2017 SMRT Grant Finalist
Conservation genomics to the rescue – saving the Dodo’s cousin!
Dr. Matt Clark, Earlham Institute
Professor Cock Van Oosterhout, University of East Anglia
Why is this the most interesting genome in the world?
The pink pigeon would be the first endangered bird species to be sequenced with PacBio’s Iso-Seq method, which would make this species a blueprint for future conservation genomic research. We are in a unique position of knowing the reasons for the pink pigeon’s continued decline – low genetic diversity reduces reproductive success and makes birds susceptible to infectious disease. With recent advances in sequencing technology, such as the Iso-Seq method, we aim to identify the causative genetic variants responsible for the decline in population numbers. This is pivotal for the genetic rescue of the population through the reintroduction of beneficial genetic variants still present in captive individuals in zoos, thereby stopping the pink pigeon from becoming the next Dodo.
What are the goals of this project?
- Use the Iso-Seq method to capture full-length coding sequences from pink pigeon tissues to fully annotate highly variable immune system genes.
- Sequence the transcriptome of blood samples of five resistant and five susceptible individuals to identify genes elevated during Trichomonas gallinae infection
- Identify candidate causative SNPs in resistant birds for further investigation using a greater number of samples (from our previous Genome Wide Association Study of ~400 birds).
- Ultimately, we aim to use this data to inform genetic supplementation and breeding programs to propagate “resistant variants”, thereby contributing to the genetic rescue of the pink pigeon in the wild and creating a conservation genomics model that can be used for other endangered species.
What is the global impact of your research?
With one-fifth of vertebrate species being listed as “threatened” by the IUCN, we are rapidly approaching the sixth mass extinction. While we seem unable to reverse the effects of habitat destruction and the introduction of novel predators and pathogens, new sequencing technologies could enable us to identify the genetic fingerprint of a species’ decline. Halting species extinction may be possible when the cause of extinction has a genetic basis, particularly when genetic variation needed to supplement and rescue the species is still available in either the captive or wild populations. Our plan uses the pink pigeon to show how this can be achieved, creating a framework that could be easily transferred to other species across the world – from Booroolong frogs to Iberian lynx.
Project Team (in addition to PIs)
- Camilla Ryan, Earlham Institute & University of East Anglia
- Dr. Lawrence Percival-Alwyn, Earlham Institute
- Professor Carl Jones, Durrell Conservation Trust
- Dr. Diana Bell, University of East Anglia
- Professor Ian Barnes, Natural History Museum (London)
- Pink Pigeon Consortium