ForBio and MEDUSA course: Systematics, Morphology and Evolution of Marine Annelids

The University Museum of Bergen (University of Bergen), Moscow State University and ForBio jointly offer an International Course on Systematics, Morphology and Evolution of Marine Annelids.

Course financial support

The course is co-financed by ForBio and the Cooperation Programme between Norway and Russia “Multidisciplinary EDUcation and reSearch in mArine biology in Norway and Russia” (MEDUSA) – funded by DIKU, the Norwegian Agency for International Cooperation and Quality Enhancement in Higher Education.

                                                   © G. Kolbasova

Course scope 

We aim to provide participants with a unique opportunity to get state of the art knowledge in various aspects of annelid biology. The course will consist of a 3-day symposium with student presentations and lectures covering three main topics: 1) Systematics and Phylogeny; 2) Morphology; 3) Development and Evolution of Life Histories in annelids. We also offer 4 one-day workshops designed to provide hands-on experience in various methods frequently used in annelid research. 

Assignment and credits

The course is equivalent to 2 ECTS. To earn credits a student must attend 3 days of symposium and in addition choose one of the two options:

a) present a talk during the symposium and attend one of the workshops with approved home assignment

b) attend two of the workshops with approved home assignment

It is not possible to attend a workshop without participating in the symposium. 

Course venue

The course will be taught online using Zoom (lectures) and Slack (workshops) platforms. The links will be provided to accepted participants. 

Course fee

There is no course fee required from ForBio members or associates.  Find out about how to become a ForBio member/associate here.

Language

English

Symposium 

April 14-16, 2021

The symposium will include keynote lectures and student presentations. Please see the preliminary program here. It will be updated after the application deadline.

All ForBio member and associates can attend the symposium after registration. Read how to become ForBio member/associate here. 

Student presentations

All course participants are invited to submit contributions to present their research. You will be asked to upload your abstract as a Word file when registering for the course. Please use the provided abstract template to format your abstract. All contributions will be oral. Talks will have 10-15 minutes plus 5 minutes for questions. We will have maximum 15 student presentations, the selection will be based on the evaluation of the abstracts by a committee. Due to funding restrictions, priority will be given to MSc and PhD students affiliated with Norwegian or Russian universities/institutes.

Keynote speakers

Alexander Tzetlin, Moscow State University

Torsten Struck, Natural History Museum, University of Oslo

Ken Halanych, Auburn University

Bruno Pernet, California State University, Long Beach

Andreas Hejnol, Department of Biological Sciences, University of Bergen

Anna Zhadan, Moscow State University

Vasily Radashevsky, National Scientific Center of Marine Biology, Russian Academy of Sciences

Elena Kupriyanova, Australian Museum

Luke Parry, University of Oxford

Chema Martín-Durán, School of Biological and Chemical Sciences, Queen Mary University of London

Conrad Helm, University of Göttingen

Nataliya Budaeva, University Museum of Bergen, University of Bergen

Nadezhda Rimskaya-Korsakova, Moscow State University

Glafira Kolbasova, Moscow State University

 

Workshop 1: Introduction to phylogenetic methods

April 19, 2021

Instructor: Torsten Struck (UiO)

Teaching assistants: Marianne Nilsen Haugen (UiO), Miguel Meca (UiB), Nataliya Budaeva (UiB)

Scope: The aim of this workshop is to provide an introduction in the phylogenetic methods for beginners. Additional, we want to make you more familiar with the general analytical steps required in a phylogenetic analysis and the minimum standard expected from phylogenetic analyses, even be it in a different research field like ecology, developmental biology or genomics.

                                       Budaeva et al. 2016

Content: As a starting point, the workshop will assume that you in some way got your assembled, quality-checked sequences of interest already. Sequencing strategies and processing reads from sequencing are not covered. We will begin with learning how we can retrieve sequences from public databases such NCBI GenBank to compile dataset for the research question at hand. The next steps will then be to learn how to align the sequences and check the quality of the alignment including masking strategies. Before the actual phylogenetic analysis, two different datasets will be combined into one. Finally, we will reconstruct a Maximum Likelihood tree using IQtree including bootstrap values and determination of the best model and the partition scheme. If time allows, we will also conduct a Bayesian analysis.

Learning outcome: At the end of this one-day workshop, you will have learned about the different steps to consider when doing a phylogenetic analysis and which resources are available for this. You will also have gotten a first introduction in how to conduct such analyses. However, the workshop is intended only as an introduction and hence cannot provide more than a starting point.

Quota: Max 8 students. Participants will be selected based on the registration form, which includes a paragraph for motivation and importance of the workshop for your study/work. Due to funding restrictions, priority will be given to MSc and PhD students affiliated with Norwegian or Russian universities/institutes.

Workshop 2: Creating illustrations for publications using Adobe Photoshop

April 20, 2021

Instructors: Katrine Kongshavn (UiB), Anna Zhadan (MSU), Alexander Semenov (MSU)

                          © K. Kongshavn

Scope: The aim of this workshop is to introduce the Adobe Photoshop workspace and to explore some of the options for creating plates of photographs suitable for scientific illustrations. The workshop aims at the beginners who have little or no experience with Adobe Photoshop and editing photographs and who want to learn a set of tools most frequently used in preparing scientific illustrations for publication in peer reviewed journals.

Content: We will combine short talks and demonstrations with practical exercises that the participants follow along and complete during the workshop.

Topics visited will be:

  • how to plan the illustrations according to a journal’s specifications (author instructions/guidelines),
  • how to choose and set up your format,
  • a brief introduction to the Photoshop workspace and the most common functions (layers, brushes, selection tools etc.),
  • adjustment of images using curves and levels,
  • some useful actions that can be applied to photos,
  • how to create panoramas and stacked images,
  • some of the most commonly used tools for removing backgrounds, including working with masks.
                                       © A. Zhadan

Learning outcome: At the end of this one-day workshop, you will be able to used basic Adobe Photoshop tools in image processing and will create a plate with multiple images, complete with annotations. Check the gallery of annelid images by A. Semenov for inspiration!

Requirements: All workshops participants are required to have Adobe Photoshop installed on their private computers (a free 7-day trial version is available on Adobe website). Workshop organizers do not provide access to a Photoshop license. We will not be able to support practical exercises in any other free software suitable for editing photographs.

Quota: Max 8 students. Participants will be selected based on the registration form, which includes a paragraph for motivation and importance of the workshop for your study/work. Due to funding restrictions, priority will be given to MSc and PhD students affiliated with Norwegian or Russian universities/institutes.

Workshop 3. Methods of 3D reconstructions based on histological sections

April 21, 2021

Instructors: Nadezhda Rimskaya-Korsakova (MSU), Elena Temereva (MSU)

Teaching assistant: Anna Mikhlina (MSU)

Scope: The one-day workshop will be devoted to practicing three-dimensional modeling of internal organs using histological sections of annelids, one of the methods widely used in morphological studies of annelids and other invertebrates.

     © T. Pimenov, E. Temereva, N. Rimskaya-Korsakova

Content: The theoretical part includes a lecture on the methods of 3D reconstruction, the principles of preparing the material and demonstration of case studies based on 3D deconstructions. During the practical part, you will become acquainted with the algorithm of the 3D reconstruction method using Amira Software 2019 (ThermoFischer Scientific): loading images of a series of sections into the program, alignment, segmentation, visualization, and analysis of a volumetric image. Participants will practice modeling skills on the provided sections of a marine annelid worm. We will also give an overview of the open-source platform Fiji (Schindelin et al., 2012, Nature) used for 3D reconstructions. This will be done as a demo as installation of this software is currently problematic in several operating systems.

Learning outcomes: At the end of the day, you will become familiar with the principles of 3D reconstructions and will create own reconstruction of a system of internal organs in an annelid species.

Requirements. Each participant must have a computer or a laptop that meets the necessary requirements. A mouse is minimally needed, but it is good if one has a pen and a tablet. We do not recommend using the touchpad. Practical exercises will be done using a free trial license of Amira provided by ThermoFischer Scientific for training purposes only. Workshop organizers do not provide access to full license. Accepted students will receive instructions on software installations several days before the workshop.

Quota: Max 8 students. Participants will be selected based on the registration form, which includes a paragraph for motivation and importance of the workshop for your study/work. Due to funding restrictions, priority will be given to MSc and PhD students affiliated with Norwegian or Russian universities/institutes.

Workshop 4 Open data publishing and BOLD tools

April 22, 2021

Instructors: Torbjørn Ekrem (NTNU), Mark Costello (Nord University), Katrine Kongshavn (UiB),  Nataliya Budaeva (UiB)

Teaching assistant: Tom Alvestad (UiB)

Scope: Research data should be open, accessible and reusable. Open data make published results transparent and reproducible, facilitates research and allow addressing global questions. Barcode of Life Data Systems (BOLD) is a repository of open barcode data aiding in correct species identification – a fundamental need for all biological research, conservation and management of biodiversity.

Content: In the beginning of the workshop, we will introduce the concept of open data publishing and provide overview of widely used sources of open data such as OBIS, GBIF, AquaMaps and related environmental data sources like Bioracle and GMED. We will also discuss CC license publishing. We will further provide participants with a more in-depth introduction to DNA barcoding through BOLD, describe its functionality as repository of genetic data and its analytical tools. Examples of recent annelid studies utilizing barcode information will be demonstrated to show advantages but also limitations of the DNA barcoding approach.

During the practical session, we will:

  • Show how DNA barcodes are produced – workflow from specimen collection to digital data
  • Introduce the Darwin Core Standard and its components
  • Practice upload of images, sequences and trace files to a BOLD project
  • Introduce the concept of Barcode Index Numbers (BINs)
  • Demonstrate analytical tools with the BOLD database

Learning outcomes: At the end of the day, you will obtain basic understanding of the potentials in DNA barcoding when applied in biodiversity and systematics research, learn how to operate BOLD systems either as a data provider or as a user of the database and DNA identification engine.

Quota: Max 8 students. Participants will be selected based on the registration form, which includes a paragraph for motivation and importance of the course for your study/work. Due to funding restrictions, the priority will be given to MSc and PhD students affiliated with Norwegian or Russian universities/institutes.

Quota: Max 8 students. Participants will be selected based on the registration form, which includes a paragraph for motivation and importance of the workshop for your study/work. Due to funding restrictions, priority will be given to MSc and PhD students affiliated with Norwegian or Russian universities/institutes.

 

Application deadline: March 14, 2021

Please register for participation in the course here.

 

Contact  Nataliya Budaeva (nataliya.budaeva@uib.no) - ForBio coordinator. 

Published Jan. 28, 2021 10:51 PM - Last modified Feb. 4, 2021 12:28 PM