campaign through the University of Guelph!    Over the past three years, the program has become an outstanding success through the constant dedication of educators, students, and supporters of the Biodiversity Institute of Ontario. Through our generous funders we have been able to reach nearly 15,000 students and over 250 schools across Canada! Furthermore, the scientific findings associated with the program are quite impressive. Over 6,500 arthropod species have been collected by participants, with 1041 of those species being new to BOLD.   As resources diminish, we are asking for support from generous donors like you so that we may keep the program alive! This year we are hoping to raise at least $10000 in order to keep the program free for participants (average cost = $1000 per participant). For more information about our program costs and our goals, please click here.   Every little bit helps! If each person who receives this email donates $15.43, we would be able to reach our goal TODAY! We ask that you kindly consider donating as well as spreading the word by forwarding this email or sharing it via social media.    To donate, please click here. All donations are eligible for a tax receipt, and you can feel good about continuing to bring modern biodiversity science to students and educators across Canada. We thank you in advance for your contribution to keep this valuable educational opportunity alive!     Sincerely, The School Malaise Trap Program Team In the past three years, over250 schools and almost15,000 students have contributed 68,000 specimens, representing6,500 different species, to BOLD (BIO’s online barcode reference library). 1,041 of these species were NEW to BOLD, having never been DNA barcoded before! Learn More about the School Malaise Trap Program