Author Archives: Jon Slate

4 year postdoc – fur seal genomics, including fieldwork in the Antarctic

Position is with Joe Hoffman (Bielefeld University, Germany).
Details here: fur seal advertisment
Note the deadline is early January.

Jon

PhD opportunity in Edinburgh

Phd with Craig Walling (Edinburgh) on the red deer population on Rum.

Details are here: Walling_PhDAdvert_ForEmail

Journals – free to a good home

Dear all

I’m planning a bit of an office tidy-up and I have a lot of journals that I want to get rid of. I don’t imagine anybody will want them, but just in case, the following are free to whoever would like them:

Molecular Ecology – 1992-2010 (all issues)
Evolution 2000-2010 (all issues)
Molecular Ecology Notes/Resources 2001-2010 (all issues)
Journal of Evolutionary Biology 2007-2010 (all issues)

I don’t imagine the library will want them, but will try there as well.

Let me know (j.slate@sheffield.ac.uk) if you would like them.
Jon

Two funded PhD projects in evolution/genetics/genomics/development of snails, Dec 8th deadline

The Davison lab at the University of Nottingham is seeking enthusiastic and well-qualified students to apply for two PhD positions, both funded by the BBSRC DTP. Full details here; apply here. I would strongly encourage good candidates to email me if you have any queries prior to the application; feel free to contact current PhD students Daniel or Hannah if you have any queries relating to lab life / the University / Nottingham.

In previous research, the Davison-lab led an international team dedicated to finding the gene that determines mirror image development (“chirality”) in the pond snail, Lymnaea stagnalis. More generally, we are using molluscan genomics, with projects dedicated to finding evolutionary interesting genes, whether chiral variation in Japanese Euhadra or the colour polymorphism / supergene of Cepaea. Field work and foreign lab work is always an option – recent students spent 5 months in a German lab or undertook field work in Japan; current PhD students are working in the Spanish Pyrenees and Hawaii. The lab also has a strong background in science communication.

Project #1: “The evolution and development of left-right asymmetry in snails”

Project supervisors: Dr Angus Davison and Dr William Brown, University of Nottingham, UK.

While invariant left/right asymmetry appears to be the rule in nearly all animals, until recently it has not been clear if the path to asymmetry is conserved. In recent research we identified the one in a billion base pair change that determines mirror image development (“chirality”) in the pond snail. As we also showed that the same gene is similarly involved in setting up asymmetry in the frog, then our work that began in snails ultimately revealed one of the earliest common symmetry-breaking steps across the whole of the Bilateria. The next stage is to ‘unravel’ symmetry breaking at the molecular and cellular level, in particular to find the set of genes that first establish asymmetry. In this exciting and fast-moving, the student will seek to understand the mechanics of the very earliest symmetry-breaking steps using Lymnaea stagnalis pond snails, or another species. Most likely, this will involve a range of techniques, from micromanipulation to genomics/bioinformatics, and possibly fieldwork – with the balance determined by the interests of the student.

The project is competitively funded through the ‘Molecules, Cells and Organisms’ stream of the Nottingham BBSRC DTP. Applicants should have, or expect to get, a First Class or Upper Second degree or equivalent in a relevant subject. Further experience, including a Masters degree, is likely to be advantageous. Applications are open to UK + EU residents (EU students will be considered and may be eligible for full funding). This project is also advertised here and here on Findaphd.

Project #2: “Genetic approaches to understanding molluscan crop pests”

Project supervisors: Dr Angus Davison, Dr Chris Wade and Dr Matt Loose, University of Nottingham, UK.

Snails and slugs cause worldwide problems, both in terms of direct damage to crops, and as intermediate vectors for diseases of farm animals. Yet, they are difficult to identify and we have little idea of what influences their distributions, hindering appropriate control measures. Genetic techniques offer a potential solution in that they can be used to understand gene-flow, the relationship and taxonomy of different species, and, ultimately, the genes involved in enabling adaptation to human-affected environments. However, molluscs in general are relatively lacking in genomic resources, partly because they generally have large genomes, but also because there is no single model mollusc to drive research forward. In this project, the student will apply population genetic, phylogenetic and genomic methods (e.g. RAD-seq) to a tropical snail species, with a view to understanding the adaptations that enable it to become invasive. With suitable resources in place, we hope to get a more general picture of invasive species and crop pests.

Note: this project and the lab rotations that come before it will be run as a ‘training triangle’, involving training in population genetics, phylogenetics and genomics. We anticipate that the final PhD research project will involve a balance of these different aspects, dependent upon the interests and skills of the students.

The project is competitively funded through the ‘AFS’ stream of the Nottingham BBSRC DTP. Applicants should have, or expect to get, a First Class or Upper Second degree or equivalent in a relevant subject. Further experience, including a Masters degree, is likely to be advantageous. Applications are open to UK + EU residents (EU students will be considered and may be eligible for full funding). This project is also advertised here

As part of the Sanger 25th anniversary celebration, the public is being asked to vote on which species should have their genome sequenced. The original plan had been to sequence ‘Jeremy’ but following an untimely death, Jeremy’s partner ‘Tomeu’ is representing the brown garden snail.

Vote snail! https://25genomes.imascientist.org.uk/2017/11/06/voting-is-open/

All about team Tomeu and the brown garden snail: https://iconic25.imascientist.org.uk/profile/browngardensnail/

Dr. Angus Davison
Reader and Associate Professor in Evolutionary Genetics
School of Life Sciences
University Park
University of Nottingham
NG7 2RD
0115 8230322

angus.davison@nottingham.ac.uk
angusdavison.org

@angus_davison (or @leftysnail)

Conservation Genetics job – Edinburgh Zoo / WildGenes

The role

Due to the expansion of our team, an opportunity has arisen for a committed researcher to join the Royal Zoological Society of Scotland WildGenes lab. Reporting to the Conservation Programme Manager – Wildgenes in our Conservation team, the successful candidate will initiate, implement and disseminate conservation genetics projects in the WildGenes laboratory. Duties include assisting with the project management and analysis of genetic data for a diverse portfolio of conservation genetic projects.

Who we are looking for

The successful candidate will have a PhD in Conservation Genetics or Population Genetics/Genomics, a proven track record of scientific publication, and a commitment to conservation. You will enjoy working at multiple levels, from complex data analysis to presenting results to a wide range of audiences. Since our projects are based across the globe, the role will involve international travel and willingness to travel to attend meetings is therefore essential.

Applicants with additional background in any of the following disciplines will be welcomed: Quantitative Genetics, Population Modelling, Bioinformatics, Project Management within the conservation sector.

Closing date:      Sunday 28 May 2017

Dr Helen Senn

WildGenes Programme Manager
0131 314 0317  hsenn@rzss.org.uk

Great postdoc position with Frank Chan (Max Planck Institute, Tubingen)

POSTDOC IN GENOMICS OF SELECTION RESPONSE IN MICE
Friedrich Miescher Laboratory, Max Planck Campus, Tübingen, Germany
A postdoctoral researcher position is available in the Chan Lab to work on a unique genomics dataset in mice, with the aim of understanding the molecular basis of phenotypic variation and response to selection in a population genetics and quantitative genetics framework.

We’re looking for a postdoc skilled in population and/or statistical genomics to take on the analysis of a replicated artificial selection experiment in mice. In order to study major morphological changes in a model organism, our collaborator, Dr. Campbell ROLIAN (Univ. of Calgary, Canada), has performed artificial selection for increased tibia length in mice (2 “Longshanks” selection lines & 1 control line, >6000 total individuals; see Marchini et al., 2014). Over 21 generations, the Longshanks selection experiment has produced 15-20% increase in tibia length but unchanged body mass relative to random-bred controls.

Having retained nearly all individuals from the entire selection experiment, we are now nearly finished with complete re-sequencing of all available breeders (~1800 individuals) in both Longshanks and control lines, with the ultimate goal of re-tracing the entire selection experiment in every individual, at every locus, in the entire genome.

You will work with the complete dataset in close coordination with Prof. Nick BARTON (IST Austria) and his team to link theory with empirical genomic data. Candidates must have a strong background in bioinformatics, including experience with genomic data analysis and strong quantitative and programming skills. Further background in population genetics and modelling will be an advantage. The postdoc will work closely with Prof. BARTON’s group, therefore she or he must show independence and ability to drive her/his own research project. You will enjoy excellent computational and sequencing support, as well as the opportunity to design and conduct functional tests in mice together with our wet-bench team members.
Our on-going work has found many loci showing very strong response to selection, with a substantial fraction of parallel response. Further dissection of top loci has identified specific mutations in limb enhancers. Our functional test in mice showed that these mutations modulate enhancer activity in a way consistent with increased tibia length.
Together with the ROLIAN and BARTON groups, we will study the selection response from multiple angles, ranging from trait mapping, population genomics, theory to developmental genetics. The Longshanks selection experiment combines quantitative, developmental and population genetics and offers a unique opportunity to study how the genome responds to strong selection in a model paradigm.
The Max Planck Campus in Tübingen, Germany is one of the leading campuses in evolutionary genomics research. The Chan Lab enjoys generous funding support by the Max Planck Society as well as the European Research Council (ERC). Our campus hosts world-class research groups, including a Nobel laureate and multiple ERC-funded teams (groups active in evolutionary genomics include Felicity Jones, Detlef Weigel, Ralf Sommer and Ruth Ley). We operate state-of-the-art sequencing (Illumina, PacBio and others) and other core facilities. All seminars and communications are in English.
For informal enquiries and applications (cover letter, CV, and two reference contacts), please e-mail frank.chan@tue.mpg.de. Consideration of applications will begin on 14 May, 2017, with a target start date of Sept 2017. The actual start is flexible.

[1] Marchini M., Sparrow, L.M., … Rolian C., BMC Evolutionary Biology 2014 14:258, doi: 10.1186/s12862-014-0258-0

[2] Cosman M.N., Sparrow, L.M., Rolian, C., Journal of Anatomy, 2016 228:6, doi: 10.1111/joa.12459


******************************

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Frank Chan
Max Planck Research Group Leader
Friedrich Miescher Laboratory of the Max Planck Society
Spemannstrasse 39
72076 Tübingen
Germany

T: +49 (0)7071 601 888
F: +49 (0)7071 601 801
@: frank.chan@tue.mpg.de
http://www.fml.tuebingen.mpg.de/chan-group.html
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PhD opportunity – Sheffield; Evolutionary dynamics of the avian sex chromosomes

Alison Wright, a NERC fellow coming to Sheffield in Jan 2017, has this PhD opportunity advertised. Details are here – AlisonWrightPhDAdvert. It’s a great opportunity to work with a rising star.

Seminar today (Friday 15th July) – Common Room 1PM

Clive Darwell (Okinawa Institute of Science and Technology Graduate University) will give a talk on:
Community Assembly in South-East Asian fig wasps.

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.

Message from Jarek Bryk (U of Huddersfield)

Dear Colleagues,

I am writing to let you know about a new funding opportunity you may not otherwise hear about. Polish National Science Centre has announced a “Polonez” funding for researchers who want to spend up to two years doing basic science research in Poland (open to all disciplines). The financial conditions are quite favourable (4350 Euro gross monthly salary with full employment, plus extras for family allowance) and research grants for up to 160000 PLN (~30000 GBP, ~40000 Euro) for two years for a life science project. The starting date is September 2016, and the deadline for applications is December 15th.

The call and more details are here: https://ncn.gov.pl/polonez?language=en and you can email me (j.bryk@hud.ac.uk) if you’re looking for a project and/or need some help or advice in selecting or contacting a potential host institution in Poland.