Population genetics of an endangered bird of prey: the Red Kite (The Student Perspective)

Student: Ilze Skujina
Company: Ecology Matters
Academic Supervisor: Dr Matthew Hegarty & Dr Robert McMahon

The genetics of the red kite by Ilze Skujina

Ilze_Skujina_PhotoI started my one year MPhil (Masters through Research) Project ‘Population genetics of an endangered bird of prey: the Red Kite’ as a KESS student in the Institute for Biological, Environmental and Rural Sciences (IBERS) of Aberystwyth University in October of 2012. The KESS scheme (Knowledge, Economy Skills Scholarships), which is mainly funded by the EU, involves the participation of a ‘commercial partner’ with the university to bring together academic expertise with business-focused research needs. The Welsh Kite Trust, in collaboration with the locally based company Ecology Matters, had identified the need for a greater understanding of the current genetic status of the Red Kite in Wales in order to provide guidance on its long-term conservation. After graduating from Aberystwyth University with a BSc degree in Equine Science it was a challenging project which confronted me when I commenced my studies last October. Also, coming from a very different background – a) being Latvian b) having my first education in Economics and c) the only animal I was at all familiar with being the horse – dealing with Red Kites and molecular genetics involved a lot of learning before commencing the research. However, by reading a tremendous amount of literature and ‘extracting the knowledge’ of my daily academic supervisors Dr Rob McMahon and Dr Matt Hegarty, as well as meeting up with Professor Mike Hayward and Tony from the Welsh Kite Trust, step by step I soon realised my mission. An indication of my enthusiasm for the project can be exemplified by the fact that late one November night when coming back home I could not miss an opportunity to pick up a fresh road-kill that in the darkness looked to me to be a Red Kite. As it was too late to get to the lab I had no choice but to store it in my boyfriend’s freezer, which I am still regularly reminded of! This carcass proved to be brilliant material to compare various tissues as a source for DNA extractions. After DNA sequencing my kite turned out to be a buzzard! I put the misidentification down to the state of the carcass after I had retrieved it from the road! However, all was not in vain as this gave us plenty of material for looking at the DNA organization of another raptor and in the process enabled even wider phylogenetic analyses.

The early part of my programme involved getting familiar with the laboratory techniques, and developing feather DNA extraction protocols, as well as trying to optimize certain assay procedures which we thought would provide new genetic markers for investigating the genetic diversity in the Red Kites of Wales. These procedural experiments we believe now have explained the initial difficulties of DNA amplification we experienced and more importantly revealed a unique biology in DNA organization, specific to the Red Kites and apparently some other raptors (see the following article on the research). By mid-February/March I had acquired DNA samples which had been collected as part of the Irish reintroduction programme together with the historical samples from the late 1980’s programme (courtesy of Dr Celia May of Leicester University). By the end of the March I had typed all the historical samples for the available genetic markers which revealed a paucity of genetic variation and hence exactly how empty-handed we were in terms of genetic tools for diversity characterization within the Red Kites. It became clear that the only solution to this problem would be to assemble entire genomes of several birds of different back grounds, compare them and hopefully be able to answer the question by this means. However spring was on its way and it was time to get familiar with the bird ‘in the field’.

The countryside around the IBERS Institute, which is located some three miles outside of Aberystwyth, is well populated by Red Kites and provided an ideal area in which to gain knowledge of the procedures adopted by the Trust to monitor the conservation status of the local kites. So in early spring, I accompanied Mike to the local nest sites to learn some practical skills and soon found out that I really enjoyed trying to spot new nest sites, and later on trying to detect the breeding progress within these nests. With my early experience I was soon able to identify potential kite nesting sites whilst out horse riding in the mountains around Aberystwyth. As the season progressed we were able to monitor the nests for hatching and growth of the chicks. When the chicks were ready to be tagged I went shadowing Tony Cross and the local Kite Watchers in the border regions of Wales, Shropshire and Herefordshire – an area of particular interest to the Trust as birds have only spread to these regions in recent years. Even though I did not manage to climb up the trees myself, holding a baby kite was a most amazing experience. What is more, the Red Kites certainly knew I was coming, as in one of the last nests Tony found a toy horse! During these field-work trips I was able to collect a decent amount of cast feathers, which proved to be an invaluable source for acquiring DNA and hence genetic information. Testing DNA extraction protocols on feathers as a DNA source was also one of the core components of my project. A large part of the feathers I used were diligently collected by many of the Kite Trust Nest Watchers and sent to me via Mike or Tony. I was pleasantly surprised about how helpful everybody was in this task and thank them most gratefully.

So, once the field-work was complete it was back to the lab. For the latter part of my research I have endeavoured to carry out the sequencing and assembly of the whole genome of the kite. This can be a cumbersome and expensive process, hence there are relatively small portions of whole genome sequences deposited in the National Gene Bank. Therefore, provision of an annotated whole genome sequence with sufficient coverage is by all means a major achievement, and as I write these lines we are nearly there. I have to admit that we were lucky that there were several auspicious conditions that all came together for this to happen: 1) the fact that IBERS had next generation sequencing (NGS) facilities and Matt with his broad expertise in this area, 2) the access to the material (some DNA that was required was again kindly provided by Dr Celia May), 3) sufficient funding thanks to the KESS scheme. Finally, during this project, I have also been working on creating a database that will contain all the information – genetic, phenotypic and demographic of all the birds that I have been able to assay. This will a) combine all the information gathered by different people and b) ensure preservation of the data. Some of the early records are still held in paper form and before they could be transcribed to the database had to be extracted from the original notebooks. To do this I visited Peter Davis (one of the founders of the Welsh Kite Trust) who kindly hosted me for the afternoon. As he was involved in the initial genetic studies, and with his long experience of working on the conservation of kites, he provided me with a lot of information that has been extremely useful for the project.

This work also took me to the “Otto Warburg International Summer School & Research Symposium on Next Generation Sequencing” that took place at the Max Plank Institute in Berlin where I presented a poster. These were an intense seven days in August, full of lectures and research talks by leading experts in their areas of genetics, and meetings with fellow students whose names I have no doubt I will see in papers soon. This was a great way to spread the word about the Red Kites and their genetics to an international audience.

My “Red Kite project” was also shortlisted as a finalist for the best KESS MPhil/PhD award 2013. So I went to Cardiff to compete for this prize by giving a presentation. I did not win the trophy, but the presentation was warmly complimented by many of listeners afterwards and the Red Kites caused a lot of interest, so I had many questions to answer after the speech.
Now, being in the final stage of the project – hurrying up with the last experiments, carrying out the analysis of the data produced in the lab, attempting to write this all up and seeing the end coming closer and closer – I already know that I will miss this work and will have very fond memories of this year.

I would like to use this as an opportunity to sincerely thank everyone for all the help that you provided, particularly those I managed to meet – Mike, Tony, Michele Frater, Leo Smith, Chris Wells, Dave Pearce and Peter Davis.