Genomic analysis of complex speciation in Heliconius

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

Abstract

Recent ideas suggest that evolution of new species (speciation) may be complex, whereby different parts of the genome separate at different times rather than a simple process consisting of a single split. Even our own species has been suggested to result from hybridization with chimpanzee lineages a few million years ago, although this conclusion is contested. Recent high-throughput genomics technologies now permit detailed investigation of complex speciation in likely non-model organism candidates, such as Heliconius butterflies. Heliconius are conspicuous warningly coloured tropical butterflies distasteful to birds. The patterns of most species also mimic those of other Heliconius or ithomiine butterflies. Some species show remarkable divergence in colour patterns between geographical races or species, but others share suspiciously similar patterns with closely related species, which they could have acquired via hybridization long after speciation. Hybridization is common: 35% of species are involved. In the melpomene/silvaniform group, almost all species are known to hybridize and backcross in both lab and in nature. This fascinating system provides an excellent test group for studying recent ideas about complex speciation. In this project, we will determine the extent to which four species (Heliconius melpomene, H. numata, H. elevatus and H. timareta) have recently exchanged parts of their genomes. This project brings together British and overseas knowledge of Heliconius butterfly biology and the latest genomic technologies to understand the genetic mechanisms that lead to the origin and maintenance of species. We propose to combine new high-throughput genomic technologies (454 and Solexa sequencing, and Illumina genotyping array chips) to map genomic regions in two focal species, H. melpomene and H. numata from Peru. Next generation sequencing technology will be used to obtain large amounts of genomic sequence data from the two species to identify thousands of genetic markers (single nucleotide polymorphisms, or SNPs). Subsequently, we will use these SNPs to produce high resolution genetic maps of each species. We will then genotype wild-caught specimens of H. melpomene, H. numata, H. elevatus and H. timareta. If complex speciation is occurring, we expect to find regions of shared polymorphism (indicating regions of recent exchange) and 'genomic islands' of fixed differences (indicating regions of older divergence probably surrounding sites of divergently selected genes such as those affecting mimicry, genomic incompatibility, mate choice, and ecological adaptations). A number of Eastern Andean taxa have recently been discovered that are close to H. melpomene, yet remain distinct from that species. The species contain some gene markers more similar to another species, H. cydno, but unlike that species they often share the local mimicry colour pattern of H. melpomene. We predict that these forms acquired their colour pattern via hybridization, which is a relatively common phenomenon in Heliconius. Using SNPs concentrated around these genes we will investigate the possibility that H. melpomene genes have been transferred to these segregate forms via hybridization, leading to the formation of new hybrid species. These SNPs will also allow investigation of colour pattern polymorphism in races of H. melpomene and H. numata The proposed research is a collaboration between Heliconius experts at a number of UK universities, The Gene Pool (Edinburgh), and the Centre for Microarray Resources (Cambridge). Further laboratory/bioinformatics support will be provided by the Max Planck Institute for Chemical Ecology (Germany). Up to now, whole-genome studies have been restricted to a few model organisms such as fruit flies and mice. Our proposal outlines a means of enabling ground breaking whole-genome understanding of evolution and speciation in a wild tropical organism for the first time.

Technical Summary

Recent studies suggest that speciation may be complex, such that different parts of the genome separate at different times, rather than in a simple, single-split process. Even our own species has been suggested to have acquired a chimpanzee X chromosome a few million years ago, although this conclusion is contentious. Few studies have investigated this possibility in any detail in likely candidate species. New genomics technologies now permit detailed investigations of complex speciation in non-model organisms such as the butterflies employed here. We will determine the extent to which four tropical American species (Heliconius melpomene, H. numata, H. elevatus and H. timareta) have recently exchanged parts of their genomes. We propose to combine high-throughput technologies (454/Solexa sequencing and Illumina SNP arrays) to produce high-resolution genomic maps of two main species, H. melpomene and H. numata from Peru; with existing BAC-end sequences these will act as scaffolds for ongoing genomics work by the Heliconius Consortium. We will genotype wild-caught specimens of the four species. If complex speciation is occurring, we expect to find regions of shared polymorphism (indicating regions of recent exchange) and 'genomic islands' of fixed differences (indicating regions of older divergence, in part protected by species isolating traits or regions of divergent selection). Higher resolution SNP maps near two colour pattern determining genes will also allow investigation of colour pattern polymorphism in races of H. melpomene and H. numata, as well as the possibility of transfer of colour pattern genes in East Andean species H. elevatus and H. timareta that share patterns with H. melpomene and are likely to have obtained them via hybridization.

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 The evolutionary importance of hybridization and introgression haslong been debated

1. Hybrids are usually rare and unfit, but even infrequent hybridization can aid adaptation by transferring beneficial traits between species. Here we use genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation

2-5. We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,669 predicted genes, biologically important expansions of families of chemosensory and Hoxgenes are particularly noteworthy. Chromosomal organizationhas remained broadly conserved since the Cretaceous period, when butterflies split from the Bombyx (silkmoth) lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, Heliconius melpomene, Heliconius timareta andHeliconius elevatus, especially at two genomic regions that control mimicry pattern. We infer that closely related Heliconius species exchange protective colour-pattern genes promiscuously, implying that hybridization has an important role in adaptive radiation.
URL http://www.heliconius.org
 
Description BBSRC Project Grant (Genome Databasing)
Amount £671,655 (GBP)
Funding ID BB/K020161/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2013 
End 11/2016
 
Title LepBase - lepidoptera genome database 
Description LepBase is a tier two ENSEMBL database for the genomes of all lepidoptera. Genome sequencing, and large-scale, population genomic analysis, has suddenly become affordable. The explosion of data presents tremendous opportunity for ground-breaking research based on integration of data from independently-organized, community-driven genome projects, but this in turn requires shared database resources. For model organisms, genome databasing efforts grew with the research communities, and there are mature portals for deep investigation across many large scale datasets - the databases themselves have become a substrate for (meta-) research of high impact. For communities new to genomic (and population genomic) approaches, the need for accessible databases is even more pressing, as researchers are less likely to be fluent in the peculiar languages of genomics and in high-throughput bioinformatics. Here we propose the founding of a community database for lepidopteran genomics, LepBase, to meet the needs of the growing community of researchers using genomics to understand Lepidoptera as crop pests, as potentially invasive species, as developmental models, and as key taxa for understanding the interplay between ecology, genomics, evolution and speciation. While initially focussed on the available lepidopteran genomes the project will meet the challenge of future genomic riches (over 20 genomes 'in the pipeline') by building a platform that focuses on the needs of the lepidopteran research community. The challenge of integrating newly developed genomic resources across taxa is not a new one, and several computational frameworks exist to support such endeavors (such as the ENSEMBL project, and the GMOD ecosystem of tools). Central, aggregative database efforts, such as ENSEMBL Genomes, provide an effective and powerful, one-size-fits-all solution to genome warehousing. Coordinating with smaller research communities to directly implement clade-specific resources is overwhelming the resources of institutions that have a mandate to generate integrated genomic databases. ENSEMBL now advocates a multi-tiered approach to the aggregation, integration, and dissemination of the rapidly increasing wealth of genomic information arising from community-driven genome projects so that species-level genomic resources can flow 'upstream' into the pan-genome database. The goals of our project are: to develop a community-wide, comparative database for the Lepidoptera using the ENSEMBL platform; to institute effective tools for ongoing community annotation of emerging genomes; to forge close links with ENSEMBL Genomes to ensure upload of lepidopteran genomes into the global resource; to implement new modes of data visualisation and analysis in the ENSEMBL framework to meet community needs; and to provide training in genomics to the community of lepidopteran researchers. The LepBase database will also be a working model of community-driven databases that drive not only clade-specific research programmes but also enable the flow of knowledge from species-specific genome projects into a comprehensive framework. The project will be based in the Blaxter bioinformatics and genomics group in Edinburgh, in association with the GenePool Genomics Facility (currently engaged in sequencing butterfly and moth species), with project partners in the Jiggins Heliconius research group in Cambridge and Dasmahapatra in York, and the support of lepidopteran researchers worldwide. Initial focus will be on the genus Heliconius, for which a complete genome sequence and abundant annotation, transcriptome and resequencing data already exist. The database will be rapidly extended into silkmoth, Bicyclus, Danaus and other species. The resource will be overseen by a Scientific Advisory Board drawn from across the range of lepidopteran researchers, and will aim for financial sustainability beyond the tenure of the award through development of a 'subscription' model of funding from research partners. 
Type Of Material Database/Collection of data 
Year Produced 2014 
Provided To Others? Yes  
Impact N/A 
URL http://lepbase.org/
 
Title ngenomes 
Description ngenomes is a database for the display of genome assemblies from the Blaxter lab. It used the genomeHubs - LepBase ENSEMBL code 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact Colleagues globally have used the database for identification of target loci, exploration of relationships and download of data. 
URL http://ensembl.ngenomes.org
 
Description Heliconius genome consortium 
Organisation University of Cambridge
Department Department of Zoology
Country United Kingdom 
Sector Academic/University 
PI Contribution Offering genomic sequencing and reseaquencing technologies; close involvement in experimental design.
Collaborator Contribution Joining the consortium has allowed GenePool to develop custom targeted resequencing technologies, and associated bioinformatics skiils, and made us much more visible across this area of science
Impact The Heliconius melpomene genome has been assembled and annotated. A manuscript describing this work is submitted for publication. On the basis of the GenePool's involvement in this consortium we have coordinated a ladybird genome consortium with 6 partner laboratories, and currently have 2 genomes in sequencing.
Start Year 2010
 
Title EasyMirror/EasyImport 
Description These tools simplify the rool out of customised ENSEMBL databases. 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact We have been inundated with requests for support and assistance in delivering these tools, and with praise for their ease of use and timeliness. 
URL http://www.genomehubs.org
 
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