Barcoding local - Contributions by course participants (4)

And yet another guest post by one of my DNA Barcoding course participants. Martha Mphatso Kalemba is a biodiversity officer responsible for coordination of Invasive Alien Species Management and other biodiversity related areas in the Department of Environmental Affairs in Malawi.

Biodiversity in Malawi just like most countries is in decline. Habitats and ecosystems are being threatened and thousands of species are at risk of extinction. Invasive species are on the rise and genetic erosion is the order of the day. My job as a biodiversity manager is to prevent this from happening. I have to identify approaches and technologies that can assist Malawi to preserve and conserve existing biodiversity and prevent further loss. Knowing that DNA Barcoding speeds up and simplifies the process of understanding what species we have, what species to prevent from invading our ecosystem and what species exist for commercial and research use was enough motivation for me to undertake this course.

Although my major motivation of taking this course was to understand how DNA barcoding can be applied in detection of invasive alien species, by going through Malawi’s National Biodiversity Strategy and Action Plan (NBSAP) I have identified a lot of areas that can benefit from DNA barcoding most of which I am directly involved in. Malawi’s NBSAP has strategies to establish an effective detection and monitoring system for invasive alien species, an effective detection and monitoring system for biotechnology and an effective system for monitoring compliance to Access and Benefit Sharing legislation. I feel that all these areas can benefit from DNA barcoding in that the basic requirement for these systems to function is to know what kind of species we want to protect preserve and manage.

Currently Malawi is developing a project on management of invasive species and one major component is to develop an inventory of all invasive species in Malawi. The output of the whole project depends on how much we know about invasive species in terms of number and characteristics. Knowing the current challenges in finding adequate experts and resources to complete such a task, DNA barcoding would be one of the most important technologies to be applied in such a project. It would ease the burden of having to search for already limited taxonomists and carefully collecting specimen to preserve their distinguishing features and spending so much time identifying a single species. With this technology the whole process of identifying invasive alien species can be sped up thereby accelerating the implementation of the project.

Similarly, applying DNA barcoding to the implementation of the Nagoya Protocol on Access and Benefit Sharing would be helpful for Malawi. Being a signatory to the Nagoya protocol, Malawi needs to ensure that it has a reliable system to monitor and track compliance of bio-prospectors. One of the first activities Malawi has planned is to come up with an inventory of all the genetic resources that are of high value and have high potential to be exploited for commercial purposes. Further, any individuals or companies that access genetic resources in Malawi need to be regulated to prevent fraud and products taken from conserved species. It is of interest for Malawi to know what genetic resources are being utilized and where they end up but that can only be done upon assessment of products to determine their genetic makeup. DNA barcoding can help Malawi in tracing products that utilize their genetic resources and ensure that there is scientific basis for incompliance claims.

Other areas that can benefit from DNA barcoding in Malawi’s NBSAP include updating the National Red Data List, production of Malawi’s valorization strategy, and identification of habitats with high species diversity, conservation of threatened and endangered species and many more. DNA barcoding can speed up process of species identification which will eventually assist us in determine further studies required and conservation approaches to be implemented on specific species and ecosystems. The only limitation would be on whether the reference database contains DNA barcodes for the species of our interest. It would be exciting for Malawi to make submissions of DNA barcodes in case of identification of new species, but from what I have gathered so far there would be a lot of quality requirements that we would need to apply before making submissions.

To set up a functional DNA barcoding system we would need to determine the minimum requirements in terms of infrastructure, skills, quality management system and capacity required. The challenge in Malawi is mainly the type of infrastructure and human resource in our laboratories and the data management systems in place. Most laboratories are not yet accredited and do not have the mandate to carry out specific testing which would need to be dealt with to ensure that tests carried out are acceptable and reliable. Further, the technology is too dependent on how well data is managed and exchanged; data management in laboratories and exchange of information between scientists is a challenge for Malawi at the moment. The question of whether our laboratories would need to be upgraded to internationally or nationally acceptable standards for DNA barcoding would also need to be clarified.

Barcoding local - Contributions by course participants (3)

And yet another guest post by one of the participants of the last DNA Barcoding Intro online course. David Hernandez-Martich is a population biologist from the Dominican Republic and describes a number of potential applications in his home country:

Several situations in the Dominican Republic have come to my mind where DNA Barcoding could be useful in addition to the application for evolution, conservation and ecology (including identification/prevention of invasive species). For instance: 

a) Fish that are highly appreciated for human consumption are confused with other less appreciated. It is a common practice to sell the latter labeled as the former in the supermarkets and restaurants;

b) between 2012 and 2013, a considerable storm happened in the Dominican population due to public attacks among DR Government agencies that claimed for/against the presence of large amounts of fecal organisms in locally made salami (this is an important component of the Dominican diet because it is cheap and the taste for it is culturally inherited by Dominicans); 

c) In the last five years,  Moringa oleifera Lam 1783, a plant traditionally used in Asia and other regions for its nutritional value and other health purposes, became popular as a natural product to prevent and cure cancer in DR and other Latin-American countries (mainly due to media reports that supposedly it cured Fidel Castro of  cancer). Dry leaves are sold locally in the informal market either whole (other plants could be sold instead because they could be confused by the layman) or ground (in capsules or bags). They are even exported to USA, Spain and other countries with large Latin-American populations; and 

d) Mamajuana (or Damajuana), an alcoholic drink that is part of the Dominican folklore, which contains spices and leaves, roots, barks and sticks from other plant species. 

All these cases have an impact on tourism, which is very important for the Dominican economy. The last three have also health implications. I chose the last situation to expand for this course assignment.

Mamajuana is used intending to cure a number of health problems, but mainly to enhance sexual performance for males and, to less extend, for women. Some of the ingredients used to make it are rum, wine, honey and spices such as cinnamon sticks and whole cloves. In addition, there is a list of parts from less than ten other plants that are not necessarily shared in all the recipes. The penis of a sea turtle (Eretmochelys imbricata) used to be added. This is not added anymore probably because it would be illegal and would not be as cheap and easy to get as it was in the past. Thus, adding it would increase selling price and reduce demand.

The procedure to make this drink is basically the manual addition of the ingredients in the bottles, and there are only a few registered brand names. At any rate, I do not think there is an effective regulation/supervision of neither the content nor the process to make it. This may lead to the use of plants that contain high levels of compounds harmful to humans rather than those plants claimed to be used. Actually, even though official records on the effects to human health may be nonexistent, some serious adverse effects have been reported. It is consumed by a large number of Dominicans and commonly bought by tourists as souvenir. The procedure to “cure” the ingredients prior to use seems to be standard, but reading the published recipes for this drink, you can tell that there is no a standard list of ingredients and their proportions are missing (and almost sure, they are not standardized either). In addition, just based on morphology, most of the plants used to make it cannot be recognized. In some cases, the manufacturers may be claiming the use of a species, but actually they may be using another that is harmful to humans or legally protected. Therefore, DNA Barcoding may help identifying those species. Even though plant identification is not enough to solve the health and conservation problems caused, it will be an essential component of the solution. Regulation, supervision and standardization are also necessary.

What's in pet food?

The pet food industry, including pet foods and other pet products and services, is a growing market in the United States. Over the past five years, U.S. pet industry expenditures have increased by approximately $10 billion, with close to $21 billion spent on pet food alone in 2012. The U.S. Bureau of Labor Statistics reports that nearly 75% of U.S. households own pets, totaling about 218 million pets, not including fish. On average, each U.S. household spends more than $500 on pets annually, equating to about 1% of household expenditures.

Although the numbers above have been estimated only for the U.S. I consider it very likely to find similar expenses in many other countries. As pet owners (we share the house with two cats) we want to ensure that our little companions live at least as well as we do and one important component is their food. It might come to no surprise that despite existing regulations for pet foods, the growth of the international trade and the globalization of the food supply increased the potential for food fraud to occur. In addition in recent years the amount of products with specific diet formulas skyrocketed. Now you can buy pet food with various combinations of ingredients. 

Two researchers Chapman University in Orange, California conducted a study in which they tested 52 wet and dry foods and treats using real-time PCR assays. The study was, in part, a response to Europe’s 2013 horse meat scandal, which involved burgers and lasagna meat sold as beef. That led to product testing in 27 countries, with horse DNA found in about 5 percent of products labeled as beef, according to the European Commission. 

Of the 52 tested products, 31 were labeled correctly, 20 were potentially mislabeled. 13 products of theses potentially mislabelled products contained meat from species not listed on the label, four lacked one or more meats listed on the label, and three had both problems. One wet cat food tested in the study contained meat from an undetermined species.

It comes to no surprise that pet food industry officials expressed doubt that the test results are a reflection of accuracy of pet food labeling in general. Indeed it is possible that mislabeling is unintended, resulting from formulation mistakes or mislabeling by suppliers. That can be prevented, in part, by requiring documentation of sources from suppliers and testing raw materials as well as by training employees to prevent product cross-contamination. But, mislabeling can not only result from sloppy operations but also through fraud. 

The authors conclude and suggest:

Although there are pet food regulations in place in the United States that are enforced by federal and state entities, there is still a lack of information on meat species authentication as well as accidental mislabeling and intentional food fraud. To date, few studies have been published on the prevalence of meat species mislabeling in pet foods. While this study suggests the occurrence of pet food mislabeling on the commercial market, further studies are needed to determine the extent of mislabeling and to identify points in the production chain where mislabeling occurs.

Discoveries of the week #36

Liolaemus scorialis, Liolaemus zabalai

The elongatus-kriegi complex is one of the most diverse clades of the Liolaemus (sensu stricto) subgenus of lizards. There are currently 29 species recognized in this group distributed between Chile and Argentina. Based on molecular evidence, there seem to be five main clades nested within this complex: the elongatus, leopardinus, kriegi, petrophilus and punmahuida clades. Liolaemus buergeri and L. kriegi, both of the kriegi clade, were believed to inhabit the surroundings of the Laja Lagoon, in the Biobío Region of Chile. Moreover, this Chilean population of L. kriegi was recently recognized as an undescribed taxon called “Liolaemus sp. A” based on molecular phylogenetics. In this work, we studied these two populations of the Laja Lagoon and provided the morphological diagnosis to describe them as two new species: L. scorialis sp. n. and L. zabalai sp. n., previously considered L. buergeri and “L. kriegi/Liolaemus sp. A” respectively. Additionally, we identified another population of L. scorialis in the vicinity of La Mula Lagoon in the Araucanía Region of Chile. Liolaemus scorialis differs from almost all of the species of the elongatus-kriegi complex by its considerably smaller size. Nevertheless, without molecular data we cannot assign it to any particular subclade. Liolaemus zabalai belongs to the kriegi clade based on published molecular phylogenies. Finally, we provide some natural history data on both species and we document for the first time the presence of L. neuquensis in Chile from a museum specimen from La Mula Lagoon.

Two new lizard species from Chile that seem to like high altitude environments. The first species was named after the habitat, which is composed of accumulations of igneous rocks from the Antuco Volcano, called “scoria” from the Greek “skoria”. The second new species is named after Patricio Zabala, collection manager of the “Colección de Flora y Fauna Patricio Sánchez Reyes, Pontificia Universidad Católica de Chile”

no DNA Barcodes (but there is cytb data available - sigh)

Coecobrya sanmingensis, Coecobrya qinae

Two new Coecobrya species, which were newly collected in 2014, are described from China. Coecobrya sanmingensis sp. n. from southeast China (Fujian) is the fourth 1+1 eyed species in the genus; it can be distinguished from other three species by the ciliate chaetae X and X2-4 on the ventral side of head, the abundant chaetae on the trochanteral organ, a large outer tooth on the unguiculus, the absence of smooth manubrial chaetae, and the dorsal chaetotaxy. Coecobrya qinae sp. n. from southwest China (Yunnan) is characterized by paddle-like S-chaetae of Ant. III organ, ciliate chaetae X, X2 and X4 posterior to labium, medial macrochaetae on the mesothorax, and 5+5 central and 2+2 lateral macrochaetae on the fourth abdominal segment. An updated key to the Chinese species of Coecobrya is given.

Two new springtail species from China. One named after the type locality and the other one after the collector.

no DNA Barcodes

Oobius minusculus, Oobius whiteorum

Oobius Trjapitzin (Hymenoptera, Encyrtidae) species are egg parasitoids that are important for the biological control of some Buprestidae and Cerambycidae (Coleoptera). Two species, O. agrili Zhang & Huang and O. longoi (Siscaro), were introduced into North America for classical biocontrol and have successfully established. Two new native North American species that parasitize eggs of Agrilus spp. (Buprestidae) are described and illustrated from the USA: O. minusculus Triapitsyn & Petrice, sp. n. (Michigan), an egg parasitoid of both A. subcinctus Gory on ash (Fraxinus spp.) and A. egenus Gory on black locust (Robinia pseudoacacia L.) trees, and O. whiteorum Triapitsyn, sp. n. (Pennsylvania), an egg parasitoid of A. anxius Gory on European white birch (Betula pendula Roth). A taxonomic key and notes on the Nearctic native and introduced Oobius species are also included.

The name of the first new species parasitoid wasp refers to its small size. The second new species is named in honor of good friends of the author’s family.

no DNA Barcodes

Lithoscaptus semperi

A new species of gall crab is described from the free-living stony coral Trachyphyllia geoffroyi. Specimens were collected during field work in Lembeh Strait (Indonesia) and off Kudat (Malaysian Borneo). This new species, here named Lithoscaptus semperi sp. n., is the ninth species assigned to the genus. It can be separated from its congeners by not having the internal orbital angle extending beyond the external orbital angle, and by the stout female P2 merus with prominent distomesial projection. In addition, the carapace surface appears smooth, despite having small tubercles on the anterior half, and is without noticeable spines, other than those on the frontal margin. The distinctive carapace pattern in life is a diagnostic character in male specimens.

This new crab species was named after the German naturalist Carl Gottfried Semper (1832–1893), who was the first to mention gall crabs occurring in the coral genus Trachyphyllia.

DNA Barcodes available

Alloscorpiops troglodytes

Among the genera of the subfamily Scorpiopinae Kraepelin, 1905 Alloscorpiops remains rather discrete. Only recently new species were added to this genus, increasing its number from two to five. Therefore, species of Alloscorpiops remain rare. One remarkable new species, Alloscorpiops troglodytes sp. n., is described on the basis of a single male specimen collected inside a cave from Song Thanh Nature Reserve, Cha Vanh Commune, Nam Giang District in Vietnam. The new species presents most features exhibited by scorpions of the genus Alloscorpiops, but it is characterized by reduced size, slender body and elongated pedipalps. This new scorpion taxon represents the third species of Scorpiopinae discovered in a cave system, and may be another endemic element in the fauna of Vietnam.

This species was found in a cave in Song Thanh Nature Reserve in Central Vietnam.The specific name refers to this origin. 

no DNA Barcodes

Psammisia pinnata, Psammisia pseudoverticillata, Psammisia sophiae, Satyria orquidiensis, Satyria pterocalyx

he inventory of the vascular plants of one of the richest and least studied floras, the Andean and Chocó regions of northwestern Colombia, targets Las Orquídeas National Park. As a result of field trips to areas never before collected, several epiphytic and small terrestrial shrubs in the family Ericaceae have been discovered in the Park’s humid forests. Five new, morphologically remarkable species of Ericaceae (tribe Vaccinieae), are here described and illustrated. In a separate phylogenetic analysis, Psammisia pinnata Pedraza, P. pseudoverticillata Pedraza, Satyria orquidiensis Pedraza, and S. pterocalyx Pedraza, were placed by molecular sequence data within clades of the non-monophyletic genera Psammisia and Satyria; phylogenetic evidence for the placement of P. sophiae Pedraza is still lacking. Their affinities are here discussed, along with their preliminary conservation status.

Five new species of the family Ericaceae and all have been found in Colombia. Several species have been named after leaf or stem features, one (P. sophiae) after the daughter of the author and another one (S. orquidiensis) after the type locality.

no DNA Barcodes

Reading Mammal Diversity from Flies

According to the Global Mammal Assessment (2008), information on the distribution and abundance of most tropical mammal species remains data-deficient, and thus some species appear to be disproportionately threatened. Lack of data on tropical mammal species can be associated with limitations of the existing monitoring approaches. Field-trapping techniques vary in efficiency and are often a biased representation of diversity. For example, identification of animal signs is laborious, requiring the input of specialists over an extended time period, and can be imprecise. Likewise, expensive camera traps cannot identify individuals to species lacking easily observed diagnostic markings. Impediments also include the challenge posed by cryptic species, which are not always morphologically distinct, and are more easily recognised by molecular techniques. Considering that the current monitoring approaches are challenged by ethics, precision, and accuracy, a new approach is urgently needed.

One alternative for monitoring mammal populations could be the analysis of non-invasively sampled vertebrate DNA. For instance, environmental DNA extracted from sediments, soil, or water samples could permit the assessment of a broad range of vertebrate diversity in a given area, for a relatively minimal sampling effort. Alternative sources are naturally shed or otherwise deposited samples, including feces, hair, and feathers. 

Perhaps there is an even more elegant solution to this. Recent studies (here and here) already suggested that mammal genetic material ingested by invertebrates (iDNA) can be used to investigate mammal biodiversity. Colleagues from Malaysia now tested the utility of blowfly-derived DNA as an effective method for local mammal monitoring. Their objectives were (i) to determine the persistence period of amplifiable mammal mtDNA in blowfly guts through a laboratory feeding experiment, and (ii) to design and test primers that can selectively amplify mammal DNA mini-barcodes in the presence of high concentrations of blowfly DNA. The animal of their choice was the oriental latrine fly (Chrysomya megacephala).

The results of this study are quite promising. The feeding experiments established that amplifiable mammal mtDNA persists in the guts of adult Chrysomya megacephala for 24 h—96 h post-feeding (89% at 48 h). The researchers also established a new primer set for DNA mini-barcodes that worked very well across all mammal groups. Actually the 205 bp COI fragment was so successful in distinguishing mammal species that it could also separating some so called “dark” bat taxa, previously recognised species that lack formal taxonomic status. This would potentially allow for the detection of cryptic taxa overlooked by other methods. The authors conclude:

Our findings suggest our new DNA mini-barcode target and a standardized trapping protocol with retrieval of blowflies every 24 h could point the way forward in the development of blowfly-derived DNA as an effective method for mammal monitoring in Peninsular Malaysia. The next step would be a comprehensive comparison of diversity measures for mammals produced by the blowfly-derived DNA approach and by traditional monitoring approaches such as cage traps, mist nets, hair traps, camera traps, or scat samples.

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.

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.

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.

Discoveries of the week #35

Hisonotus vespuccii

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

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.

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Savarna kraburiensis

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.

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Cyphastrea kausti

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).

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Sarothrias sinicus

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.

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Critoniopsis narinoensis, Critoniopsis tausae

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.

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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:

Set up at M.C. Knoll Elementary School:

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.

Niche partitioning in diatoms

Life on Earth is diverse and abundant, and there's no need to look any farther than the ocean's surface for proof. There are over 200,000 species of phytoplankton alone, and all of those species of microscopic marine plants that form the base of the marine food web need the same basic resources to grow--light and nutrients. This diversity of phytoplankton has puzzled researchers for a long time. The many different species coexist in this relatively stable environment, competing for the same resources but no species seems to out-compete others.

A study by a team of researchers from the Woods Hole Oceanographic Institution (WHOI), University of Rhode Island (URI), and Columbia University, reveals how diatom species - one of the several major types of marine phytoplankton - use resources in different ways to coexist in the same community. The colleagues used a novel approach combining new molecular and analytic tools to investigate how similar species utilize resources differently - known as niche partitioning - in Narragansett Bay, R.I.  In conjunction with the sequencing analysis, the research team developed a new bioinformatic approach that uses data from nutrient amendment experiments to help interpret signals from the environment.

Here, we use quantitative metatranscriptome analyses to examine pathways of nitrogen (N) and phosphorus (P) metabolism in diatoms that co-occur regularly in an estuary on the east coast of the United States (Narragansett Bay).

Using these data the researchers e.g. observed two species of chain-forming diatoms--Skeletonema spp. and Thalassiosira rotula--coexisting in the same subset of water, but doing fundamentally different things with available nutrients, specifically nitrogen and phosphorus. Skeletonema is the more dominant species of the two and has specialized on inorganic nitrogen sources, like nitrate and nitrite. The less dominant species, Thalassiosira, is bringing in nitrogen from organic sources, such as amino acids.

We have long suspected that even closely related phytoplankton must have ways of distinguishing their needs from that of their neighbors, for example using different forms phosphorus or nitrogen, but this has been hard to track in the environment, as most approaches are not species-specific...Part of the challenge is that you would need to track species-specific patterns in resource utilization to compare one diatom to another.

The annotation of RNA sequences via "pattern matching" was facilitated by the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP), which has sequenced the genetic material of more than 300 marine species. In this study, a new database that is part of the MMETSP was leveraged to identify species-specific signals. In addition the team developed a way to normalize those signals to be able to compare quantitatively between species.

Finalists for GBIF Ebbe Nielsen Challenge

The Global Biodiversity Information Facility (GBIF) officially established in 2001 is an international open data infrastructure, funded by various governments. It allows anyone, anywhere to access data about all forms of life on Earth, shared globally and openly.

Last year GBIF launched the GBIF Ebbe Nielsen Challenge, an open incentive competition seeking for the best and most innovative applications of open-access biodiversity data by scientists, informaticians, data modelers, cartographers and other experts. GBIF wanted to encourage use of the more than half a billion species occurrences and other data mobilized through and related to GBIF’s international network.

The competition goes through two rounds. Round one has just been finished and the jury selected six finalists from among 23 submissions received, inviting their creators to compete for €25,000 during the innovation prize’s second and final round. 

Here they are and it will be a tough choice for the jury as all are pretty cool and innovative ideas. 

#myGBIF

Developed by Tom August

This service leverages location information from Twitter users who use the the hashtag #myGBIF—“One hashtag, infinite possibilities”, as August suggests. Functioning as a hyper-local personalized biodiversity assessment, the call to #myGBIF retrieves species occurrence data from the user’s area, mashes them up with common names and IUCN extinction risks via the Encyclopedia of Life, and promptly tweets a resulting infographic back to the user.

BioGUID.org

Developed by Richard Pyle

Biodiversity informatics needs reliable, persistent and actionable digital identifiers, but the community has made little progress toward resolving its glut of multiple identifiers and sources for any given data object. BioGUID.org provides a common service for indexing and cross-linking a wide range of identifiers, making it easier to cross-link biodiversity datasets, and making them more powerful by harnessing identifiers.

ecoSpace

Developed by Miguel Porto

Promising “a new way of looking at species occurrence datasets”, this dynamic web application lets users navigate the relationships within regional species groups that are displayed as an ecologically meaningful network. Its interactive interface shows species’ ecological or biogeographical affinities based on user-selected bioclimatic variables and expands at each step to reveal the network’s complexity.

GBIF dataset metrics

Developed by Peter Desmet, Bart Aelterman & Nicolas Noé

This team has created a ready-to-use browser extension for Google Chrome, offering quick insights about the datasets available through GBIF.org. Its chart-based visual approach provides at-a-glance assessments of the occurrences contained in a dataset, enabling a user to assess its fitness for his or her use without having to download, filter and clean the data.

GBIF Soundscape

Developed by Ben Raymond & Peter Neish

This application taps the rich if unconventional stream of information available in sound recordings associated with some occurrence records. Drawing on the GBIF API, it reconstructs the natural "soundscapes" using audio files associated with bird and frog occurrences in selected regions.

Wallace (beta v0.1): Harnessing Digital Biodiversity Data for Predictive Modeling, Fueled by R

Developed by Robert P. Anderson, Matthew Aiello-Lammens, Bob Muscarella, Bruno Vilela & Jamie Kass

This submission combines data from the GBIF network with two recently developed tools developed in R, a high-powered programming language for statistical computing and graphics, allowing users to generate predictive distribution models. The web application enables researchers working online or offline to map, filter and remove occurrence records and build, evaluate and visualize complex predictions.

Here is what Rod Page, member of the jury had to say about the winners. He calls this quote rather cheesy but I let you be the judge of that. 

The creativity and ambition displayed by the finalists is inspiring. My biggest hope for the challenge was that the biodiversity community would respond with innovative - even unexpected - entries. My expectations have been exceeded, and the jury is eager to see what the finalists can achieve between now and the final round of judging.

I really like to encourage everyone to play around with these new tools. Most of them are in working condition and what will take place next is refinement. 

Discoveries of the week #34

Chaerilus pseudoconchiformus

A new species, C. pseudoconchiformus sp. n., is described from Xizang, China. The present new species is distinguished from its congeners by a body length of 32−40 mm, carapace with the anterior margin straight, chela with length/width ratio average of 3.3 in males (3.2−3.4, two adults), and 2.5 in females (2.3−2.6, nine adults), eight or nine (eight usually) rows of denticles on fixed and movable fingers of pedipalp chelae, five pectinal teeth in males and three or four in females. To date, the chaerilid species fauna of China consists of nine species. An updated identification key to Chaerilus from China is presented.

The first of two newly described scorpion species. The species name of this new member of a small monotypic family refers to the geographically and morphologically most closely related species Chaerilus conchiformus, by adding the Greek prefix “pseudo".

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Scorpiops ingens

A new species, Scorpiops ingens sp. n., from Xizang, is described and illustrated. Scorpiops ingens sp. n. is characterized by yellow-brown color, large size (length of adults above 70.0 mm), small and dense granules on tegument, a pair of small median eyes, 17 external trichobothria (5 eb, 2 esb, 2 em, 4 est, 4 et), and 7 or 8 (usually 7) ventral trichobothria in the pedipalp patella, chela with a length/width ratio average of 2.2 in males and females, pedipalp chela fingers on adult females and males scalloped, pectinal teeth count 6–8, pectinal fulcra absent. With the description of this new species, the number of known species of Scorpiops from China is raised to 12. An updated identification key to Scorpiops from China is presented.

This is the second new scorpion from China. The species name refers to its size. The Latin word "ingens' means huge.

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Neomida diminuta

Neomida diminuta sp. n. is described, based on a single male specimen from Colombia, and a redescription of N. suilla (Champion) is given. Data on the morphology of the aedeagus for both species, and on the female abdominal terminalia for N. suilla are provided. New records of N. suilla from Atlantic Forest remnants in the states of Espírito Santo and Minas Gerais, Brazil are given.

This new species of darkling beetle belongs to genus of strict fungivorous beetles that live in hard conks of wood decomposing fungi. The species name “diminuta” means small, referring to its minute size (1.7 mm total length).

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Stephos geojinensis, Stephos projectus

Stephos geojinensis

Two new species of benthopelagic copepods of the genus Stephos T. Scott, 1892, belonging to the family Stephidae G.O. Sars, 1902, are described based on specimens collected in the stagnant water flooding the burrows excavated by ocypodid crabs in two intertidal mud-flats, and from near-bottom shallow waters in Korea, respectively. They can be easily diagnosed based on the ornamentation of both the female genital double-somite and genital operculum; the morphology of the distal segment of the male right P5; the presence/absence of a tiny pointed process on the distomedial angle of second segment of female P5; and the condition (seta or spine) of the lateral armature element on the distal segment of female fifth legs, among other features. This is one of the few cases reported of calanoid copepods living as commensals of other invertebrates, and raises to six the number of members of the genus reported from Asia. This is also the first record of the family Stephidae in Korea.

These two new species are first records of the calanoid family Stephos in Korean waters. One was named after the type locality Geojin Port, Gosung-gun, Gangwon-do, Korea. The second species go tits name from some dorsolateral spiniform projections present on the female genital apparatus.

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Paepalanthus serpens

We describe and illustrate Paepalanthus serpens, a microendemic species of Eriocaulaceae from the Espinhaço Range. The species is known from a single population growing in rocky areas of the Serra do Cipó, Minas Gerais. It is placed in Paepalanthus ser. Paepalanthus, and is easily distinguished from its congeneric species by its elongated, lignescent stem, thickened by the marcescent sheaths of the linear leaves, which are arranged in a rosette at the stem apex, scapes equalling the leaf height, and capitulae with straw-coloured involucral bracts. Comparisons with the morphologically similar species are provided, as well as comments on distribution, ecology, phenology and conservation status.

This new perennial species is known only from one population at the western slopes of the Serra do Cipó in Brazil. The name "serpens" refers to the serpent-like growth, with an unbranched, thick woody stem that slowly elongates and becomes creeping, with an erect apex.
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Indigofera magnifica, Indigofera asantasanensis

Indigofera magnifica

Two new species of Indigofera L. (Leguminosae) are described from the Sneeuberg Centre of Floristic Endemism on the southern Great Escarpment, Eastern and Western Cape Provinces, South Africa. Both species are localised high-altitude endemics. Indigofera magnifica Schrire & V.R. Clark is confined to the summit plateau of the Toorberg–Koudeveldberg–Meelberg west of Graaff-Reinet, and complements other western Sneeuberg endemics such as Erica passerinoides (Bolus) E.G.H. Oliv. and Faurea recondita Rourke & V.R. Clark. Indigofera asantasanensis Schrire & V.R. Clark is confined to a small area east of Graaff-Reinet, and complements several other eastern Sneeuberg endemics such as Euryops exsudans B. Nord & V.R. Clark and E. proteoides B. Nord. & V.R. Clark. Based on morphology, both new species belong to the Cape Clade of Indigofera, supporting a biogeographical link between the Cape Floristic Region and the Sneeuberg, as well as with the rest of the eastern Great Escarpment.

The first of these two new high altitude species is named for its magnificent, showy, vivid fuchsia-pink flowers and the second for the Asante Sana Private Game Reserve, the owners and managers of which have been generous and instrumental in facilitating biodiversity research in the Sneeuberg region. The known range of this species is almost entirely confined to this property.
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