PhD in Conservation genomics of Asian elephants

PhD in Conservation Genomics of Asian Elephants

Are you passionate about using your genomics and bioinformatics skills for real conservation impact? This PhD opportunity could be the perfect fit!

PhD Position in Genomic Compatibility of Endangered Asian Elephant Populations

The section Ecology & Evolution, part of the Amsterdam Institute for Life and Environment (A-LIFE) at the Vrije Universiteit Amsterdam, invites applications for an exciting PhD position that will combine innovative bioinformatics and genomic tools to study the genomic compatibility of endangered Asian elephant populations.

We are in the UN’s decade of ecosystem restoration, which requires a better understanding of the recovery potential of threatened species. As part of the NWO-VIDI ExPANsion project, you will employ a pangenomics approach for the conservation and restoration of an endangered species, the iconic Asian elephant. You will work on developing novel genomic parameters focused on assessing the risks and benefits of population hybridization for the genetic rescue, conservation, and recovery of threatened species.

The successful PhD candidate will be embedded in an experienced team of collaborators, including Dr. Mirte Bosse, an expert in the emerging field of conservation genomics; Jeroen Kappelhof, the EAZA (European Association of Zoos and Aquaria) studbook keeper of the zoo population of Asian elephants; Dr. Reeta Sharma, who has extensive field experience and species knowledge; and Dr. Martijn Derks and Dr. Sandra Smit, supporting the bioinformatics. The PhD candidate will be embedded in the Ecology & Evolution section at the Vrije Universiteit Amsterdam in close collaboration with Rotterdam Zoo and Wageningen University. The candidate will have the opportunity to frequently work from Rotterdam Zoo.

Your Duties

• Develop a high-quality reference genome for each Asian elephant population using nanopore technologies
• Explore structural genomic differences between populations by combining de novo assemblies into a pan-genome graph
• Perform population genomics analyses on re-sequenced animals, supported with long and short reads, to better understand genetic load from SNPs and Structural Variants
• Develop a framework for decision-making on planned connectivity based on genomic information
• Author and co-author 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 in range countries

Your Profile

• MSc in one of the following fields: Biology, Genetics, Animal Breeding, Conservation Sciences and/or Bioinformatics, or a related field
• Good command-line skills and programming experience (in Python or bash)
• Experience with next- and third-generation sequencing technology such as Illumina, PacBio, or Oxford Nanopore, especially with downstream analysis of sequence data
• Ideally, experience with pan genomics of vertebrates
• Experience with the Asian elephant model system is an advantage, but not necessary
• Good ability to speak, write, and read English
• Affinity with outreach activities and working in an international multidisciplinary team

What We Offer

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

• A salary of €3.059,00 (PhD) up to €3.881,00 (PhD) gross per month in the fourth year, for a full-time employment
• An employment contract of initially 1 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 attractive fringe benefits and arrangements, including:

• 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
• Solid pension scheme (ABP)
• Contribution to commuting expenses
• A wide range of sports facilities which staff may use at a modest charge

About Ecology & Evolution

The PhD position is embedded in the section Ecology & Evolution, which focuses on answering fundamental questions regarding the mechanisms by which organisms respond and adapt to environmental change, including ecological and evolutionary effects on species interactions, behaviour, and community composition. We make innovative contributions to the fundamental research field of Ecology and Evolution worldwide and bring new insights to issues of societal relevance. The section comprises a dynamic community of researchers and provides an excellent research environment with state-of-the-art facilities and high-quality training. The section Ecology & Evolution is part of the Amsterdam Institute for Life and Environment (A-LIFE) in the Faculty of Science of the Vrije Universiteit. A-LIFE aims to advance the fundamental understanding of the interplay between life and its environment, connecting properties and emergent behaviors across all scales, from molecules to ecosystems, including human populations.

About Rotterdam Zoo

Rotterdam Zoo is a zoological and botanical garden based in Rotterdam (The Netherlands) focusing on nature restoration and species conservation. Due to our long history with Asian elephants and the associated expertise we gained, the Asian elephant is one of our key species. We coordinate the EAZA breeding program (EEP) for Asian elephants and have close ties with organizations and researchers in situ and ex situ, who are working on Asian elephant conservation. In addition to the studbook for Asian elephants, we coordinate seven other EAZA breeding programs, for amongst others red pandas and Rüppell’s vultures. For these other breeding programs, we are also working on genomic research together with the Vrije Universiteit Amsterdam and Wageningen University & Research.

Faculty of Science

Working at the Faculty of Science means collaborating with students, lecturers, and researchers who are focused on their field, yet have a broad view of the world. We are proud of a positive and inclusive workplace culture within the faculty, where we work together with great energy and a pragmatic attitude to tackle social challenges. At the Faculty of Science, scientists and students work on fundamental and complex societal issues for a sustainable, healthy, and just future.

From forest fires to big data, from obesity to malnutrition, from helium to the universe and from genetics to medicine: our education and research cover the full breadth of science, from molecules to mankind. Our academic education and research are highly experimental, technical, and interdisciplinary in nature. That is why we collaborate extensively with leading scientific institutes and industry. The faculty has more than 8,000 students studying in one of the 39 programs and employs more than 1,400 staff across 10 scientific departments, making us one of the largest science faculties in the Netherlands.

Vrije Universiteit Amsterdam

Vrije Universiteit Amsterdam stands for values-driven education and research. We are open-minded experts with the ability to think freely—a broader mind. Maintaining an entrepreneurial perspective and concentrating on diversity, significance, and humanity, we work on sustainable solutions with social impact. By joining forces, across the boundaries of disciplines, we work towards a better world for people and planet. Together we create a safe and respectful working and study climate, and an inspiring environment for education and research.

We are located on one physical campus, in the heart of Amsterdam's Zuidas business district, with excellent location and accessibility. Over 6,150 staff work at the VU and over 31,000 students attend academic education.