Monthly Archives: November 2015

Lab Meeting: December 1st, 11:30pm, Common Room

The next Molecular Ecology lab meeting will take place on December 1st at 11:30am in the Common Room. D floor, Alfred Denny Building. This month we will hear from Anna Krystalli and Malika Ihle.

Anna will present “Don’t just sit there, interact!: Building interactive exploratory data apps with shiny and plotly in R”

Malika will present “The fitness benefits of love”

Her PhD research has focused on testing whether there is any kind of mate choice for genetic compatibility: do females avoid breeding with their siblings? Do they choose genetically compatible males with whom they do not get a high rate of embryo mortality? Or can they compensate any genetic incompatibility with their partner by engaging in extra-pair copulation? Additionally or alternatively, do they choose behaviorally compatible males with whom they are better able to raise chicks?

She will present here only one of the experiments she ran during her PhD: a four year experiment recently published in PLoS Biology and entitled ‘the fitness benefits of mate choice for compatibility in a socially monogamous species’.

Welcome to Lara Meade and Andy Buxton

Lara and Andy are visiting the Facility. Lara will study sexual selection in stalk-eyed flies and Andy will use eDNA to assess the abundance of great crested newts.

R packages for population genetics

Thought might be useful for many people:

http://nescent.github.io/popgenInfo/

https://github.com/NESCent/r-popgen-hackathon

Cheers,
Ludo

PhD opportunity – foraging patterns of albatrosses and petrels

NERC DTP PhD opportunity (joint between BAS and Cambridge University Dept. of Zoology)

Details of the project and how to apply can be found at:

B213: Constraint and compromise: the importance of intrinsic and extrinsic factors in shaping the foraging patterns of albatrosses and petrels

http://essdtp.esc.cam.ac.uk/programme/biology-theme/b213-constraint-and-compromise

Congratulations to Bilal and family

Bilal’s wife had a baby boy on Tuesday night (2 weeks late).
It was a normal delivery and all went well. Mum, Dad and Sister are all delighted.

year, full time postdoctoral researcher in School of Biological Sciences, Bangor, UK

Understanding the ecological relevance of eDNA in freshwater lotic ecosystems

We are looking for a dynamic researcher to fulfil a leading role in a new, collaborative and multidisciplinary team working at the leading edge of environmental DNA (eDNA) analyses in order to advance our knowledge of the ecological relevance of eDNA in freshwater systems. Molecular biodiversity identification is emerging as a high throughput and cost effective alternative to traditional approaches and in particular, the analysis of ‘free’ environmental DNA (eDNA) provides an opportunity to measure biodiversity in space and time at unprecedented scales. Understanding how sources of eDNA relate to living biodiversity, land use and associated ecological function are focal aims of the project. The 4 year, £1.25M project led by Dr. Si Creer (http://mefgl.bangor.ac.uk/staff/si.php) is funded by the first round of NERC Highlight Topic funding (http://www.nerc.ac.uk/research/portfolio/strategic/topics/) and features collaborations with Cardiff University (Isabelle Durance; Steve Ormerod), the NERC Centre for Ecology and Hydrology (Jack Cosby, Bridget Emmett) and the Birmingham Joint Centre for Environmental – Omics (JCEO – John Colbourne). The project will utilise novel molecular ecological workflows, including genomic approaches to assess biodiversity, bioinformatics and ecological modelling working with a large team of collaborators and an international steering committee comprising leading representatives from the field of eDNA (including David Lodge, Mike Pfrender, Pierre Taberlet, Holly Bik, Peter Kille, Kristy Deiner and Xin Zhou), end-users and stakeholders.
Candidates should possess a doctoral degree in related areas such as natural sciences, ecology, evolution/genomics and should have previous experience of fieldwork, molecular ecology, high throughput sequencing, bioinformatics and modelling. The ability to drive, in addition to being physically fit to undertake fieldwork, and excellent team working and communication skills are essential.
The successful candidate (£31,656 – £37,768 pa; Grade 7) will be expected to commence in January 2016, or as soon after this as possible. Applications will only be accepted via the on-line recruitment website (https://jobs.bangor.ac.uk/; ref: BU01021). However, in cases of access issues due to disability, paper application forms are available by telephoning +44 (0) 1248 383865. Closing date for applications: 6th December, 2015 with interviews aimed to schedule first week in January.
Please contact Si Creer (s.creer@bangor.ac.uk; http://mefgl.bangor.ac.uk/staff/si.php; @spideycreer) in the first instance, copied to Mark De Bruyn (markus.debruyn@gmail.com) and Gary Carvalho (g.r.carvalho@bangor.ac.uk) for further information.

Lara looking for a room

Hello,

I am a PhD student visiting from UCL and looking to find a spare room for my stay. I will be arriving on the 23rd of November and staying until the 9th of December. If you have, or know anybody that has a spare room that I would be able to stay in, please contact me at lara.meade .13 (at) ucl.ac.uk

Thanks!

Lara

Course on Programming for Evolutionary Biology

When: February 10th – February 27th 2016

Location: Leipzig, Germany

Application deadline: December 20th 2015

Detailed information about the course content and how to apply:

http://evop.bioinf.uni-leipzig.de/

In this intensive 18 days course, students will learn how to survive in a
Linux environment, get hands-on experience in two widely used programming
languages (Python and R), and statistical data analysis. The classes will be
given by experts in the field and consist of lectures and exercises with
the computer. The aim of the course is to provide the students with the
necessary background and skills to perform computational analyses with a
focus on solving research questions related to genomics and evolution. The
philosophy of the course will be “learning by doing”, which means that the
computational skills will be taught using examples and real data from
evolutionary biology for the exercises. During the course, students will
also propose projects of their own interest and perform them as final
projects in small groups under the supervision of a teaching assistant.
This summer school is open for students from all countries and targeted
toward PhD students and postdocs of evolutionary biology or related
research fields with no or little programming experience who want to
become proficient in computational evolutionary biology in a couple of
weeks.

The course takes place at the University of Leipzig.

Postdoc position available on fungal adaptation

Please find below a two-years postdoc position open to any non-French citizen.

Ludo

A two-year postdoctoral position in molecular plant pathology at INRA Angers, France (non-French citizens only)

Applications are invited for a postdoctoral position to study molecular
determinants underlying adaptation of pathogenic fungi to their host plants, in the EcoFun team of the Horticulture and Seed Research Institute (IRHS). Our lab conducts research on the interaction between the scab fungus Venturia inaequalis and its host plants, including domesticated and wild apple trees, and firethorn. Host shifts between these hosts have been reported, making this pathosystem an adequate model to identify genes involved in fungal adaptation to different host plants. The research will employ interdisciplinary approaches, including molecular biology, microscopy and RNA-seq analyses. The first task of this position will be to take ownership of population genomic resequencing data to identify genes present in isolates that are pathogenic on a single host only. The second task will be to determine at which stages of the infection process genes involved in adaptation to different host plants are expressed, using confocal and MEB microscopy of incompatible interactions. This knowledge will be
used in a third task to harvest infected leaves for deep transcriptome sequencing (RNA-seq) and identify genes that are specifically expressed on a given host. The successful candidate is also expected to contribute to the writing of research publications and to help with student supervision.

Job requirements
Candidates should have or expected to obtain a PhD in Biology, Molecular Biology, Functional Genomics, or a closely related subject. Skills in Next Generation Sequencing data analysis are highly desirable. Candidates with a PhD in Bioinformatics are also highly encouraged to apply. Experience in fungi and practical knowledge in molecular biology, microscopy and bioinformatics are advantageous. Candidates must have proficiency in oral and written English. This position is available for non-French citizens only.

Job details
The position is full-time for 24 months and is available to start as early as 1st January 2016. Basic gross salary on appointment will be between €2,200 and €3,100 per month depending on experience. The applicant will have the possibility to obtain an additional mobility allowance from the AgreenSkills and AgreenSkills+ schemes, ranging from €1,300 to €1,700 per month depending on experience (www.agreenskills.eu).

Application
The position is open until filled.
Applications should include a cover letter summarizing your experience and describing your research interests, a curriculum vita, and at least two references.
Applications should be emailed to jerome.collemare@angers.inra.fr.
For further information, please contact Dr. J. Collemare
(email: jerome.collemare@angers.inra.fr; tel.: +33(0) 2 41 22 57 15)

Organization description
Institut de Recherche en Horticulture et Semences (IRHS)
UMR1345 INRA – Université d’Angers – Agro Campus Ouest
Evolutionary Ecology of Fungi (EcoFun)
42 rue Georges Morel
49071 Beaucouzé Cedex

http://www6.angers-nantes.inra.fr/irhs/Recherche/EcoFun

The candidate will be located in IRHS, Angers, which leads research on Rosaceae plants and seeds in France, including research on fungi and bacteria pathogenic on apple, pear and rose. The position will provide access to local excellent technical centres in molecular biology and microscopy (laser-scanning confocal microscope, table electron-scanning microscope). The candidate will have the opportunity to interact with other research teams within the institute; and will
interact with scientists with knowledge in functional genomics, population genetics and genomics, epidemiology and modelling within the EcoFun team.

Life in the Loire Valley
The laboratory is located near Angers, in the Loire Valley. This region is often called the garden of France because of fruits and vegetables production, and green calm landscapes. It is also famous for a gentle way of life, high quality regional food and wines. The banks of the Loire River are very touristic in summer, they offer diverse outdoor activities, including biking and visiting the numerous castles.

Facility visitor looking for a room from 23rd Nov

Dear All,

My name is Andrew Buxton, I am a PhD candidate with DICE at the University of Kent, I work with environmental DNA and Great Crested Newts. I will be visiting the NBAF facility in Sheffiled on and off over the next year with my first stint from the 23rd of November until mid to late February. If any body knows of a room to rent please let me know, my email is asb40 (at) kent.ac.uk

Thank you