CBD GTI Training Course on Rapid Identification of Invasive Alien Species is back

In 2015 The Secretariat of the Convention on Biological Diversity launched a capacity-building “training for trainers” course in DNA Barcoding available to interested Parties to the Convention. With generous financial support from the Government of Japan, the Secretariat will support a second round of the training course in 2016 on the application of DNA barcoding in the detection and monitoring of priority invasive alien species, pests and zoonotic disease vectors for interested Parties. This course will provide opportunities for Parties to develop national capacity in the detection and management of invasive alien species, pests and disease vectors that threaten habitats, ecosystems or the health of plants, animals and humans. 

The training course has two major components: an 8-week online distance education course on DNA barcoding methodological approaches and technologies, and a 4-week hands-on training course in standard DNA barcoding protocols for selected trainees at the Biodiversity Institute of Ontario, University of Guelph, Canada.  Applicants should be nominated by the National Focal Point for the Convention on Biological Diversity. National Focal Points are encouraged to consult with the national or regional plant protection organization (NPPO or RPPO) to recommend appropriate individuals to take the training course. The course is open to additional self-funded experts from countries that are not eligible for SCBD financial support.

The call for applications was announced last week on the CBD GTI website. For inquiries on eligibility, selection criteria, and application procedure, please contact the CBD Secretariat.

As per usual the online training component of this course is open to everyone else. This particular run of the course is exceptional as it draws in such a huge international audience which is a great learning environment. So mark your calendar - the online course starts April 11th, 2016.

Spider evolution

Spiders are an ancient and diverse group comprising over 45,000 described species with probably three times as many awaiting discovery. In addition to their remarkable diversity, ecology, and abundance, spiders are known for some extraordinary compounds, such as venoms and silks. Although few spider venoms are dangerous to humans, they potentially hold some medical promise as insecticides and therapeutics. And, no other animal can claim a more varied and elegant use of silk a super strong material we are started to explore more in order to use it to create biometic material such as artificial nerve constructs, implant coatings, and drug delivery systems.

Despite all that, our understanding of spider evolution was rather poor. The orb web, the spiral wheel shaped web made by many spider species, was once considered "the crowning achievement of aerial spiders" and consequently researchers believed it to have evolved independently at least twice across the group's evolutionary history. However, studies in the 1980s suggested the opposite and many colleagues concluded that the orb web and the taxa that spin it all shared a common ancestor. 

Well, this thought will likely change once again. Colleagues in the US conducted a massive phylogenetic study of spiders using next generation sequencing technologies. Perhaps I should start calling them HTS - High Throughput Sequencing which seems to become the new standard. The researchers generated a genomic data set composed of nearly 3,400 genes for 70 spider taxa that represented a wide breadth of the order's diversity. The resulting phylogenetic tree confirms earlier suspicions that all orb weaving spiders are, in fact, not closely related to one another. Although these data could be interpreted to mean that the orb web evolved more than once the team finds this hypothesis highly unlikely. 

Our results are relatively clear that while orb weaving taxa are not as closely related as previously thought, our data do support the notion that the orb web itself has evolved only once. What we are calling the "ancient origin hypothesis" for the web, simply means that the largest branch on the spider tree of life had an ancestor that constructed an orb web but most of its descendants abandoned it for other more seemingly more lucrative prey hunting strategies.

Further diversification analyses actually showed that the mostly ground-dwelling, web-less spiders diversified faster than orb weavers. Molecular dating estimates show a major increase in biomass of non-flying insects during the Cretaceous Terrestrial Revolution 125–90 million years ago favoring diversification of spiders that feed on running rather than flying prey. 

A very interesting read and as it has been noted by a couple of colleagues via Twitter that the new PeerJ graphical abstracts (image above) are pretty cool, too.

Freshwater biodiversity boosts global food security

Inland waters are the most threatened systems globally, with dams, water extraction, pollution and invasive species as well as overharvesting of the fisheries themselves recognised as some of the biggest threats. It is imperative that the relationships we explored should be considered within freshwater and fisheries management; the protection and conservation of species diversity in freshwater systems is a win-win outcome for human food security and conservation efforts to preserve freshwater ecosystems.

At least two billion people depend directly on inland freshwaters for the provision of food. However, despite thousands of freshwater species contributing to food security, the relationship between biodiversity and yield remains poorly understood.

A new study from the University of Southampton and the International Union for Conservation of Nature (IUCN) now shows that freshwater environments with a greater fish biodiversity have higher-yielding and less variable fisheries. Using datasets from the Food and Agriculture Organization of the United Nations (FAO) and IUCN covering 100 countries in Africa, Europe and parts of Asia, the researchers have conducted the first large-scale test of the impact of freshwater biodiversity on fishery yields and the variability of yield over time.

After taking into account other factors that would be expected to have an effect on yield, such as fishing effort, the size of lakes, and temperature and precipitation, the colleagues found that fisheries with a higher number of species are also producing higher yields. In addition, they showed that in regions with a higher number of fish species there was also more stability in the year to year yield. Countries with such strong relationships were Tanzania, Democratic Republic of Congo, Vietnam and Thailand.

The results suggest that fish biodiversity may deliver benefits for human well being. As such, these results provide a powerful argument for placing biodiversity conservation centrally within fisheries management, particularly in countries with the highest yielding inland fisheries as these also tend to have high freshwater biodiversity.

Beyond food security, the researchers say that understanding the degree to which biodiversity underpins freshwater fisheries has particular policy relevance because freshwater systems are of major importance for the conservation of biodiversity. Freshwater habitats are disproportionately species rich given that they cover only 0.8% of the Earth's surface but contain 10% of all species described to date and as many as a third of all vertebrates.

The root cause of tropical forest diversity

Oreomunnea mexicana Photo: James Dalling

Tropical forests are renowned for their high diversity, yet in many sites a single tree species accounts for the majority of the individuals in a stand. An explanation for these monodominant forests remains elusive, but may be linked to mycorrhizal symbioses.

The types of beneficial fungi that associate with tree roots can alter the fate of a patch of tropical forest, boosting plant diversity or, conversely, giving one tree species a distinct advantage over many others. A new study sought to explain this phenomenon that occurs in some tropical forests: Small patches of "monodominant forest," where one species makes up more than 60 percent of the trees, form islands of low diversity in the otherwise highly diverse tropical forest growing all around them. These patches dominated by a single species are rare but understanding how monodominant forests arise and persist could help explain how tropical forests otherwise maintain their remarkable diversity.

The new study focused on mountain forests in Panama that harbor hundreds of tree species, but which include small patches dominated by the tree species Oreomunnea mexicana. A team of US researchers focused on two types of fungi that form symbiotic relationships with trees: arbuscular mycorrhizas and ectomycorrhizas. Arbuscular mycorrhizas grow inside the roots of many different tree species, supplying phosphorus to their tree hosts. Ectomycorrhizas grow on the surface of tree roots and draw nitrogen from the soil, some of which they exchange for sugars from the trees. Ectomycorrhizas cooperate with only a few tree species, 6 % or less, of those that grow in tropical forests.

The researchers tested three hypotheses to explain the high abundance of Oreomunnea. First, they tested the idea that Oreomunnea trees are better able to resist species-specific pathogens than trees growing in more diverse forest areas. They actually found the opposite: The trees suffered more from pathogen infection when grown in soil from the same species than in soil from other species.

The researchers next tested whether mature Oreomunnea trees supported nearby Oreomunnea seedlings by sending sugars to them via a shared network of ectomycorrhizal fungi. But they found no evidence of cooperation between the trees.

In a third set of experiments, the team looked at the availability of nitrogen inside and outside the Oreomunnea patches. They found three-fold higher soil nitrate and ammonium concentrations outside than inside Oreomunnea-dominated forest and a correlation between soil nitrate and Oreomunnea abundance in plots.

Ectomycorrhizal fungi make some of their nitrogen available to the trees while starving other plants and soil microbes of this essential nutrient. The lack of adequate nitrogen means bacteria and fungi are unable to break down organic matter in the soil, causing most other trees to suffer because they depend on the nitrogen supplied by the microbial decomposers.

Bird identification - use your phone

Researchers of the Jena University in Germany have developed an algorithm that allows the software to memorize the appearance of a variety of animal and plant species and thereby developing the ability to discriminate between them. The visual fine-grained project not only aims to develop a new precise way of pattern recognition but also to deliver the parameter the software develops during the learning process.

The algorithm uses deep learning and big data methods for pattern recognition and by including images of many different perspectives it can recognize e.g. birds and dogs even while they move.

The algorithm we developed is able to automatically distinguish between different types of birds, flowers, dog breeds, and in general very similar object categories. It is based on computer vision and machine learning techniques that learn the appearance of object categories from a given set of images together with their annotations. Very recent ideas from the deep learning area allow for estimating very complex visual models and boost the recognition performance up to 82% for a dataset with 200 different bird categories. 

One potential outcome would be an app that would enable all of us to identify species in the field as using only a cell phone camera. There is already one less versatile one available. The Merlin app, a tool used in North American to identify birds now lets you upload an image of a bird that you’ve photographed, and if the photo shows one of the supported species, it returns the correct species in the top 3 results, 90% of the time. It currently supports 400 species in North America and needs good photographs of the animal. 

MIDORI Prize for Biodiversity nominations

Maybe you know of somebody who should be nominated.  The AEON Environmental Foundation opened nominations a few days ago for the MIDORI Prize for Biodiversity 2016:

The MIDORI Prize, a biennial international prize, was established by the Foundation in 2010 in order to extend the developmental influence of individuals’ efforts to various projects relating to biodiversity throughout the world, and to raise awareness about biodiversity.  In 2009, the Foundation established “The Japan Awards for Biodiversity,” a domestic prize.  This prize is also biennial and these two prizes are awarded alternately.  This year marks the fourth time that the MIDORI Prize has been presented.

The aim of the MIDORI Prize is to honor distinguished individuals who have made outstanding contributions to the conservation and sustainable use of biodiversity.  Each prize winner is awarded a wooden plaque, a commemorative gift and a monetary prize of 100,000 US dollars.

The conservation of biodiversity and the prevention of climate change are two of the greatest challenges of our time. In order to achieve the Aichi Biodiversity Targets during the United Nations Decade on Biodiversity 2011-2020, AEON Environmental Foundation will make further efforts in support of biodiversity issues through conducting various projects including award-presenting activities.

Period of Nomination: 15 February – 30 June

Award Ceremony:

The Prize will be awarded at a special ceremony organized in conjunction with the thirteenth meeting of the Conference of the Parties to the Convention on Biological Diversity (COP 13) in Cancún, Mexico in December 2016.  Following the Award Ceremony, the Winners’ Forum will be held in Tokyo, Japan, in the same month of the year.

DNA Barcoding to fight song bird slaughter

I don't know if you ever heard of Ambelopoulia, which is a traditional dish of grilled, pickled or boiled songbirds served on Cyprus. I find the idea of such a dish disgusting to begin with but what is really concerning is that the birds are caught by using non-selective methods such as mist nets and limesticks during the migration period in autumn but also in the spring. Trappers mainly target blackcaps but also other birds such as bee-eaters and shrikes. In contrast the list of trapped bird species is over 150 species long and includes 78 species listed as threatened by BirdLife International and the EU Birds Directive. According to Birdlife Cyprus over 1.5 million migrating songbirds are killed annually, and the number is increasing each year.

To be clear, this practice is outlawed by the EU and national legislation but it is a highly lucrative local commodity which means it is secretly served and birds are obtained through black market sources. Once prepared it is very difficult to determine what bird was actually used. However, DNA Barcoding is the new hope for the song birds. A new project aims to establish the method as a test if restaurant owners are trying to pass off illegally trapped birds as chicken or other legal species.

The project is a three-year collaboration between researchers at the University of Pisa, Italy, and the University of Cyprus, Nicosia, as well as the Ministry of the Interior's Cyprus Game and Fauna Service and the conservation group BirdLife Cyprus. So far, the team's unpublished work has shown that sequences from COI are enough to distinguish 81 bird species. This worked even when the DNA was extracted from meat baked at 90 °C, and cooked with salt or vinegar — a method that matches local gastronomy but that could degrade the DNA. 

With the help of their colleagues in Pisa, the team at the University of Cyprus was able to set up a laboratory to conduct DNA Barcoding on site. Furthermore, as part of the project two game-service officers were trained to enable them to testify on DNA evidence in court cases. This approach seems to be successful as the method has already been used in two pending court cases.

It is encouraging that methods such as DNA Barcoding can actually help to make a difference in such cases. However, lets be clear on that - the real change will only happen if humans start to develop respect for the species they share the planet with. We are not talking about a crucial source for food without the local human population can't obtain essential nutrients. This is an example for something completely unnecessary only maintained illegally because there are enough people that pay good money to have this dish. It reminds me a lot of the shark-fin soup that has no nutritional value and is still served with the excuse that it is an old deeply rooted tradition in local culture which is also a pro argument for Ambelopoulia. Well, I am curious if someone asked the younger generation about that kind of tradition. I met and talked with a number of students (school and university) who all reject these kinds of dishes, that are part of their respective culture, for what they are - unnecessary, brainless slaughter of animals. There is hope.