PhD in Conservation genomics of endangered red pandas

The section Ecology & Evolution, part of the Amsterdam Institute for Life and Environment (A-LIFE) at the Vrije Universiteit Amsterdam invites applications for an ambitious PhD position that will combine innovative bioinformatics and genomic tools to study captive and wild red panda genomes for conservation. Are you interested? Keep reading and apply at Vrije Universiteit Amsterdam!

Understanding the population structure of (sub)species is crucial for both wildlife conservation and effective population management of back-up populations in zoos, given the potential harm hybridization poses to the reintroduction potential of zoo animals. The red panda (Ailurus fulgens) is an endangered mammal with only 2,500 to 10,000 individuals in the wild. Debate is ongoing whether the species should be split into two distinct species: Ailurus fulgens fulgens and Ailurus fulgens styani. This project aims to assess the genetic health of the worldwide zoo population and determine the taxonomic origin of its founders. Additionally, the candidate will explore genomic compatibility between populations to predict the potential effect of hybridization. In collaboration with the international studbook keeper of the red panda zoo population, based at Rotterdam zoo, we will use long- and short read whole genome sequence data from key individuals from the zoo population with an additional reference dataset of re-sequenced wild individuals. This project will develop a genomics-informed framework for conservation and reintroduction of red pandas, and could potentially set a new standard for the field of conservation genomics.

The successful applicant will bring together the expertise of Dr. Mirte Bosse, who is in the forefront of the exciting new field of conservation genomics, and Janno Weerman, who is the international studbook keeper of the worldwide zoo population of red pandas. The PhD candidate will be embedded in the Ecology&Evolution group at the VU in close collaboration with Rotterdam Zoo and the Animal Breeding and Genomics group of Wageningen University. The candidate will have the opportunity to frequently work from Rotterdam Zoo, and will engage in a research network with international academic partners, zoos and NGOs.

Your duties

• develop a high-quality reference genome for each red panda (sub)species using nanopore technologies
• explore structural genomic differences between populations by combining de novo assemblies with long and short reads
• perform population genomics analyses on re-sequenced animals to better understand population structure in situ and ex situ
• analyze genetic load in the zoo population in comparison with the wild, and develop framework to implement this information in the breeding programme
• developing a framework for decision-making on planned reintroductions based on genomic information.
• authoring and co-authoring manuscripts submitted to high quality journals
• provide support to teaching of the section (<10% of your time)
• frequently present your work at internal and external (national or international) meetings, and to non-academic stakeholders

Requirements:

• MSc in one of the following fields: Biology, Genetics, Animal Breeding, Conservation sciences and/or Bioinformatics, or a related field
• you should have at least experience with bioinformatics and genomics (details below):
• experience (or affinity) with programming in Python, R, bash
• experience (or affinity) with next- and third generation sequencing technology such as Illumina, PacBio or Oxford Nanopore and some experience with downstream analysis of sequence data
• experience with the red panda model system is an advantage, but not necessary
• a good ability to speak, write and read English
• affinity with outreach activities and working in an international multidisciplinary team

As a university, we strive for equal opportunities for all, recognising that diversity takes many forms. We believe that diversity in all its complexity is invaluable for the quality of our teaching, research and service. We are always looking for talent with diverse backgrounds and experiences. This also means that we are committed to creating an inclusive community so that we can use diversity as an asset.

We realise that each individual brings a unique set of skills, expertise and mindset. Therefore we are happy to invite anyone who recognises themselves in the profile to apply, even if you do not meet all the requirements.

Salary Benefits:

A challenging position in a socially engaged organisation. At VU Amsterdam, you contribute to education, research and service for a better world. And that is valuable. So in return for your efforts, we offer you:

• a salary of € 2.770,00 (PhD) and maximum € 3.539,00 (PhD) gross per month in the fourth year, for a full-time employment.
• an employment contract of initially one year. If there is sufficient perspective, this will be extended to a total of 4 years. Your dissertation at the end of the fourth year forms the end of your employment contract..

We also offer you attractive fringe benefits and arrangements. Some examples:

• A full-time 38-hour working week comes with a holiday leave entitlement of 232 hours per year. If you choose to work 40 hours, you have 96 extra holiday leave hours on an annual basis. For part-timers, this is calculated pro rata.
• 8% holiday allowance and 8.3% end-of-year bonus
• contribution to commuting expenses
• solid pension scheme (ABP)
• a wide range of sports facilities which staff may use at a modest charge

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