PhD Position in Ecology (VU University of Amsterdam)

Your function 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 genomic compatibility of endangered Asian elephant populations. Are you interested? Keep reading and apply at Vrije Universiteit Amsterdam! We are in the UN’s decade of ecosystem restoration, which requires a better understanding about 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, who is 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 developing a framework for decision-making on planned connectivity 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 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 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. What do we offer? 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 € 3.059,00 (PhD) and maximum € 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 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 solid pension scheme (ABP) contribution to commuting expenses a wide range of sports facilities which staff may use at a modest charge About us 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. A-LIFE seeks to connect 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) who is 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 we have close ties with organizations and researchers in situ and ex situ, who are working on Asian elephant conservation. Next to the studbook for Asian elephants, we coordinate seven other EAZA breeding programs, for amongst others red pandas and Rüppells vultures. Also for these other breeding programs we are 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. 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. Diversity is the driving force of VU Amsterdam. VU wants to be accessible and receptive to diversity in disciplines, cultures, ideas, nationalities, beliefs, preferences and worldviews. We believe that trust, respect, interest and differences lead to new insights and innovation, to sharpness and clarity, to excellence and a broader understanding. We stand for an inclusive community and believe that diversity and internationalisation contribute to the quality of education, research and our services. Therefore, we are always searching for people whose backgrounds and experience contribute to the diversity of the VU community. Interested? Are you interested in this position and do you believe that your experience will contribute to the further development of our university? In that case, we encourage you to submit your application. You are requested to write a letter in which you describe your abilities and motivation, accompanied by your curriculum vitae, a list of grades of your MSc and the names and contact details of two scientific referees. Please compile all this together in one document and convert it to pdf. You can apply via the application button and upload your documents as mentioned above until December 15th, 2025. Interviews will take place in January 2026. Applications received by e-mail will not be considered. Acquisition in response to this advertisement is not appreciated. Questions about the vacancy? Please contact Dr. Mirte Bosse Assistant Professor Send an email If you apply for this position please say you saw it on Bioloxy

Your function

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 genomic compatibility of endangered Asian elephant populations. Are you interested? Keep reading and apply at Vrije Universiteit Amsterdam!

We are in the UN’s decade of ecosystem restoration, which requires a better understanding about 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, who is 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
developing a framework for decision-making on planned connectivity 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 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
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.

What do we offer?

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 € 3.059,00 (PhD) and maximum € 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 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
solid pension scheme (ABP)
contribution to commuting expenses
a wide range of sports facilities which staff may use at a modest charge

About us

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. A-LIFE seeks to connect 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) who is 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 we have close ties with organizations and researchers in situ and ex situ, who are working on Asian elephant conservation. Next to the studbook for Asian elephants, we coordinate seven other EAZA breeding programs, for amongst others red pandas and Rüppells vultures. Also for these other breeding programs we are 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.

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.

Diversity is the driving force of VU Amsterdam. VU wants to be accessible and receptive to diversity in disciplines, cultures, ideas, nationalities, beliefs, preferences and worldviews. We believe that trust, respect, interest and differences lead to new insights and innovation, to sharpness and clarity, to excellence and a broader understanding.

We stand for an inclusive community and believe that diversity and internationalisation contribute to the quality of education, research and our services.

Therefore, we are always searching for people whose backgrounds and experience contribute to the diversity of the VU community.

Interested?

Are you interested in this position and do you believe that your experience will contribute to the further development of our university? In that case, we encourage you to submit your application. You are requested to write a letter in which you describe your abilities and motivation, accompanied by your curriculum vitae, a list of grades of your MSc and the names and contact details of two scientific referees. Please compile all this together in one document and convert it to pdf.

You can apply via the application button and upload your documents as mentioned above until December 15th, 2025. Interviews will take place in January 2026.

Applications received by e-mail will not be considered.
Acquisition in response to this advertisement is not appreciated.