Monthly Archives: December 2015

iCASE PhD studentship: Next-generation sequencing in birds of prey

please see attached for details.
CAM iCASE advert

Assistant Professor and ‘Senior scientist’ positions in Vienna

See attached for details

Funded PhD on senescence in European badgers, U Leeds

Early-life environment effects on telomere dynamics in European badgers

Lead supervisor: Dr Hannah Dugdale (U Leeds)
Co-supervisors: Dr Amanda Bretman (U Leeds), Prof David Macdonald (U Oxford), Dr Chris Newman (U Oxford)

Death is inevitable, but the quality of life prior to death varies enormously. This is because individuals differ in the point and rate at which they senesce – senescence being the loss of function with age, from the cellular to the organism level. Our understanding of the factors that affect senescence is limited: Within a species, are some individuals better able to buffer against senescence due to physiological adaptations (such as greater oxidative damage resistance and longer protective chromosome caps – termed telomeres), environmental effects (e.g. born in years with high food availability), or social conditions (e.g. low levels of intra-sexual competition)? This PhD project will investigate these questions, using data from a natural population subject to variable environmental and social conditions. This will generate critical knowledge that will improve our understanding how and why some individuals live longer, healthier lives than others, potentially contributing to both human and animal health interventions.

This PhD has the exciting opportunity to use long-term data from a wild population of European badgers in Wytham Woods, Oxford, UK. These badgers live in social groups of variable size that on average have six adult males and six adult females. Within this population female badgers show an earlier onset and a shallower rate of reproductive senescence than males, but it is not clear why these sex differences in senescence occur. In another UK badger population, sex differences in somatic senescence rates have been linked to the level of intra-sexual competition that individuals experience in the first two years of adulthood. It is also apparent that stressful environmental conditions in early life, such as low food availability and exposure to disease, can accelerate senescence. This PhD will therefore use telomeres as a bio-molecular measure of senescence, in relation to somatic, actuarial and reproductive senescence. This is important as we currently have very little understanding of how both the onset and the rate of senescence, from the bio-molecular to reproductive levels, are influenced by environmental conditions.

The student wil

2 Funded PhDs on Seychelles warblers

1) Conservation genomics of the Seychelles warbler

Lead supervisor: Prof Terry Burke, Sheffield.
Co-supervisors: Prof Steve Paterson, Liverpool; Dr Hannah Dugdale, Leeds

In the 1960s, the Seychelles warbler was reduced to a single population of <30 birds on Cousin Island. The population later recovered ten-fold due to habitat restoration and has since increased through translocations to four other islands. The global population was however historically vastly larger and an intensive 20-year study of the life history of the entire Cousin population has recorded negative effects of inbreeding on fitness. As the bottleneck in this species was recent and the contemporary population size remains historically small, we hypothesize that genetic variation will continue to be eroded by inbreeding. This project will conduct one of the first conservation genomic analyses, assessing regions of the Seychelles warbler genome that contribute to inbreeding effects. It will model the population size required to maintain extant genomic diversity and so inform future management plans of this and other species of conservation concern. Applicants should have a keen interest in learning field and laboratory skills, including next generation sequencing techniques. They will be trained in population bioinformatics, statistics, conservation genetics, and evolutionary theory. Along with the standard application, applicants should submit a one-page PhD proposal. This PhD project is part of the NERC funded Doctoral Training Partnership “ACCE” (Adapting to the Challenges of a Changing Environment). This is a partnership between the Universities of Sheffield, Liverpool, York and the Centre for Ecology and Hydrology. For more information, visit: Application: via Deadline: Monday, January 11, 2016 2) Offspring or survival: Antagonistic effects and the maintenance of genetic variation in an isolated island population of Seychelles warblers

Lead supervisor: Dr Richardson, University of East Anglia.
Co-supervisors: Dr Hannah Dugdale, Leeds; Prof Terry Burke, Sheffield; Prof Jan Komdeur, Groningen

This project will investigate how different mechanisms – including antagonistic effects on survival and reproduction – interact to maintain genetic variation within a population of the Seychelles warbler.

Genetic variation provides the building blocks for evolution and underpins biodiversity. It is key to the adaptive potential of populations, affecting their probability of extinction. How genetic variation is maintained in natural populations, especially small ones, is therefore a fundamental question in evolutionary and conservation biology. Nowhere is diversity more important than at immune genes, which underpin the ability of individuals and populations to combat pathogens. However we still do not understand how different mechanisms interact to maintain such diversity within natural populations. Only by using modern molecular tools in conjunction with detailed information on individual fitness within populations will we resolve these issues.

Our long-term study of an island population of Seychelles warblers provides an excellent system in which to do this. We have shown that major histocompatibility complex (MHC) variation has been maintained in this bottlenecked species through a combination of natural and sexual selection. Moreover, a single MHC allele can provide individuals with a five-fold greater life expectancy but, intriguingly, the frequency of this allele in the population has not increased. These contradictory results suggest the presence of antagonist effects that counterbalance the positive effect of this allele on survival by negative effects on reproduction.

Now we need a researcher to test the interacting effects of MHC variation on survival and reproduction, and the role of pathogens, using the amazing dataset available for the Seychelles warbler.

This interdisciplinary project will develop an exceptional range of skills in the successful candidate including fieldwork techniques, molecular tools, bioinformatics and analytical expertise.

This project has funding by the EnvEast NERC Doctoral Training Partnership, comprising the Universities of East Anglia, Essex and Kent, with twenty other research partners. To apply:

Don’t just sit there, interact! Building interactive exploratory data apps with shiny and plotly in R

Anna Krystalli’s talk slides are now available online, including links to some great resources and tools for data management and visualisation:

special seminar this Thurs: >40 years of butterfly host shifts

Dear All,

There will be a special seminar this Thursday (1oth) from 1-2pm in the D-floor common room, by Professor Mike Singer. Mike is nothing short of a living legend, having studied butterfly ecology and evolution in California for >40 years. It should be a refreshing display of integration of ‘old school’ and modern approaches to biology. Title etc. below.

Hope to see you there.

cheers, Patrik

Patterns in space and time: a geographic mosaic of host association and six independent host shifts by a Californian butterfly

Mike Singer, Plymouth University

Studentship, Imperial College, with Dr Julia Schroeder

Information available:

Terry’s group meeting tomorrow 4/11, 1.30pm BMS seminar room1