Friday, April 24, 2015

Wanna know about climate change? Ask a beetle.

We have been logging changes in weather patterns and temperatures in the Arctic for quite some time. What is more difficult is to measure how these changes in climate are affecting biodiversity. According to some colleagues from McGill's Dept. of Natural Resource Sciences one of the best places to look may be down at our feet, at beetles. 

The team of researchers was able to identify more than 460 different species of Arctic beetles in locations ranging from the edge of the boreal forest in Northern Ontario to Ellesmere Island in the far north. More significantly, they found that there were clear differences in what beetles are found where along this north-south gradient, and the ecological roles they fulfilled differed depending on the latitude in which they lived. The beetles are diverse in feeding habits and what they eat is closely linked to the latitude in which they are found.

Species and functional diversity have significant negative relationships with latitude, which are likely explained by the mediating effects of temperature, precipitation, and plant height. Assemblages within the same ecoclimatic zone are similar, and there is a significant relationship between assemblage structure and latitude. Species and functional assemblage structure are significantly correlated with many of the same climatic factors, particularly temperature maxima and minima. At a large spatial extent, the diversity and assemblage structure of northern beetles show strong latitudinal gradients due to the mediating effects of climate, particularly temperature.

The discovery that Arctic beetles may be especially sensitive to temperature has implications for future climate change monitoring.

As temperatures in northern regions rise or become more variable, there is a strong possibility that the beetle communities will undergo significant changes in response. Whether these changes will have positive or negative effects on Arctic ecosystems and the other animals and plants living there remains to be seen, but it is clear that beetles' sensitivity to climate make them ideal targets for long-term biodiversity monitoring in the far north.

Thursday, April 23, 2015

Sofja Kovalevskaja Award - Deadline 31 July

Fresh from the inbox:

With the Sofja Kovalevskaja Award, the Alexander von Humboldt Foundation is offering promising young researchers from all over the world attractive career prospects in Germany. Junior research talents of all disciplines from abroad are given the opportunity to establish working groups of their own at German research institutions.

The Sofja Kovalevskaja Award recognises outstanding talent and creative research approaches with exceptional conditions: With an award amount of up to €1.65 million each winner receives valuable starting capital to spend five years pursuing an innovative research project at a research institute of his or her choice – untroubled by administrative constraints. In addition, the establishment of their own junior research team enables the award winners to lay an important foundation for a promising academic career at a very early stage. Eight awards are expected to be granted.

Outstandingly qualified junior academics of all disciplines from abroad who completed their doctorate less than six years ago are eligible to apply for the Sofja Kovalevskaja Award. It is also possible to submit applications immediately after finishing one’s doctoral studies. Applications must be submitted by 31 July 2015.

We should be very grateful if you would support our search for young international research personalities by disseminating this announcement at your institution and also asking your colleagues to draw the attention of appropriately qualified research talents to this academic award.

Details of the application procedure for the Sofja Kovalevskaja Award can be found on our website. For individual questions, you are also welcome to contact us via email.

h/t Torbjørn Ekrem

Barcoding local - Contributions by course participants (2)

Here is the second contribution by one of my current DNA Barcoding course participants. Joanna Werner-Fraczek is an associate professor at Moreno Valley College, California. She is looking at DNA Barcoding as an educational tool and presents how it was implemented into the college's undergraduate program.

Does DNA barcoding belong in community colleges? “To be or not to be” is the question I would like to answer first, since I am an associate professor at a community college in Southern California who believes that research-based learning is the best approach to teach biology. My six-year teaching experience tells me that the biological message is even more powerful if it is supported with new technology. DNA barcoding seems to be the perfect fit; the technique is fairly straight-forward (collect samples, isolate DNA, amplify the fragment of interest, send off for sequencing, identify the species in BOLD, supplement with morphological/phenotypic data), yet it uses database searches that bring the flavor of doing something really smart. Even more, when students collect an insect or grow a plant, it becomes their own “pet”, therefore they immediately develop an attachment to it. Now they love what they do; biology becomes an intriguing engaging science. It is a win-win situation.

The second question is how to integrate DNA barcoding into teaching, so it creates a meaningful tool for a bigger cause. This is what I have developed. Every year, my college experiences the migration of cliff swallows coming from Central or South America to breed. They build multiple nests around campus, utilizing the nearby lake as a water source, and the surrounding hills as a mud source for their nests. The Flying With Swallows (FWS) undergraduate research project proposes two avenues of investigations. The first one, Ecosystem Survey, includes fauna observations on a year-round basis to monitor the presence of all birds with an emphasis on cliff swallows, mammals, reptiles and insects on the campus. The annual fauna fluctuations will be recorded on a dynamic “living” map available on the college website, constructed using ArcGIS Online, constantly updated using a smartphone application. The second path of the FWS project focuses on Ecosystem Investigation, where conducted research goes beyond observations, and includes biological magnification studies using swallows as monitoring organisms for pollutants. The FWS project is designed to integrate research into Biology and Chemistry courses with a common research theme. The DNA barcoding technique has been employed by biology major students to identify insects present on the campus and to identify swallows on a molecular level. DNA barcoding allows for introduction of major molecular biology techniques to a course such as DNA extraction, PCR, electrophoresis, concentration check and database searches. With the project umbrella over the course, students develop the sense of research continuation, and the individual labs are not a random collection of “who knows what for” techniques.

The third question a reader might ask now, is how smooth the incorporation and integration have been. Well, there is some level of complexity to everything we do. The incorporation-related problem is the cost. With colleges being chronically underfunded, purchase of kits for DNA extraction, and gel purification is an issue that currently can only be solved by outside funding (please, wish me luck with this task). However, what motivated me to take this course is the trouble I ran into when I tried DNA barcoding the first time last year for insect identification. We were able to identify campus insects down to the genus only, not to a species. So what I am eventually hoping to learn is the practical knowledge on how to use BOLD so the samples can be identified by the species name. Considering the fact that I am in the community college, our research will never reach the levels of discussions we had in this course, however, it represents the use of DNA barcoding for everyday life including teaching.

Wednesday, April 22, 2015

Barcoding local - Contributions by course participants (1)

The Introduction to DNA Barcoding course I am teaching is in its final week but we have already lined up another one running from June 1 to July 24, 2015. One of the weekly assignments of the course is an essay that combines what participants learned in the first 7 weeks and what they are doing at their home institution. This is one of the highlights of the course for me as it provides me with some unique insights into the work of colleagues world wide but it also shows me how well I did with teaching to that point. 

There are usually so many very interesting contributions that I always thought it would be a loss to the community at large if not shared more broadly. Therefore, I asked the participants of this course if they would give me permission to share their work through this blog. 

This is what I ask the participants in the respective unit:
Consider what you have learned so far about the application of DNA barcoding in several socio-economic fields. Try to come up with an application of the method in your professional or social environment. Your main motivation to take this course might be related to such an issue. Describe the issue at hand and how DNA barcoding could help. Assess how difficult or easy it might be to implement the new technology.

The first one who agreed to share his answer is Charuwat Taekul, head of the insect collection at the Insect Museum Thailand which is part of the Federal Department of Agriculture located in Bangkok. 

The development of a DNA barcoding knowledge base can help alleviate the situation of current trade negotiation. The International Plant Protection Convention (IPPC) currently plays a vital role in trade negotiations after non-tariff barriers have been established by the WTO. This means all members of the WTO not only are free to trade but also cannot limit the import/export of commodities unless there are scientifically proven health concerns or other reasons. The IPPC calls this subject "Sanitary and Phytosanitary (SPS)." However, this issues results in several issues when it comes to trade between countries. For example, EU countries claim that certain species of insects contaminate agricultural products and because these species do not occur in the EU member states, those products are banned from import into the EU. However, we are currently not sure these claims stem from actual research or trade barriers. To resolve such issues, the IPPC established experimental procedures, which all member countries can uniformly employ, the International Standard Phytosanitary Measures (ISPMs).

A number of protocols using DNA Barcoding are applied into ISPMs, e.g., ISPM No.27: Diagnostic Protocols for Regulated Pests. This protocol deals with the detection of Thrips palmi using real-time PCR since this species represents a trade barrier for import into the EU as it is a recognized invasive species. My research focuses on establishing ideal conditions for real-time PCR to detect Thrips palmi in Thailand to support the ISPM. 

DNA barcoding may help in pest control strategies as well as save the governmental money. A couple years ago, Thailand had critical pest problems with the coconut black-headed caterpillar, Opisina arenosella and the Pink sugarcane mealybug Saccharicoccus sacchari. These two species play an important role as invasive alien species and had a huge impact on the federal budget due to the large scale import of their natural enemies to control them. This classical control was applied without investigating the species richness of native natural enemies since the damage is quite widespread and uncontrollable. Nevertheless we might have saved a lot of money by investigating if suitable biocontrol agents are already available from native sources before importing them from elsewhere. Obtaining the information for both native pests and their natural enemies is important.

The formation of the ASEAN Economic Community (AEC) and ASEAN+3 (China, South Korea, and Japan) in late 2015 will bring the major changes to the economy, businesses, the workforce and society. The AEC is not only establishing free trade zones within Asia but also generating a single market and production zone to boost the competitiveness, thereby unequivocally creating free mobility of goods, services, investments, and skilled labors. DNA barcoding could help develop national capacities in detection and management of invasive alien species and plant pests as well as utilize the knowledge base to other research areas. After all, Thailand provides suitable conditions for many  alien species which might allow them to establish quite well. 

Despite the fact that DNA barcoding could play a significant role in trade facilitation as well as pest control and invasive species management, only little financial support has been provided for the program. A taxonomic proposal for pest and natural enemies has been suspended. The national science foundation claims that it is not a pressing issue and that the results cannot be applied at this moment. The main problems here are the lack of financial support from the government and the lack of recognition from the other fields of the scientific community.

Tuesday, April 21, 2015

Discoveries of the week #35

A new species of Hisonotus is described from the rio São Francisco basin. The new species can be distinguished from congeners by having (1) a unique coloration pattern of caudal fin with one black spot extending from its origin to the ventral lobe and two dark spots at the end of the lobe’s rays; (2) odontodes forming longitudinally aligned rows on head and trunk; (3) a functional V-shaped spinelet; (4) a single rostral plate at the tip of the snout; (5) by lacking contrasting dark geometric spots on the anterodorsal region of the body; (6) a lower caudal-peduncle depth; and (7) lower counts of the lateral median plates and (8) higher premaxillary and dentary teeth. The new species is the second described species of the genus Hisonotus in the rio São Francisco basin. It was found inhabiting the marginal vegetation of the rio São Francisco and three of its tributary, rio das Velhas, rio Paraopeba and rio Formoso.

And yet another new loricariid species. This one was named after Amerigo Vespucci, navigator and explorer who discovered the Rio São Francisco in 1501, which is the type locality of the species.
no DNA Barcode

Taxidiotisoma portabile gen. n., sp. n. is described from scattered populations in New South Wales, Victoria and Tasmania, Australia. Populations of T. portabile in Victoria, Tasmania and parts of New South Wales occur in urban, suburban and agricultural areas, with no collections of the species in natural habitats in the same district. Taxidiotisoma portabile is likely to be a native exotic species whose home range is in eastern New South Wales.

Not only a new millipede species but also a new genus. The genus name means travelling body and refers to the fact that the only species of this genus is perhaps a species that moved into new areas. The species name has a similar meaning referring to the fact that this species is almost certainly being transported to new areas in Australia by cars or trucks.
no DNA Barcode

The small genus Savarna Huber, 2005 only contains three species: Savarna baso (Roewer, 1963) from Sumatra, Indonesia, S. tesselata (Simon, 1901) from Malaysia, and S. thaleban Huber, 2005 from Thailand (World Spider Catalog 2014). In this paper, we describe one more, a new species from Ranong, Thailand.

A new spider species from Thailand named after the type locality district.
no DNA Barcode

A new scleractinian coral species, Cyphastrea kausti sp. n., is described from 13 specimens from the Red Sea. It is characterised by the presence of eight primary septa, unlike the other species of the genus, which have six, ten or 12 primary septa. The new species has morphological affinities with Cyphastrea microphthalma, from which it can be distinguished by the lower number of septa (on average eight instead of ten), and smaller calices and corallites. This species was observed in the northern and central Red Sea and appears to be absent from the southern Red Sea.

This new scleractinian coral species was discocvered at the coast of Saudi Arabia. This species is named after the King Abdullah University of Science and Technology (KAUST).
no DNA Barcode

The family Jacobsoniidae Heller (短跗甲科) is newly recorded from China upon the discovery of Sarothrias sinicus Bi & Chen, sp. n. (中华短跗甲) from Motuo, Southeast Xizang. Description and illustrations of the habitus and major diagnostic features of the new taxon are provided. A key to the species of Sarothrias and some ecological notes on the new species are presented.

This new species is named after the country of the type locality, China.
no DNA Barcode

Critoniopsis bogotana is more precisely delimited, and two related Colombian species are described as new. The form of trichomes on the abaxial surfaces of the leaves is found to be of major importance. A short key to the C. bogotana group is provided.

Two new species from the Northern Andes. One has been named after a department of Columbia, Nariño, and the other one is named after the type locality, Municipality de Tausa.
no DNA Barcode

Monday, April 20, 2015

School Malaise Trap Program - Spring 2015

Today was the day. All participants of the School Malaise Trap Program deployed and 'armed' their traps. The weather hasn't been optimal this year to say the least but over the last few weeks things started to get better and most importantly warmer. We pitched a trap here at our institute and there are already quite a few insects trapped in it. My guess is that the majority of them are the infamous Chironomids as those always seem to be the first ones out after the Winter.

As last Fall we encouraged students and their teacher to let us know via Blog and Twitter what they are up to and how their traps are doing. Here is a selection of some pretty cool entries to our program blog and Facebook page.

Here a video from Blair Outdoor Education Centre not far from here:


big excitement at the Chedabucto Education Centre:

and even a cheer from John Polanyi Collegiate Institute:


DOPA Explorer

The Digital Observatory for Protected Areas (DOPA) has been developed to support the European Union’s efforts to substantially strengthen the effectiveness of international governance for biodiversity and ecosystem services and more generally for strengthening the capacity to mobilize and use biodiversity data, information and forecasts so that they are readily accessible to policymakers, managers, experts and other users. DOPA is conceived as a set of web based services to provide a large variety of end users with means to assess, monitor and possibly forecast the state of, and pressures on protected areas at local, regional and global scale.

I have to admit that until very recently I didn't know much about this very interesting biodiversity information system which was developed over the last five years at the Joint Research Centre of the European Commission in collaboration with other international organizations, such as GBIF, UNEP-WCMC, Birdlife International and RSPB. DOPA is not only designed to assess the state and pressure on protected areas and to prioritize them accordingly, in order to support decision making and fund allocation processes, but it is also conceived as a monitoring and ecological forecasting service, through e-Habitat, its core web processing service. The use of open standards and of open source programming languages for the development of the core functionalities of the system were expected to encourage the participation of the scientific community beyond existing partnerships and to favor the sharing of such an observatory which could be installed anywhere.

The first of the proposed tools, DOPA Explorer  has been released in early April:

The main purpose of the DOPA Explorer is to provide simple means to explore, analyse and compare the existing reference information on species and ecosystems that is available on protected areas at the country and ecoregion levels. End-users can use DOPA Explorer to identify the protected areas with the most unique ecosystems and species or assess the level of pressure coming from agriculture or population.

The web interface provides users with simple means to explore nearly 16 000 of the world's protected areas. Although the system is currently frequently overloaded it provides some very interesting mapping tools and one can certainly see its value for a lot of applications. 

In a recent letter of the United Nations Convention on Biological Diversity (CBD), the Executive Secretary encourages all the Parties to the CBD to make use of the DOPA Explorer in their actions towards achieving Aichi Biodiversity Target 11:

By 2020, at least 17 per cent of terrestrial and inland water, and 10 per cent of coastal and marine areas, especially areas of particular importance for biodiversity and ecosystem services, are conserved through effectively and equitably managed, ecologically representative and well connected systems of protected areas and other effective area-based conservation measures, and integrated into the wider landscapes and seascapes.