Monthly Archives: November 2017

clearout of B71 office – rackets

badminton, squash and tennis rackets and tennis balls – all good working order.

Will be donated to charity shops tomorrow.

2 PhD positions available

If you’re interested, please send which position you are interested in, your CV, a short letter of motivation, and e-mail addresses of two academic referees, to Julia.schroeder@imperial.ac.uk before 30 December 2017.

1)

Exciting opportunity to get top-notch quantitative analytical skills. In collaboration with Dr Danica Greetham from Reading University, and Terry Burke from UoS, we offer a PhD postion on linking infidelity with social networks in birds! Apply if you like stats and birds! Deadline 30 December 2017

https://goo.gl/kVkps5

Infidelity is common among many taxa with prevailing social monogamy, but we still do not know what shapes variation in, and drives the evolution of, extra-pair behaviour. Males are expected to reap fitness benefits from siring extra-pair offspring, because extra-pair fathers do not expend resources on costly parental care. This is, however, not the case for females who raise the resulting extra-pair young, posing the question of why females take part in extra-pair matings. The indirect benefits hypothesis explains female infidelity, where females benefit indirectly from better, or more compatible genes for their offspring. However, this hypothesis is not well supported empirically, evidenced by two contradictory meta-analyses on the topic, and ongoing discussion in the field. Specifically, only one long-term study that quantified life-time reproductive success supports the indirect fitness benefits hypothesis. Contradicting this result, extra-pair males have not been found to be superior, or more compatible, than a female’s within-pair male. Females were found to incur no indirect benefits, and even fitness costs by mating outside of their pair bond, suggesting that that this hypothesis does not satisfactorily explain why females cheat. Recently suggested novel, testable hypotheses provide a fresh perspective. These hypotheses explain female infidelity with intra- and intersexual antagonistic pleiotropy, and remain largely untested. This project aims to empirically test these hypotheses by using the powerful combination of long-term data from a wild population, state-of-the-art social network analysis and manipulative experiments on captive birds. This project will reap the benefits from long-term data in the wild, where precise fitness data and a genetic pedigree allow fitness costs and benefits to be measured, and quantitative genetic analyses. Given the long-standing conundrum of female extra-pair behaviour, this project has the potential forward this field significantly.

2)

Very cool project on trans-generational effects. We’ll use RNA sequencing experiments on sparrow sperm to detect epigenetic, trans-generational effects. This project on the forefront of epigenetics is super exciting because we have long-term data available, and the expertise from researchers at the Sanger Institute (Dr Katharina Gapp) and the Gurdon Institute University Cambridge (Prof Eric Miska) on board! If you like the lab, and birds, and field work, this is for you! Deadline 30 December 2017

https://goo.gl/iMDbtW

The current speed at which environmental conditions change is unprecedented, endangering vulnerable populations and species. A novel idea for how organisms can sustainably respond to rapid environmental changes are environmentally induced adaptations that are heritable. Such trans-generational, potentially epigenetic effects can, with high precision mediate evolutionary rescue of populations that experience rapidly changing environments. These advantages put TAGs at the forefront of mechanisms leading to adaptations to global change. This project will use long-term data from a wild population of passerines, and focused experiments on birds in captivity, to disentangle phenotypic plasticity induced during development from epigenetic TAGs, to better understand the epigenetic mechanism, and evolution of TAGs. We will use state-of-the art RNA-sequencing experiments (to be performed in the Sanger institute) to pinpoint TAGs in RNA methylation patterns in sparrow sperm, using focused experiments in captive and wild birds.

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

First footage of a wild otter in the Peak District !!

https://www.sheffield.ac.uk/news/nr/wild-otters-peak-district-population-study-1.744398

PhD position available at Imperial College London

Linking infidelity with behaviour in social networks

Project Description

Infidelity is common among many taxa with prevailing social monogamy, but we still do not know what shapes variation in, and drives the evolution of, extra-pair behaviour. Males are expected to reap fitness benefits from siring extra-pair offspring, because extra-pair fathers do not expend resources on costly parental care. This is, however, not the case for females who raise the resulting extra-pair young, posing the question of why females take part in extra-pair matings. The indirect benefits hypothesis explains female infidelity, where females benefit indirectly from better, or more compatible genes for their offspring. However, this hypothesis is not well supported empirically, evidenced by two contradictory meta-analyses on the topic, and ongoing discussion in the field. Specifically, only one long-term study that quantified life-time reproductive success supports the indirect fitness benefits hypothesis. Contradicting this result, extra-pair males have not been found to be superior, or more compatible, than a female’s within-pair male. Females were found to incur no indirect benefits, and even fitness costs by mating outside of their pair bond, suggesting that that this hypothesis does not satisfactorily explain why females cheat. Recently suggested novel, testable hypotheses provide a fresh perspective. These hypotheses explain female infidelity with intra- and intersexual antagonistic pleiotropy, and remain largely untested. This project aims to empirically test these hypotheses by using the powerful combination of long-term data from a wild population, state-of-the-art social network analysis and manipulative experiments on captive birds. This project will reap the benefits from long-term data in the wild, where precise fitness data and a genetic pedigree allow fitness costs and benefits to be measured, and quantitative genetic analyses. Given the long-standing conundrum of female extra-pair behaviour, this project has the potential forward this field significantly.

For more information, contact julia.schroeder[a]imperial.ac.uk

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)

25 genomes competition

Please go to this site and vote for your favourite species to be sequenced. Of course, that should be the scaly cricket!

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

PhD – Leibniz IZW, Berlin -Deadline 15/11

The Leibniz Institute for Zoo and Wildlife Research (Leibniz IZW) in Berlin is Germany’s premier wildlife research institute. The Leibniz IZW focuses on the life histories and mechanisms of evolutionary adaptations of mammals and birds, their limits and their conservation in natural and anthropogenically influenced environments. The institute operates within the fields of evolutionary ecology, evolutionary genetics, wildlife diseases, reproduction biology and reproduction management. For an interdisciplinary externally funded project on

Epigenetic stability and plasticity of social environmental effects

the Leibniz IZW offers

1 PhD-position (50%) in Bioinformatics, Metagenomics and Computational Biology.

The health consequences to hosts of the microbiome, i.e. intestinal bacteria, and of the eukaryotic biome, i.e. the intestinal community of fungi and other protozoans plus unicellular and multicellular eukaryotes, are receiving increasing attention. Intestinal biomes can have both beneficial and pathogenic effects. The aim of this PhD project is to determine how social status, and most intriguing, changes in social status, influence the composition, diversity and gene content of intestinal biomes in a highly social carnivore, the spotted hyena (Crocuta crocuta). In spotted hyenas as in other socially structured mammalian societies, social status determines access to food resources and thus profoundly affects key physiological processes, including investment in immunity, and Darwinian fitness. It is currently unknown whether social mobility over-rides life history trajectories set by the previous social environment.

Already collected faecal samples will be used to assess the composition and diversity of intestinal biomes in terms of mutualists, commensals and parasites under the supervision of Prof. Heitlinger. To identify differences in the gene content of the intestinal biome, a metagenomic approach will be used under the supervision of Prof. Soen. Status-specific differences in bacterial genes will then be related to status-specific differences in metabolism, host gene expression and immunity, which will be investigated in other project sections.

The position involves collaborative research between Prof. Emanuel Heitlinger, who holds a joint junior professorship position at Humboldt University Berlin/Leibniz Institute for Zoo and Wildlife Research (IZW) and Prof. Yoav Soen, who is the head of the Department of Biomolecular Sciences at the Weizmann Institute of Science in Israel. Longer, regular visits to the Weizmann Institute are required.

Prerequisites:

? Completed MSc in bioinformatics, computational biology, or biology;

? Programming skills (e.g. Python, R) and proficiency working in a Unix/Linux command line environment;

? Background in statistical data analysis and good understanding of underlying mathematical principles;

? Experience in analyses of large scale sequencing datasets are beneficial, ideally for gut microbiome analyses, transcriptomics or similar;

? Experience working in a molecular biology laboratory is required, ideally experience in metagenomics;

? Experience with databases for computational biology;

? Reliability, high motivation and efficiency; ability to work independently and as part of a team;

? Strong organisational and communication skills; willingness to engage in collaboration for successful and timely implementation of the project and publication of results;

? Proficiency in English.

We offer state-of-the-art methodology and a stimulating research environment in an interdisciplinary, collaborative project. The position will start January 1st, 2018 and is limited to three years. Salary is 50 % according to TVöD (Bund). The place of employment is the Leibniz Institute for Zoo and Wildlife Research (Leibniz IZW), Alfred-Kowalke-Str. 17, 10315 Berlin (Germany).

As a member of the Leibniz Association the Leibniz IZW is an equal opportunity employer, determined to increase the proportion of women in successful scientific careers, and particularly encourages women to apply. Preference will be given to disabled applicants with the same qualifications. Enquiries or further questions should be directed to Prof. Emanuel Heitlinger (emanuel.heitlinger@hu-berlin.de) and Prof. Yoav Soen (yoavs@weizmann.ac.il).

Applicants should upload a letter explaining their interests in and particular skills for this position, a CV, copies of relevant degrees, list of publications and names and contact details of two referees preferably before 15th of November 2017 (with interviews scheduled to be at the Leibniz IZW on the 5th December 2017 from 9 am onwards) via IZW’s online-job- application facility http://www.leibniz-izw.de/jobs-training.html) button Apply online”.