Monday, May 15, 2017

From the inbox - metabarcoding course in Russia

International course in DNA Metabarcoding: Part 1 – Field collecting and Molecular laboratory.

Tromsø Museum (University of Tromsø, Norway), Forest Research Institute, Karelian Centre, Russian Academy of Sciences (Petrozavodsk, Russia), ForBio (Research School in Biosystematics), and SIU (Norwegian Centre for International Cooperation in Education) jointly offer an International Course in DNA Metabarcoding. The course will link its teaching program to the current research projects at the partner institutes to strengthen the connection between education and cutting age research methodologies by taking students through consecutive stages of the research process such as field collecting, plant community descriptions, laboratory set up and bioinformatic data analyses.

Time and place:  Aug. 7, 2017 9:30 AM - Aug. 19, 2017 4:30 PM, Forest Research Institute, Karelian Centre, Russian Academy of Sciences (Petrozavodsk, Russia).

DNA metabarcoding is a rapid method of biodiversity assessment utilizing environmental DNA (DNA obtained from sediments, soils, water, etc) which combines two technologies: DNA based species identification and high-throughput DNA sequencing. We include applications of DNA metabarcoding to ancient and recent plant community or species composition assessment using lake sediments as well as in diet study of the reindeer - one of the last remnants of the Beringian megafauna in the Arctic, keystone species, with high cultural and economic value for indigenous residents. The field collecting will be done in Karelia and Murmansk region of Russia, the laboratory work will be partially conducted in the field as well as using molecular laboratory facilities at the UiT. The computer classes for data processing and bioinformatic analyses will be held at the Tromsø Museum. The Tromsø-based Part 2 of the course will be organized in February 2018 and announced later. The detailed schedule of the programme including field work itinerary is upcoming.

Teachers:
Charlotte Clarke, University of Southampton, U.K.;
Eric Coissac, Laboratoire d’Écologie Alpine, Grenoble, France (Part 2: Data processing and Bioinformatics);
Galina Gusarova, Tromsø museum, University of Tromsø, Norway;
Stefaniya Kamenova, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway;
Alexey Kravchenko Forest Research Institute, Karelian Centre, Russian Academy of Sciences, Petrozavodsk, Russia;

Financial aid: Only students affiliated with the universities from the partner countries in the High North Programme (Norway, Canada, China, Japan, Russia and U.S.A.) may be funded through the project funds. All expenses of the participants from the partner countries, including travel, accommodation, meals and bench fee are fully covered. Other applicants will have to cover return travel to St Petersburg (Russia). Additional expenses, including the local train tickets as well as food and lodging at two nature reserves, amount to 660 EUR in total. This amount will have to be transferred to the Tromsø Museum, University of Tromsø, before 1 July 2017, as we will book travel within Russia for all the participants together.

Registration: please fill out the online application form

Maximum number of participants is 15.
Application deadline is June 1, 2017.
The results will be announced by e-mail on June 8, 2017.

Please contact Galina Gusarova for more information.

Friday, May 5, 2017

From the inbox

Online questionnaire on the openness and ethics of data in life sciences

Dear colleague,

I need your help.

I am doing a study with my colleague Dimitris Damalas on the openness and ethics of data in life sciences. Thus we have prepared an online questionnaire

The objective of this questionnaire is to gain a better understanding of what researchers think on sharing and archiving, as well as barriers to the sharing and archiving of research data. The results of this survey will be published in a special issue on ‘The ethics and practice of openness in life science data’ of the international journal of Ethics in Science and Environmental Politics (Editors: Konstantinos Stergiou, Dimitrios Damalas).

The questionnaire takes less than 5 min to fill it. Can you please devote these 5 min and fill it?

Thank you in advance.

Prof. Kostas Stergiou

Director of the Institute of Marine Biological Resources and Inland Waters
Hellenic Center for Marine Research, Athens - Greece
Department of Biology
Aristotle University, Thessaloniki - Greece

Friday, April 28, 2017

Last chance - submit your abstract today

TODAY THE ABSTRACT DEADLINE ENDS


The African Centre for DNA Barcoding (ACDB), the University of  Johannesburg (UJ), International Barcode of Life Project (iBOL), and the Department of Environmental Affairs (DEA) are proud to announce and welcome delegates to our hosting of the 7th International Barcode of Life Conference, 20 – 24 November 2017. This is the first time that this event will be held on the African continent. The venue for the hosting of this prestigious event will be the Nombolo Mdhluli Conference Centre,
Skukuza.


The major theme of the conference is exploring mega-diverse biotas with DNA barcodes. A series of presentations and workshops will focus on the use of DNA to understand diversity patterns and ecological processes in species-rich and complicated ecosystems. The conference also provides a
general forum for presentations, posters, and discussion on the wider field of DNA barcoding.
Delegates are encouraged to register as soon as possible as space is limited.
Abstracts should be submitted here today.

More information at:
Website: http://dnabarcodes2017.org
Facebook: @DNABarcodes2017
Twitter: @DNABarcodes


Tuesday, April 25, 2017

Tuesday reads

Happy DNA Day! Has been a little while since the last post but I have been busy with a lot of different tasks and working myself into new projects. Here is hope that things will go back to normal slowly. Lots of interesting reads today starting with two of my own.

The School Malaise Trap Program (SMTP) provides a technologically sophisticated and scientifically relevant educational experience that exposes students to the diversity of life, enhancing their understanding of biodiversity while promoting environmental stewardship. Since 2013, the SMTP has allowed 15,000 students at 350 primary and secondary schools to explore insect diversity in Canadian schoolyards. Students at each school collected hundreds of insects for an analysis of DNA sequence variation that enabled their rapid identification to a species. Through this hands-on approach, they participated in a learning exercise that conveys a real sense of scientific discovery. As well, the students contributed valuable data to the largest biodiversity genomics initiative ever undertaken: the International Barcode of Life project. To date, the SMTP has sequenced over 80,000 insect specimens, which includes representatives of 7,990 different species, nearly a tenth of the Canadian fauna. Both surprisingly and importantly, the collections generated the first DNA barcode records for 1,288 Canadian species.

To date the global initiative to barcode all fishes, FISH-BOL, has delivered barcodes for approximately 14,400 of the 30,000 fish species; there is still much to do to attain its ultimate goal of barcoding all the world’s fishes. One strategy to overcome local gaps is to initiate short but intensive efforts to collect and barcode as many species as possible from a small region – a barcode ‘blitz’. This study highlights one such event, for the marine waters around Lizard island in the Great Barrier Reef (Queensland, Australia). Barcode records were obtained from 983 fishes collected over a two-week period. The resulting dataset comprised 358 named species and another 13 species that presently can only be reliably identified to genus level. Overall, this short expedition provided DNA barcodes for 13% of all marine fish species known to occur in Queensland.

The difficulty of censusing marine animal populations hampers effective ocean management. Analyzing water for DNA traces shed by organisms may aid assessment. Here we tested aquatic environmental DNA (eDNA) as an indicator of fish presence in the lower Hudson River estuary. A checklist of local marine fish and their relative abundance was prepared by compiling 12 traditional surveys conducted between 1988–2015. To improve eDNA identification success, 31 specimens representing 18 marine fish species were sequenced for two mitochondrial gene regions, boosting coverage of the 12S eDNA target sequence to 80% of local taxa. We collected 76 one-liter shoreline surface water samples at two contrasting estuary locations over six months beginning in January 2016. eDNA was amplified with vertebrate-specific 12S primers. Bioinformatic analysis of amplified DNA, using a reference library of GenBank and our newly generated 12S sequences, detected most (81%) locally abundant or common species and relatively few (23%) uncommon taxa, and corresponded to seasonal presence and habitat preference as determined by traditional surveys. Approximately 2% of fish reads were commonly consumed species that are rare or absent in local waters, consistent with wastewater input. Freshwater species were rarely detected despite Hudson River inflow. These results support further exploration and suggest eDNA will facilitate fine-scale geographic and temporal mapping of marine fish populations at relatively low cost.

We report the discovery of a non-native gammarid, Gammarus fossarum (Koch, 1836) (Crustacea, Amphipoda), in UK rivers. Gammarus fossarum is a common freshwater gammarid in many parts of mainland Europe, but was previously considered absent from the UK. Gammarus fossarum was detected in a number of UK rivers following DNA metabarcoding of a mini-barcode region of the COI gene in macroinvertebrate kick samples, and environmental DNA (eDNA) from water and sediment samples. Subsequent morphological analysis and standard DNA barcoding showed that the species could be reliably identified and separated from Gammarus pulex (Linnaeus, 1758), the most dominant and widespread native freshwater gammarid in the UK. Our data demonstrate extensive geographical coverage of G. fossarum in the UK, spanning distant river catchments. At present there is no data to confirm the likely origin of G. fossarum’s introduction. Subsequent re-examination of historic archive material shows the species to have been present in the UK since at least 1964. This study is among the first to demonstrate the potential of eDNA metabarcoding for detection of new non-native species. 

Consumption of frog legs is increasing worldwide, with potentially dramatic effects for ecosystems. More and more functioning frog farms are reported to exist. However, due to the lack of reliable methods to distinguish farmed from wild-caught individuals, the origin of frogs in the international trade is often uncertain. Here, we present a new methodological approach to this problem. We investigated the isotopic composition of legally traded frog legs from suppliers in Vietnam and Indonesia. Muscle and bone tissue samples were examined for δ15N, δ13C, and δ18O stable isotope compositions, to elucidate the conditions under which the frogs grew up. We used DNA barcoding (16S rRNA) to verify species identities. We identified three traded species (Hoplobatrachus rugulosus, Fejervarya cancrivora and Limnonectes macrodon); species identities were partly deviating from package labeling. Isotopic values of δ15N and δ18O showed significant differences between species and country of origin. Based on low δ15N composition and generally little variation in stable isotope values, our results imply that frogs from Vietnam were indeed farmed. In contrast, the frogs from the Indonesian supplier likely grew up under natural conditions, indicated by higher δ15N values and stronger variability in the stable isotope composition. Our results indicate that stable isotope analyses seem to be a useful tool to distinguish between naturally growing and intensively farmed frogs. We believe that this method can be used to improve the control in the international trade of frog legs, as well as for other biological products, thus supporting farming activities and decreasing pressure on wild populations. However, we examined different species from different countries and had no access to samples of individuals with confirmed origin and living conditions. Therefore, we suggest improving this method further with individuals of known origin and history, preferably including samples of the respective nutritive bases.

Biological diversity is depleting at an alarming rate. Additionally, a vast amount of biodiversity still remains undiscovered. Taxonomy has been serving the purpose of describing, naming, and classifying species for more than 250 years. DNA taxonomy and barcoding have accelerated the rate of this process, thereby providing a tool for conservation practice. DNA barcoding and traditional taxonomy have their own inherent merits and demerits. The synergistic use of both methods, in the form of integrative taxonomy, has the potential to contribute to biodiversity conservation in a pragmatic timeframe and overcome their individual drawbacks. In this review, we discuss the basics of both these methods of biological identification- traditional taxonomy and DNA barcoding, the technical advances in integrative taxonomy, and future trends. We also present a comprehensive compilation of published examples of integrative taxonomy that refer to nine topics within biodiversity conservation. Morphological and molecular species limits were observed to be congruent in ~41% of the 58 source studies. The majority of the studies highlighted the description of cryptic diversity through the use of molecular data, whereas research areas like endemism, biological invasion, and threatened species were less discussed in the literature.

Effective vector and arbovirus surveillance requires timely and accurate screening techniques that can be easily upscaled. Next-generation sequencing (NGS) is a high-throughput technology that has the potential to modernise vector surveillance. When combined with DNA barcoding, it is termed 'metabarcoding'. The aim of our study was to establish a metabarcoding protocol to characterise pools of mosquitoes and screen them for virus. Pools contained 100 morphologically identified individuals, including one Ross River virus (RRV) infected mosquito, with three species present at different proportions: 1, 5, 94%. Nucleic acid extracted from both crude homogenate and supernatant was used to amplify a 269 bp section of the mitochondrial cytochrome c oxidase subunit I (COI) locus. Additionally, a 67 bp region of the RRV E2 gene was amplified from synthesised cDNA to screen for RRV. Amplicon sequencing was performed using an Illumina MiSeq, and bioinformatic analysis was performed using a DNA barcode database of Victorian mosquitoes. Metabarcoding successfully detected all mosquito species and RRV in every positive sample tested. The limits of species detection were also examined by screening a pool of 1000 individuals, successfully identifying the species and RRV from a single mosquito. The primers used for amplification, number of PCR cycles, and total number of individuals present all have effects on the quantification of species in mixed bulk samples. Based on the results, a number of recommendations for future metabarcoding studies are presented. Overall, metabarcoding shows great promise for providing a new alternative approach to screening large insect surveillance trap catches. 

The potential of DNA barcoding approaches to identify single species and characterize species compositions strongly depends on the marker choice. The prominent "Folmer region", a 648 basepair fragment at the 5' end of the mitochondrial CO1 gene, has been traditionally applied as a universal DNA barcoding region for metazoans. In order to find a suitable marker for biomonitoring odonates (dragonflies and damselflies), we here explore a new region of the CO1 gene (CO1B) for DNA barcoding in 51 populations of 23 dragonfly and damselfly species. We compare the "Folmer region", the mitochondrial ND1 gene (NADH dehydrogenase 1) and the new CO1 region with regard to (i) speed and reproducibility of sequence generation, (ii) levels of homoplasy and (iii) numbers of diagnostic characters for discriminating closely related sister taxa and populations. The performances of the gene regions regarding these criteria were quite different. Both, the amplification of CO1B and ND1 was highly reproducible and CO1B showed the highest potential for discriminating sister taxa at different taxonomic levels. In contrast, the amplification of the "Folmer region" using the universal primers was difficult and the third codon positions of this fragment have experienced nucleotide substitution saturation. Most important, exploring this new barcode region of the CO1 gene identified a higher discriminating power between closely related sister taxa. Together with the design of layered barcode approaches adapted to the specific taxonomic "environment", this new marker will further enhance the discrimination power at the species level.

Monday, April 24, 2017

From the inbox: Postdoc @ Kartzinel Lab at Brown

Position Title: Postdoctoral Research Associate in Environment and Society: Molecular Ecology/Conservation Biology

Location: Department of Ecology and Evolutionary Biology; Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA

Position Description: The Kartzinel Lab at Brown University is seeking a postdoctoral research associate in molecular ecology and conservation biology to collaborate on studies of the ecology and evolution of animal diets, especially in African savannas (http://www.kartzinellab.com/). The postdoctoral project will emphasize conceptual and analytical advances in our understanding of plant-herbivore, predator-prey, and/or host-microbe interaction networks using DNA- based analyses. These results will be placed in the context of manipulative field experiments, broad geographic gradients, and different land use histories in order to illuminate the biological processes that determine population and community dynamics in a changing world. The postdoc will have ample opportunities to integrate both field and lab-based research on wildlife in Kenya, and other potentially relevant field sites. The Department of Ecology and Evolutionary Biology and Institute at Brown for Environment and Society are home to a diverse community of scholars and world-class scientific resources.

Qualifications: The successful candidate will have a recent Ph.D. and relevant experience in molecular ecology, such as environmental DNA analysis, microbiome analyses, DNA (meta) barcoding, metagenomics, or related approaches. A strong interest in community ecology and conservation is required, and prior field experience is a plus. Responsibilities include: helping develop and coordinate laboratory and field research activities; data management; analysis of ecological and molecular data; publication of manuscripts and dissemination of results. Candidates should demonstrate strong communication skills and an ability to work both independently and collaboratively with groups from diverse backgrounds.

Applicants should submit: (1) a cover letter describing research interests, qualifications, and motivations, (2) a CV, and (3) contact information for three references. Applications will be reviewed starting May 12, 2017, and accepted until the position is filled. The ideal start date is September 2017, but flexible. The initial appointment will be for one year with an opportunity for extension based on satisfactory performance. Please contact Tyler Kartzinel directly with any questions.


Equal Employment Opportunity Statement: Brown University is committed to fostering a diverse and inclusive academic global community; as an EEO/AA employer, Brown considers applicants for employment without regard to, and does not discriminate on the basis of, gender, race, protected veteran status, disability, or any other legally protected status.

Tuesday, April 18, 2017

Metabarcoding and Metagenomics journal

Not too long ago I posted a call for participation at a questionnaire which solicited feedback and suggestions for a new open access journal focusing on metabarcoding and metagenomics. Today, just a few months later the journal out in the open and ready for submission:

Metabarcoding and Metagenomics (MBMG) is an innovative open access journal which facilitates the publication of articles on metabarcoding and metagenomics both in basic and applied context. The journal welcomes submissions representing all stages of the research cycle: data, models, methods, workflows, software, perspectives, opinions, and conventional research articles. The journal will consider manuscripts for publication related (but not limited) to the following topics: Environmental MBMG, Microbial MBMG, Applied MBMG (biomonitoring, quarantine, environmental assessment, nature conservation, eDNA, species invasions and others), and other emerging fields related to MBMG. Submissions of bioinformatic approaches to MBMG (algorithms, software) are also encouraged.

So, if you are currently working on a metabarcoding or metagenomics study and looking for a home for your publication you might want to consider this new option.


Thursday, April 13, 2017

FINAL CALL FOR ABSTRACTS

7th International Barcode of Life Conference, 20 – 24 November 2017 at Kruger National Park



**FINAL CALL FOR ABSTRACTS**

The African Centre for DNA Barcoding (ACDB), the University of  Johannesburg (UJ), International Barcode of Life Project (iBOL), and the Department of Environmental Affairs (DEA) are proud to announce and welcome delegates to our hosting of the 7th International Barcode of Life Conference, 20 – 24 November 2017. This is the first time that this event will be held on the African continent. The venue for the hosting of this prestigious event will be the Nombolo Mdhluli Conference Centre, 
Skukuza.

The major theme of the conference is exploring mega-diverse biotas with DNA barcodes. A series of presentations and workshops will focus on the use of DNA to understand diversity patterns and ecological processes in species-rich and complicated ecosystems. The conference also provides a 
general forum for presentations, posters, and discussion on the wider field of DNA barcoding.

Delegates are encouraged to register as soon as possible as space is limited.

Abstracts should be submitted here before or on 28th April 2017.

More information at:

Website: http://dnabarcodes2017.org
Facebook: @DNABarcodes2017
Twitter: @DNABarcodes