Genetic basis of reproductive and plumage polymorphism in the ruff

Lead Research Organisation: University of Edinburgh
Department Name: Sch of Biological Sciences

Abstract

Individual animals usually exhibit flexibility in their behaviour, but some behaviours are genetically determined. An extreme example of genetically fixed alternative behaviours occurs in a wading bird, the ruff. The ruff has a "lek" mating system in which males invest all their energy into attracting females to mate with them, and none into parental care. Territorial breeding males have spectacular plumes around their neck and head, and vary enormously in colouration, so that each male at the lek is distinguishable. Other nonterritorial "satellite" males, which are distinguishable by their white feathers, concentrate on "stealing" matings from territorial displaying males. Whether a male becomes a territorial or satellite individual is genetically determined. Satellites are essentially parasitic on territorials, though there is evidence that territorials may benefit from the presence of a small number of satellites. A third type of male, which mimics females, was recently discovered. This parasitic male is able to "hide" from the other males at the lek, so avoiding territorial aggression, and also succeeds by stealing matings from the resident males.

The purpose of this study is to use genome sequencing to identify the genes that make the males behave in these three different ways. We want to understand how the three different strategies can coexist in the population, and how they have evolved. We also plan to discover the genetic mechanism to explain why males are so diverse in their plumage. These mechanisms are likely to be the same ones that produce some of the similar variation that we normally only see between species. Finally, we want to discover the mechanism that ensures that the plumage pattern and behaviour are co-inherited.

Technical Summary

The objectives will be achieved by collaboration among three research groups. David Lank (Simon Fraser University) has studied the reproductive behaviour of ruffs in a captive population for 18 generations, and will provide tissue samples to Terry Burke and Jon Slate (University of Sheffield) to enable completion of the ruff pedigree and study of gene expression. Mark Blaxter and colleagues (University of Edinburgh) will support the work by providing new-generation sequencing and associated bioinformatic expertise. Specifically, we will use high-density RAD sequencing to search for genetic markers associated with the three genetically determined reproductive strategies and with plumage patterning. We will use low-density RAD screening of the entire available pedigree to map each trait. The ruff genome will be sequenced and assembled so that we can locate the RAD markers. In combination, we expect to identify the causative loci for both reproductive and plumage traits. We will investigate the expression of the identified loci in the brain and feather follicles. We will investigate the mechanism that maintains the association between behaviour and morphology, and also use standard population genetic tools to test for evidence of selection at the identified loci.

Planned Impact

RAD sequencing as a genome discovery tool

The new approach of RAD sequencing is just beginning to get established as an efficient and cost-effective gene discovery tool, and we anticipate that this project will be one of the first to demonstrate the use of RAD to discover the genetic basis of multiple Mendelian genes. MB and colleagues have promoted RAD to the academic community through annual workshops. We now propose to share the knowledge we have gained, and particularly the experience that we will gain in the proposed study, with the wider non-academic user community. The most obvious potential users belong to the plant and animal breeding community.

Mendelian traits are of particular significance in agriculture and horticulture, but relatively few such traits have as yet been identified at the molecular level or even mapped in the genome. This project will demonstrate the power of using RAD to identify the molecular basis of such traits. This may be particularly important in the commercial protection of new traits and for understanding the epistatic physiological effects of mutants. Additionally, breeders have increasingly used molecular approaches such as gene mapping and marker assisted selection to assist the development of new breeds and strains. The efficiency of mapping can be improved through the use of RAD sequencing, and gene identification potentially allows direct selection as an improvement over the marker-assisted approach.

We therefore anticipate significant potential interest from the plant and animal breeding community and will host a workshop aimed at their needs, plus offer additional direct specific advice to interested potential end users in the form of one-to-one tutorial or surgery sessions. The workshop will include speakers from overseas and we anticipate that Floragenix, the US company that owns the patent to the RAD technology, would be one of the contributors.

Outreach

The ruff's impressively visual reproductive biology and morphology lends itself beautifully to public communication. We believe that the results from this proposed work would provide an unusually accessible opportunity to showcase the link between genomic and organismal biology. We therefore propose to produce a high quality free-standing display stand that would include large LED video of displaying ruffs and other aspects of the work, accompanied by ruff specimens and feathers. This stand would be offered to appropriate scientific events and exhibitions and otherwise housed in one of the University's public exhibition spaces. These are being actively developed as part of the University's increasing outreach activities.

Budget

We have budgeted £7000 to cover the costs of hosting the workshop (£4000) and the travel costs to enable interactions with interested companies (either direct visits to companies or participation in breeding industry meetings, £1000), in producing a display stand (£2000) and one additional month of PDRA time to cover the cost of organizing the workshop, participating in meetings, and in outreach activities.

Publications

10 25 50
 
Title Transmissions exhibition 
Description The Blaxter lab collaborated closely wth artists-in-residence (see http://www.ascus.org.uk/ciie-micro-residency-artists-announced/) in the Centre for immunity Infection and Evolution to inspire and be part of the final exhibition "Transmissions". Mark Blaxter appears in the film work produced by Anne Milne, and the work of the lab inspired Jo hodges and Robbie Coleman to produce a piece dedicated to the lab. 
Type Of Art Artwork 
Year Produced 2014 
Impact 'Transmissions' was showcased to the general public within a group exhibition 'Parallel Perspectives' in Summerhall as part of the Edinburgh International Science Festival 2015 art programme, How The Light Gets In . This exhibition of work susequently travelled LifeSpace, Dundee, returning to Edinburgh to showcase at the Tent Gallery, Edinburgh College of Art. 
URL http://www.ascus.org.uk/ciie-micro-residency-2/
 
Description We found that the three different kinds of males in the ruff, a common wading bird, are controlled by a large set of genes that have been trapped together by a rare major genetic change. This finding reveals one of the meany mechanisms operating in evolution to generate and maintain biotic diversity. It is likely that many of the "jumps" observed in evolution may be similarly the consequence of major genetic changes - rearrangements in the genome - that allow chance sets of gene strapped together by the insulation to evolve to generate new phenotypes. These step changes, and especially how they can be maintained in the face of sexual recombination when individuals with one trait mate with individuals carrying the other trait. The ruff model also identifies how unexpected evolutionary systems - in this cases a species with three contrasting kinds of males - can arise and be maintained.
Exploitation Route The next step is to fully understand the mechanisms behind the control of the different morphs. The collaborating laboratories are using the extensive work that underpins this project to develop new ways of approaching this question.
Sectors Environment

 
Description Blaxter group - presentations and outreach 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact The Blaxter group presented work at a wide range of national and international conferences, including PopGroup, the Arthropod Genomics Workshop, The C. elegans International Meeting, The Hydra Helminthology meeting, The European Society for Nematology, The UK Genome Science meeting, and others. At many of these venues, in addition to offering platform or poster presentations, we also presented workshops or training activities.
Year(s) Of Engagement Activity 2016
 
Description Blaxter group presentations and outreach 2015 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Mark Blaxter and research team communication and outreach 2015

Globodera genomics and blobtools software
25/02/2015 JHI Postgraduate Student Competition 2015 James Hutton Institute, Aberdeen, UK A tale of Two Peaks: Analysing Genomic Data from Potato Cyst Nematodes Talk
26/03/2015 JHI Cell and Molecular Sciences (CMS) seminar James Hutton Institute, Invergowrie, Dundee, UK Frustration and happiness : (De)-constructing parasite genomes Talk
16/06/2015 JHI Dundee effector consortium (DEC) meeting 2015 Birnam Arts and Conference Centre, Birnam, UK Variation within the Globodera pallida species complex: preliminary results Talk
03/09/2015 Molecular and Cellular Biology of Helminth Parasites IX Bratsera Hotel, Hydra, Greece Inter- and intra-specific analyses of the effector complement in potato cyst nematodes Poster
18/09/2015 UoE Postgraduate Poster Day University of Edinburgh, Edinburgh, UK Inter- and intra-specific analyses of the effector complement in potato cyst nematodes Poster
26/09/2015 Edinburgh University Doors Open Day University of Edinburgh, Edinburgh, UK Potato Cyst Nematodes (PCN) - Nematode parasites of potatoes Poster
30/11/2015 NextGenBug University of Edinburgh, Edinburgh, UK Blobtools: Blobology 2.0 Talk
01/12/2015 UK pollinator genomics meeting Roslin Institute, Edinburgh, UK Bees and Blobs Talk

LepBase
06/03/2015 EMARES Cambridge, UK The Bicyclus Genome Project Talk
06/03/2015 EMARES Cambridge, UK An introduction to Lepbase Talk
17/06/2015 Arthropod Genomics Manhattan, Kansas, USA Lepbase - A multi genome database for the Lepidoptera Poster
24/07/2015 10th Heliconius Meeting Gamboa, Panama Lepbase - A multi genome database for the Lepidoptera (API demonstration) Workshop
24/07/2015 10th Heliconius Meeting Panama Lepbase - A multi genome database for the Lepidoptera Poster
26/07/2015 10th Heliconius Meeting Panama Lepbase Workshop Talk
04/09/2015 Edinburgh Bioinformatics Edinburgh, UK Lepbase - A multi genome database for the Lepidoptera Talk
26/09/2015 Open Doors Day "Make a butterfly" interactive exhibition
26/09/2015 Edinburgh University Doors Open Day Edinburgh, UK Lepbase Multiple Sequence Alignments game Poster+Game
28/10/2015 NextgenBUG Dundee, UK Lepbase - an Ensembl (and more) for the Lepidoptera Talk

Nematode genomics
24.06.2015 20th International C. elegans Meeting Los Angeles USA A new evolutionary framework for the phylum Nematoda: a case study of HOX cluster evolution Poster
24.06.2015 20th International C. elegans Meeting Los Angeles USA Caenorhabditis Genomes Project Workshop (organiser and chair) Talk
24.06.2015 20th International C. elegans Meeting Los Angeles USA Current status of the CGP in Edinburgh Talk

Meloidogyne genomics
10-14 August 2015 ESEB Lausanne-Switzerland Genomic consequences of hybridization and the loss of meiotic recombination in Root-knot nematodes poster
15-18 December 2015 PopGroup Edinburgh-UK Genomic consequences of hybridization and the loss of meiotic recombination in Root-knot nematodes talk
23 February 2016 NextGenBug Edinburgh-UK Genomics of Root-knot nematodes talk
Year(s) Of Engagement Activity 2015
 
Description Blaxter lab workshops 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The Blaxter lab took our software products and research tools to various venues (Arthropod Genomics, UK Genome Science meeting, Butterfly Genomics) to present as workshops, training events or interactive sessions
Year(s) Of Engagement Activity 2016
 
Description Press releases and website 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact We have engaged actively with the University press office to promote press coverage of our research outcomes, particularly major publications (which have had coverage in national and international newspapers) and in blogs and other online media. We have also promoted major new initiatives such as additional core funding of the Edinburgh genomics facility.

Increased visibility of Edinburgh Genomics within the community; requests for comment by funders and government on matters pertaining to genomics.
Year(s) Of Engagement Activity 2009,2010,2011,2012,2013,2014,2015,2016