Monthly Archives: November 2013

PhD in Nottingham

Funding is available for a four year BBSRC DTP PhD studentship (deadline 5th January), to be awarded on a competitive basis within the University of Nottingham, to investigate the speciation of snails using next generation DNA sequencing methods

Speciation on a snail’s scale
Snails and slugs are a major crop pest, with a few introduced species causing massive worldwide problems. They are difficult to identify, and part of the second most species-rich animal group - yet we have no good idea of how this biodiversity has come about. This project will use next generation sequencing methods to investigate the speciation of snails, especially with respect to characters under natural and artificial selection (e.g. shell colour and banding or molluscide resistance), and including methods that may help identify cryptic species. Although the precise nature of the project will be determined by the state of play when the project begins and the interests of the student, I envisage that he/she will use mapping and expression methods to home in on the genes in question. He/she may also develop new species/models to study (possibly involving fieldwork in Europe or Asia), enabling deeper comparative analyses. The student will receive training in standard molecular lab methods, next generation sequencing and bioinformatic methods.

Representative publications from existing students
Richards, PM, Liu, MM, Lowe, N, Davey, JW, Blaxter, ML and Davison, A (2013) RAD-Seq derived markers flank the shell colour and banding loci of the Cepaea nemoralis supergene. Molecular Ecology 22: 3077-3089. http://onlinelibrary.wiley.com/doi/10.1111/mec.12262/full

Grindon, AJ and Davison, A (2013). Irish Cepaea nemoralis land snails have a cryptic Franco-Iberian origin that is most easily explained by the movements of Mesolithic humans. PLoS One 8, e65792. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0065792

Applicants should have, or expect to receive, a good degree in a relevant subject, and an interest and enthusiasm for evolution. In the first instance, prospective students should send a CV and an indication of general area of interest to angus.davison@nottingham.ac.uk; see also angusdavison.org

Funding details:

Funding is available for four years from Autumn 2014. A full award would be fees plus an annual stipend.

Eligibility:
Eligibility for full funding is restricted to UK residents (fees and stipend). EU students are eligible for fees only awards, unless the applicants fulfil the residency criteria for a full award. To be eligible applicants must have (or be expected to achieve) a first or upper second class UK honours degree, or the equivalent qualifications gained outside the UK and/or a postgraduate Masters degree in a relevant subject. For full eligibility criteria visit: http://www.bbsrc.ac.uk/web/FILES/Guidelines/studentship_eligibility.pdf

How to apply:
Applicants should go to www.nottingham.ac.uk/bbdtp to download the application and reference forms. Note that an important part of this BBSRC DTP scheme is a lab rotation during the first year. A full list of the possible projects is here, http://www.nottingham.ac.uk/graduateschool/doctoral-training-centres/bbsrc-doctoral-training-programme-in-biosciences/prospective-students/available-projects/available-projects-new.aspx

Dr. Angus Davison
Reader in Evolutionary Genetics
School of Life Sciences
Life Sciences Building
University Park
University of Nottingham
NG7 2RD

0115 8230322
angus.davison@nottingham.ac.uk
www.angusdavison.org

Genomics Software Repository on Iceberg, the High Performance Computing Cluster at the University of Sheffield

To develop and support the analytical infrastructure of the Molecular Ecology Group at the University of Sheffield, a Genomics Software Repository has been established.

The Genomics Software Repository is a shared folder on Iceberg, the High Performance Computing Cluster at the University of Sheffield. The aim of the Genomics Software Repository is to facilitate NGS data and population genetic/genomic analyses using the Iceberg platform. The shared folder contains installed and enabled NGS and population genetic/genomic softwares (e.g. BEAST, Colony, STACKS, GATK). Softwares can be run by including a directory pathway to the software in the job submission script. The advantage is it removes the necessity for the user to install softwares to their personal folder. Additionally the shared folder contains example job submission scripts for various analyses that can be copied and modified by the user and some tutorials for how to run softwares.

The Genomics Software Repository shared folder is accessible from this directory:  /usr/local/extras/Genomics

Example job submission scripts are available to copy to your user profile from this directory:

/usr/local/extras/Genomics/submit_scripts

All Iceberg users have access to Genomics Software Repository; however, to access you must be on a worker node (and not the head node).

For more information and a list of installed softwares, access the Genomics Software Repository website from following Genomics link at:

http://www.shef.ac.uk/molecol/software/

We’re launching the Genomics Software Repository and website today to coincide with the final session of the High Performance Computing Course at APS that is supporting training to access these communal resources for NGS and population genetic/genomic analyses.

Best of luck with your future research!

Caitriona McInerney and Victor Soria-Carrasco

Molecular ecology group meeting Tuesday 3rd December, 10am B52

Dear all,

Our next molecular ecology group meeting will take place the next week on Tuesday 3rd December, 10am at B52.
We will hear talks from Jun-Mo Kim and Haris Pilidis.

Jun-Mo: “Development of high-density SNP Chip for the great tit bird”

There are currently 30-min slots available for speakers to give presentations on January 7th and from April 1st on. I am afraid February and March are now full. Please let me know if you wish to give a talk (m.montano@sheffield.ac.uk).

Kind regards,

Mauricio Montaño-Rendón

Improvements in extracting DNA from feathers

Bayard De Volo et al. 2008 AN IMPROVED EXTRACTION METHOD TO INCREASE DNA YIELD FROM MOLTED FEATHERS. The Condor 110(4):762-767

If anyone tests this method, please let me know how it works out.
thanks
debs

message from Julia Schroeder re PhD positions

The International Max Planck Research School (IMPRS) for Organismal Biology offers several fully-funded PhD positions. The IMPRS is based in southern Germany and is jointly organized by the Max Planck Institute for Ornithology in Seewiesen and Radolfzell and the University of Konstanz. Outstanding students of all nationalities with a deep commitment to basic research in Organismal Biology are invited to apply.  More than 25 internationally recognized research groups actively participate in the PhD program and offer challenging, cutting-edge PhD projects in the fields of Behavioral Biology, Ecology, Evolutionary Biology, Physiology, and Neurobiology. For a list of all available PhD projects visit www.orn.mpg.de/projects.  All students accepted to the program will be supported by stipends or contracts. The program offers a dedicated teaching program, high quality research experience, and outstanding research facilities in an inspiring research and living environment. The working language is English. Each PhD student receives individual supervision and mentoring and is guided in her/his research work by a PhD advisory committee.  Deadline for the application is January 15, 2014. Interviews with the applicants are scheduled for Mid-March. Candidates accepted into the program may start latest September 2013. The Max Planck Society and the University of Konstanz are equal opportunity employers.  Qualification: Applicants should hold a MSc or equivalent degree in biology or a related discipline at the point of enrollment.  Queries should be mailed to the program office: IMPRS@uni-konstanz.de Application: For the online application process visit www.orn.mpg.de/application .  More information at www.orn.mpg.de/IMPRS and www.facebook.com/OrganismalBiology .  IMPRS <IMPRS@uni-konstanz.de>

Celine has moved to lab office

Dear all,

I’ve moved to the lab office in B71. This is where you can find me if you need to organise a meeting with Terry!

Celine

Pop Group conference – earlybird deadline tomorrow 22nd

PopGroup47 will be taking place in the historic city of Bath from the 7th to the 10th of January 2014.

The Population Genetics Group (PGG or PopGroup) is a yearly international meeting held in the UK. Despite its name, the meeting covers all aspects of Evolutionary Genetics. You can get good feel for the typical content can be gained by downloading some of the previous years¢ programmes (http://www.populationgeneticsgroup.org/index.php?page=previous_meetings). Popgroup is an informal meeting, with typically 200-250 participants, and an excellent place for PhD students to present their work.

We are delighted that this PopGroup installment will also host the Fisher award lecture by Prof. William Hill.

Other plenary speakers include:
Prof. Josephine Pemberton, Dr Lilach Hadany and Dr Fyodor Kondrashov

Registration is open and will remain so until the 2nd of December.
Costs = if registering before the 22nd of November – £180 for regular participants and £150 for students
registering between November 22nd and December 2nd – £200 for regular participants and £170 for students
with a £10 discount for Genetics Society members.

Deadline for abstract submission is on the 2nd of December.

Please visit the PopGroup website (www.populationgeneticsgroup.org) for more details.

Best regards and hope to see you all here at Bath this winter.
Nicholas Priest, Araxi Urrutia and the rest of the Popgroup47@BATH team.

1st Young Natural History scientists’ Meeting

Hi all,

below is an announce for the first Young Natural History scientists’ Meeting hosted at the MNHN, Paris, France on February 12th-14th, 2014.

The Bureau des Doctorants et Étudiants du Muséum (association for students and young researchers working at the Muséum national d’Histoire naturelle, Paris) is pleased to announce the opening registration (for free) and abstract submission to the first Young Natural History scientists’ Meeting hosted at the MNHN, Paris, France on February 12th-14th, 2014.

We invite submissions for oral and poster presentations on all aspects of natural history within four broad themes:

- Biodiversity Dynamics and Conservation
- Earth and Planetary Sciences
- Mankind, Prehistory, Nature and Societies
- Systematics, Evolution and Comparative Anatomy

Abstract should include name(s) of author(s) and their address(es), a succint title and a text (no more than 300 words), sent by email (indicating if you want to present a talk or a poster) to assobdem@mnhn.fr. Abstract submission deadline is January 19th, 2014.

More information can be found in the first circular, attached to this email.

Please feel free to circulate to colleagues who may be interested in attending, and don’t hesitate to get in touch if you have any questions about the meeting (assobdem@mnhn.fr).

We look forward to meet you in Paris!

Kind regards,

Lab Christmas Meal!

Christmas is coming! Time for the most important decision you’ll make this year… Your food choice for the Molecular Ecology Lab Christmas Meal!

This year, by popular demand, the meal will be at the Scotsman’s Pack in Hathersage, at 2pm on Friday 13th December.

Transport will be by train or bus, or you’re welcome to make your own arrangements. We’ll send out a more detailed travel plan nearer the time. For now, we just need your food choices by Friday 29th November :)

The menus – one for Christmas food and two for standard pub food (inc. veggie options) – can be perused by the central doors in the lab, or in the coffee room.

Please write down your choices on the list in the lab, or if you’re away, just email ndosremedios@hotmail.co.uk.

Lastly, making a come back this year will be Secret Santa! Please let us know whether you’d like to take part, along with your food choices, by Friday 29th November.

Christmassy wishes!

Natalie & Katy

Accommodation needed

PhD student from Seewiesen is looking for a furnished room to rent for the next 3 weeks. Best would be in walking distance to the department. I am already in the lab, and ideally would like to move places asap. I am afraid, I have a limited budget, so rent incl. all bills should not exceed 60 GBP per week. I am aware that this is very short notice, but maybe somebody has a spare room, or knows somebody who has?
I look forward to hearing from you.

Sincerely, Antje Girndt