BIG4 News

The new release of the OpenBiodiv-LOD

Wed, 05 Jan 2022 11:09:00 +0200

A recently published article in the open-access Biodiversity Data Journal introduces the new release of the OpenBiodiv-LOD (Linked Open Dataset).

IGNITE and BIG4 researchers successfully created the new OpenBiodiv-LOD through information extraction and modelling of additional biodiversity entities. Furthermore, they made additional developments to OpenBiodiv-O ontology.

OpenBiodiv is a biodiversity knowledge graph that includes OpenBiodiv-LOD, a synthetic linked open dataset that integrates academic literature knowledge with the taxonomic backbone utilised by the Global Biodiversity Information Facility.

In this paper, researchers discuss how to utilise the LOD for biodiversity informatics use cases and give examples by providing solutions to several competency questions. They also investigate performance issues that arise due to the large amount of inferred statements in the graph and conclude that OWL-full inference is impractical for the project and that unnecessary inference should be avoided.

The authors envision OpenBiodiv-LOD as an integral part of the existing semantic network of biodiversity knowledge, based on HTTP identifiers and controlled vocabularies. By semantically enhancing and linking knowledge in OpenBiodiv to existing machine-readable data, biodiversity data quality and its potential for reuse are improved.

Photo: Information flows in the OpenBiodiv system. Red arrows show the workflows outlined in the paper. Two projects associated with the OpenBiodiv system are also shown: the Pensoft Annotator (Dimitrova et al. 2020) and a prototype workflow for generation of biodiversity nanopublications.

You can read the full article here.

Hall of FameLab

Fri, 22 Nov 2019 13:33:00 +0200

by Viktor Senderov, Marie-Sklodovska-Curie PhD Student in Artificial Intelligence and Bioinformatics, on Oct 27, 2019. Natural History Museum, London.

From left to right Tim Slingsby: Director of Skills and Education at Lloyd's Register Foundation, London; Christina Melidou: Partnership manager at FutureLearn, FameLab Greece participant 2008; Anne-Marie Imafidon MBE: Co-founder and CEO of Stemettes.

Yours truly, participated successfully in the science communication event boldly named Hall of FameLab that took place during European Researchers’ Night (a MSCA event) this Oct 27 at the Natural History Museum in London.

FameLab is a science communication competition organized annually since 2005 by the British Council in over 30 countries. Their challenge to the participants is: "Could you inspire and educate a live audience about your work in science, technology, maths or engineering – in just three minutes?"

The regional rounds take place in spring, and then the national winner goes on to participate at the international finals at the Cheltenham festival. I didn’t make it to Cheltenham, but even the participation in the national rounds was amazing as I discovered that I know how to inspire people about science.

Then, I was quite surprised to be selected for a special invitation-only FameLab event, Hall of FameLab, at the Natural History Museum in London. The motto of the event was "the collaborative work of scientists around the world is helping us to understand the interconnected nature of our planet and to conserve the web of natural connections that we depend on to survive." Lyubov Kostova and Ivaylo Slavov from the British Council thought that my work on computer languages and phylogenetics might be relevant to the topic. With the help of some props obtained from Costco’s (a pineapple), I was able to entertain the three judges (photo) and two hundred or so science-hungry museum goers. You can see it all here https://youtu.be/zDRCGTtqgXk.

My talk was about my childhood fascination with the shared ancestry of everything on the Planet. We are literally all relatives: humans and pineapples, even! The second idea of the talk was that language is one of the most powerful instruments that we, as scientists, have to reason about inter-connections. As an illustration, I present a computer language on which I am working, TreePPL.

I am grateful to the public for funding my research, which inevitably helps us, as Homo sapiens, understand our revolutionary place, even if this research has to do with other living organisms. Needless to say, my BIG4 experience in Pensoft shaped me as a scientist and a public speaker and I believe all current Marie-Curie fellows ought to engage in this or in some other form of science communication.

Our successful computational biologist Viktor Senderov shares a recipe for a thriving scientific career

Wed, 13 Nov 2019 17:00:00 +0200

Viktor Senderov, a young computational biologist, was distinguished by the national contact point for research programmes of the EU Net4Mobility+ for his work as a Marie Skłodowska-Curie PhD Candidate in Bioinformatics of the BIG4 Consortium. The BIG4 project is specialized in providing biosystematics, informatics and genomics training and workshops for young researchers. Recently, he also became the Bulgaria FameLab 2019 finalist, a global competition finding and supporting the world's most talented new science, technology, engineering and maths (STEM) communicators.

While working on his PhD, Viktor Senderov was a data scientist at Pensoft Publishers with the aim of building the Open Biodiversity Knowledge Management System (OpenBiodiv).

Today, he is working on cutting-edge phylogenomics modelling at the Ronquist lab in the Museum of Natural History, Stockholm. His work at Pensoft is now continued by Mariya Dimitrova.

"Taxonomists investigate the Planet’s biodiversity and publish their findings as research papers or monographs in peer-reviewed scientific literature. Access to these findings is difficult as a lot of papers have been published in the 18th and 19th centuries and have not been digitized. Biodiversity informaticians’ top priority in the last twenty years has been to create a unified system to access biodiversity data. Such a system will diminish the time they spend in manual archival work and will enable them to concentrate on ecological, conservation, and evolution questions", he elaborated.

Viktor Senderov explained that being part of ITN is beneficial for young researchers as they participate in the international exchange of ideas and get to extend their professional networks. The generous scholarship allowed him to go back to his home country and to simultaneously do science at an international level.

He recommended the ITN program to everybody but remarked that the enthusiastic scientists have to get well-acquainted in advance with the scientific and administrative aspects of their future project so that you have the right expectations. Especially if they have decided to do science in a widening country which is harder than in Western Europe but can be highly rewarding for people with high independence.

The mystery of insects is unveiled - now in six languages

Thu, 21 Mar 2019 15:21:00 +0200

BIG's Results in Brief are available in English, French, German, Italian, Polish and Spanish.

The project studied the four largest insect groups represented by beetles, bees, flies and butterflies and the services they could potentially provide by combining genomics, phylogenetics, informatics, taxonomy, semantic, biodiversity publishing and citizen science.

BIG4's valuable contribution to healthy ecosystems made it part of the Results in Pack on Biodiversity, published by CORDIS.

With regard to the future, project coordinator Prof Solodovnikov believes that "BIG4 broke the established bias of investigating bigger yet less abundant organisms. The cohort of trained young researchers, who will soon start their own research teams, will continue this legacy and invest in future insect research.″ BIG4 stressed the demand for resources to further tackle this hidden biological mega-diversity, to get a bigger picture of the living world and its functions.

Greetings from the 9th International Congress of Dipterology in Namibia

Mon, 11 Feb 2019 13:21:00 +0200

This article was written by Trevor O. Burt.

I am happy to report back from the 9^th International Congress of Dipterology (ICD9), which took place in November, 2018, in Windhoek, Namibia.The International Congress of Dipteralogy (ICD) is a meeting that brings together dipterists from all around the world every four years to present their scientific findings, discuss and debate the latest research projects, converse and collaborate with colleagues, and for students and scientists to develop new network branches in the Diptera community.

The 9th edition of the congress was dedicated to the launching of the first two of four volumes of the Manual of Afrotropical Diptera, which is a ground-breaking leap forward in the study of flies. The congress theme was centered on Afrotropical dipterology, though research from all regions was presented. Over 273 delegates and students from 51 countries from around the world were in attendance presenting 321 abstracts for oral or poster presentations, across 23 symposia.

I myself gave two presentations in the "Advances in Diptera phylogenomics" symposium. My first talk was titled "Is this the end of Syrphoidea? – Flower flies (Syrphidae) and big-headed flies (Pipunculidae) are not sister-groups." This talk served to present results from our paper (Pauli et al. 2018). My second talk was titled "Big Data, big challenges – resolving the phylogenetic relationships of the subfamily Syrphinae (Syrphidae) with target DNA enrichment." This one presented the early results of a long-term, collaborative Syrphidae of the World project using target enrichment techniques to generate large genomic data sets with the goal of generating phylogenetic trees to explore the subfamilial and genera-level relationships of hoverflies. This particular talk focused mainly on the genera-level relationships of the subfamily Syrphinae.

Trevor Burt (left) and Dr. Jens-Hermann Stuke (right)

Overall, the congress was a great success and yielded many opportunities for future collaborative projects. The many symposia were extremely varied, ranging from taxonomy, phylogenomics, to medical and forensic dipterology, to pollination and ecology studies. This variety gave delegates and students alike a good sense of research undertaken by scientists from around the world and a chance to converse directly with presenters.

The ICD9 experience was scientifically incredibly satisfying. The people I met and talked to, and the relationships I was able to develop were invaluable.

Hard work is being acknowledged

Wed, 06 Feb 2019 13:09:00 +0200

We are happy to announce that Anne-Sarah Ganske received a grant from the "Network of Biological Systematics Austria" (NOBIS Austria) for her research entitled "Lithobius - A big genus in a small subphylum: phylogeny and evolutionary history", which she carried out within the BIG4 project. NOBIS Austria is a network for scientists working in the broad field of biological systematics – on evolutionary research, phylogeny and taxonomy – theoretically, philosophically and pragmatically.
Anne-Sarah presented and discussed first results of her PhD-project at the NOBIS Annual Meeting, held on 22-23 November 2018 in the Museum of Nature South Tyrol in Bolzano. Congratulations!

Dr. Elisabeth Haring (left) and Dr. Sabine Agatha (right) with NOBIS-fellowship holder Anne-Sarah Ganske (center).

When dreams come true

Wed, 02 Jan 2019 10:40:00 +0200

The New Year 2019 has just begun! In this year, BIG4’s training network will formally not exist anymore. The generous EU Horizon 2020 ITN grant, awarded to us in 2015, was completed on December 31^st 2018. There are still some important reporting activities ahead and many project-bound students continue to work on the projects, but technically the grant is over.

As the BIG4 coordinator, I have to admit I am a bit sad about this. We had really fun years with 15 early stage researchers and several scientific advisors from universities, natural history museums and three international companies working together. It was an opportunity we are very thankful for, and glad to report about.

A few weeks ago, Si-Pei defended her PhD thesis on adaptations to various modes of flight in insects. Si-Pei, you are our first student with the PhD diploma already in your hands and we are very proud of you! Josh, Janina, Trevor and Viktor are also pretty much done with their theses and awaiting the PhD defense soon. Igor must hand in his thesis in one month. What a busy and responsible start of the year, for you, Igor! Adam, who joined the network for one year, soon landed a competitive position as a researcher and curator at the Canadian National Collection of Insects and Arthropods, and Ashish now works in India on data visualisations. Other students enrolled later or having longer PhD programs, still have months to work on their projects based on collateral agreements and co-funds from their universities. Following the progress of these lucky fellows with more time available, I am sure that Elsa, Hamid, Erik, Miroslav, Daniel, Emmanuel, Mathias and Anne-Sarah, you all will do fine, even though your projects are challenging.

As always in science and technology, there is some time lag before one can harvest results. Ideas that were brewed during BIG4 will continue to materialise as papers or applications for years after the network is finished. Still, I am proud to see a long list of peer review papers we already published – check out our ‘Publications’.

Miroslav produced not only papers during BIG4, but a baby as well. Well done, Miroslav, and enjoy your paternity leave, something nice to have as an EU program-bound student! I hope others will follow your work-life balance approach – entomologists must grow in numbers to keep up with the mega-diversity of insects that our network has as a target.

Speaking of the opportunities and benefits the network gave us, I must say that sometimes it was difficult to read EU grant rules and regulations, or deal with the Participant Portal. However, the University of Copenhagen coordinator’s support office always saved when we had doubts or (nearly) missed deadlines. Thanks to Sree, Karin and Fabienne it was seldom when Patricia E. Rischitor, our Brussels-bound project adviser, had to give us a notch. When you, Patricia, did so, we always smoothly moved forward.

And now, even though our network is formally completed, we still go together as a community. I am glad to see continuing interactions among students and PIs, and long lasting friendships. BIG4 made one of my dreams come true!

I wish all of you, BIG4-bound researchers, to dream big and move our science about insect mega-diversity forward in 2019 and onwards. Happy New Year!

Alexey Solodovnikov, BIG4 scientific coordinator

BLOG POST: OpenBiodiv: The Semantic Web comes to biodiversity informatics

Tue, 25 Sep 2018 10:11:00 +0300

This post was written by Viktor Senderov.

The Semantic Web is a vision for the future of the web where not only documents but also data are connected. As part of the Semantic Web, the goal of the Pensoft-based OpenBiodiv project is to create a system for management of biodiversity knowledge extracted from scientific articles and shared as Linked Open Data. The system consists of our ontology OpenBiodiv-O, a knowledge graph, the RDF4R package and related source-code, and a front-end user interface available at http://openbiodiv.net.

First of all, it is useful to understand the term knowledge management system both by looking at some explicit definitions and by looking at several examples in practice. Variations of the term were already widely discussed by the 1980's and early nineties and were understood to mean the utilization of ideas from both database management systems (DBMS) and artificial intelligence (AI) to create a type of computer system called knowledge base management system (KBMS). Knowledge-bases differ from traditional databases in the fact that they contain "prestored rules and facts from which useful inferences and conclusions may be drawn by an inference engine." In other words, using a knowledge-base, it is not only possible to retrieve and filter information stored in a database, but it is also possible to obtain facts that have been inferred (logically deduced) from what is already stated in the knowledge-base. For example, using FactForge one can find all airports in a given radius around London. More examples of modern knowledge-bases include Freebase, which recently migrated to WikiData, DBPedia, and what most people have seen without realizing the mechanism behind it: the infoboxes that appear next to Google searches.

There has also been progress in incorporating statistical techniques into databases and representing knowledge under uncertainty. In such probabilistic databases, new knowledge is not logically deduced but is rather inferred under uncertainty with techniques from Bayesian statistics. However, the architecture chosen for the OpenBiodiv project is one of a classical rule-based knowledge-base.

Modern knowledge-based systems also incorporate Linked Open Data (LOD) principles to emphasize the community aspects of knowledge sharing and to make data more interconnected and reusable. Tim Berners-Lee, the creator of the World Wide Web writes that similar to how the hypertext web functions, "with linked data, when you have some of it, you can find other, related, data."

OpenBiodiv’s store rises up to the challenge of LOD by interlinking data from three sources: more than 5000 biodiversity-related articles published in Pensoft’s journals, data extracted from legacy literature provided by from Plazi, and the Global Biodiversity Information Facility (GBIF). In order to illustrate the capabilities of OpenBiodiv and draw attention to the impact of the tragically lost collection of the Museu Nacional de Rio de Janeiro (MNRJ), I can ask our system to give me the number of times a specimen from that collection was used in a taxonomic article, and in which ones. It turns out that MNRJ has been mentioned 195 times in our system in a total of 22 articles published by Pensoft. Perhaps more interestingly, we can see specimens of which taxa may have been lost. Examples include the insects (Xestoblatta, Charinus, Lamproclasiopa, etc.), nematode worms (Paracamallanus, Cucullanus, Pseudascarophis, etc.), birds (Ichthyouris), fish (Sphoeroides), and many others for a total of 6,127 distinct names mentioned in taxonomic articles whose materials methods include MNRJ. I believe a similar analysis may prove helpful in the effort to rebuild MNRJ’s collection by highlighting what may have been lost and giving access to the primary literature describing the lost species. Imagine what detailed inventory we could have build if OpenBiodiv contained knowledge extracted from all taxonomic literature!

It is hard for me in such a short format to describe all of the results of OpenBiodiv. Perhaps the reader is well advised to look directly at the text of my dissertation, which I develop in open access, for a full treatment and at the system itself at http://openbiodiv.net. Nevertheless, I would like to highlight the tool-development work that I have been doing as part of the OpenBiodiv. The knowledge graph is stored as a GraphDB triple store, whereas the input data comes in the form of XML files published by Pensoft and Plazi and a huge CSV file in the case of GBIF’s taxonomic backbone. In order to convert XML to RDF I wrote an R library called RDF4R, whose usage is described in a vignette. During the development process I learnt a lot about free and open source software development and how frustrating and fun it can be at the same time. Perhaps the fun part is best illustrated by a feature of the library called query_factory. It is a functional-programming inspired widget that "magically" transforms a given input SPARQL query s and a given SPARQL access point a into an R function f. f’s invokation executes the query s parameterized by f’s arguments on the access point a. However, neither the query nor the access point are arguments of f itself! The "magic" becomes apparent when one understands functions as closures, i.e. an execution sequence and an execution environment—the query and access point are enclosed in f from its parent query_factory.

I think it must have become clear so far that thanks to the programming I did as a part of BIG4 I became even more of a geek that I had been. It cemented my desire to look for a career combining science and programming in the future. This blog post came so late (amongst other reasons) as I just submitted a Marie Skłodowska Curie individual fellowship to do a postdoc in probabilistic programming for phylogenetics at a BIG4 project partner: the Ronquist lab at the Swedish Natural History Museum in Stockholm. BIG4 is responsible for not only this great connection but also many other professional and personal friendships that I made. Certainly, I am indebted for life to the friendly and professional people at Pensoft, and in particular to my advisor Lyubomir Penev, as well as Kiril Simov, and hope to maintain my connection to the project who will from now on be lead by Pensoft’s new Ph.D. student, Maria Dimitrova.

Publications within Viktor's project:

Senderov, Viktor et al. 2018. "OpenBiodiv-O: Ontology of the OpenBiodiv Knowledge Management System." Journal of Biomedical Semantics 9(1). https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0174-5 (February 13, 2018).
Senderov, Viktor, and Lyubomir Penev. 2016. "The Open Biodiversity Knowledge Management System in Scholarly Publishing." Research Ideas and Outcomes 2: e7757. http://rio.pensoft.net/articles.php?id=7757 (July 22, 2017).
Cardoso, Pedro et al. 2016. "Species Conservation Profiles Compliant with the IUCN Red List of Threatened Species." Biodiversity Data Journal 4: e10356. http://bdj.pensoft.net/articles.php?id=10356 (March 15, 2018).
Senderov, Viktor, Teodor Georgiev, and Lyubomir Penev. 2016. "Online Direct Import of Specimen Records into Manuscripts and Automatic Creation of Data Papers from Biological Databases." Research Ideas and Outcomes2: e10617. http://rio.pensoft.net/articles.php?id=10617 (March 15, 2018).

BLOG POST: Taking the right steps is good, showing the path to others is even better

Mon, 17 Sep 2018 12:16:00 +0300

This post was written by Miroslav Valan.

Human impact on nature causes insects to die out and disappear at a faster pace than they can be studied. Any survey on biodiversity requires expertise, but those who may help with identifications - taxonomists - are always in shortage. Thanks to new technologies in computer vision and machine learning, which could automatically interpret objects captured in the images, and together with the members of the general public we could finally start making bigger steps towards saving our planet.

In my thesis titled "Accelerating taxonomic research using image analyses and citizen science contribution", I firstly focused on a project aimed to provide a reliable of-the-shelf tool for taxon delimitation and/or taxon identification. This tool could be used by any expert or non-expert for taxa of interest, without the need for knowing underlying machine learning algorithms. This work is under review.

The knowledge I gained while working on aforementioned tool is widely applicable. That motivated me to take part in Datathon 2018 together with another BIG4 fellow Viktor Senderov, where we won the 1st place in computer vision and the 2nd overall on a task to build up an image recognition that reliably recognises which type of vegetable the customer has selected. Besides, I won the 3rd place on a challenge Fungi2018 from the workshop organized by Google and Microsoft, the FGVC5 (The Fifth Workshop on Fine-Grained Visual Categorization). Here, the goal was to build an automated taxon identification tool for nearly 1,500 wild mushrooms species, which have been spotted and photographed by the general public in Denmark.

The second part of my PhD is focused on citizen science. For this reason I initiated the Nyckelpigeforsoket2018 (Ladybird research 2018), which has two main goals (1) to educate the target group - school pupils - about AI and ladybirds and (2) to build a tool for automated identification of the ladybirds occuring in Sweden.

Over 15 000 pupils across Sweden and others interested to participate are contributing by taking pictures of one of our most popular insects - ladybirds. This project would not be possible without the help from Vetenskap & Allmänhet, Naturhistoriska riksmuseet, Entomological Society Stockholm and Savantic AB. The project is ongoing, so If you would like to contribute just download the Nyckelpigeforsoket2018 app, available for download in the App Store and on Google Play. You can also learn how to "catch a ladybird like a pro" from this short video done by Swedish National Television (in Swedish, starts at 1:04).

It has been pleasure to be part of such a great group such as BIG4 (actually, we students refer to it BIG4-ever). I was honored and excited from the moment I was chosen for the interview with one of the most cited scientists in the 21st century who eventually became my supervisor. The excitement never ended.

In the light of many positive outcomes, being a BIG4 fellow at Savantic AB is something that I appreciate the most. This enabled me to enter the field of machine learning during the exciting era (I knew nothing about it beforehand) and helped me to get a higher understanding of what is within reach with the technological advancements and what limitations should be surpassed to unlock new possibilities. This fellowship enabled me to develop a set of skills which made me feel ready for upcoming challenges and made me lose all the fears for ever being unemployed. In addition to conferences and symposia that allowed me to listen to, learn from, connect and discuss with prominent scientist, I am immensely indebted to all of those small, everyday scientific discussions with more than 20 PhD students that worked and mainly still work at Savantic (I am the only non-PhD at Savantic, but not for long *laugh*). I truly believe I could not benefit more from any other host.

BLOG POST: Investigating the mysteries of gall-wasps biology

Thu, 13 Sep 2018 10:43:00 +0300

This post was written by Erik Gobbo.

Among gall-making insects, the Cynipidae (gall-wasps) are probably the most fascinating, for many reasons: they are capable of inducing extremely complex galls that often constitute a small ecosystem of their own, they are extremely diverse (counting more than 1300 known species) and most importantly, the nature of their gall-induction process still eludes our understanding. Although it is still unclear how such biological complexity evolved, the most recent molecular phylogenies suggest that the family has been subjected to several independent transitions affecting their life-cycle.

The main focus of my research is to identify the genetic elements responsible for such evolutionary events in the hope that they will shed some light on the molecular mechanism of gall-making. In order to achieve this goal, I focus on the analysis of the genome of closely related species showing major differences on their gall phenotype. My main model is the Japanese species Synergus itoensis.

All members of the extremely species-rich genus Synergus were believed to be inquiline wasps, which means they make their gall from the gall of another wasp (the primary gall-inducer), and are seemingly unable to initiate one on their own. However, S. itoensis has been demonstrated to be a true gall inducer, meaning it probably became capable of initiating the gall formation relatively recently in evolutionary terms. I therefore traveled to Japan and collected some specimens of this insect and of its closely related species S. gifuensis, an inquiline. I then sequenced their genomes and compared the orthologous genes of the gall-inducer to those of S. gifuensis and the other two species for which a genome was available, S. japponicus and S. umbraculus. The underlying assumption is that those genes that are responsible for gall initiation would show evidence of recent positive selection on S. itoensis but not on the inquilines.

Surprisingly, despite the fact that a transition from an inquiline to a gall-inducing biology is often regarded as a major evolutionary event, I found so far no significant difference between the coding sequences of the two categories: standard analysis have not revealed any special selective pressure on the branch were the different life cycle emerged. It would appear that the transition relies on very few genetic changes and can therefore occur easily and smoothly.

However, a pattern emerged once I repeated the analysis with a more elaborate tool that was being developed by a collaborator (as a matter of fact, my dataset was used to test the new program). I can now see that the number of genes that are showing traces of positive selection on the gall inducer is slightly but significantly bigger compared to the other species (on a side note, because of a bug in the first version of the program, I originally concluded that there was no difference). Although more elaborate analysis are needed to confirm the validity of the method, these findings might provide some insight on the genetic of gall induction.

My work was possible thanks to the BIG4 network: since I was trained as a molecular biologist, I had nearly no experience about field work. All the other members of the network have a completely different background, most of them being morphologists. Comparing ideas and points of view has been an invaluable asset. Moreover, most of my research is done at the informatics level rather than in the lab, but thanks to the many BIG4 workshops and a two-month secondment at our expert partners at the University of Edinburgh, I received all the training that I needed. The skills that I learned will surely prove useful regardless of what kind of research I will work on in the future.

BLOG POST: Can we resolve the evolutionary relationships of the world’s largest animal family? - Challenge accepted!

Mon, 10 Sep 2018 17:41:00 +0300

This post was written by Janina Lisa Kypke.

You might be wondering what animals am I talking about and how large is the largest animal family? Meet the rove beetles or Staphylinidae!

If you have never heard of them, here are the cornerstone facts:
- Rove beetles consist of more than 63.137 fossil and living species. This is the last official number published in 2017, which means it is already outdated by now since more species are being described every year.
- Rove beetles can be found on every continent except Antarctica, their preferred habitat is shady and moist as can be found e.g. in leaf litter, at shores or in the dung. They vary in size and can be as small as only 0.5 mm and up to 5 cm long.
- Most of the rove beetles are easily identifiable because their hind wings are shortened and wings are folded underneath. This makes them much more flexible and faster than other beetles and might be why they are such efficient and numerous predators.

The best way to understand evolutionary relationships amongst organisms is to reconstruct their phylogenetic tree. This can be done either by comparing the beetles and using morphological characters or by analyzing their genetic material. Since both methods have their own benefits and flaws, ideally, both data sources should be combined. Additionally, it helps to add fossils to the analysis: 1) because they might bear unknown ancestral characters or show transitional states between lineages that exist today and 2) because if we know their age we can use it to date the phylogeny.

Oh, and Jurassic Park was wrong. Unfortunately we are not able to extract DNA from fossils, not even from comparatively young amber fossils. Sorry to burst that bubble, I know it would have been amazing.

At this point I am very happy to tell you that the first Staphylinid phylogeny based on (mostly) genomic data is about to be finished. This work was done in a collaborative effort with members of the 1KITE team, CSIRO, and the Bioinformatics Institute in St Petersburg where we managed to obtain close to 4000 genes for 33 transcriptomes and genomes across all Staphylinoidea. More taxa with fewer genes that have already been published are added to have a more complete representation of the group.

Getting these results is super exciting since they will shed light on the higher-level relationships amongst the subfamilies and groups of subfamilies. Among the answers I am hoping to find are for example whether there are indeed four distinct groups of subfamilies as morphology suggests or which subfamilies are the oldest/ youngest from an evolutionary point of view. These results can help us to begin to understand how this family of beetles could become so large and omnipresent and successful.

Rove beetle amber fossil with corresponding line drawing and its placement in a phylogenetic tree

During my research I was able to expand my background in ecology not only to bioinformatics for phylogenomics but I also had the chance to study amber fossils both using traditional light microscopy as well as X-ray computed microtomography (µCT) and I described my first species!

BIG4 have undoubtedly expanded my scientific and private network. During the meetings we were able to freely discuss our research, share ideas and make plans for the future. Since the network is interdisciplinary, I got the chance to expand my knowledge not only in my field of research but also beyond. I am very grateful to have been part of the BIG4 and cannot wait to see how we will continue to shape the future.

Publications within Janina's project:

J.L. Kypke, A. Solodovnikov, A. Brunke, S. Yamamoto, D. Zyla (2018) The past and the present through phylogenetic analysis: the rove beetle tribe Othiini now and 99 Ma, Systematic Entomology. DOI:10.1111/syen.12305.
First phylogeny for Staphylinidae based on genomic data. (In preparation)
X-ray µ-CT helps to identify first fossil Orsunius sp. in Baltic amber. (In preparation)
Baltic amber fossils reveal an ancient connection between disjunct distribution of recent species. (In preparation)

BLOG POST: Visual exploration of taxonomic, phylogenomic and biodiversity data

Mon, 03 Sep 2018 11:33:00 +0300

This post was written by Ashish Tomar.

A tree or hierarchical representation of data is commonly observed in biology. This is due to interlinked information, and the complex hierarchical nature of biological systems. Advanced data visualization in scientific communities is becoming a trend to help researchers discover hidden pattern in such systems.

The aim of my project was to create novel, innovative and interactive visualization of hierarchical data in biology. My work depends heavily on JavaScript and D3.js library, which allow document data manipulation and help create powerful visualization. D3.js gives a layout for hierarchical data visualization, providing functionality to create multiple types space filling and node link diagrams.

During my secondments to the Natural History Museums in Stockholm and Copenhagen, BIG4 supervisors Fredrik and Alexey helped me narrow down exact biological problems that could be addressed through visualization. The main outcome of my project is the Danish Beetle Atlas visual interface and Taxonomy tree editor web application. The Danish Beetle Atlas is a visualization rich project as the beetle occurrence data are very rich and have multiple dimensions to get visual insight.

The taxonomy tree editor application is the most interesting work as currently there is no tool that can help researchers edit and compare two taxonomies. It is also the most challenging work as large taxonomy data files are heavy to handle on client side. An interesting feature is that the user can "drag and drop" a node from a reference taxonomy to working taxonomy.

Figure 1: Visual interface for "Danish beetle Atlas" project

Figure 2: Taxonomy Editor for visual editing of taxonomy trees in the web browser

Description of my additional visualization projects:

Phylogenomics tree visualization library: A JavaScript library using D3.js for integrative visualization of phylogenetic tree along with metadata in web browser.
Metagenomics visualization: A hierarchical data visualization prototype web application to help the user to view multiple data samples with synchronous interaction.
Geo-coordinates spatial data visualization: A web app to map biodiversity geo-coordinates to the geographical location.
Metabarcoding visualization: A prototype visualization for comparative analysis of multiple metabarcoding data.

I am glad to be part of such an amazing group, which is working in basic biology to advance data science. This project helped me explore the visual dimension of biology. It also made me realize how important biodiversity and ecology is for our planet and what we can do using the advancement of technology. I recently developed a hobby of taking photos of wild flowering plants and love for butterflies.

I would like to thank all people from BIG4 for the wonderful discussions and for helping me out in difficult situations. I would also like to thank EU Horizon2020 for supporting this project and providing a research environment where a researcher can pursue their passion and contribute to the betterment of society.

All the codes are available at github and big4-project gitlab repository.

BLOG POST: Butterfly and Moth Diversification Dynamics

Thu, 30 Aug 2018 09:48:00 +0300

This post was written by Hamid Reza Ghanavi.

Lepidoptera (i.e. moths and butterflies) is one of the four most diverse orders of organisms - BIG4 - on earth. Despite a wide variety of research being undertaken, there is still a lot to discover about them. Scientists are discovering new species, studying ecosystem interactions, and the list goes on.

I am interested in addressing questions such as: How are they related? When did a particular species appear or go extinct? What was the speed of these processes in different periods? When were particular areas colonized?

To answer these questions, I first need to receive samples from all over the world. I then need to obtain the genetic information of a few genes and combine it with available data to construct a phylogeny of the group. I use the resulting tree to study the evolution of different branches through time. Using statistical models, I estimate the diversity of the study group at different time periods. And finally, I try to answer the question: is it possible to see the effect of mass extinctions in the history of this group? During this process I will hopefully be able to answer some of my questions, but I also expect a lot of new questions to arise.

So far, my main focus has been on the time calibrated phylogeny of the Geometrid moth family. This group of moths is one of the most diverse families within Lepidoptera, but very little has been done to resolve their phylogeny. To obtain a good time-calibrated phylogeny and study the diversification dynamics of this family, some additional challenges exist, for example the sampling bias. It is normally a lot easier to obtain samples from developed countries, as the fauna here is usually better studied. Due to this bias, the diversity present in the developing countries is usually under-sampled and underestimated. This occurs because of the cost associated with sampling at these locations and the lack of local specialists. Nevertheless, in order to better understand global questions, we really need better global sampling.

Due to our networks of partners around the world, we have been able to obtain samples from hard to access locations. Our dataset, is the largest obtained for this family, consisting of 1200 samples and covering around 5% of the groups diversity. It is also the best dataset in terms of sampling homogeneity of the global diversity of the family. So, stay tuned to hear a lot of exciting results about diversification of the group in a few months!

Being an evolutionary biologist BIG4 project opened my eyes to all the interesting possibilities the amazing world of insects offer us to study different evolutionary questions. Apart from the very interesting scientific value of this experience I discovered a small community where we all became very good friends. This priceless network enriches both professional and personal development of all of us which hopefully will result in more and better future collaborations.

My next steps will be to perform similar analyses with other families of Lepidoptera, so we can compare the diversification patterns, allowing us to get a broader idea of evolutionary paths butterflies and moths followed to reach the diversity we see today.

Apart from the analytical and biologically interesting results that we obtain in this project, we are also working on the development of new methods to overcome one of the biggest challenges we usually encounter in similar studies: high costs of obtaining big amounts of genetic data for large numbers of samples. The new methods we have designed can be used by many other groups to produce genetic information without any major first investment, i.e. using their normal molecular lab material. This also can help to avoid new samplings as old DNA extracts and small amount of them will also be enough to produce the amount of information we are interested in.

So next time you see a nice butterfly or moth, why not stop and ponder where it has come from, in terms of evolutionary history, diversity and challenges they have overcome.

BLOG POST: An integrative approach helps us understand the phylogeny of a challenging centipede taxon

Mon, 27 Aug 2018 15:52:00 +0300

This post was written by Anne-Sarah Ganske.

The main goal of our BIG4 project is to shed light on the phylogeny of the species-rich genus Lithobius Leach, 1814, which belongs to the centipedes (Myriapoda). On the pursuit of this mission, we are searching for new morphological characters and acquiring molecular data from representatives of the genus Lithobius and other Lithobiidae mainly from the European continent.

One achievement in this project is the generation of a morphological character matrix with information from an existing set of characters and new information based on scanning electron microscopic data obtained from mouth parts of the centipedes. The first step towards obtaining this information, was the dissection of the mouth parts from the head of the animal. The structures are tiny, measuring just some hundred micrometers, and calm hands were essential to handle the samples before observing them with the microscope. Afterwards, the comparison and evaluation of the structures between the examined species was the next step to describe new characters and establish a matrix for following phylogenetic analyses. Preliminary analyses of the morphological matrix are at hand and provide a first overview on the species interrelationships of the genus resolving it non-monophyletic.

A second milestone is the acquisition of sequence data of four genes from freshly collected centipede material (e.g. from excursions in Carinthia, Austria and La Palma, Spain). During a five-week long research stay in the Zoological Museum at the University of Turku (Finland), I learned how to extract DNA from centipedes, how to compile polymerase chain reactions for gene amplification, how to edit and align the obtained sequences and how to analyze those molecular data sets. The acquisition of sequences continued at the University of Vienna (Department of Integrative Zoology) and is now finished. The analysis of the molecular data sets is ongoing, also in combination with the morphological data mentioned earlier.

Collecting centipedes together with Dr. László Dányi from the Hungarian Natural History Museum Budapest during a field trip in Carinthia, Austria.

Besides the pure research, the popular science and outreach aspect were also present. That is why I participated in a photo competition called "My research in one picture" at the University of Vienna, Austria. It was requested to present my research in one image together with an abstract of my work. Honestly, it was a challenging experience to extract data and make it accessible to the broader audience. The result was rewarding as my image was among the ten finalists. Furthermore, some of the SEM-images inspired us to write an article in the popular magazine UNIVERSUM (in press) showcasing that images taken for scientific purposes may fringe broader aspects and even art.

Presenting the SEM-image for "My research in one picture" at the University of Vienna, Austria

BIG4 enabled me to participate in international meetings and organize workshops, which made me realise that research is sustainable. It also enabled me to develop nice collaborations, which will hopefully continue after the project. I worked in stimulating scientific environments with experts in the field of centipede research and learned new methods and strengthened my methodological skills.

BIG4 also made it possible for me to dive into different biological fields like taxonomy, systematics, phylogeny, morphology, evolutionary and molecular biology and to combine those in different aspects. During these international meetings and events, I took the chance to compete with my peer colleagues from other institutes and was honored with a poster prize during the International Congress of Myriapodology in Thailand and the "Carl-von-Schreibers-Forschungspreis" (neugier!wissen!schafft!) for the best poster at the NHM-Vienna. Lately, I was awarded with a research grant from the Network of Biological Systematics Austria (NOBIS).

My supervisor Dr. Nesrine Akkari and me at the International Congress of Myriapodology in Krabi, Thailand.

Publications within the project:

Ganske A-S, Edgecombe GD, Akkari N (2018). The peristomatic structures as a source of systematic characters in the genus Lithobius Leach, 1814 (Myriapoda, Chilopoda). In: Stoev P, Edgecombe GD (Eds) Proceedings of the 17th International Congress of Myriapodology, Krabi, Thailand. ZooKeys 741: 49-75. https://doi.org/10.3897/zookeys.741.21706
Akkari N, Ganske A-S (2018). Two centipedes new to the fauna of La Palma (Canary Islands, Spain) and notes on the Lithobiomorpha of the island (Chilopoda, Myriapoda). Biodiversity Data Journal 6: e26746. https://doi.org/10.3897/BDJ.6.e26746
Akkari N, Ganske A-S, Komerički A, Metscher B (2018). New avatars for Myriapods: Complete 3D morphology of type specimens transcends conventional species description (Myriapoda, Chilopoda). PLOS ONE 13(7): e0200158. https://doi.org/10.1371/journal.pone.0200158
Ganske A-S, Akkari N (in press). Auf der Schwelle zur Kunst – wie wissenschaftliche Bildgebung versteckte Schönheiten offenbart. UNIVERSUM Magazin, Das Naturhistorische, Krems/Wien, Austria.

BLOG POST: Building from the ground up – towards a classification of the rove beetle subtribe Amblyopinina

Thu, 23 Aug 2018 09:48:00 +0300

This article was written by Josh Jenkins Shaw.

The rove beetle subtribe Amblyopinina is a signature group of about 400 species in the southern hemisphere with major species diversity in Australia, New Guinea, New Zealand, New Caledonia and South America. Most Amblyopinines are free-living rove beetles, which can be found in leaf litter and other decaying materials. About 65 species are adapted to live in the fur and burrows of mammals where they are predators on mammal ectoparasites such as fleas. Despite being an important component of the southern hemisphere biodiversity, having an interesting transcontinental distribution and expressing a unique relationship with mammals, the group has never been thoroughly explored in a phylogenetic context.

Looking for beetles in sifted leaf litter in Queensland, Australia with Dr. Alexey Solodovnikov and Aslak Hansen.

The major goals of my PhD based at the Natural History Museum of Denmark and the University of Copenhagen are to taxonomically revise the subtribe at the generic level, to reconstruct the first phylogeny of the subtribe based on morphological and molecular data and to taxonomically revise the Amblyopinine fauna of Lord Howe Island. The taxonomic and phylogenetic research I am undertaking is the first step towards making Amblyopinines a model group for studies in evolutionary biology, biogeography and other fields of natural science. With morphological and molecular data now in place, recent developments have been the construction of the first phylogenetic trees, which show several interesting things, which will be published in due course.

For me, one of the most rewarding and educational aspects of my PhD research has been the opportunity to visit the places where Amblyopinines and other organisms live. In early 2017, I spent 2 weeks on Lord Howe Island, an oceanic island in the Tasman Sea 780km North-east of Sydney and 2 weeks in the rainforests of Queensland.

Looking out over the Northern part of Lord Howe Island

On both occasions the focus was collecting beetles for molecular and taxonomic work, however being immersed in the environment and biodiversity allowed me to develop a much stronger understanding of where the beetles live and some of the issues facing the environment and biodiversity more broadly. Such experiences have also been essential for generating ideas and hypotheses on current and future research projects.

BIG4 allowed me to meet and learn from both early career researchers and established scientists. The workshops, formal and informal discussions enabled the exchange of ideas and the development of collaborative research. BIG4 helped me learn about future career opportunities outside academia. I will utilize the amazing source of knowledge that BIG4 gave me for the rest of my scientific career.

Publications within this project:

Jenkins Shaw, J & Solodovnikov, A. 2016. Systematic and biogeographic review of the Staphylinini rove beetles of Lord Howe Island with description of new species and taxonomic changes (Coleoptera: Staphylinidae). ZooKeys 638: 1-25. DOI: https://doi.org/10.3897/zookeys.638.10883
Solodovnikov, A & Jenkins Shaw, J. 2016. Remarkable Australian rove beetle genus Myotyphlus: its cryptic diversity and significance for exploring mutualism among insects and mammals (Coleoptera: Staphylinidae: Staphylininae). Austral Entomology 56: 311-321. DOI: https://doi.org/10.1111/aen.12233
Jenkins Shaw, J., Żyła, D. & Solodovnikov, A. 2017. A spectacular new genus of Staphylinini rove beetle from the Tropical Andes and its phylogenetic assessment (Coleoptera: Staphylinidae). Invertebrate Systematics 31 (6): 713-722. DOI: https://doi.org/10.1071/IS17020

BLOG POST: Evolution of leaf-litter insect fauna as a bioindicator of evolutionary change

Mon, 20 Aug 2018 09:59:00 +0300

This post was written by Matthias Seidel.

In my project I investigate the systematics, phylogenetics and biogeography of terrestrial water beetles across the Southern Hemisphere. This relict group of beetles is called Cylominae and it is restricted to New Zealand, Australia, South Africa, Chile and Peru. In our fieldwork in New Zealand and South Africa we discovered many new species and genera that will result in several publications.

We described the new South African genus and species Relictorygmus trevornoahi, the only genus of the subfamily in Africa. We also explored the biology of the flower visiting water beetle Rygmodus. Our results revealed that beetles are pollen feeding with larvae that live in aquatic habitat, a combination that is absolutely unique for water beetles. After finishing all the molecular work, we will reconstruct the migratory and vicariant events that shaped the diversity of this Gondwanan group.

With the fieldwork in New Zealand and South Africa I was able to experience the habitats of my beetles as well as the culture of the countries. BIG4 inspired me to continue working in taxonomy and phylogenetics and showed me that this basic science offers great career opportunities.

To get a more detailed view on short-term evolutionary change of Southern hemisphere beetles we started a project in cooperation with the BIG4 student Daniel Marquina and biogeographer Dr. Isabel Sanmartin. We focused on the evolution and its biogeographic implications of leaf litter beetles across North and South Island in New Zealand. New Zealand is famous for its endemism and landscape diversity that has resulted in the evolution of some enigmatic animals such as the kiwi. Since research on beetles, especially the leaf litter communities, is scarce it perfectly suits our purpose and might result in much deeper understanding of the evolutionary drivers in New Zealand. Currently, we have 40 samples of leaf litter beetle communities from our 2016 fieldwork. With environmental DNA extraction techniques and next generation sequence we generated sequences of three mitochondrial genes that will be the basis of upcoming analyses.

BIG4 enabled me to meet my scientific heroes on conferences and to connect with scientist around the world. With those new cooperators and the BIG4 workshops I learned a lot about the morphology of my focus groups as well as the molecular methodology to study them in a broader evolutionary context.

Publications within the project:

Seidel, M., Arriaga-Varela, E., & Fikáček, M. (2016). Establishment of Cylominae Zaitzev, 1908 as a valid name for the subfamily Rygmodinae Orchymont, 1916 with an updated list of genera (Coleoptera: Hydrophilidae). Acta Entomologica Musei Nationalis Pragae, 56(1), 159-165.
Minoshima, Y. N., Seidel, M., Wood, J. R., Leschen, R. A., Gunter, N. L., & Fikáček, M. (2018). Morphology and biology of the flower‐visiting water scavenger beetle genus Rygmodus (Coleoptera: Hydrophilidae). Entomological Science.
Seidel, M., Minoshima, Y. N., Arriaga-Varela, E., & Fikáček, M. (2018, June). Breaking a disjunct distribution: a review of the Southern Hemisphere genera Cylorygmus and Relictorygmus gen. nov. (Hydrophilidae: Cylominae). In Annales Zoologici (Vol. 68, No. 2, pp. 375-402). Museum and Institute of Zoology, Polish Academy of Sciences.
Toussaint E. A. F., Seidel M., Arriaga-Varela E., Hájek J., Král D., Sekerka L., Short A. E. Z. & Fikáček M. (2017) The peril of dating beetles. Systematic Entomology 42(1): 1-10

BLOG POST: BIG4 Phylogenomic research on Syrphidae: Scope and Collaboration

Thu, 16 Aug 2018 10:03:00 +0300

This post was written by Trevor Burt.

Over the last couple of decades, the global syrphid community has been progressing towards a focused picture of the origin and diversification of hoverflies (Diptera: Syrphidae). Given the growing concerns about climate change and biodiversity loss, this work, along with revising the taxonomy of hoverflies, is extremely important. Syrphids are also critical pollinators of flower plants and crops underscoring their value. In recent years multi-phase projects were developed to take advantage of new Target Enrichment techniques in hopes of generating high-confidence molecular data that would cement subfamily relationships (with particular focus on the subfamily Syrphinae) and shed light on some genera within the Syrphidae.

My BIG4 project’s main focus is to develop baits to target informative genes of Syrphidae. This undertaking required a large scale global collaboration with scientists and syrphid workers from multiple labs, collections, and museums from several nations. Some of the wet lab work was divided among several labs including the Canadian National Collection of Insects, Arachnids and Nematodes (CNC), Ottawa, Canada; The Royal Museum for Central Africa (RMCA), Tervuren, Belgium, and the target enrichment wet lab was completed at the Alexander Koenig Research Museum (ZFMK), Bonn, Germany. 192 syrphid species were selected and targeted using a bait kit designed specifically for Syrphidae from a Transcriptome library provided by the 1Kite project (Bonn, Germany). This process was rather tedious and took roughly 3 months to complete, including the receival of raw sequences.

This is where the real fun began. When processing raw sequences at this scale, serious bioinformatic background is paramount. The pipeline has been developed and reshaped many times, as new challenges arise. There is a lot of stop-start, stop-start, two steps forward and five steps back. This can feel very defeating and frustrating, but our goal propels us and thankfully there is no shortage of support in the community. Our efforts have yielded roughly 1300 genes across all taxa targeted (this will constitute the largest data set ever developed for Syphidae)!

Magnetic plate used in purification

We are now in the stages of aligning COI sequences to collate with our genomic data. Our aim is to generate large matrices to produce phylogenetic trees to better understand the relationships of the genera within the subfamilies of Syrphidae.

Overall, working on this project within the larger scope of the BIG4 has shown me the benefit and pitfalls of collaboration. A project of this scale simply cannot be undertaken or completed without community input, especially given the wide variety of expertise from many disciplines required (collections, private collectors, bioinformatics, technical lab expertise, etc.).

After all the work is behind us and we are able to look plainly at our raw sequences, gain a good alignment, establish a section of our pipeline, and begin to make out the ghost of a result, it’s a great feeling!

Publications within Trevor's project:

Burt, T.O. & Mengual, X. 2017. Origin and diversification of hoverflies: a revision of the genera Asarkina and Allobaccha – A BIG4 Consortium PhD project. Research ideas and Outcomes 3: 1-16.
Pauli, T. Burt, T.O., Meusemann, K., Bayless, K., Donath, A., Podsiadlowski, L., Mayer, C., Kozlov, Vasilikopoulos, A., Liu, S., Zhou, X., Yeates, D., Misof, B., Peters, R.S. and Mengual, X. 2018. New data, same story: Phylogenomics does not support Syrphoidea (Diptera: Syrphidae, Pipunculidae). Systematic Entomology 43: 447-459.
Burt, T.O. & Mengual, X. 2018. New records of Melanostoma fumivenosum Doesburg (Diptera: Syrphidae) with the description of the male. Australian Entomologist 45: 209-216.

BLOG POST: An X-ray vision into the evolution of Hydrophilidae

Mon, 13 Aug 2018 09:40:00 +0300

This post was written by Emmanuel Arriaga Varela.

In order to understand the Hows, the Whens and the Whys of the evolution of insects and other animal groups, it is necessary to take a look at the past. Fossils embedded in amber give us the unique opportunity to take a deep and intimate look at a moment frozen in time. Through careful examination of the morphology of these organisms and a comparison with extant groups it is possible to place them within the framework of an evolutionary tree. Moreover, the morphological, geological and biogeographical aspects of the fossil record are invaluable in the reconstruction of a comprehensive evolutionary history.

The global aim of my PhD project at Charles University in Prague is to understand the biodiversity explosion of the terrestrial water scavenger beetles (Family Hydrophilidae, tribe Megasternini). I am reconstructing the phylogenetic relationships within this group based on the genetic information and complemented by the main morphological traits of the organisms. Any knowledge about the extinct members of this group and their close relatives is crucial on the way towards understanding of evolutionary patterns.

Sometimes the quality of amber embedded fossils is not optimal for its study with conventional tools.

The fossil record for this tribe is, unfortunately, very scarce. Only one member of the tribe has been reported, and even from other hydrophilid groups just a handful of amber fossils are known in the collections. The fact that most of the available amber hydrophilid fossils are in a suboptimal condition is aggravating the situation; contracted limbs, milky clouds and cracks in the amber piece obscure the most important characters rendering its examination with conventional tools almost impossible. Therefore, we decided to use advance technology for its study.

3D reconstruction of micro-CT scans allow us to study the morphology of fossils specimens in amazing detail.

All the available hydrophilid fossils from Baltic amber from the Eocene epoch were scanned using micro computerized tomography in the laboratory of Brian Metscher at the Department of Theoretical Biology, University of Vienna. As part of my BIG4 secondment, I visited the laboratory of Adam Brunke in the Canadian National Collection of Insects, Arachnids, and Nematodes at the Agriculture and Agri-Food Canada, Ottawa. Adam, a successful graduate of the BIG4 project himself, made an exemption to his "Staph only" policy and diverged from his beloved staphylinids instructing me in the use of specialized software for the construction of 3D models from the X-ray micro-CT scans. These reconstructions allowed us to examine the morphological structures in a way that otherwise would be impossible. Now, we will be able to use this information for the calibration of the branching events in the evolutionary tree of Hydrophilidae.

As part of the BIG4 project I had the chance to learn modern methods for the study of insect diversity and I was lucky to meet and even to collaborate with many of the top scientists in this area of knowledge. I will definitely utilize this acquired knowledge and connections in the future.

After the examination of the only known potential member of my subject of study group, we discovered that it is actually not even a hydrophilid, but a member of a distant beetle family. However, in the study of extinct and extant biodiversity any discovery that bring us closer to the truth is a step forward, and that is something that should makes us all happy.

Publications within the project:

Arriaga-Varela E, Wong SY, Kirejtshuk A, Fikácek M (2018) Review of the flower-inhabiting water scavenger beetle genus Cycreon (Coleoptera, Hydrophilidae), with descriptions of new species and comments on its biology. Deutsche Entomologische Zeitschrift 65(1): 99-115. https://doi.org/10.3897/dez.65.26261
Arriaga-Varela, E., Seidel, M., Fikáček, M. 2018. A new genus of coprophagous water scavenger beetle from Africa (Coleoptera, Hydrophilidae, Sphaeridiinae, Megasternini) with a discussion on the Cercyon subgenus Acycreon. African Invertebrates 59(1): 1-23. https://doi.org/10.3897/AfrInvertebr.59.14621
Arriaga-Varela, E., Seidel M., Deler-Hernández A., Senderov V. & Fikacek M. 2017. A review of Cercyon Leach (Coleoptera, Hydrophilidae, Sphaeridiinae) of the Greater Antilles. ZooKeys 681: 39-93
Toussaint E. A. F., Seidel M., Arriaga-Varela E., Hájek J., Král D., Sekerka L., Short A. E. Z. & Fikáček M. 2017: The peril of dating beetles. Systematic Entomology 42(1): 1-10. DOI: 10.1111/syen.12198

BLOG POST: Raiders of the Lost Museums – Next-Generation Sequencing for museum specimens

Thu, 09 Aug 2018 11:43:00 +0300

This post was written by Elsa Call.

Natural museum collections around the world are extremely abundant. All of these specimens are highly valuable for a wide range of research applications, such as systematics and taxonomy, biodiversity studies, habitat loss and investigations into the history of infectious diseases or environment contaminants. For a long time, these museum specimens were only used to study morphology because their DNA was seen as too degraded to be used. However, the appearance of the Next-Generation sequencing method allows sequencing of very short fragments of DNA, thereby opening the door to new possibilities, like sequencing of both ancient DNA and museum specimens.

Nowadays, we have examples of successful sequencing of extinct taxa (including Neanderthals, mammoths and cave bears), as well as museum specimens with a main focus on mammals and birds, and a few examples of plants. Studies on insects, however, are limited, as they are considered too small and too difficult to extract DNA from.

The main idea of my project is to develop Next-Generation sequencing for museum specimens of Lepidoptera (moths and butterflies), and also to investigate the level of DNA preservation in museum specimens of various ages. The second part of the project is to use these methods to explore the relationships among families of the superfamily of moths, Geometroidea. Within this superfamily, three families are rare and difficult to collect nowadays, but there is an extensive collection of representative species for them in museums (such as Copenhagen, Bonn, Tokyo, Paris, etc.). The idea is to sample as many of the species from these families as we can and to include them in our phylogenomic study.

A funny anecdote that happened in the lab was when the specimens were so dry, they were floating above the DNA extraction liquid. It made us realize we first needed to re-hydrate the samples, before extraction. We soaked them in some drops of water (depending on the specimen size) and let them absorb the water for a while.

Abdomen of one of our samples above the extraction liquid

So far, the protocols (extractions and library preparations) have been optimized for Whole-Genome Sequencing (WGS). Six butterfly specimens from the 40’s have been successfully sequenced with 2 different sequencing machines (MiSeq and HiSeq) and good mitochondrial genome coverage was obtained. Currently, I am processing more samples and more data is yet to come.

Representatives of some of the rare Geometroidea families

I also want to learn an alternative method to Whole-Genome Sequencing, because in terms of evolutionary questions the more taxa, the merrier. Not only because WGS can be expensive for several different species but also because for phylogenomics, we don’t need the whole genome, targeted loci are enough. With this in mind, I learned the Target Enrichment approach. I successfully prepared 32 specimens of 19 different species and targeted 1,900 genes. The samples are currently being sequenced.

BIG4 has brought me a lot, both on a professional and personal level. Thanks to this amazing network I was able to meet very interesting fellow researchers, and I had the possibility to travel for courses, visit other research teams and laboratories, attend congresses and considerably expand my network. I also met wonderful colleagues that are now very good friends of mine! The BIG4 meetings were always cheerful moments, with a lot of fascinating and interesting discussions on our respective projects, future ideas for collaborations and career development.

Publications within the project:

Mitochondrial Museomics. (In preparation)
Investigate the relationships of families in the super family Geometroidea based on museum specimens.

BLOG POST: Metabarcoding approach answers key questions about our ecosystem

Mon, 06 Aug 2018 16:07:00 +0300

This post was written by Daniel Marquina.

How unique is this habitat? Is this a biodiversity hotspot? Should we invest public resources in preserving it? Is this a healthy environment? Have our conservation efforts done any good? How does the food web look like in this habitat? How many species are there?

Answering this type of questions is a key point for an ecologist, a nature reserve manager or even for the government, to be able to do their job. Whether it is for the purpose of research on the biodiversity of a certain area, the monitoring of the habitat or the decision to protect the place or not, it is fundamental to have a clear view of how the ecosystem is structured. And the most basic part of this structure is the number of species that coexist in it. The way to find the answer might vary depending on the group of organisms: walking around a delimited area counting different species (for plants), observing with a pair of binoculars during a transit (birds, amphibians), setting up a remote sensing camera during the night (mammals) or electrofishing in a river (fish). For insects, this kind of direct observation is much more difficult because they are much smaller and most of the time, species identification requires detailed analysis of the morphology of, for instance, the dissected reproductive organs. Thus, it is common to use different types of traps when sampling insects to collect as much as one can, with the Malaise trap being the most popular one (developed by the Swedish entomologist René Malaise).

Malaise traps are usually left in the field for one or two weeks, and then the insects are collected and brought to the laboratory for identification.

Until recently, the only way to identify them was for an expert taxonomist to examine specimens one by one. This process, apart from relying on the availability of taxonomists for all the different insect groups, is extremely slow, sometimes taking tens of years to identify all the specimens from a collection campaign. However, taking advance of the Next Generation Sequencing platforms, we are now able to amplify and sequence a short fragment of any gen from thousands of individuals at a time. Certain genes have the property of being very similar in their nucleotide sequence between individuals of the same species, but significantly different between individuals of different species. They are what we call ‘barcoding genes’, and they allow us to assign any insect to the correct species by comparing their sequence with a previously created reference database. This technique is called ‘metabarcoding’.

BIG4 has given me the opportunity to expand my research horizons, landing into the field of entomology, where there is much to learn that is already known, but so much more unknown. The way people are connecting thanks to the consortium, makes us eager to keep collaborating between teams, even after the project comes to an end.

In this project, we focused on the technical aspect of metabarcoding of insects, although our protocols can be applied for any other animal group. One of the most important components of this work pipeline is to use good primers (small fragments of DNA that can be artificially synthetized, that make the gen amplification reaction possible for the posterior sequencing), since they have to be able to bind equally well to the DNA of all the species present in the sample. This is particularly difficult because of the huge variability in the target sequence, and a bad primer design can cause inability to identify species that are actually present in our sample. Using a set of computational tools, we have designed and evaluated new and already existing primers, using the most comprehensive reference database to date with more than 2000 sequences belonging to approximately 1100 species. With this material, we have identified better regions of these barcoding genes, easier to amplify and with the same identifying capacity than the most used and more difficult to amplify gen. We have concluded that the combined use of these regions two-by-two enhances the detection capacity of metabarcoding applied to insects over the use of a single gen. These primers are currently being used in different case-study surveys, and we will soon have data on their in vitro performance.

On the other hand, we are nowadays testing and developing different DNA extraction methods from whole samples that allow us to preserve the morphology of the insects intact for further examination. The usual protocol consists of grinding the insects to make a soup or a paste, which is chemically treated to extract the entire DNA. In case of unknowingly dealing with a new species in our sample, such protocol would destroy the possibility of formally describing it, a huge mistake in these times of biodiversity loss. With the optimization of the non-destructive DNA extraction we are conducting, we will be able to pinpoint a new species from the perspective of DNA sequencing, and later examine and describe it, since the morphology of the insect will be preserved.

Publications within the project:

Marquina, D., Andersson, A. F., & Ronquist, F. (2018). New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods. bioRxiv, 325688.

BLOG POST: One hand is tradition, one hand is innovation – morphological challenges in present times

Mon, 30 Jul 2018 10:26:00 +0300

This post was written by LIU Si-Pei.

To adapt to different environments, some of the BIG4 insects - which usually fly well - abandon their flight ability and develop some other specialised structures. With modern morphological techniques such as scanning electron microscope (SEM), computer based 3D-reconstruction and traditional hand drawings, I demonstrated these specialized thoracic structures in detail.

The reduced or absent flight related skeletomuscular structures are generally significant thoracic features of flightless insects. Meanwhile, some other modified body structures such as enlarged female ovaries, highly movable coxal articulations, etc., become a trade-off for the adaptation to specialized environments.

I am very happy that I could broaden my vision on entomology thanks to BIG4. As a PhD student in a morphological laboratory, I was deeply shocked by all the other subjects including phylogenomics, computer-based publication, mathematics etc.

The interdisciplinary approach motivated me to learn many new perspectives and to figure out how to combine the traditional morphological research with different fields. I began to realise that learning new things is a mission of my whole life.

Currently, I am dealing with a very interesting non-biting midge (Chironomidae), which lives on the ocean surface and has no flight ability. I would like to demonstrate the thoracic structure and compare that with the other alate families of "lower Diptera", and then find out the most specialized characteristics of this species.

Wingless female Nyssiodes lefuarius (Lepidoptera: Geometridae) has a very narrow thorax and enlarged ovaries (3D reconstruction)

How the Orectochilus villosus (Coleoptera: Gyrinidae) fly based on its simplified thoracic structures (hand drawing)

Besides anatomy, I also analyzed the morphological evolution of Lepidoptera and Hippoboscidae, based on parsimony. Important changes in the thoracic characters system are linked to the evolution of basal Lepidoptera. The monophyly of Hippoboscoidea, Pupipara and bat flies group are confirmed based on 44 thoracic morphological characters, which are nearly the same as the phylogenomic results. Meanwhile, the structure replacement is another interesting topic. I analyzed a whirligig beetle species (Gyrinidae), which has very simplified thoracic structures to support the flight ability. I also inferred the functions of some reduced sclerites or muscles replaced by others.

BIG4 was also a brilliant chance for me to make so many friends around world! We come together and freely discuss our researches, ideas and career expectations.

Publications within Si-Pei's project:

Liu, S.-P., Wipfler, B., Niitsu, S. & Beutel, R.G. (2017) The thoracic anatomy of the male and female winter moth Nyssiodes lefuarius (Lepidoptera: Geometridae) and evolutionary changes in the thorax of moths and butterflies. Organisms Diversity & Evolution, 17(3): 565–594.
Liu, S.-P., Wipfler, B. & Beutel, R.G. (2018) The unique locomotor apparatus of whirligig beetles of the tribe Orectochilini (Gyrinidae, Coleoptera). Journal of Zoological Systematics and Evolutionary Research, 56(2): 196–208.
Liu, S.-P., Friedrich, F., Petersen, D.S., Büsse, S., Gorb, S.N. & Beutel, R.G. The thoracic anatomy of the swift lousefly Crataerina pallida (Diptera) – functional implications and character evolution in Hippoboscidea. Zoological Journal of the Linnean Society. (https://doi.org/10.1093/zoolinnean/zly032)
Liu, S.-P., Richter, A. & Beutel, R.G. The thoracic anatomy of Myrmecia nigrocincta workers and evolutionary transformations in Formicidae (Hymenoptera). Arthropod Systematics & Phylogeny. (submitted)
Beutel, R.G., Pohl, H.W., Yan, E.V., Anton, E., Liu, S.-P., Slipinski, A., McKenna, D. & Friedrich, F. The phylogeny of Coleopterida (Hexapoda) – morphological characters and molecular phylogenies. Systematic Entomology. (in press)

BLOG POST: Getting close to the first major phylogenetic analysis of Aleocharinae

Wed, 25 Jul 2018 14:38:00 +0300

This post was written by Igor Orlov.

Aleocharinae are one of the biggest monophyletic groups of living organisms on Earth and include about 16,200 described species worldwide. They are a subfamily of Staphylinidae, a mega-diverse insect group, also known as Rove Beetles. Although this group is an important component of the biosphere and several species are used in the biological control of pests in agriculture, the poor knowledge and undeveloped taxonomic system do not allow us to make more exciting discoveries within this group.

Almost two hundred years have passed since the first Aleocharinae Rove Beetle was described but only a few limited molecular and morphological studies have been carried out in the last decade and we still do not understand what the major phylogenetic lineages within Aleocharinae are and how they related to each other.

My project within BIG4 aims to shed more light towards the phylogenetic relationships of the higher taxa within Aleocharinae, which is not an easy task. Even a little advance in understanding of the tribal relationships within a group like that can only be achieved with a great effort.

Being part of the BIG4 group, I got the great opportunity to see and learn the most modern methods in biology, which can be used to solve this issue. Two main ways of working towards the phylogeny of Aleocharinae were chosen - morphological and molecular. Observing tiny characters on the beetle body with a Scanning Electron Microscope (SEM) during my secondment to Prof. Dr. Rolf Beutel's lab in Friedrich-Schiller-Universität in Jena brought me a lot of new ideas of understanding of the characters in a phylogenetic context. An absolute majority of the SEM pictures were obtained first time ever for this group.

Even though SEM is a great and promising method, light microscopy is more accessible. In my home lab in Copenhagen I made hundreds of full body dissections of tiny and minute specimens of Aleocharinae to see phylogenetically important characters and score into a data matrix for the subsequent analysis with a special software. The usual size of Aleocharinae is about 1-4 millimeters and over a hundred specimens were dissected into 40-50 parts and mounted in Euparal for careful examination and long storage. A fresh DNA-grade material for the molecular study was loaned from Dr. Martin Fikáček lab and I currently use it to get insights in Aleocharinae tribal phylogeny as well. The molecular work is based on previous research and the main idea is to combine existing molecular data from GenBank with my own newly generated sequences. So far, I have obtained molecular data for 5 genes for around 60 taxa from different tribes and I am getting very close to the first major phylogenetic analysis of Aleocharinae.

ESM: Orphnebius sp. tarsal claws

Aleocharinae microslide collection

All this and many more activities would be impossible outside the BIG4 community within such a short period of time. It is true to say that during the last two-three years we began to be a close community of scientific workers driven by common ideas and love for nature.

But this is only beginning. In the future I would like to continue and further expand my work on the Aleocharinae systematics and phylogeny and I am pretty sure this question can be satisfyingly solved within next 15-20 years. I am happy that my current PhD project within BIG4 is building the basis for future work!

Publications within the project:

Systematics and Biogeography of the Subantarctic Leptusa (Coleoptera: Staphylinidae: Aleocharinae: Homalotini). (Under Review in "Systematics and Biodiversity" Journal)
Towards Aleocharinae phylogeny based on morphology. (In preparation)

BIG4's fifth and last workshop is taking place in Sofia, Bulgaria

Mon, 16 Apr 2018 16:00:00 +0300

Starting today, 16 April 2018, the last BIG4 workshop will take place over three busy days in Sofia, Bulgaria, where our MSCA fellows will have the chance to present their results and learn from invited professionals in the scientific, business and publishing fields alike.

Close to the end of a very successful project where 15 early career researchers had the opportunity to be part of 15 PhD projects, focused on the biosystematics, informatics and genomics of 4 insect groups, our fellows have the chance to meet again and discuss plans and strategies for their future career development.

Together with BIG4's scientific supervisors, coming from top research institutions across Europe, a number of professionals from more business-oriented fields will present insights on important skills and strategies for BIG4's participants academic and professional future.

Special focus will be put on training the young researchers for successful grant applications, as well as showing them the tricks to succeed in a modern start-up environment. The participants will also have the chance to learn the latest development in high-tech open access publishing and related modern workflows and tools.

BIG4 Fall Workshop in La Palma, Canary Islands, Spain, Oct 29- Nov 3 2017- By Trevor O. Burt

Thu, 09 Nov 2017 15:45:00 +0200

The BIG4 Autumn workshop was held October 29^th to the 3^rd of November on the idyllic La Palma of the Canary Islands, Spain. A better backdrop could not have been selected for all BIG4 students, supervisors and many other participants to discuss and workshop a number of subjects relating to phylogeography, citizen science, publication and manuscript development, and entrepreneurship. Students were also granted opportunity to outline progress in their projects and address any future goals and challenges. This year’s workshop was organized by Niklas Wahlberg, PhD fellows: Elsa Call, and Hamid Ghavani of the Lund Systematics Biology Group, Sweden.

On the first day, Sunday, October 29^th, all students presented their progress and had a chance to have an open discussion about any challenges some might have faced in the last year. It was also a wonderful opportunity to take a moment to celebrate the many successes and milestones students have experienced (such as publications) before beginning the workshop.

The workshop lectures and tutorials were presented by BIG4 project supervisors Niklas Wahlberg and Fredrik Ronquist with associate lecturers Isabel Sanmartin (Senior Research Scientist of Plant Biology and Systematics; Spanish National Research Council, Madrid, Spain), Nicolas Chazot (Postdoctoral Fellow of the Systematic Biology Group (Lepidoptera), Lund, Sweden), with special guest lecturer Brent Emerson (Consejo Superior de Investigaciones Científicas (CSIC), at the Instituto de Productos Naturales y Agrobiología (IPNA) in La Laguna).

The workshop, though intense, was very thorough, covering a range of subjects on biogeography with great practical depth. Students were exposed to comprehensive tutorials focused on Parsimony-Based Tree Fitting, Dispersal-Vicariance Analysis, Probabalistic models (Dispersal-Extinction-Cladogenesis (DEC)), geographic speciation and extinction, lineage diversification (GeoSSE), Bayesian paramentric biogeography (including Bayesian-Island-Biogeography (BIB) modelling), using a variety of software packages and modeling schemes such as DIVA, R (BioGeoBEARS, DiversiTree), Lagrange, BEAST v1.8.3-4, and RevBayes. Students left with a better grasp of how to assess patterns of speciation, including rates of dispersal, how to explore mechanisms of diversification, and dating phylogenetic trees with the fossil record (pros and cons).

Though the workshop was intense students and supervisors had sufficient time to socialize in the evenings over late dinners, filling dimly lit coastal restaurants with the jubilant reverberations of good friends and colleagues. Some took opportunity to walk the black sand shoreline, or swim in the lukewarm ocean. Accommodations at El Cerrito were very comfortable, with a crystal blue wading pool, and an open air atmosphere conducive to relaxation, laughter, and late night discussions. Some students participated in a Star Gazing tour organized by Daniel Marquina, while others explored more terrestrial attractions, including visiting the national park: Caldera de Taburiente. The workshop overall was a very useful, well-rounded, and enjoyable experience – nothing short of a success!

Thanks are given to the instructors and organizers (Niklas Wahlberg, PhD fellows: Elsa Call, and Hamid Ghavani) for putting together an immense program and selecting such an exotic and interesting setting. On behalf of the BIG4 students a special thank you is offered to Isabel Sanmartin and Nicolas Chazot who did a magnificent job presenting important concepts and the practical applications used to address biogeographic (among many other) questions. Thank you to Brent Emerson for his in depth presentation on approaches to taxonomy and systematics uniquely fitted to his work on the Canary Islands.

The El Cerrito resort personnel deserve a special thank you for their cheerful and accommodating attitude and for striving to provide an atmosphere that would ensure the success of this year’s workshop.

With a lot of legs in the backpack to the 17th International Congress of Myriapodology, Krabi, Thailand - By Anne-Sarah Ganske

Tue, 29 Aug 2017 15:49:00 +0300

Despite being an outlier among the insect-focused BIG4-project, myriapods are a highly interesting group of animals to study and to discuss about. From July 23^rd to 26^th 2017, myriapodologists from all over the world met in Krabi (Thailand) to present their research on these fascinating creatures during the 17^th International Congress of Myriapodology organized by members of the Chulalongkorn University, Bangkok. That was a great opportunity for me and my supervisors Dr. Nesrine Akkari (NHM-Wien) and Dr. Gregory D. Edgecombe (NHM London) to present our first results from the BIG4-project: "Lithobius: a big genus of a small subphylum (Arthropoda, Myriapoda) - phylogenetics and evolutionary history". As preliminary results, we presented the variation and new characters with phylogenetic potential of cephalic microstructures from species of the genus Lithobius.

Besides a great amount of cultural impressions in Thailand, I had the opportunity to listen to interesting scientific talks on myriapods and onychophorans and to give an oral and poster presentations during the 17^th ICM. It was an occasion for constructive feedback and stimulating discussions, which are helpful for further project-related research. During the congress’ farewell party, I had the honour to receive the award for the best student poster for my work entitled "Investigation of the mandibular structures and evaluation of their phylogenetic significance in the genus Lithobius (Lithobiomorpha: Lithobiidae)" (DOI: 10.13140/RG.2.2.34492.54401), co-authored by my supervisors. Finally, this meeting was a great chance to discuss the BIG4-project with world’s leading experts on Myriapodology and to contribute a first scientific output of our ongoing research.

UPCOMING EVENT : BIG4 Workshop - Phylogeography OCT/NOV 2017

Wed, 16 Aug 2017 14:34:00 +0300

The planning of the next BIG workshop is currently underway and will be held on La Palma, Canary Islands. The workshop is scheduled to start from the 29th Oct untill 3th Nov 2017. Further updates and information about the workshop will be coming soon. You may also contact the organisers, Niklas Wahlberg, Elsa Call or Hamid Ghavani.

My secondment to Australia - By Josh Jenkins Shaw

Thu, 13 Jul 2017 11:45:00 +0300

Late January saw me switch the Danish winter for Sydney’s warm climate of around 38C. As part of my BIG4 PhD, I spent several months at the Australian Museum for a ‘change of environment’ and my research stay abroad. I was based next to the museums insect collection and supervised by Dr Chris Reid, a research scientist working mostly on leaf beetles (Coleoptera: Chrysomelidae). The main aim of my stay was to join Chris and the Australian Museum on a field trip to Lord Howe Island which was very successful and important for my project and resulted in other exciting finds (see here). We spent two weeks on the island collecting beetles, including finding all targets for my PhD project. A particular highlight was finding two species my supervisor (Alexey Solodovnikov) and I had described as new to science just a few months earlier: Quediopsis howensis and Cheilocolpus olliffi (paper here). These and other specimens will be vital in phylogenetic reconstruction and understanding the biogeography of Lord Howe Island. During my time at the museum, I also studied the insect collection and alcohol collection, finding important specimens for my project that had been collected on earlier expeditions to LHI. At the end of March a small team from Copenhagen flew out and we convened in Cairns for more fieldwork, this time in the rainforests of Queensland. This was another great field trip, experiencing the sights and sounds of Australia’s rainforests and finding many beetles crucial for my project. After a couple of weeks three of us headed to the Queensland Museum (Brisbane) for several days to study their important collections. We were helped along by great hospitality from Geoff Monteith whom we are very grateful to. After Brisbane I went back to Sydney to continue working in the Australian Museum with a couple of days hiatus at the Australian National Insect Collection (CSIRO, Canberra) to study the DNA-grade beetles and insect collection. Overall it was a very successful trip which enabled me to gather important beetle specimens, experience fieldwork in a new place, meet new friends and colleagues working in systematics and visit new institutions and see how they work.

BIG4 Spring Workshop in Vienna, 8-13 May 2017 - By Si-Pei Liu

Mon, 22 May 2017 13:08:00 +0300

After recent rise and domination of the phylogenomics and bioinformatics, the chance for charming morphology come-back to insect systematics has arrived! During the second week of May in beautiful Vienna, all BIG4 students and supervisors attended the 4^th workshop "Morphology of invertebrates: 3D imaging and novel approaches for Biosystematics".

Morphological characters are the most visual monitors reflecting the evolutionary changes and organismal diversity. Combined with computer science, the current science of morphology demonstrates strong advances compared to the traditional tedious dissection and hand drawing. Energetic Dr. Brian Metscher from the University of Vienna gave a series of brilliant seminars for deep understanding of electronic imaging. Dr. Sergei Tarasov from the National Institute of Mathematical and Biological Synthesis at Knoxville, USA further explained how to deal with the famous Maddison "red tail" and "blue tail" problem using multiple Markov chains. Meanwhile Arn Rytter Jensen, a fresh graduate from the University of Copenhagen introduced many useful skills of scientific illustration with Adobe software. Finally Dr. Evgeny Yan from Phylogenetic Museum in Jena gave a short talk about the 3D fossil illustration based on 2D drawings. We also would like to thank Prof. Rolf Beutel, Dr. Gregory Edgecombe, Dr. Sarah Faulwetter, Prof. Lyubomir Penev, Prof. Andreas Wanninger, coming from various countries for their wonderful presentations on the first day showing how to observe, analyze and publish morphological result. The students practiced extant and fossil specimen 3D reconstruction with microCT and Amira/Drishti under the instruction of Dr. Brian Metscher and Dr. Sarah Faulwetter and were introduced to SEM, digital photography and computer illustration by Dr. Nesrine Akkari and Dr. Dap Topa in the museum. On Saturday morning, some students briefly presented their interesting results, such as 3D reconstruction of a rove beetle in the amber with strange blue color…

Of course the biggest "danke schön" goes to our sweet Dr. Nesrine Akkari and her student Anne-Sarah Ganske, who successfully organized this workshop in the Natural History Museum Vienna, under the caring gaze of Maria Theresia, beside the "Blauen Donau".

More photos from the workshop can be found here.

COMING SOON! BIG4 Workshop in Vienna, May 8th – 13th 2017 NHMW, Austria

Fri, 07 Apr 2017 12:17:00 +0300

Morphology of invertebrates: 3D imaging and novel approaches for Biosystematics

The motto of this project is innovation: how to create and manipulate complex 3D data, approach novel statistical models, master techniques like multifocus imaging, as well as SEM and digital illustration, including software to create and assemble images for publications. Monday 8^th will be an open day devoted to inspirational talks on the legacy and prospects of morphology in systematics and evolutionary biology, naturally with the stress on BIG FOUR and allied. We will have some BIG4 supervisors as lecturers, as well as guest speakers, e.g. Prof. Dr. Andreas Wanninger, Dr. Sergei Tarasov and Dr. Sarah Faulwetter, who will also be involved in the teaching during the week. From Tuesday on, the workshop will be more or less restricted to BIG4 members and focus on seminars and practice of the various techniques. To make this workshop an exciting and busy event, BIG4 students will have a chance to collaborate on small projects and present their results on Saturday!

For further information and updates please check the workshops’ webpage:

https://anne-sarahganske.wixsite.com/big4workshopvienna

BIG4 Fall Workshop in Sweden, 10 -19 Oct 2016 - By Janina Lisa Kypke

Wed, 26 Oct 2016 15:32:00 +0300

Between 10-19 October 2016 all BIG4 students, supervisors and a number of outside participants got together again for a workshop on phylogenetics, phylogenomics, citizen science and entrepreneurship, as well as for the mid-term meeting. This time the workshop was organized by Fredrik Ronquist and his ‘three wise men’: the BIG4 PhD fellows Daniel Marquina, Erik Gobbo and Miroslav Valan. They had the outstanding idea to place the workshop at Tovetorp Research Station, approximately 90km southwest of Stockholm between Gnesta and Nyköping, where we could enjoy the autumn colors of the forest surrounding us and see pheasants and deer strolling around the field station while dining.
During the workshop we were introduced to Bayesian phylogenetic inference, Markov chain Monte Carlo simulation, different dating methods and how to use MrBayes and RevBayes. We also learned about metabarcoding, including an exercise where we designed primers, basic commands to handle bioinformatics data in a unix environment as well as de-novo genome sequencing, assemblies and how this information can be used for phylogenetic inference. The second part of the workshop covered the areas of entrepreneurship and citizen science where we could benefit from the experience of a number of invited speakers that were successful in these fields. We discussed the process of having an idea to selling a final product, failures and successes and even got to brainstorm about our own ideas.
The mid-term meeting took place on Friday and gave every BIG4 fellow the opportunity to talk about his/her own projects. It was the first time our newest member Anne-Sarah Ganske and her co-supervisor Gregory Edgecombe could introduce themselves and her project. Welcome to our network! For this special day EU Officers were listening in to evaluate our network and individual progress.
While we covered a lot of different topics during these 10 days, there was still a lot of time to socialize, discuss (e.g. how to become a successful scientist), and to make plans on how our network can become even stronger in the next years to come - no doubt that the idyllic landscape, the sauna, the outdoor hot-tub, volleyball -and floorball filed and last, but not least, the delicious food have made their positive contribution to that!
Our thanks go to Fred and his three wise men for organizing this wonderful workshop and for teaching us, to all invited speakers for sharing their knowledge and expertise with us and to the staff at the field station who made sure that we lacked in nothing.

COMING SOON! Stockholm workshop: Tovetorp field station south of Stockholm, 9th Oct- 19th Oct 2016

Thu, 29 Sep 2016 13:43:00 +0300

BIG 4 Fall Workshop 2016

Phylogenetics, phylogenomics, citizen science and entrepreneurship

The BIG4 fall workshop 2016 has two main themes. One theme is focused on phylogenetics, phylogenomics and bioinformatics, and is intended to provide students with an introduction to these topics, focused on skills that will be useful in their PhD research projects. There will be a mixture of lectures and practicals; students are encouraged to bring their own datasets and analysis problems. The other theme is citizen science and entrepreneurship, and this part of the course will provide broad introductions, exercises, and inspiration for students interested in pursuing these subjects as part of their current or future activities.

The workshop is primarily aimed at BIG 4 students but (except for the Friday morning session) is open to outside participants as well. We have room for up to 10 additional outside participants on a first come first served basis. Outside participants may choose to come for only part of the course, if they wish.

Venue and practical information

The Tovetorp research station (http://www.zoologi.su.se/tovetorp/) belongs to Stockholm University and was founded in 1969. It hosts courses and research projects, primarily in ecology and ethology. It is situated about 95 km southwest of Stockholm. For driving directions and maps that will help you get there, see http://www.zoologi.su.se/tovetorp/hitta.php [in Swedish]. In English: Take E4 south from Stockholm. Between Järna and Nyköping, you take the "Lästringe" exit and follow signs to Nyköping. After about 10 km, take a right towards Aspa and Öster-Malma. Follow signs towards Öster-Malma until you get to a yellow sign pointing to Tovetorp to your left, close to Öster-Malma. If you need more detailed instructions, you should have no problems finding "Tovetorp forskningsstation" on Google Maps.

Students should be prepared to share rooms. Please note that outdoor shoes are not allowed inside the station. We recommend you to bring slippers for indoor use. There is a hot tub and an indoor recreation area with a floorball court (complete with goals, balls and sticks) and a sauna (unisex). We recommend that you bring indoor sport shoes, gym clothes, swimsuit, and a big towel for sauna use.

Transportation

The most convenient option coming from abroad is probably to fly to Stockholm Arlanda airport. From there you can choose express train (Arlanda Express) bus to downtown Stockholm (or taxi if you prefer). There is also the regional commuter train, but it is the slowest option and is not recommended unless you have the time to spare. You can enquire about details and buy tickets at Arlanda airport.

An alternative option is to fly into Stockholm Skavsta airport south of Stockholm (used by Ryan air). From there, you can take the bus to downtown Stockholm. Skavsta airport is actually fairly close to Tovetorp field station, so if you are adventurous there is also the possibility of taking public transport (bus) from Skavsta to the vicinity of Tovetorp (expect a 2 km walk from nearest bus stop). Alternatively, you can rent a car at Skavsta and drive (about 30–40 min. drive from there to Tovetorp).

For those students and teachers who will only participate in part of the course, you may want to take the train to Gnesta Station (36 min. from Stockholm central station with regional trains). We will organize transports between Gnesta railway station and Tovetorp, as needed.

We have arranged common transportation for BIG 4 students. Bus to Tovetorp will leave Stockholm central station (?) on Sunday, October 9th at 7:30 PM. Bus from Tovetorp to Stockholm central station (?) will leave Tovetorp on October 19th 8:30 AM (after breakfast). The bus drive will take approximately an hour and a half. Outside students are encouraged to use these buses if they plan to participate in the entire course, or in the starting or ending part of the course.

Preparations

Bring your own computer with wireless access and an ssh client. For Windows machines we recommend MobaXTerm (http://mobaxterm.mobatek.net/). For Mac computers, simply make sure you know where to find the Terminal application.

Some basic familiarity with Unix will be highly beneficial for the first week. This is one of many unix tutorials for beginners on the web: http://www.ee.surrey.ac.uk/Teaching/Unix/. It includes eight short tutorials that cover all the necessary basics, and more.

Teachers

Fredrik Ronquist (Professor, Swedish Museum of Natural History), Chris Wheat (Professor, Stockholm University), Rodrigo Esparza-Salas (PhD, Technician at the DNA-lab, Swedish Museum of Natural History), Johan Nylander (Bioinformatician, Swedish Museum of Natural History), Erik Gobbo (PhD student, Swedish Museum of Natural History), Daniel Marquina (PhD student, Swedish Museum of Natural History); Karin Carlsson (Business Developer, Savantic AB), Miroslav Valan (PhD student, Savantic AB/Swedish Museum of Natural History). [Miroslav and Karin to complement this list with teachers/discussion participants for the part on citizen science and entrepreneurship].

Pre- or post-course activities

Students interested in sightseeing in Stockholm or visits to the Swedish Museum of Natural History before or after the course, please contact a member of the local organizing committee (Erik, Daniel, Miroslav, Fredrik).

Course registration and fee

Register for the course no later than September 28 using the form at this web site: http://bit.ly/2c6i6v0. Outside student participation will be confirmed on September 29. If you cancel past that date, we may very well have to charge you the course fee anyway.

There will be a fee for course, accommodation and food. We expect the total cost to be approximately 2,000 SEK/day for students participating for part of the course, and approximately 15,000 SEK in total for those students taking the entire workshop. Students will receive an invoice after the course is finished.

Schedule

Coffee breaks are scheduled all days at 10:15-10:45 and 14:30-15:00.

Sunday October 9

19:30                  Bus to Tovetorp leaving from Stockholm Central Station

21:00 (appr.)     Arrival at Tovetorp Field Station

Monday October 10

07:30–08:30      BREAKFAST

09:00–12:00      Fredrik Ronquist. Introduction to statistical inference. Bayesian phylogenetic inference and Markov chain Monte Carlo simulation.

12:00–13:00      LUNCH

13:00–17:00      Fredrik Ronquist. Stochastic models of evolution. Introduction to MrBayes. Exercises using MrBayes.

18:00–19:00      DINNER

19:30–21:00      Continued exercises. Questions. Discussion.

Tuesday October 11

07:30–08:30      BREAKFAST

09:00–12:00      Fredrik Ronquist. Divergence time estimation: node dating and total-evidence dating. Statistical biogeography. Model testing, model averaging and other special topics.

12:00–13:00      LUNCH

13:00–17:00      Fredrik Ronquist. Phylogenetic graphical models. Introduction to RevBayes. Exercises using MrBayes and RevBayes.

18:00–19:00      DINNER

19:30–21:00      Continued exercises. Questions. Discussion.

Wednesday October 12

07:30–08:30      BREAKFAST

09:00–12:00      Erik Gobbo. De novo genome sequencing: next generation sequencing and genome assembly.

12:00–13:00      LUNCH

13:00–17:00      Chris Wheat. Gene finding, genome annotation and phylogenomic inference.

18:00–19:00      DINNER

19:30–21:00      Questions. Discussion.

Thursday October 13

07:30–08:30      BREAKFAST

09:00–12:00      Chris Wheat, Erik Gobbo. Genome assembly, gene finding, genome annotation and phylogenomics exercises.

12:00–13:00      LUNCH

13:00–17:00      Rodrigo Esparza-Salas. Introduction to metabarcoding.
Daniel Marquina. Metabarcoding: special topics.

18:00–19:00      DINNER

19:30–21:00      Continued exercises. Questions. Discussion.

Friday October 14

07:30–08:30      BREAKFAST

08:30–12:30      BIG 4 Midterm Review [Only BIG 4 participants].

12:30–13:30      LUNCH

13:30–17:00      Daniel Lundin, Daniel Marquina. Metabarcoding exercises.

18:00–19:00      DINNER

19:30–21:00      Continued exercises. Questions. Discussion.

Saturday October 15

07:30–08:30      BREAKFAST

09:00–12:00      Johan Nylander. Handling bioinformatics data in a unix environment. Bioinformatics exercises. Bring your own data and questions!

12:00–13:00      LUNCH

13:30–17:00      Continued exercises. Questions. Discussion.

18:00–19:00      BANQUET DINNER

Sunday October 16

Free day for social activities. Food will be served as usual.

07:30–08:30      BREAKFAST

12:00–13:00      LUNCH

18:00–19:00      DINNER

Monday October 17

07:30–08:30      BREAKFAST

09:00–10:15      TBA. Why you should become an entrepreneur.

10:45–12:00      Several contributors. Round table discussion: insights from experienced entrepreneurs in biosystematics, informatics and genetics.

12:00–13:00      LUNCH

13:30–17:00      Karin Karlsson (Savantic AB). Training session: Steps in the entrepreneurship process.

18:00–19:00      DINNER

Tuesday October 18

07:30–08:30      BREAKFAST

09:00–10:15      Karoly Makonyi. A personal view on citizen science.
Karin Carlsson. Gamification and viral effects: a case study.

10:45–12:00      Jakob Jönsson. Citizen science in cosmology.

12:00–13:00      LUNCH

13:30–17:00      TBA. [Contribution from Chalmers].
Emma Lundberg. [Title TBA].
Miroslav Valan. [Title TBA].

18:00–19:00      DINNER

Wednesday October 19

07:30–08:30      BREAKFAST

08:30                  Bus to Stockholm from Tovetorp

10:00 (appr.)     Arrival at Stockholm Central Station

Successful BIG4 field workshop in the Czech Republic, 6-10 June 2016 - By Joshua Max Jenkins Shaw

Tue, 21 Jun 2016 12:25:00 +0300

All students of the BIG4 consortium along with some supervisors and external collaborators convened on the idyllic surroundings of the Podyjí National Park near Havraníky in the South Moravian region on the Czech Republic. The workshop, successfully organized by Martin Fikáček from the National Museum of Prague, was the first opportunity for many students and supervisors to catch up after the kick-off meeting in Copenhagen in September 2015. In addition to enabling an open dialogue to share successes, problems and ideas of projects between students and supervisors, a series of field days and lectures were held to introduce four of the major insect groups (Coleoptera, Hymenoptera, Lepidoptera and Diptera) and collecting techniques for obtaining specimens for further study. Fortunately, the weather was on our side and we enjoyed the sunny, warm days, perfect for being in the forest looking for insects and other organisms. The warm days were equally perfect for evenings around a fire with local Czech wine and further discussions about topics such as collecting legislation, modern systematic research methods, vouchers and types and species concepts. I think I speak for all students when I say we left having further built on relationships within the BIG4 family and were suitably tired from fieldwork in an impressive location.

Entomological expedition to Western Cape region, South Africa- By Emmanuel Arriaga Varela

Mon, 09 May 2016 12:07:00 +0300

The southernmost corner of Africa, the Cape Region, is home of one of the most peculiar ensembles of living organisms in the globe. The systematic study of the highly endemic beetle fauna of this area is crucial for the understanding of the evolution and historical biogeography of many taxa. For this reason the members of the Fikáček lab of the National Museum in Prague, and of the Zoological department of the Charles University at Prague, in the Czech Republic: Emmanuel Arriaga-Varela, Matthias Seidel and Martin Fikáček and Dominik Vondráček, organized, from November 18th to December 13, 2015, an expedition to Western Cape province of the Republic of South Africa, in order to collect specimens of the Hydrophilidae family, key for the ongoing research projects of the members of the expedition.
Our journey began in the Nature Reserve of Diepwalle, which is composed by one of the largest reservoirs of the highly decimate southern afrotemperate forest, as well as by colorful montane fynbos vegetation. We sifted as much forest litter as we could and regularly checked dung from various mammal species, even under unfavorable weather conditions.
The next stop, The De Hoop Nature Reserve, gave us the chance to explore a different scenario: coastal fynbos, savanna-like vegetation and plenty of aquatic and semiaquatic environments. In the search for copro-necrophilous beetles, we, naturally, did not missed the opportunity to scan the savanna for zebra dung to put our fingers in and antelope corpses to inspect, with a little bit more caution, of course.
Then we moved to the region of Swellendam for having access to the natural areas of Grootvaderbosch and Boosmanbos, where we looked at the leaf-litter of the afrotemperate forest for elusive hydrophilids. The wet rocks surrounding the abundant waterfalls of the zone offered a unique environment which we scrutinized in detail for small beetles. Not only the natural forested zones provided us with interesting specimens, but the farms of the zone provided us with kilogram after kilogram of fresh cow and horse dung, that we diligently sorted with fabulous results; among the hundreds of beetles swarming int the nutritious dung, we obtained many specimens of a new genus, member of the tribe Megasternini (Hydrophilidae: Sphaeridiinae). The elucidate evolution of this tribe is the main objective of my PhD project. For this reason such finding are of a vital importance for my studies.
Our journey (almost) finished in the Hermanus area. The beautiful sandy beaches of this enclave gave us the chance of diving into piles of rotten kelp in the quest for highly specialized Cercyon (Megasternini) species, to the surprise and puzzlement of the bathers. In the nearby rivers we succeed finding a few specimens of Cylorygmus a rare genus of Hydrophilidae, key to the understanding of the evolution of the Rygmodinae subfamily, which almost exclusively inhabit the southernmost spots of the globe: New Zealand, Australia, Chile and south Africa.
We said goodbye to this wonderful country with a night excursion to the most exotic locality on the expedition: the green areas of the suburbs of Cape Town. We returned to the Czech Republic with lots of interesting specimens that will enrich our researches, but also with tons of edifying experiences and a nice tanned skin.

More photos here!

COMING SOON! BIG4 field workshop in the Czech Republic, 6th June-10th June 2016

Thu, 07 Apr 2016 15:49:00 +0300

The aim of the workshop is for all members of the BIG4 consortium to meet and catch-up with each other’s progress, celebrate first achievements, discuss difficulties and problems & to experience a practical field-based exposure to diversity of BIG4 with the focus on the dominating insect families.

Location: The workshop will take place in the National Park Podyjí at the Czech-Austrian border, with the base at the field station in the small village Havraníky

Program summary:
June 6: BIG4 progress overview with short (ca. 15 min) student’s projects progress-reports talks, get familiar with the area
June 7: Introduction to major collecting methods and trap installation
June 8: Sorting and identification of the first bulk samples, mixed with expert short talks about some most diverse insect families, ad hoc short nearby collecting excursions.
June 9: Continuing trap-based and hand-based collecting, as well material sorting and identification.
June 10: Finalizing sorting/identification, completing the summary of collected material, discussion on results and field activities, social even in the evening.

For more details, please contact: Martin Fikáček at mfikacek@gmail.com

Student Conference on Conservation Science (SCCS)

Wed, 02 Mar 2016 16:59:00 +0200

After the first successful Student Conference on Conservation Science (SCCS) Hungary in 2015, the MTA Centre for Ecological Research announces the second SCCS Hungary to take place from 30 Aug to 2 Sep 2016, in Tihany (Lake Balaton).

SCCS Hungary offers young conservationists the opportunity to meet renowned plenary speakers, to attend career-enriching trainings, workshops and field trips and to have fun at the largest lake in Central Europe, Lake Balaton in a student-friendly low price.

Find more about the conference and register here.

Why I decided to publish my PhD Project Plan, a guest post by Viktor Senderov

Tue, 12 Jan 2016 15:02:00 +0200

According to Was ist Open Science? there are six leading principles of Open Science: open methodology, open source, open data, open access, open peer review, and open educational resources. If I am to have an open thesis, then I have to strive to apply those six principles to my own work. In the spirit of this effort, I and my advisor, Prof. Penev, have decided to publish my PhD project plan as a RIO article.

RIO (Research Ideas and Outcomes) is a new academic journal, which aims to publish results from all steps of the research continuum. Therefore, a PhD project plan was a very good candidate for it, as it is the first output of my PhD research so far.

By publishing my PhD research plan I achieve several things. First, since we’re being funded through a Marie-Curie grant (No. 542241), we achieve visibility of where the public financing goes. Second, we have invited several known experts to review my submission and we’ve got invaluable comments, which will help us steer the research into a better direction. Third, by publishing the research plan in RIO and sharing it in social media, we hope to attract comments from the public, which again will help me steer my research into a better direction, and might turn out to be valuable contributions. Fourth, we are more motivated to be on track, when we know that the plan is public.

You can find the plan here and even an official press release! This is in a nutshell why we decided to publish my PhD Project Plan. In the remainder of this post, I will share with you some more thoughts on open theses.

Having an open thesis consists of two parts: first, have an open license allowing for the unhindered access and distribution of the text and a second, optional part, which consists of drafting the thesis in the open. By publishing my PhD research plan I am making the first step towards drafting my thesis in the open. Further steps could be, should I decide that this is the most appropriate direction, the opening up of lab notebooks, and the gradual publication of the chapters of my thesis as they become available. For this purpose, I have started using the Open Science Framework to host my lab notebooks and other project documentation. Should I decide that I want to publish the chapters of my PhD thesis, I could setup a github repository and push updates as I write them.

The Wikipedia page on open thesis lists two theses that are being drafted in the open right now: that of Max Klein and that of Patrick Hadley.

If you’ve read the research plan and want to comment, don’t hesitate to post here, or mention me @vsenderov in Twitter or email me at datascience at pensoft dot net.

FOLLOW-UP from BIG4 Kick-Off in Copenhagen

Mon, 23 Nov 2015 16:14:00 +0200

Talks and images from our network meeting is now available on the BIG4 webpage. Please find them respectively in Agenda & Minutes and Images under RESOURCES.

First Impressions and First Results by Viktor Senderov (@vsenderov, http://openbkms.blogspot.com)

Thu, 15 Oct 2015 11:31:00 +0300

I recently blogged on my PhD thesis blog about the BIG4 kick-off meeting in Copenhagen. Here, I will revisit this topic and give my first impressions as well as report some first BIG4-relevant results.

As I pointed out, the format of the meeting was two days of presentations by students and PI’s about individual projects, then a field-trip day, then two more days of presentations and entomology-related workshops lead by senior lecturers. Certainly, one of the more memorable moments for me was the Friday workshop, when the students got to examine and document parts of the Fabricius collection at the Natural History Museum of Denmark.

The whole symposium was very well organized thanks to Sree and Alexey. I am certainly looking forward to the next one that will be probably in the Czech Republic.

On the scientific side, I think we have good mix of entomologists and molecular researchers - me being squarely in the second camp. I am looking forward to the next half a year or so when first data begin to be generated so that I have material to work on. In the mean-time, I will be doing some interconnections between data portals and Biodiversity Data Journal (BDJ) in order to learn the Pensoft system, laying the ground-work for an open thesis, and working on different research agendas for my project.

Some of those interconnections have been already engineered and I’d like now to introduce two new workflows. The first workflow facilitates the import of metadata into BDJ as a data paper. What it does is that it allows an author in BDJ to initialize her data paper manuscript from an EML text file containing metadata belonging to a dataset. In other words, given a dataset and its metadata, we convert the structured information about the dataset found in the metadata to a journal-style formatted manuscript ready for submission for review in BDJ after modifications have been made. The other workflow facilitates the import of occurrence records into a taxonomic manuscript at BDJ. As you can see, it is now possible to copy occurrence records from GBIF, BOLD Systems and iDigBio into your taxonomic manuscript by just typing their ID’s in a dialog.

These two workflows could be used by BIG4 students and PI’s to write data papers about the datasets that are generating and in taxonomy papers. An easy way to utilize them would be that all BIG4 member labs install a copy of GBIF’s Integrated Publishing Toolkit (IPT) on their lab server and share their biodiversity datasets with the community via IPT. Then should the authors decide to publish in Biodiversity Data Journal they would be able to both create a data paper about their dataset based on GBIF’s EML format and import the individual occurrences into a taxonomic paper.

In terms of the big picture, they would be most useful for species redescriptions and more specifically to extend the morphological descriptions of old taxa with genomic data. I also plan in the future, together with the ARPHA engineers, to write an importer for occurrence data from Darwin Core-Archive (DwCA). This will allow for an almost universal exchange of occurrences between databases and BDJ.

We would certainly be very happy to hear from other BIG4 students and PI's and also from the general public. Therefore, I will cross-post this blog entry on the BIG4 Google+ page, and on my PhD thesis blog, where you can start a discussion.

SEPTEMBER 14-18, 2015: Successful BIG4 Kick-off in Copenhagen, Denmark

Thu, 01 Oct 2015 15:19:00 +0300

BIG thank you, all participants of the BIG4 Kick-off!

We held our first all network meeting, with all students having a chance to meet each other and every BIG4 supervisor. The meeting involved a variety of scientific activities and social events including presentations of each individual BIG4 project, talks about BIG4’s fellow’s rights and obligations, ITN financing rules, and network work packages. Finally, ITN fellows had a workshop on museum entomological collections, their management and curation. As practical exercise, they successfully digitized ca. 1/3 of the Cerambycidae collection of the Natural History Museum of Denmark.
All in all, it was a great opportunity to strengthen working relations among all members of the BIG4 consortium and wish all student fellows good luck in their projects.

More images and video will be coming up!

UPCOMING EVENT : BIG4 Kick-off in Copenhagen, DENMARK (UPDATES!)

Thu, 10 Sep 2015 13:18:00 +0300

The BIG4 Kick off meeting will be held in Copenhagen from the 14th to 18th of September 2015.
It will start off at the International House with talks from the project Coordinator, EU officer, project supervisors and some students. During final days, a collections-related workshop will take place at the Zoological Museum, with talks about entomological collections by speakers from various natural history museums. The scientific program of the meeting will be complimented by networking events for all participants, including a dinner club, excursion to Røsnæs and canal-tour in the city of Copenhagen. Please refer to the meeting schedule attached for more details. We are looking forward to meeting all participant soon. Vi ses i København!

Job Announcement - Marie Skłodowska-Curie PhD Position in Bioinformatics

Thu, 12 Feb 2015 09:49:00 +0200

We are pleased to announce а PhD position in bioinformatics at Pensoft, as а part of the BIG4 international cross-disciplinary training consortium (BIG4: ‘Biosystematics, Informatics and Genomics of 4 big insect groups’) funded by the European Union‘s Marie Skłodowska-Curie Innovative Training Network Program (ITN). More information at: www.pensoft.net/Marie-Curie-PhD-position