PhD in Conservation genomics of endangered red pandas

Are you interested in genomics, but also passionate about wildlife conservation? This PhD opportunity might be the perfect fit!

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 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

Your profile

  • 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.

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 € 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

About us

About the department and project

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.

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 Red Panda and the associated expertise we gained, red panda is one of our key species. We coordinate the international studbook (GSMP) for red pandas and we have close ties with Red Panda Network in Nepal and other organizations and researchers in situ and ex situ, who are working on red panda conservation. Next to the studbook for red pandas, we coordinate five other European breeding programs, for amongst others Asian elephants 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
Researchers and students at VU Amsterdam’s Faculty of Science tackle fundamental and complex scientific problems to help pave the way for a sustainable and healthy future. From forest fires to big data, from obesity to malnutrition, and from molecules to the moon: we cover the full spectrum of the natural sciences. Our teaching and research have a strong experimentally technical, computational and interdisciplinary nature.

We work on new solutions guided by value-driven, interdisciplinary methodologies. We are committed to research, valorisation and training socially engaged citizens of the world who will make valuable contributions to a sustainable, healthy future.

Are you interested in joining the Faculty of Science? You will join undergraduate students, PhD candidates and researchers at the biggest sciences faculty in the Netherlands. You will combine a professional focus with a broad view of the world. We are proud of our collegial working climate, characterised by committed staff, a pragmatic attitude and engagement in the larger whole. The faculty is home to over 11,000 students enrolled in 40 study programmes. It employs over 1,600 professionals spread across 10 academic departments.

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. Learn more about our codes of conduct

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.

Diversity
Diversity is the driving force of the VU. The 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.

Submitting a diploma and a reference check are part of the application process.

Applications received by e-mail will not be considered.

Acquisition in response to this advertisement is not appreciated.

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 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

Your profile

  • 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.

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 € 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

About us

About the department and project

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.

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 Red Panda and the associated expertise we gained, red panda is one of our key species. We coordinate the international studbook (GSMP) for red pandas and we have close ties with Red Panda Network in Nepal and other organizations and researchers in situ and ex situ, who are working on red panda conservation. Next to the studbook for red pandas, we coordinate five other European breeding programs, for amongst others Asian elephants 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
Researchers and students at VU Amsterdam’s Faculty of Science tackle fundamental and complex scientific problems to help pave the way for a sustainable and healthy future. From forest fires to big data, from obesity to malnutrition, and from molecules to the moon: we cover the full spectrum of the natural sciences. Our teaching and research have a strong experimentally technical, computational and interdisciplinary nature.

We work on new solutions guided by value-driven, interdisciplinary methodologies. We are committed to research, valorisation and training socially engaged citizens of the world who will make valuable contributions to a sustainable, healthy future.

Are you interested in joining the Faculty of Science? You will join undergraduate students, PhD candidates and researchers at the biggest sciences faculty in the Netherlands. You will combine a professional focus with a broad view of the world. We are proud of our collegial working climate, characterised by committed staff, a pragmatic attitude and engagement in the larger whole. The faculty is home to over 11,000 students enrolled in 40 study programmes. It employs over 1,600 professionals spread across 10 academic departments.

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. Learn more about our codes of conduct

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.

Diversity
Diversity is the driving force of the VU. The 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.

Questions about the vacancy?

Please contact

Dr. Mirte Bosse

Assistant Professor

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.

Submitting a diploma and a reference check are part of the application process.

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

Application procedure

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