Testing repeatability in the evolution of complex traits: the genetics of convergent structural colour

Lead Research Organisation: University of Sheffield
Department Name: Animal and Plant Sciences

Abstract

How repeatable is the evolutionary process and would the same evolutionary pathways always be used to reach a given end-point? Recent work on the genes responsible for adaptation in the wild suggests that certain genes are particularly likely to be the target of selection. This may be because these genes have large effects on the traits under selection without having effects on other traits. However, some adaptive differences are due to the combined effects of many genes. In these cases it is less clear how repeatable the evolutionary process will be and if the same sets of genes will be used when evolving similar traits. Organisms that that have converged on similar phenotypes can help us to answer these questions because they represent independent evolutionary trajectories towards the same endpoint.

The Heliconius butterflies are one of the most striking examples of evolutionary convergence. They have bright colour patterns that warn predators of their distastefulness and several species have converged on near identical colour patterns. This reduces the number of patterns that predators have to learn, so benefitting all individuals that share them. This provides a "natural experiment" in which to test whether the same genes are used when evolving the same phenotypes. Results from this system have shown that the same major switch genes have independently been used in two species to produce the same colour patterns. However, these genes do not explain all of the evolutionary changes. Some populations of these two species have evolved an iridescent blue colour, which is controlled by many genes. I will identify what these genes are and if they are the same or different between species. If the same genes have been independently used in both species it will suggest that evolution is predictable, so when evolving a certain trait a particular set of genes are likely to always be used. On the other hand if different genes are used then it will suggest that traits that are controlled by multiple genes are more flexible in their evolution. Given that many important traits are controlled by large numbers of genes, such as size and behaviour, this has important implications for our understanding of the evolutionary process. If evolution can proceed down multiple routes in order to arrive at the same endpoint, then it is likely to be easier and faster than if it is constrained to use particular genes.

Iridescent colours like those of the peacock and blue morpho butterfly are some of the most spectacular in the animal kingdom. They are produced by sub-micron-scale structures that cause coherent scattering of light, rather than the absorption of light by pigments. Although these types of colours are often used in animal signalling, nothing is currently known about the genes controlling them. Identifying the genes responsible for controlling these colours in Heliconius will shed some light on the genetics and development of these traits and provide candidate genes for their control in other systems. There is commercial interest in replicating these types of colours artificially, for use in anticounterfeiting and advanced materials technologies. If the genetic basis of these traits can be understood, this will be an important step towards understanding how such structures are assembled in natural systems, which will allow the problem of how to synthesise materials with similar properties to be approached from an entirely new angle.

Planned Impact

1. Who will benefit from this research?

1.1 This research will benefit conservation policy makers and practitioners.

1.2 This research will benefit those working in applied uses of structural colours.

1.3 This research will benefit those working in science education, particularly those preparing educational materials, museum and live animal exhibits.

1.4 This research will benefit innovation and wider society by helping to inspire the next generation of scientists (particularly young female scientists).

2. How will they benefit from the research?

2.1 The work will shed light on the evolutionary process and in particular the importance of constraint. This will influence our understanding of how easily organisms can adapt to changing environments and so how best to mitigate human influences on habitats, including habitat destruction and climate change.

2.2 There have been many proposed technological uses for structural colour and much research effort in being channeled into finding ways to synthesise them. An understanding of how these structures are produced in natural systems is currently lacking. By addressing this question this research will provide information that could be used to find novel methods are artificial synthesis of such structures.

2.3 Butterfly wing colour patterns and mimicry are evolutionary examples that have captured the public imagination every since Bates, Darwin and Wallace first described them. Therefore the outcomes of this research will contribute to the public understanding of evolutionary biology and appreciation of the natural world. I will seek to capitalise on this through public engagement activities and direct collaborations with schools to help to incorporate these examples into educational materials (see pathways to impact). In addition, Heliconius butterflies are frequently present in butterfly houses and exhibits. Therefore, the managers of these could increase the educational content of such exhibits by including elements of this research.

2.4 Science is a crucial driver of innovation and the economy. In recent years there has been a decline in interest in science among young people. The vivid and appealing evolutionary examples in this research make it an excellent system for inspiring young scientists. From the outset of the project, I will undertake outreach activities (see pathways to impact). I particular I hope this will help to inspire young women, who are still grossly under-represented in the scientific community, to take an interest in future careers in science.

Publications

10 25 50
 
Title Mimicry magic and iridescence 
Description The artist Sarah Jane Palmer worked with the scientists on the project to capture some of the scientific concepts and results of the research in several pieces of artwork. This included 2 large lenticular prints, a video that were on display in the Millennium Gallery and a performance during the Festival of the Mind in Sheffield in March 2018. The prints and video are now in display in the Alfred Denny Museum. 
Type Of Art Artwork 
Year Produced 2018 
Impact The exhibition in the Millennium gallery had thousands of visitors 
URL http://festivalofthemind.group.shef.ac.uk/mimicry-magic-and-iridescence-the-heliconius-butterfly/
 
Description To date there have been key findings in 6 areas:
1) We have identified a gene that controls colour pattern differences in Heliconius butterflies. This gene has been repeatedly targeted by natural selection not only multiple times in Heliconius but also in moths to produce changes in colour pattern. This suggests that certain genes may be particularly important in adapting animals to their environments. This was published in Nature and received extensive media attention.
2) We have identified scale structure differences between species and subspecies of Heliconius butterflies that are responsible for producing colour differences. This has revealed that similar colour-producing structures have repeatedly evolved in different species. However, some aspects of scale structure appear to evolve faster than others. This tells us something about the limitations of producing structural colours that may exist in natural systems. This was published in the Journal of the Royal Society, Interface.
3) We have identified the genetic architecture of iridescent colour, showing that it is controlled by multiple loci, one or more of which are sex linked in Heliconius erato. These results have been published in the Journal of the Royal Society, Interface Focus, as part of a special issue on structural colour.
3) We have identified genetic loci controlling parallel variation in iridescent colour in 2 mimetic species. This has demonstrated that the genetic basis is different in the 2 species, suggesting that divergence in quantitative traits is less predictable in its evolution than divergence in discrete traits. Ongoing work aims to identify specific genes controlling structural colour. These will be among the first genes involved in producing structural colours to be identified in nature. We have also shown that the genetic basis of quantitative colour pattern variation has limited parallels between species (published in the Journal of Evolutionary Biology).
4) We have investigated the selective pressures acting on iridescent structural colour in Heliconius butterflies in the wild and found evidence of divergent selection in the wild. However, the selection acting on one species appears to be stronger than the other. These results also shed light on the evolution of quantitative traits, which are controlled by multiple genes, and how selection can act on these to cause them to diverge in populations that are exchanging genetic material. This has broader implications for how biological diversity and local adaptation can arise and be maintained. These results are published in Molecular Ecology.
5) We have found evidence that iridescent colour in Heliconius erato and Heliconius sara may be a sexually selected trait, because it shows differences between the sexes. This is interesting because the colour is also known to been under selection for deterring predators. By investigating this further we can understand how multiple selection pressures, possibly acting in different directions, can shape the evolution of traits.
Exploitation Route Understanding the evolutionary process is important to predicting how animal populations could respond to environmental change. Our results so far suggest that having genetic variation at certain key genes may be important, but that this may only apply to certain discrete traits not to continuously varying traits.

Structural colours have several unique properties as compared to pigment based colour, which makes them interesting from an industrial perspective. Identifying how these very fine scale structures are modulated between closely related species tells us how nature has been able to modify these structures to produce colour in relatively short evolutionary time-scales, which could give useful insights into how to modulate such colours in artificial systems.

An understanding of the genetic basis of these traits will tell us how such colours are produced in nature, again giving insights into how to replicate this process.

I will also continue to work with schools, museums and tourism to ensure that my research is disseminated widely, and used to educate, inform and for the enjoyment of others.
Sectors Aerospace, Defence and Marine,Agriculture, Food and Drink,Creative Economy,Education,Energy,Environment,Leisure Activities, including Sports, Recreation and Tourism,Manufacturing, including Industrial Biotechology,Culture, Heritage, Museums and Collections,Retail

URL http://nadeau-lab.group.shef.ac.uk/
 
Description My findings have been used to develop educational materials for schools (primary and secondary). I have also been involved in developing displays and activities using my research outputs to communicate scientific ideas. My research has been conducted in partnership with an eco-tourism lodge in Ecuador and presentations on my research have been used to enhance the visitor experience to the lodge. My research has been used by a local artist, inspiring the production of a set of artworks.
Sector Creative Economy,Education,Leisure Activities, including Sports, Recreation and Tourism,Culture, Heritage, Museums and Collections
Impact Types Cultural,Societal

 
Description International Exchanges Scheme 2014/R2
Amount £12,000 (GBP)
Funding ID IE140619 
Organisation The Royal Society 
Sector Charity/Non Profit
Country United Kingdom
Start 01/2015 
End 01/2017
 
Description Revealing the interplay of genetics and biomechanics underlying butterfly scale morphogenesis
Amount $1,095,000 (USD)
Funding ID RGP0034/2021 
Organisation Human Frontier Science Program (HFSP) 
Sector Charity/Non Profit
Country France
Start 09/2021 
End 09/2024
 
Title Data from: Müllerian mimicry of a quantitative trait despite contrasting levels of genomic divergence and selection 
Description Hybrid zones, where distinct populations meet and interbreed, give insight into how differences between populations are maintained despite gene flow. Studying clines in genetic loci and adaptive traits across hybrid zones is a powerful method for understanding how selection drives differentiation within a single species, but can also be used to compare parallel divergence in different species responding to a common selective pressure. Here, we study parallel divergence of wing colouration in the butterflies Heliconius erato and H. melpomene, which are distantly related Müllerian mimics that show parallel geographic variation in both discrete variation in pigmentation, and quantitative variation in structural colour. Using geographic cline analysis, we show that clines in these traits are positioned in the roughly the same geographic region for both species, which is consistent with direct selection for mimicry. However, the width of the clines varies markedly between species. This difference is explained in part by variation in the strength of selection acting on colour traits within each species, but may also be influenced by differences in the dispersal rate and total strength of selection against hybrids between the species. Genotyping-by-sequencing also revealed weaker population structure in H. melpomene, suggesting the hybrid zones may have evolved differently in each species; which may also contribute to the patterns of phenotypic divergence in this system Overall, we conclude that multiple factors are needed to explain patterns of clinal variation within and between these species, although mimicry has probably played a central role. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL http://datadryad.org/stash/dataset/doi:10.5061/dryad.dz08kprv5
 
Title Gene expression data 
Description RNA sequence data from developing butterfly wings 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact It was used for a publication identifying genes controlling structural colour variation. Can be used by other researchers for genome annotation and further investigations of gene expression. 
URL https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE190378
 
Title Genomic data 
Description Short read sequences of genomes of wild Heliconius butterflies sampled from across a hybrid zone 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact We are using this data to understand the genes controlling structural colour. It has also been used by collaborators investigating other aspects of evolution of this butterflies, for example adaptation to altitude. It has been made public on the European Nuceotide Archive 
URL https://www.ebi.ac.uk/ena/data/view/PRJEB32848
 
Title Genomic data from crosses 
Description Genomic data from crosses use to map phenotypic variation 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact These data have been used for two publications identifying genes underlying quantitative trait variation 
URL https://www.ebi.ac.uk/ena/browser/view/PRJEB38330
 
Title Heliconius butterfly collection records in the Chocó-Darien Rainforest (Ecuador, Colombia, Panama) 2014-2016 
Description These data comprise collection records of Heliconius butterfly samples collected in the Chocó-Darien ecoregion between the Andes and the Pacific in Ecuador and Colombia, and the Pacific coast of the Darien region of Panama. Samples were collected over five sampling trips between 2014 and 2016. Data were collected for a study of clinal variation across this region in Heliconius erato and Heliconius melpomene, so focus on these two species. However, in most cases all observed Heliconius species were collected. The dataset includes photographs of the wings of most of the specimens, which were used for an analysis of colour and pattern variation. Many of these individuals also have genomic information available for them on the European Nucleotide Archive (ENA) - the data includes ENA accession numbers. Data were collected as part of a NERC fellowship project (NE/K008498/1). 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL https://catalogue.ceh.ac.uk/id/cb23c552-caee-4221-bdd3-83b172139ae1
 
Title Heliconius-iridescence 
Description Data and scripts for linkage mapping - part of Brien et al. "The genetic basis of structural colour variation in mimetic Heliconius butterflies" 
Type Of Material Data handling & control 
Year Produced 2021 
Provided To Others? Yes  
Impact Was used for two publications on the genetics of quantitive trait variation. The dta and scripts could be used by other researchers to investigate other traits that segregate in these crosses. The Scripts could be used by other researchers wanting to perform QTL mapping in other systems. 
URL http://github.com/mnbrien/Heliconius-iridescence
 
Title Images of Heliconius erato and Heliconius melpomene crosses 
Description Photographs in raw format of dorsal and ventral wings of Heliconius erato and Heliconius melpomene butterflies. Includes F1 and F2 offspring of crosses between H. e. cyrbia and H. e. demophoon, and H. m. cythera and H. m. rosina. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact These data have been used for two publications revealing the genetics of quantitative trait variation. 
 
Title Small angle x-ray scatterning data 
Description Small-angle x-ray scattering data from butterfly scale structures 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Data used to measure scale features in Heliconius erato individuals. 
 
Title The genetic basis of structural colour variation in mimetic Heliconius butterflies 
Description Raw USAXS data from discal region of Heliconius butterflies (H. erato and H. melpomene). The data comes from wings of individuals of two intercross families, one from each species and was used to estimate scale structure variation and a QTL analysis. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact These data have been used for two publications revealing the genes controlling structural colour variation 
URL https://zenodo.org/record/5747416
 
Title USAXS data handelling 
Description This is a set of modules and functions written to analyse Ultra Small Angle X-ray Scattering (USAXS) data collected on butterfly wings to study scale ultrastructure. 
Type Of Material Data analysis technique 
Year Produced 2020 
Provided To Others? Yes  
Impact Used for two publications on the genetic basis of structural colour variation. Could be used by other researchers using this type of data to characterise structural variation in materials. 
URL https://github.com/juanenciso14/butterfly_usaxs
 
Title analysis of SAXS data 
Description Code used to calculate ultrastructure measurements in the scales of the butterfly Heliconius erato from small-angle x-ray scattering data. The estimates are obtained by fitting the peaks of scattered intensity to bell-shaped functions and taking their centre as the magnitude of the scattering vector. 
Type Of Material Data handling & control 
Year Produced 2018 
Provided To Others? Yes  
Impact Publication describing ultra-structural variation found in Heliconius wing scales 
 
Title butterfly collections 
Description Collection of wild and captive bred Heliconius butterflies 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact The collection will be used to explore the physical structures underlying variation in iridescence and its genetic control. Also being used by other research groups studying other aspects of population genetics, dispersal and community composition. Being used for a study of butterfly adaptation to altitude. 
URL https://heliconius.ecdb.io/Default.aspx#ViewID=Unit_ListView&ObjectClassName=EarthCape.Module.Core.U...
 
Description Ecuador, UTI and Mashpi 
Organisation Technological University Indoamerica
Country Ecuador 
Sector Academic/University 
PI Contribution Providing expertise and resources to conduct research on butterfly genetics and evolution.
Collaborator Contribution Providing access to field facilities for rearing butterflies and local staff and expertise to maintain butterfly stocks.
Impact samples of butterflies for analysis
Start Year 2014
 
Description IKIAM 
Organisation Amazon Regional University
Country Ecuador 
Sector Academic/University 
PI Contribution Design and co-ordinate the research project Manage the project budget PDRA, PGRA and PhD student working on the project
Collaborator Contribution Provide access to facilities, including insectaries for butterfly rearing and two temperature-controlled chambers, to all staff and students of the University of Sheffield participating in the project. Hire a research technician to work on the project Help obtain all the necessary legal permits to allow researchers from the University of Sheffield and Ikiam to work and collect data in Ecuador, as well as to export samples. Support the Postdoctoral Research Associate (PDRA) and the Postgraduate Research Assistant (PGRA), hired by the University of Sheffield, to carry out the research and obtain visas and permissions to work in Ecuador Collaborate in the preparation of reports that include the activities in which Ikiam participates.
Impact Contributed to collection of biological specimens, which have been databased. Increasing the Profile of both Sheffield University and IKIAM University
Start Year 2017
 
Description MIT 
Organisation Massachusetts Institute of Technology
Country United States 
Sector Academic/University 
PI Contribution We are investigating the genetics underlying structural colour and using genetic and developmental tools to test model predictions
Collaborator Contribution The partners are using predictive modelling to investigate mechanical parameters that may influence scale structure morphology
Impact The collaboration is multi-disciplinary between biologists, physicists and materials scientists.
Start Year 2021
 
Description Rosario 
Organisation Del Rosario University
Country Colombia 
Sector Academic/University 
PI Contribution We are working with researchers to collect samples in the field. We and analysing these samples phenotypically and genetically.
Collaborator Contribution Working with us on this project. They have organised access to remote field sites and assisted with planning and sample collection.
Impact Samples collected Publications as listed under publications
Start Year 2015
 
Description STRI, Panama 
Organisation Smithsonian Institution
Department Smithsonian Tropical Research Institute
Country Panama 
Sector Academic/University 
PI Contribution Conducting research into butterfly evolution and genetics
Collaborator Contribution Access to in-country resources in Panama, assistance with obtaining permits.
Impact Butterfly samples for analysis
Start Year 2014
 
Description Biomimetics meeting 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Meeting of around 30 researchers from academia and industry with interests in using biological systems to improve the performance or develop new optical systems. I was one of a small number of biologists. Researchers from physical sciences and engineering expressed an interest in using my research findings to develop new engineering solutions.
Year(s) Of Engagement Activity 2017
URL https://www.iopconferences.org/iop/frontend/reg/thome.csp?pageID=564921&eventID=1026&eventID=1026&CS...
 
Description Butterfly wing colour media coverage 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Publication and press release received widespread media attention including: BBC news, ABC news (Australia), The New York Times,
The Washington Post, El Pais (Spain), The Mirror
Year(s) Of Engagement Activity 2016
URL http://www.bbc.co.uk/news/science-environment-36424768
 
Description CPD event for teachers 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact 7 secondary school teachers from 6 local schools attended a training day at the university organised by myself and a teacher-facilitator. All the teachers reported that the event improved their skills and knowledge and that it would have an impact on their teaching.
Year(s) Of Engagement Activity 2018
URL https://www.stem.org.uk/cpd/ondemand/46217/geneticsgenomics
 
Description Discovery night and Researchers night 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? Yes
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Annual events for the general public at the university, typically getting over 100 visitors. Sparked questions, discussion and interest

Visitors reported increased interest in science and the natural world
Year(s) Of Engagement Activity 2014,2017
 
Description In our time BBC radio 4 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Panel member on BBC Radio 4 programme "In Our Time" episode about hybrids
Year(s) Of Engagement Activity 2019
URL https://www.bbc.co.uk/programmes/m0009t41
 
Description Mashpi talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Participants in your research and patient groups
Results and Impact Local guides and staff in Ecuador showed interest and asked questions after the talk.

Local Ecuadorians showed an increased interest and appreciation of their natural resources and felt able to talk to tourists about it's importance and on-going research in the area, helping to generate sustainable income.
Year(s) Of Engagement Activity 2014
 
Description Nature Podcast 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Nature Podcast - released on the nature website and iTunes.
Year(s) Of Engagement Activity 2016
URL http://www.nature.com/nature/podcast/index-2016-06-02.html
 
Description Royal Society Summer Science 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Visitors to the Royal Society Exhibit included 2,540 school students and 10,447 members of the public. We estimate that at our stand we interacted with around 5,000-6,000 visitors. Our interactions sparked many questions and discussions.

We had some teachers saying they would use some of our web-based resources in the classroom. A survey conducted by the Royal Society showed that 94% of the school students agreed or strongly agreed that they enjoyed talking to the scientists and 61% of students felt that the Exhibition had made them more interested in science, and more interested in the possibility of a science-based career.
Year(s) Of Engagement Activity 2014
URL http://sse.royalsociety.org/2014/butterfly-evolution/
 
Description Schools mentoring 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Working with teachers to integrate the latest research into their classes and develop classroom and STEM club activities
Year(s) Of Engagement Activity 2015
 
Description Science festival (Sheffield) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact The exhibit and our presence gained lots of interest and sparked lots of questions and discussion.

Lots of the participants were passers buy and their questions suggested that they would not normally think about science in their day-to-day lives so I think many of them went away with an improved understanding and appreciation of science.
Year(s) Of Engagement Activity 2015
URL http://www.scienceweeksy.org.uk/
 
Description Whizz Pop Bang 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact Article about my research in the children science magazine "Whizz Pop Bang". Intended to interest children in science and inspire them to pursue scientific careers. My profile was specifically included to encourage girls in science.
Year(s) Of Engagement Activity 2016
URL http://www.whizzpopbang.com/