ForBio course: Phylogenomics – Extended deadline

The ForBio course: Phylogenomics has an extended application deadline: September 1st!

ForBio course: Phylogenomics
http://www.forbio.uio.no/events/courses/2016/phylogenomics.html

Time and place: Nov 14, 2016 – Nov 18, 2016, Natural History Museum, University of Oslo, Norway.
Teachers: Torsten Hugo Struck, NHM, UiO and Patrick Kück, NHM London.

Objectives: Advances in high-throughput sequencing and genomics have revolutionized research in evolutionary biology and systematics. The use of genomics data in phylogenetic analyses has brought new challenges in terms of data handling and analysis. This course aims to help those that have basic experience in bioinformatics and molecular phylogenetics, and have projects focused on high-throughput sequencing data and phylogenetics, to become acquainted with tools, programs and pipelines for phylogenomics and want to contact phylogenomic studies beyond the standard also addressing potentially confunding biases in their datasets.

Prerequisites: Basic knowledge of command line interaction, regular expressions, UNIX, sequence data and alignments, model-based phylogenetic analyses, model testing, Bayesian inference, is a prerequisite for participation. Pre-course exercises on command line, regex and UNIX will need to done, submitted and passed to ensure that all participants have an equal minimum level at start.

NB: This course consists of two parts, week I (14-18 Nov 2016) and week II (in March or April 2017). We will provide the exact dates as soon as possible. The first week covers the basic foundation of phylogenomic studies. Lectures and labs in week II will build upon this and focus on dissecting the phylogenetic signal in the dataset and detecting possible misleading biases such as long branches and compositional heteroegenities. Strategies for thorough sensitivity analyses in phylogenomic studies will be part of this week.

Maximum number of participants is 26.

Application deadline is September 1, 2016.

For more information and application go to the website: http://www.forbio.uio.no/events/courses/2016/phylogenomics.html

Contact Hugo de Boer (hugo.deboer@nhm.uio.no) or Torsten Hugo Struck (t.h.struck@nhm.uio.no) for more information.
All the best,

ForBio/Hugo

GU and ForBio course: Life and Earth History

The evolution of life on Earth is inevitably linked with the geological and climatic history that has dramatically changed available habitats and resources over time. In this course we will explore how geological and paleoclimatic evidence and paleontological and neontological data can be combined to better understand the interplay between Earth history and the evolution and biogeography of organisms. We will provide key concepts about biostratigraphy and fossil preservation and their crucial role in dating events in deep time. We will touch upon several major events of climate changes and landmass dynamics in different part of the world and at different geological times, such as the formation of the Himalayan mountain range, the Paleocene–Eocene Thermal Maximum (PETM; ~ 55 Ma), and the formation of a land bridge connecting the North and South American continents. A special focus will be given to the effects of these events on local and global biodiversity and its spatial distribution. Further, we will demonstrate computational methods that can help us investigating the dynamics of origination, dispersal, and extinction of organisms using fossil occurrence data. This course will also include practicals providing training in computational (paleo)biology to infer macroevolutionary dynamics and instill or reinforce skills in python and R computing.

Course content
The course includes: 1) formal lectures on earth history and its links to biodiversity dynamics; 2) workshops on the use of computational methods to infer macroevolutionary processes from fossil data with hands-on practicals; 3) visiting the “The history of life and its teeming diversity” exhibition at the Natural History Museum of Gothenburg.

Outcomes
After completion of the course the PhD student will have gained insights on important geological and climatic events that have characterized Earth history and inevitably impacted biodiversity and evolution. They will also have a better understanding of the paleontological and geological evidence that these events left and how they can be used to understand the origin and history of life on Earth, at different geographic and temporal scales. Finally, participants will learn how to setup and carry out macroevolutionary analyses using the software PyRate (https://github.com/dsilvestro/PyRate) to infer origination, extinction and preservation rates from fossil occurrence data.

Required reading
A list of scientific publications required for the course will be distributed among confirmed students two weeks before the start of the course.

Assessment
Preparation of a short research proposal (powerpoint presentation and two page executive summary) to be presented and submitted 10 days after course completion.

Course teachers
Christine D. Bacon, Carina Hoorn, Carlos Jaramillo, Daniele Silvestro

The University of Gothenburg course plan can be found here.

Application deadline is August 12th, 2016. Apply here. Plan to book travel arrangements that weekend.

A 1.5 ECTS course certificate will be given to students that pass the course, either by GU or ForBio depending on registration.

Contact the course leaders Daniele Silvestro or Christine D. Bacon, or ForBio leader Hugo de Boer for more information.

Research School in Biosystematics – ForBio: course overview

The Research School in Biosystematics – ForBio is organising a number of relevant courses in the summer and autumn this year, and we invite you to apply to these courses, or forward this overview to interested colleagues for further dissemination to students and postdocs.

Looking forward to seeing you at our courses! Hugo – ForBio

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Transmitting Science and ForBio course: Introduction to Electron Microscopy for Life Sciences
Time and place: Jul 5, 2016 09:00 AM – Jul 8, 2016 06:00 PM, Universitat Autònoma de Barcelona (UAB), Barcelona (Spain).
http://www.forbio.uio.no/events/courses/2016/electronmicroscopy.html

SIU and ForBio course: Dead Wood Course
Time and place: Aug 8, 2016 – Aug 11, 2016, Lammi Biological Station, Finland
http://www.forbio.uio.no/events/courses/2016/Deadwood

ForBio and STIRs course: DNA barcoding – from theory to applications
Time and place: Aug 22, 2016 – Aug 26, 2016, Zoology building, Medicinaregatan 18, Gothenburg
http://www.forbio.uio.no/events/courses/2016/barcoding.html

ForBio course: Marine Annelids in the Norwegian Sea
Time and place: Sep 4, 2016 – Sep 10, 2016, NTNU, Sletvik Field Station , Norway
http://www.forbio.uio.no/events/courses/2016/Annelid%20field%20course

SIU and ForBio course: Polypores as tools in forest conservation
Time and place: Sep 19, 2016 – Sep 23, 2016, Lammi Biological Station, Finland
http://www.forbio.uio.no/events/courses/2016/Polypores

ForBio and UiO: Mycology field course
Time and place: Sep 26, 2016 – Sep 30, 2016, Biological Station Drøbak, Norway
http://www.forbio.uio.no/events/courses/2016/mycology.html

ForBio course: Introduction to Bioinformatics for Biosystematics
Time and place: Oct 3, 2016 – Oct 7, 2016, Biological Station Drøbak, Norway
http://www.forbio.uio.no/events/courses/2016/bioinfointro_2016.html

DEST and ForBio course: Philosophy of Biological Systematics
Time and place: Oct 10, 2016 – Oct 14, 2016, Biological Station Drøbak
http://www.forbio.uio.no/events/courses/2016/philbiolsyst.html

DEST and ForBio course: Basics of Taxonomy – describing, illustrating and communicating biodiversity
Time and place: Oct 10, 2016 09:00 AM – Oct 21, 2016 06:00 PM, Zoology house, Medicinaregatan 18, Gothenburg, Sweden
http://www.forbio.uio.no/events/courses/2016/Basics%20of%20Taxonomy.html

ForBio course: Species Concepts and Species Delimitation
Time and place: Oct 24, 2016 – Oct 28, 2016, NTNU, Trondheim, Norway
http://www.forbio.uio.no/events/courses/2016/Species%20delimitation

SIU and ForBio course: Biodiversity data management and open data
Time and place: Oct 31, 2016 – Nov 4, 2016, Tartu, Estonia
http://www.forbio.uio.no/events/courses/2016/Open%20data

ForBio course: Phylogenomics
Time and place: Nov 14, 2016 09:00 AM – Nov 18, 2016 05:00 PM, Natural History Museum, University of Oslo
http://www.forbio.uio.no/events/courses/2016/phylogenomics.html

ForBio course: Species Concepts and Species Delimitation

The Research School in Biosystematics – ForBio invites you to:

ForBio course: Species Concepts and Species Delimitation
http://www.forbio.uio.no/events/courses/2016/Species%20delimitation

Time and place: Oct 24, 2016 – Oct 28, 2016, NTNU, Trondheim, Norway
Teachers: Kevin de Queiroz, Smithsonian Institution, Washington; Joan Pons, Mediterranean Institute for Advanced Studies (IMEDEA), Balearic Islands, Paschalia Kapli, Heidelberg Institute for Theoretical Studies

Course content
What is a species? Are they real entities we can define and diagnose? In this course you will learn about philosophical, conceptual, theoretical and practical issues around species concepts and the implication of their different definitions in ecological and conservation studies. Species boundaries in many organism groups are still in a state of flux, and for empirical species delimitation, finding appropriate character sets and analytical tools are among the greatest challenges. We will review the advantages and disadvantages of different types of data for species assessment and you will be introduced to the different methods for species delimitation based on DNA sequence data and interpretation of results. Students will gain hands-on-experience about distance and tree based methods for species delimitation, including the use of software such as CROP, ABGD, UCLUST, PTP, GMYC and BPP. We will generate stimulating discussion about the interpretation of results and the advantages and limitations of these methods.

Learning targets
• Understanding the implications of the different species concepts
• Pros and cons of different types of data for species assessments
• Gain an overview of different methods for species delimitation using DNA sequence data, and their advantages and limitations.
• Hands-on experience with distance and tree based approaches.

Credits: 3 ECTS
Level: PhD students, postdocs and researchers – with experience in phylogenetic analyses.
Participants: Maximum number of participants is 18.
Registration: http://www.forbio.uio.no/events/courses/2016/Species%20delimitation
Application deadline: October 1, 2016

ForBio/Hugo and Maria

University of Gothenburg and ForBio workshop: Target capture for NGS sequencing

The Research School in Biosystematics – ForBio invites you to the University of Gothenburg and ForBio workshop: Target capture for NGS sequencing

This workshop will cover the methodology currently in use for generating DNA sequence data from multiple loci and individuals. It will cover all steps from design of probes to phasing of alleles. Emphasis will be put on basic understanding of the whole procedure, which pitfalls there may be, and demonstration of the use of software for different assembly, mapping, and phasing steps.

The format of this course requires students to have the specific objective of using these methods in their research, and students with PhD projects that include target capture will be prioritized.

Course teachers are: Isabel Liberal, Tobias Hofmann, Mats Töpel, Patrik Cangren
Credits: A 2 ECTS course certificate will be given to students that pass the course, either by GU or ForBio depending on their registration.
Time and place: Mar 21, 2016 – Mar 24, 2016, Botanhuset, Göteborg
Application deadline: March 1, 2016.
Information and registration: http://www.forbio.uio.no/events/courses/2016/target_capture.html

Contact Bengt Oxelman (bengt.oxelman@bioenv.gu.se) or Hugo de Boer (hugo.deboer@nhm.uio.no) for more information.

All the best,

ForBio/Hugo

ForBio Annual Meeting 2016 in Trondheim

ForBio is organising its annual meeting in Trondheim and registration is now open. ForBio annual meetings aim to gather scientists and students working on or interested in biosystematics in order discuss about current projects and results, share experience on methods and strengthen networking within the scientific community. This year, the meeting will be held in Trondheim, Norway, from Monday April 25th to Wednesday 27th. Registration deadline March 1st.

Keynote speakers will be invited to this meeting and will give valuable talks on the state of the art within the field of taxonomy and systematics, with the objective to inspire members on how cutting edge methods can innovate our field. We encourage attendees to use this meeting as an opportunity to present and discuss their own research as it provides a platform for exchange and dialogue about biosystematics.

There is no registration fee and you are all welcome to participate. ForBio members (PhD students and Postdocs) presenting their research (oral or poster) will have free travel and shared accommodation booked through ForBio.

For more information and registration please visit the website:
http://www.forbio.uio.no/events/meeting/2016/meeting2016.html

Best, Hugo/ForBio

PhD position in Systematic Botany at the Bergen University Museum

At the University Museum of Bergen, Department of Natural History, a temporary position as research fellow is open within the field of systematic botany. The position is for a fixed-term period of 4 years, of which 25% is work duty in the herbarium.

About the project/work tasks

The aim of the PhD-project is to improve our understanding of phylogenetic relationships within the species rich Potentilla argentea group. The project will address the role of polyploid and reticulate evolution in the group and clarify species delimitations. The work will include plant collecting in the field, molecular lab work, including the development of new markers, and phylogenetic analysis. The candidate will be a member of the research group Phylogenetic Systematics and Evolution.

Qualifications and personal qualities

• The applicant must hold a master’s degree or equivalent in evolutionary biology with relevance to Systematic Botany. Thesis work must be completed and graded before the application deadline.

• Experience with molecular and phylogenetic methods is necessary.

• Experience with plant morphological studies and taxonomic work is desirable.

• Experience with next generation sequencing methods is an advantage.

• Ability to work independently and in a structured manner, and to cooperate with others is expected.

• Proficiency in both written and oral English is required.

About the research training

As a PhD Candidate, you must participate in an approved educational programme for a PhD degree for a period of 3 years. A final plan for the implementation of the research training must be approved by the faculty within three months after you have commenced in the position. It is a condition that you satisfy the enrolment requirements for the PhD programme at the University of Bergen. The PhD fellow will become a member of the Norwegian-Swedish research school in Biosystematics (http://www.forbio.uio.no).

We can offer

• A good and professionally challenging working environment.

• A modern laboratory with diverse research activities.

• Salary at pay grade 50 upon appointment (Code 1017, NOK 430.500). Further promotions are made according to length of service in the position.

• Enrolment in the Norwegian Public Service Pension Fund.

• A position in an inclusive workplace (IA enterprise).

• Good welfare benefits.

 Your application must include

• A brief account of the applicant’s research interests and motivation for applying for the position.

• The names and contact information for two referees. One of these must be the main advisor for the master’s thesis or equivalent thesis.

• CV.

• Transcripts and diplomas showing completion of the bachelor’s and master’s degrees.

• Relevant certificates.

• A list of any works of a scientific nature (publication list).

• Any publications in your name.

The application and appendices with certified translations into English or a Scandinavian language must be uploaded at Jobbnorge.

General information:

Detailed information about the position can be obtained by contacting: Associate Professor Jenny Smedmark, phone +47 55 58 33 51 / e-mail jenny.smedmark@uib.no.

The state labour force shall reflect the diversity of Norwegian society to the greatest extent possible. Age and gender balance among employees is therefore a goal. It is also a goal to recruit people with immigrant backgrounds. People with immigrant backgrounds and people with disabilities are encouraged to apply for the position.

We encourage women to apply. If multiple applicants have approximately equivalent qualifications, the rules pertaining to moderate gender quotas shall apply. The University of Bergen applies the principle of public access to information when recruiting staff for academic positions. Information about applicants may be made public even if the applicant has asked not to be named on the list of persons who have applied. The applicant must be notified

if the request to be omitted is not met. The successful applicant must comply with the guidelines that apply to the position at all times.

https://www.jobbnorge.no/en/available-jobs/job/120496/phd-position-in-systematic-botany-at-university-museum

The Tromsø University Museum, University of Tromsø (UiT), is recruiting a ForBio coordinator/researcher in Biosystematics

This is a four year research position that includes 50% research and 50% coordination of ForBio.

We are looking for an enthusiastic and active researcher willing to organize ForBio courses and meetings and participate in teaching activities. The role of ForBio coordinators is to continue, expand and improve the work that ForBio has done during the last five years, by training the next generation of biosystematist in Scandinavia, strengthen their networks and improve the quality of the scientific outcomes. The full announcement with requirements and specifications is here: http://www.jobbnorge.no/nn-no/ledige-stillingar/stilling/119862/researcher-in-biosystematics-at-tromsoe-university-museum
Application deadline is January 3rd 2016.

The position’s affiliation
This position is attached to the Department of Natural Sciences, which is responsible for developing and maintaining scientific collections of objects (animals, plants, fossils and minerals) as well as public outreach including Tromsø Arctic Alpine Botanical Garden. The department has a permanent staff of 16, of which 9 are in academic positions. The department includes a research group in taxonomy and biodiversity, which focuses on diversity, phylogeography and taxonomy of northern organism using molecular as well as traditional methods. The department has laboratories for modern and ancient DNA analyses, and is currently involved in two large project: “Ancient DNA of Norwest Europe” and “Norwegian Barcode of Life”. The latter includes full genome sequencing of the entire Norwegian flora. For more information about the Department of Natural Sciences, visit: https://en.uit.no/om/enhet/tmu

The position’s field of research and other duties
The position is funded the Nordic Research School in Biosystematics, ForBio (http://www.forbio.uio.no/). ForBio is a teaching and research initiative coordinated by the Natural History Museum (University of Oslo), with Bergen Museum (University of Bergen), Tromsø University Museum (UiT The Arctic University of Norway) and the Museum of Natural History and Archaeology (Norwegian University of Science and Technology) as collaborators. ForBio is funded by the Research Council of Norway and the Norwegian Taxonomy Initiative/Norwegian Biodiversity Information Centre. Most students at our courses are postgraduate students (PhD or post doc students), but some are graduate students and professionals.

For further information, please contact Prof. Inger Greve Alsos, e-mail inger.g.alsos@uit.no<mailto:inger.g.alsos@uit.no>, tel +47 77 62 07 96, head of Department of Natural Sciences, Karl Frafjord, e-mail karl.frafjord@uit.no<mailto:karl.frafjord@uit.no>, tel + 47 77 64 57 25, or Museum Director Marit Anne Hauan, e-mail marit.hauan@uit.no<mailto:marit.hauan@uit.no>,  tel. + 47 77 64 50 30. For further information about the work for ForBio, contact ForBio leader Hugo de Boer, hugo.deboer@nhm.uio.no<mailto:hugo.deboer@nhm.uio.no>, tel +47 98 12 60 30.

Please forward to relevant candidates!

Best, Hugo

ForBio and UiB course: Introduction to phylogenetic methods

Time and place: Nov 2 – Nov 6, 2015, University of Bergen

ForBio opens for participation of up to 8 students from Nordic universities in the regular University of Bergen (UiB) course Phylogenetic methods (http://www.uib.no/en/course/BIO332).

The course is aimed primarily at students who will do phylogenetic computation in their thesis work, but who have no hands-on experience with some of the more frequently used software applications. Introductory lectures will cover topics such as properties of data and trees, models of evolutionary change, phylogenetic signal, model testing, and hypothesis testing. The students will learn how to prepare their data, explore the properties of the data, how to use distance, parsimony, likelihood and Bayesian methods in computation in packages such as PAUP*, MrBayes, BEAST, RaxML, and how to present results with graphical applications.

Click here for more information about the course.

Application deadline is October 5th, 2015, and applications should be sent directly by email to: endre.willassen@uib.no. The application must indicate the academic background of the applicant and the topic and the present state of progress in the thesis work. Please add a recommendation from your supervisor.

Contact Endre Willassen (endre.willassen@uib.no) for questions about the course or Hugo de Boer (hugo.deboer@nhm.uio.no) for more information about ForBio.

ForBio workshop: Bayesian inference using BEAST

Time and place: Nov 2, 2015 09:00 AM Nov 6, 2015 05:00 PM, Natural History Museum, University of Oslo

The workshop aims to help those that have some experience of Bayesian model-based phylogenetics. The course focuses on issues relating to identification of priors, and the impact of different priors on posterior results.

Maximum number of participants is 26. If there are more than 26 applicants priority will be given to ForBio applicants best fulfilling the prerequisites given.

Application deadline is September 18, 2015.

For more information about the course: http://www.forbio.uio.no/events/courses/2015/beast_workshop_2015.pdf

To apply: https://nettskjema.uio.no/answer/67500.html

Contact Hugo de Boer (hugo.deboer@nhm.uio.no) or Stephan Nylinder (stephan.nylinder@nrm.se) for more information.