Genetically guided breeding plan for chimpanzees

Wednesday 07 Nov 18
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Danish researcher, Peter Frandsen, and his colleagues at Copenhagen Zoo are coordinating the European breeding programme for chimpanzees under the European Association of Zoos and Aquaria (EAZA). For his research Peter is using Computerome, the Danish National Supercomputer for Life Sciences. 

Watch the video below to know more about Peter's research and how Computerome is helping to analyse large amounts of conservation genetic data.

What does your research hope to discover? 

We hope to discover suitable (non-admixed) individuals to strengthen the current breeding programs for the Western and Central subspecies of chimpanzee in European Zoos. We further hope to identify potential candidate individuals to establish breeding programs for the two remaining subspecies.

Lastly, we hope to be able to re-assign geographical origin of a panel of confiscated chimpanzees from the illegal trade and with the hope to help to ensure that they can return to the region of Africa where they came from, as each subspecies are uniquely adapted to survive in their original habitat. 

How Computerome is helping with this research?

 

We quickly realized that we did not have the computational capacity and expertise to run our analyses with the desired scrutiny here at the Zoo or with any of our collaborating partners.

With Computerome we can analyze all our hundreds of tested individuals up against a large reference panel of previously published chimpanzee genomes in a fraction of the time it would take otherwise. 

My project aims to develop ways to apply genetics in conservation management of endangered great apes.

Using Computerome, we have also finished the first large project that looks to implement a genetically guided breeding plan for chimpanzees in European Zoos as well as aiding the battle against illegal pet trade of wild chimpanzees by inferring geographical origin of confiscated chimpanzees.

Are there any benefits or risks involved in this study?

The benefits are that we set a new standard for a sustainable management of breeding populations and provide the means to conservation authorities in Africa to pinpoint where chimpanzees were taken from there in wild. 

 

The biggest risk is that our algorithms are emerging and there is constant development so there is a lot Research and Development work and that we make mistakes. This is, personally, also part of what sparked my interest in applied conservation genetics, as any result we produce goes directly into practice and any mistake could have irreversible consequences. To avoid this, our strategy has to include a lot of sample cross-validation and we run our analyses with a lot of attention to detail and in many more replicates than would normally be required.  

 

Who is involved?

The project involves contributions from Zoos across Europe and wildlife sanctuaries in Africa, where the scientific involvements counts a great team of research groups in Copenhagen Zoo, Copenhagen University, Århus University, and Universitat Pompeu Fabra in Barcelona.

 

What first sparked your interest in the chimpanzees?  

My curiosity sparked by early work done at Zoo Copenhagen, where my colleague Christina Hvilsom tried with success to transform the management of chimpanzees in Zoo populations by applying a genetic layer to breeding programs as a replacement to traditional studbook or register methods.

Here, I saw an opportunity to use my background in population genetics to solve a practical challenge that would help to conserve an endangered species and set a new benchmark for how to manage captive populations of species in general.

What are your expectations for the future?

 

In the future, we are planning to expand our genetic approach to breeding programs for other endangered species. We are currently collaborating with Antwerp Zoo, in Belgium, to establish a similar project with the closest living relative to chimpanzees (and us), the bonobo. A great ape facing similar conservation challenges.

As well as having a closer cooperation with the Computerome Center. 

 About Computerome

The Danish National Life Science Supercomputing Center, Computerome is a HPC Facility specialized for Life Science. Users include Research groups from all Danish Universities and large international research consortiums as well as users from industry and the public Health Care Sector. They all benefit from the fast, flexible and secure infrastructure and the ability to combine different types of sensitive data and perform analysis.


Researchers from any Danish university may submit a call of interest for a project to become a DeIC National eScience Pilot Project. Read more about pilot projects

 

Computerome is physically installed at the DTU Risø campus and managed by a strong team of specialists from DTU. The computer hardware is funded with grants from the Technical University of Denmark (DTU), University of Copenhagen (KU) and the Danish e-infrastructure Cooperation (DeiC).

 

 

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