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Orteu A, Kucka M, Gordon IJ, Ng’iru I, van der Heijden ESM, Talavera G, Warren IA, Collins S, ffrench-Constant RH, Martins DJ, Chan YF, Jiggins CD, Martin SH. Transposable Element Insertions Are Associated with Batesian Mimicry in the Pantropical Butterfly Hypolimnas misippus. Mol Biol Evol 2024; 41:msae041. [PMID: 38401262 PMCID: PMC10924252 DOI: 10.1093/molbev/msae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/26/2024] Open
Abstract
Hypolimnas misippus is a Batesian mimic of the toxic African Queen butterfly (Danaus chrysippus). Female H. misippus butterflies use two major wing patterning loci (M and A) to imitate three color morphs of D. chrysippus found in different regions of Africa. In this study, we examine the evolution of the M locus and identify it as an example of adaptive atavism. This phenomenon involves a morphological reversion to an ancestral character that results in an adaptive phenotype. We show that H. misippus has re-evolved an ancestral wing pattern present in other Hypolimnas species, repurposing it for Batesian mimicry of a D. chrysippus morph. Using haplotagging, a linked-read sequencing technology, and our new analytical tool, Wrath, we discover two large transposable element insertions located at the M locus and establish that these insertions are present in the dominant allele responsible for producing mimetic phenotype. By conducting a comparative analysis involving additional Hypolimnas species, we demonstrate that the dominant allele is derived. This suggests that, in the derived allele, the transposable elements disrupt a cis-regulatory element, leading to the reversion to an ancestral phenotype that is then utilized for Batesian mimicry of a distinct model, a different morph of D. chrysippus. Our findings present a compelling instance of convergent evolution and adaptive atavism, in which the same pattern element has independently evolved multiple times in Hypolimnas butterflies, repeatedly playing a role in Batesian mimicry of diverse model species.
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Affiliation(s)
- Anna Orteu
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Marek Kucka
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Ian J Gordon
- Centre of Excellence in Biodiversity, University of Rwanda, Huye, Rwanda
| | - Ivy Ng’iru
- Mpala Research Centre, Nanyuki 10400, Laikipia, Kenya
- School of Biosciences, Cardiff University, Cardiff CF 10 3AX, UK
- UK Centre for Ecology and Hydrology, Wallingford OX10 8BB, UK
| | - Eva S M van der Heijden
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, Barcelona, Catalonia, Spain
| | - Ian A Warren
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Steve Collins
- African Butterfly Research Institute, Nairobi, Kenya
| | | | - Dino J Martins
- Turkana Basin Institute, Stony Brook University, Stony Brook, NY 11794, USA
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Simon H Martin
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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2
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Van Belleghem SM, Ruggieri AA, Concha C, Livraghi L, Hebberecht L, Rivera ES, Ogilvie JG, Hanly JJ, Warren IA, Planas S, Ortiz-Ruiz Y, Reed R, Lewis JJ, Jiggins CD, Counterman BA, McMillan WO, Papa R. High level of novelty under the hood of convergent evolution. Science 2023; 379:1043-1049. [PMID: 36893249 PMCID: PMC11000492 DOI: 10.1126/science.ade0004] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 02/08/2023] [Indexed: 03/11/2023]
Abstract
Little is known about the extent to which species use homologous regulatory architectures to achieve phenotypic convergence. By characterizing chromatin accessibility and gene expression in developing wing tissues, we compared the regulatory architecture of convergence between a pair of mimetic butterfly species. Although a handful of color pattern genes are known to be involved in their convergence, our data suggest that different mutational paths underlie the integration of these genes into wing pattern development. This is supported by a large fraction of accessible chromatin being exclusive to each species, including the de novo lineage-specific evolution of a modular optix enhancer. These findings may be explained by a high level of developmental drift and evolutionary contingency that occurs during the independent evolution of mimicry.
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Affiliation(s)
- Steven M. Van Belleghem
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico
- Ecology, Evolution and Conservation Biology, Biology Department, KU Leuven, Leuven, Belgium
| | - Angelo A. Ruggieri
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico
| | - Carolina Concha
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
| | - Luca Livraghi
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Laura Hebberecht
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- School of Biological Sciences, Bristol University, Bristol, UK
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Edgardo Santiago Rivera
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Department of Biomaterials, Universität Bayreuth, Bayreuth, Germany
| | - James G. Ogilvie
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Joseph J. Hanly
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Ian A. Warren
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Silvia Planas
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Yadira Ortiz-Ruiz
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Robert Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - James J. Lewis
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | | | | | - W. Owen McMillan
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
| | - Riccardo Papa
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan, Puerto Rico
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, Puerto Rico
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3
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Yen EC, McCarthy SA, Galarza JA, Generalovic TN, Pelan S, Nguyen P, Meier JI, Warren IA, Mappes J, Durbin R, Jiggins CD. Correction to: A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning. Gigascience 2021; 10:6409162. [PMID: 34687311 PMCID: PMC8538893 DOI: 10.1093/gigascience/giab073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Eugenie C Yen
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Shane A McCarthy
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.,Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Saffron Walden CB10 1SA, UK
| | - Juan A Galarza
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Tomas N Generalovic
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Sarah Pelan
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Saffron Walden CB10 1SA, UK
| | - Petr Nguyen
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic.,University of South Bohemia, Faculty of Science, Branišovská 1645/31A, 370 05 České Budějovice, Czech Republic
| | - Joana I Meier
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.,St John's College, University of Cambridge, St John's Street, Cambridge CB2 1TP, UK
| | - Ian A Warren
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Johanna Mappes
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.,Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Saffron Walden CB10 1SA, UK
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.,St John's College, University of Cambridge, St John's Street, Cambridge CB2 1TP, UK
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4
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Livraghi L, Hanly JJ, Van Bellghem SM, Montejo-Kovacevich G, van der Heijden ESM, Loh LS, Ren A, Warren IA, Lewis JJ, Concha C, Hebberecht L, Wright CJ, Walker JM, Foley J, Goldberg ZH, Arenas-Castro H, Salazar C, Perry MW, Papa R, Martin A, McMillan WO, Jiggins CD. Cortex cis-regulatory switches establish scale colour identity and pattern diversity in Heliconius. eLife 2021; 10:e68549. [PMID: 34280087 PMCID: PMC8289415 DOI: 10.7554/elife.68549] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/14/2021] [Indexed: 12/14/2022] Open
Abstract
In Heliconius butterflies, wing colour pattern diversity and scale types are controlled by a few genes of large effect that regulate colour pattern switches between morphs and species across a large mimetic radiation. One of these genes, cortex, has been repeatedly associated with colour pattern evolution in butterflies. Here we carried out CRISPR knockouts in multiple Heliconius species and show that cortex is a major determinant of scale cell identity. Chromatin accessibility profiling and introgression scans identified cis-regulatory regions associated with discrete phenotypic switches. CRISPR perturbation of these regions in black hindwing genotypes recreated a yellow bar, revealing their spatially limited activity. In the H. melpomene/timareta lineage, the candidate CRE from yellow-barred phenotype morphs is interrupted by a transposable element, suggesting that cis-regulatory structural variation underlies these mimetic adaptations. Our work shows that cortex functionally controls scale colour fate and that its cis-regulatory regions control a phenotypic switch in a modular and pattern-specific fashion.
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Affiliation(s)
- Luca Livraghi
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
| | - Joseph J Hanly
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
- The George Washington University Department of Biological Sciences, Science and Engineering HallWashingtonUnited States
| | - Steven M Van Bellghem
- Department of Biology, Centre for Applied Tropical Ecology and Conservation, University of Puerto RicoRio PiedrasPuerto Rico
| | | | - Eva SM van der Heijden
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
| | - Ling Sheng Loh
- The George Washington University Department of Biological Sciences, Science and Engineering HallWashingtonUnited States
| | - Anna Ren
- The George Washington University Department of Biological Sciences, Science and Engineering HallWashingtonUnited States
| | - Ian A Warren
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
| | - James J Lewis
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell UniversityIthacaUnited States
| | | | - Laura Hebberecht
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
| | - Charlotte J Wright
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
| | - Jonah M Walker
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
| | | | - Zachary H Goldberg
- Cell & Developmental Biology, Division of Biological Sciences, UC San DiegoLa JollaUnited States
| | | | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences, Universidad del RosarioBogotáColombia
| | - Michael W Perry
- Cell & Developmental Biology, Division of Biological Sciences, UC San DiegoLa JollaUnited States
| | - Riccardo Papa
- Department of Biology, Centre for Applied Tropical Ecology and Conservation, University of Puerto RicoRio PiedrasPuerto Rico
| | - Arnaud Martin
- The George Washington University Department of Biological Sciences, Science and Engineering HallWashingtonUnited States
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
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5
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Generalovic TN, McCarthy SA, Warren IA, Wood JMD, Torrance J, Sims Y, Quail M, Howe K, Pipan M, Durbin R, Jiggins CD. A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia illucens L.). G3 (Bethesda) 2021; 11:jkab085. [PMID: 33734373 PMCID: PMC8104945 DOI: 10.1093/g3journal/jkab085] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/09/2021] [Indexed: 01/15/2023]
Abstract
Hermetia illucens L. (Diptera: Stratiomyidae), the Black Soldier Fly (BSF) is an increasingly important species for bioconversion of organic material into animal feed. We generated a high-quality chromosome-scale genome assembly of the BSF using Pacific Bioscience, 10X Genomics linked read and high-throughput chromosome conformation capture sequencing technology. Scaffolding the final assembly with Hi-C data produced a highly contiguous 1.01 Gb genome with 99.75% of scaffolds assembled into pseudochromosomes representing seven chromosomes with 16.01 Mb contig and 180.46 Mb scaffold N50 values. The highly complete genome obtained a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness of 98.6%. We masked 67.32% of the genome as repetitive sequences and annotated a total of 16,478 protein-coding genes using the BRAKER2 pipeline. We analyzed an established lab population to investigate the genomic variation and architecture of the BSF revealing six autosomes and an X chromosome. Additionally, we estimated the inbreeding coefficient (1.9%) of the lab population by assessing runs of homozygosity. This provided evidence for inbreeding events including long runs of homozygosity on chromosome 5. The release of this novel chromosome-scale BSF genome assembly will provide an improved resource for further genomic studies, functional characterization of genes of interest and genetic modification of this economically important species.
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Affiliation(s)
| | - Shane A McCarthy
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Ian A Warren
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Jonathan M D Wood
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - James Torrance
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Ying Sims
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Michael Quail
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Kerstin Howe
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Miha Pipan
- Better Origin, Entomics Biosystems Limited, Cambridge CB3 0ES, UK
| | - Richard Durbin
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
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6
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Darragh K, Orteu A, Black D, Byers KJRP, Szczerbowski D, Warren IA, Rastas P, Pinharanda A, Davey JW, Fernanda Garza S, Abondano Almeida D, Merrill RM, McMillan WO, Schulz S, Jiggins CD. A novel terpene synthase controls differences in anti-aphrodisiac pheromone production between closely related Heliconius butterflies. PLoS Biol 2021; 19:e3001022. [PMID: 33465061 PMCID: PMC7815096 DOI: 10.1371/journal.pbio.3001022] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/30/2020] [Indexed: 02/07/2023] Open
Abstract
Plants and insects often use the same compounds for chemical communication, but not much is known about the genetics of convergent evolution of chemical signals. The terpene (E)-β-ocimene is a common component of floral scent and is also used by the butterfly Heliconius melpomene as an anti-aphrodisiac pheromone. While the biosynthesis of terpenes has been described in plants and microorganisms, few terpene synthases (TPSs) have been identified in insects. Here, we study the recent divergence of 2 species, H. melpomene and Heliconius cydno, which differ in the presence of (E)-β-ocimene; combining linkage mapping, gene expression, and functional analyses, we identify 2 novel TPSs. Furthermore, we demonstrate that one, HmelOS, is able to synthesise (E)-β-ocimene in vitro. We find no evidence for TPS activity in HcydOS (HmelOS ortholog of H. cydno), suggesting that the loss of (E)-β-ocimene in this species is the result of coding, not regulatory, differences. The TPS enzymes we discovered are unrelated to previously described plant and insect TPSs, demonstrating that chemical convergence has independent evolutionary origins. Plants and insects often use the same compounds for chemical communication, but little is known about the convergent evolution of such chemical signals. This study identifies a novel terpene synthase involved in production of an anti-aphrodisiac pheromone by the butterfly Heliconius melpomene. This enzyme is unrelated to other insect terpene synthases, providing evidence that the ability to synthesise terpenes has arisen multiple times independently within the insects.
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Affiliation(s)
- Kathy Darragh
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Smithsonian Tropical Research Institute, Panamá, Panamá
- * E-mail:
| | - Anna Orteu
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Daniella Black
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Kelsey J. R. P. Byers
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Smithsonian Tropical Research Institute, Panamá, Panamá
| | - Daiane Szczerbowski
- Institute of Organic Chemistry, Department of Life Sciences, Technische Universität Braunschweig, Braunschweig, Germany
| | - Ian A. Warren
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ana Pinharanda
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - John W. Davey
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | | | | | - Richard M. Merrill
- Smithsonian Tropical Research Institute, Panamá, Panamá
- Division of Evolutionary Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Stefan Schulz
- Institute of Organic Chemistry, Department of Life Sciences, Technische Universität Braunschweig, Braunschweig, Germany
| | - Chris D. Jiggins
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Smithsonian Tropical Research Institute, Panamá, Panamá
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7
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Byers KJRP, Darragh K, Fernanda Garza S, Abondano Almeida D, Warren IA, Rastas PMA, Merrill RM, Schulz S, McMillan WO, Jiggins CD. Clustering of loci controlling species differences in male chemical bouquets of sympatric Heliconius butterflies. Ecol Evol 2021; 11:89-107. [PMID: 33437416 PMCID: PMC7790645 DOI: 10.1002/ece3.6947] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 12/23/2022] Open
Abstract
The degree to which loci promoting reproductive isolation cluster in the genome-that is, the genetic architecture of reproductive isolation-can influence the tempo and mode of speciation. Tight linkage between these loci can facilitate speciation in the face of gene flow. Pheromones play a role in reproductive isolation in many Lepidoptera species, and the role of endogenously produced compounds as secondary metabolites decreases the likelihood of pleiotropy associated with many barrier loci. Heliconius butterflies use male sex pheromones to both court females (aphrodisiac wing pheromones) and ward off male courtship (male-transferred antiaphrodisiac genital pheromones), and it is likely that these compounds play a role in reproductive isolation between Heliconius species. Using a set of backcross hybrids between H. melpomene and H. cydno, we investigated the genetic architecture of putative male pheromone compound production. We found a set of 40 significant quantitative trait loci (QTL) representing 33 potential pheromone compounds. QTL clustered significantly on two chromosomes, chromosome 8 for genital compounds and chromosome 20 for wing compounds, and chromosome 20 was enriched for potential pheromone biosynthesis genes. There was minimal overlap between pheromone QTL and known QTL for mate choice and color pattern. Nonetheless, we did detect linkage between a QTL for wing androconial area and optix, a color pattern locus known to play a role in reproductive isolation in these species. This tight clustering of putative pheromone loci might contribute to coincident reproductive isolating barriers, facilitating speciation despite ongoing gene flow.
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Affiliation(s)
- Kelsey J. R. P. Byers
- Department of ZoologyUniversity of CambridgeCambridgeUK
- Smithsonian Tropical Research InstitutePanamaPanama
- Present address:
Department of Cell and Developmental BiologyJohn Innes CentreNorwichUK
| | - Kathy Darragh
- Department of ZoologyUniversity of CambridgeCambridgeUK
- Smithsonian Tropical Research InstitutePanamaPanama
- Present address:
Department of Evolution and EcologyUniversity of California DavisDavisCAUSA
| | - Sylvia Fernanda Garza
- Smithsonian Tropical Research InstitutePanamaPanama
- Present address:
Department of Collective BehaviourMax Planck Institute of Animal BehaviourKonstanzGermany
| | - Diana Abondano Almeida
- Smithsonian Tropical Research InstitutePanamaPanama
- Present address:
Institute for Ecology, Evolution and DiversityGoethe UniversitätFrankfurtGermany
| | - Ian A. Warren
- Department of ZoologyUniversity of CambridgeCambridgeUK
| | | | - Richard M. Merrill
- Smithsonian Tropical Research InstitutePanamaPanama
- Division of Evolutionary BiologyLudwig‐Maximilians‐Universität MünchenMunichGermany
| | - Stefan Schulz
- Institute of Organic ChemistryDepartment of Life SciencesTechnische Universität BraunschweigBraunschweigGermany
| | | | - Chris D. Jiggins
- Department of ZoologyUniversity of CambridgeCambridgeUK
- Smithsonian Tropical Research InstitutePanamaPanama
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8
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Valencia-Montoya WA, Elfekih S, North HL, Meier JI, Warren IA, Tay WT, Gordon KHJ, Specht A, Paula-Moraes SV, Rane R, Walsh TK, Jiggins CD. Adaptive Introgression across Semipermeable Species Boundaries between Local Helicoverpa zea and Invasive Helicoverpa armigera Moths. Mol Biol Evol 2020; 37:2568-2583. [PMID: 32348505 PMCID: PMC7475041 DOI: 10.1093/molbev/msaa108] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Hybridization between invasive and native species has raised global concern, given the dramatic increase in species range shifts and pest outbreaks due to anthropogenic dispersal. Nevertheless, secondary contact between sister lineages of local and invasive species provides a natural laboratory to understand the factors that determine introgression and the maintenance or loss of species barriers. Here, we characterize the early evolutionary outcomes following secondary contact between invasive Helicoverpa armigera and native H. zea in Brazil. We carried out whole-genome resequencing of Helicoverpa moths from Brazil in two temporal samples: during the outbreak of H. armigera in 2013 and 2017. There is evidence for a burst of hybridization and widespread introgression from local H. zea into invasive H. armigera coinciding with H. armigera expansion in 2013. However, in H. armigera, the admixture proportion and the length of introgressed blocks were significantly reduced between 2013 and 2017, suggesting selection against admixture. In contrast to the genome-wide pattern, there was striking evidence for adaptive introgression of a single region from the invasive H. armigera into local H. zea, including an insecticide resistance allele that increased in frequency over time. In summary, despite extensive gene flow after secondary contact, the species boundaries are largely maintained except for the single introgressed region containing the insecticide-resistant locus. We document the worst-case scenario for an invasive species, in which there are now two pest species instead of one, and the native species has acquired resistance to pyrethroid insecticides through introgression.
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Affiliation(s)
- Wendy A Valencia-Montoya
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA
| | - Samia Elfekih
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, VIC, Australia
- Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Henry L North
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Joana I Meier
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Ian A Warren
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Wee Tek Tay
- CSIRO Land and Water, Black Mountain Laboratories, Canberra, ACT, Australia
| | - Karl H J Gordon
- CSIRO Land and Water, Black Mountain Laboratories, Canberra, ACT, Australia
| | | | | | - Rahul Rane
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, VIC, Australia
- Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Tom K Walsh
- CSIRO Land and Water, Black Mountain Laboratories, Canberra, ACT, Australia
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
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9
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Yen EC, McCarthy SA, Galarza JA, Generalovic TN, Pelan S, Nguyen P, Meier JI, Warren IA, Mappes J, Durbin R, Jiggins CD. A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning. Gigascience 2020; 9:giaa088. [PMID: 32808665 PMCID: PMC7433188 DOI: 10.1093/gigascience/giaa088] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/03/2020] [Accepted: 07/27/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Diploid genome assembly is typically impeded by heterozygosity because it introduces errors when haplotypes are collapsed into a consensus sequence. Trio binning offers an innovative solution that exploits heterozygosity for assembly. Short, parental reads are used to assign parental origin to long reads from their F1 offspring before assembly, enabling complete haplotype resolution. Trio binning could therefore provide an effective strategy for assembling highly heterozygous genomes, which are traditionally problematic, such as insect genomes. This includes the wood tiger moth (Arctia plantaginis), which is an evolutionary study system for warning colour polymorphism. FINDINGS We produced a high-quality, haplotype-resolved assembly for Arctia plantaginis through trio binning. We sequenced a same-species family (F1 heterozygosity ∼1.9%) and used parental Illumina reads to bin 99.98% of offspring Pacific Biosciences reads by parental origin, before assembling each haplotype separately and scaffolding with 10X linked reads. Both assemblies are contiguous (mean scaffold N50: 8.2 Mb) and complete (mean BUSCO completeness: 97.3%), with annotations and 31 chromosomes identified through karyotyping. We used the assembly to analyse genome-wide population structure and relationships between 40 wild resequenced individuals from 5 populations across Europe, revealing the Georgian population as the most genetically differentiated with the lowest genetic diversity. CONCLUSIONS We present the first invertebrate genome to be assembled via trio binning. This assembly is one of the highest quality genomes available for Lepidoptera, supporting trio binning as a potent strategy for assembling heterozygous genomes. Using our assembly, we provide genomic insights into the geographic population structure of A. plantaginis.
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Affiliation(s)
- Eugenie C Yen
- Department of Zoology, University of Cambridge, Downing
Street, Cambridge CB2 3EJ, UK
| | - Shane A McCarthy
- Department of Genetics, University of Cambridge, Downing
Street, Cambridge CB2 3EH, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus,
Hinxton, Saffron Walden CB10 1SA, UK
| | - Juan A Galarza
- Department of Biological and Environmental Science, University of
Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Tomas N Generalovic
- Department of Zoology, University of Cambridge, Downing
Street, Cambridge CB2 3EJ, UK
| | - Sarah Pelan
- Wellcome Sanger Institute, Wellcome Trust Genome Campus,
Hinxton, Saffron Walden CB10 1SA, UK
| | - Petr Nguyen
- Biology Centre of the Czech Academy of Sciences, Institute of
Entomology, Branišovská 1160/31, 370 05 České Budějovice, Czech
Republic
- University of South Bohemia, Faculty of Science, Branišovská
1645/31A, 370 05 České Budějovice, Czech Republic
| | - Joana I Meier
- Department of Zoology, University of Cambridge, Downing
Street, Cambridge CB2 3EJ, UK
- St John's College, University of Cambridge, St John's Street,
Cambridge CB2 1TP, UK
| | - Ian A Warren
- Department of Zoology, University of Cambridge, Downing
Street, Cambridge CB2 3EJ, UK
| | - Johanna Mappes
- Department of Biological and Environmental Science, University of
Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Downing
Street, Cambridge CB2 3EH, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus,
Hinxton, Saffron Walden CB10 1SA, UK
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Downing
Street, Cambridge CB2 3EJ, UK
- St John's College, University of Cambridge, St John's Street,
Cambridge CB2 1TP, UK
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10
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Martin SH, Singh KS, Gordon IJ, Omufwoko KS, Collins S, Warren IA, Munby H, Brattström O, Traut W, Martins DJ, Smith DAS, Jiggins CD, Bass C, ffrench-Constant RH. Whole-chromosome hitchhiking driven by a male-killing endosymbiont. PLoS Biol 2020; 18:e3000610. [PMID: 32108180 PMCID: PMC7046192 DOI: 10.1371/journal.pbio.3000610] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/23/2020] [Indexed: 12/30/2022] Open
Abstract
Neo-sex chromosomes are found in many taxa, but the forces driving their emergence and spread are poorly understood. The female-specific neo-W chromosome of the African monarch (or queen) butterfly Danaus chrysippus presents an intriguing case study because it is restricted to a single 'contact zone' population, involves a putative colour patterning supergene, and co-occurs with infection by the male-killing endosymbiont Spiroplasma. We investigated the origin and evolution of this system using whole genome sequencing. We first identify the 'BC supergene', a broad region of suppressed recombination across nearly half a chromosome, which links two colour patterning loci. Association analysis suggests that the genes yellow and arrow in this region control the forewing colour pattern differences between D. chrysippus subspecies. We then show that the same chromosome has recently formed a neo-W that has spread through the contact zone within approximately 2,200 years. We also assembled the genome of the male-killing Spiroplasma, and find that it shows perfect genealogical congruence with the neo-W, suggesting that the neo-W has hitchhiked to high frequency as the male-killer has spread through the population. The complete absence of female crossing-over in the Lepidoptera causes whole-chromosome hitchhiking of a single neo-W haplotype, carrying a single allele of the BC supergene and dragging multiple non-synonymous mutations to high frequency. This has created a population of infected females that all carry the same recessive colour patterning allele, making the phenotypes of each successive generation highly dependent on uninfected male immigrants. Our findings show how hitchhiking can occur between the physically unlinked genomes of host and endosymbiont, with dramatic consequences.
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Affiliation(s)
- Simon H. Martin
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Kumar Saurabh Singh
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, United Kingdom
| | - Ian J. Gordon
- Center of Excellence in Biodiversity and Natural Resource Management, University of Rwanda, Huye, Rwanda
| | - Kennedy Saitoti Omufwoko
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States of America
- Mpala Research Centre, Nanyuki, Kenya
| | - Steve Collins
- African Butterfly Research Institute, Nairobi, Kenya
| | - Ian A. Warren
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Hannah Munby
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Oskar Brattström
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Walther Traut
- Institut für Biologie, Universität Lübeck, Lübeck, Germany
| | - Dino J. Martins
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States of America
- Mpala Research Centre, Nanyuki, Kenya
| | | | - Chris D. Jiggins
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Chris Bass
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, United Kingdom
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Byers KJRP, Darragh K, Musgrove J, Almeida DA, Garza SF, Warren IA, Rastas PM, Kučka M, Chan YF, Merrill RM, Schulz S, McMillan WO, Jiggins CD. A major locus controls a biologically active pheromone component in Heliconius melpomene. Evolution 2020; 74:349-364. [PMID: 31913497 PMCID: PMC7027519 DOI: 10.1111/evo.13922] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/20/2019] [Accepted: 01/03/2020] [Indexed: 12/23/2022]
Abstract
Understanding the production, response, and genetics of signals used in mate choice can inform our understanding of the evolution of both intraspecific mate choice and reproductive isolation. Sex pheromones are important for courtship and mate choice in many insects, but we know relatively little of their role in butterflies. The butterfly Heliconius melpomene uses a complex blend of wing androconial compounds during courtship. Electroantennography in H. melpomene and its close relative Heliconius cydno showed that responses to androconial extracts were not species specific. Females of both species responded equally strongly to extracts of both species, suggesting conservation of peripheral nervous system elements across the two species. Individual blend components provoked little to no response, with the exception of octadecanal, a major component of the H. melpomene blend. Supplementing octadecanal on the wings of octadecanal-rich H. melpomene males led to an increase in the time until mating, demonstrating the bioactivity of octadecanal in Heliconius. Using quantitative trait locus (QTL) mapping, we identified a single locus on chromosome 20 responsible for 41% of the parental species' difference in octadecanal production. This QTL does not overlap with any of the major wing color or mate choice loci, nor does it overlap with known regions of elevated or reduced FST . A set of 16 candidate fatty acid biosynthesis genes lies underneath the QTL. Pheromones in Heliconius carry information relevant for mate choice and are under simple genetic control, suggesting they could be important during speciation.
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Affiliation(s)
- Kelsey J. R. P. Byers
- Department of ZoologyUniversity of CambridgeCambridgeCB2 3EJUnited Kingdom
- Smithsonian Tropical Research InstitutePanamaPanama
| | - Kathy Darragh
- Department of ZoologyUniversity of CambridgeCambridgeCB2 3EJUnited Kingdom
- Smithsonian Tropical Research InstitutePanamaPanama
| | | | - Diana Abondano Almeida
- Smithsonian Tropical Research InstitutePanamaPanama
- Current address: Institute for Ecology, Evolution, and DiversityGoethe Universität60323FrankfurtGermany
| | - Sylvia Fernanda Garza
- Smithsonian Tropical Research InstitutePanamaPanama
- Current address: Department of Collective BehaviorMax Planck Institute of Animal Behavior78315KonstanzGermany
- Current address: Centre for the Advanced Study of Collective BehaviorUniversity of Konstanz78464KonstanzGermany
| | - Ian A. Warren
- Department of ZoologyUniversity of CambridgeCambridgeCB2 3EJUnited Kingdom
| | - Pasi M. Rastas
- Institute of BiotechnologyUniversity of Helsinki00014HelsinkiFinland
| | - Marek Kučka
- Friedrich Miescher LaboratoryMax Planck Society72076TübingenGermany
| | | | - Richard M. Merrill
- Division of Evolutionary BiologyLudwig‐Maximilians‐Universität München80539MunichGermany
| | - Stefan Schulz
- Department of Life SciencesInstitute of Organic Chemistry, Technische Universität Braunschweig38106BraunschweigGermany
| | | | - Chris D. Jiggins
- Department of ZoologyUniversity of CambridgeCambridgeCB2 3EJUnited Kingdom
- Smithsonian Tropical Research InstitutePanamaPanama
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12
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Warren IA, Naville M, Chalopin D, Levin P, Berger CS, Galiana D, Volff JN. Evolutionary impact of transposable elements on genomic diversity and lineage-specific innovation in vertebrates. Chromosome Res 2016; 23:505-31. [PMID: 26395902 DOI: 10.1007/s10577-015-9493-5] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Since their discovery, a growing body of evidence has emerged demonstrating that transposable elements are important drivers of species diversity. These mobile elements exhibit a great variety in structure, size and mechanisms of transposition, making them important putative actors in organism evolution. The vertebrates represent a highly diverse and successful lineage that has adapted to a wide range of different environments. These animals also possess a rich repertoire of transposable elements, with highly diverse content between lineages and even between species. Here, we review how transposable elements are driving genomic diversity and lineage-specific innovation within vertebrates. We discuss the large differences in TE content between different vertebrate groups and then go on to look at how they affect organisms at a variety of levels: from the structure of chromosomes to their involvement in the regulation of gene expression, as well as in the formation and evolution of non-coding RNAs and protein-coding genes. In the process of doing this, we highlight how transposable elements have been involved in the evolution of some of the key innovations observed within the vertebrate lineage, driving the group's diversity and success.
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Affiliation(s)
- Ian A Warren
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France.,Department of Genetics, University of Georgia, Athens, Georgia, 30602, USA
| | - Perrine Levin
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Chloé Suzanne Berger
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Delphine Galiana
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France.
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13
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Naville M, Warren IA, Haftek-Terreau Z, Chalopin D, Brunet F, Levin P, Galiana D, Volff JN. Not so bad after all: retroviruses and long terminal repeat retrotransposons as a source of new genes in vertebrates. Clin Microbiol Infect 2016; 22:312-323. [PMID: 26899828 DOI: 10.1016/j.cmi.2016.02.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/05/2016] [Accepted: 02/06/2016] [Indexed: 12/24/2022]
Abstract
Viruses and transposable elements, once considered as purely junk and selfish sequences, have repeatedly been used as a source of novel protein-coding genes during the evolution of most eukaryotic lineages, a phenomenon called 'molecular domestication'. This is exemplified perfectly in mammals and other vertebrates, where many genes derived from long terminal repeat (LTR) retroelements (retroviruses and LTR retrotransposons) have been identified through comparative genomics and functional analyses. In particular, genes derived from gag structural protein and envelope (env) genes, as well as from the integrase-coding and protease-coding sequences, have been identified in humans and other vertebrates. Retroelement-derived genes are involved in many important biological processes including placenta formation, cognitive functions in the brain and immunity against retroelements, as well as in cell proliferation, apoptosis and cancer. These observations support an important role of retroelement-derived genes in the evolution and diversification of the vertebrate lineage.
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Affiliation(s)
- M Naville
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - I A Warren
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - Z Haftek-Terreau
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - D Chalopin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France; Department of Genetics, University of Georgia, Athens, GA, USA
| | - F Brunet
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - P Levin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - D Galiana
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - J-N Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France.
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14
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Dreier S, Redhead JW, Warren IA, Bourke AFG, Heard MS, Jordan WC, Sumner S, Wang J, Carvell C. Fine-scale spatial genetic structure of common and declining bumble bees across an agricultural landscape. Mol Ecol 2014; 23:3384-95. [PMID: 24980963 PMCID: PMC4142012 DOI: 10.1111/mec.12823] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/07/2014] [Accepted: 05/21/2014] [Indexed: 02/04/2023]
Abstract
Land-use changes have threatened populations of many insect pollinators, including bumble bees. Patterns of dispersal and gene flow are key determinants of species' ability to respond to land-use change, but have been little investigated at a fine scale (<10 km) in bumble bees. Using microsatellite markers, we determined the fine-scale spatial genetic structure of populations of four common Bombus species (B. terrestris, B. lapidarius, B. pascuorum and B. hortorum) and one declining species (B. ruderatus) in an agricultural landscape in Southern England, UK. The study landscape contained sown flower patches representing agri-environment options for pollinators. We found that, as expected, the B. ruderatus population was characterized by relatively low heterozygosity, number of alleles and colony density. Across all species, inbreeding was absent or present but weak (FIS = 0.01-0.02). Using queen genotypes reconstructed from worker sibships and colony locations estimated from the positions of workers within these sibships, we found that significant isolation by distance was absent in B. lapidarius, B. hortorum and B. ruderatus. In B. terrestris and B. pascuorum, it was present but weak; for example, in these two species, expected relatedness of queens founding colonies 1 m apart was 0.02. These results show that bumble bee populations exhibit low levels of spatial genetic structure at fine spatial scales, most likely because of ongoing gene flow via widespread queen dispersal. In addition, the results demonstrate the potential for agri-environment scheme conservation measures to facilitate fine-scale gene flow by creating a more even distribution of suitable habitats across landscapes.
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Affiliation(s)
- Stephanie Dreier
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK; School of Biological Sciences, University of Bristol, Woodland Road, Bristol, BS8 1UG, UK
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15
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Warren IA, Ciborowski KL, Casadei E, Hazlerigg DG, Martin S, Jordan WC, Sumner S. Extensive local gene duplication and functional divergence among paralogs in Atlantic salmon. Genome Biol Evol 2014; 6:1790-805. [PMID: 24951567 PMCID: PMC4122929 DOI: 10.1093/gbe/evu131] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2014] [Indexed: 12/30/2022] Open
Abstract
Many organisms can generate alternative phenotypes from the same genome, enabling individuals to exploit diverse and variable environments. A prevailing hypothesis is that such adaptation has been favored by gene duplication events, which generate redundant genomic material that may evolve divergent functions. Vertebrate examples of recent whole-genome duplications are sparse although one example is the salmonids, which have undergone a whole-genome duplication event within the last 100 Myr. The life-cycle of the Atlantic salmon, Salmo salar, depends on the ability to produce alternating phenotypes from the same genome, to facilitate migration and maintain its anadromous life history. Here, we investigate the hypothesis that genome-wide and local gene duplication events have contributed to the salmonid adaptation. We used high-throughput sequencing to characterize the transcriptomes of three key organs involved in regulating migration in S. salar: Brain, pituitary, and olfactory epithelium. We identified over 10,000 undescribed S. salar sequences and designed an analytic workflow to distinguish between paralogs originating from local gene duplication events or from whole-genome duplication events. These data reveal that substantial local gene duplications took place shortly after the whole-genome duplication event. Many of the identified paralog pairs have either diverged in function or become noncoding. Future functional genomics studies will reveal to what extent this rich source of divergence in genetic sequence is likely to have facilitated the evolution of extreme phenotypic plasticity required for an anadromous life-cycle.
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Affiliation(s)
- Ian A Warren
- School of Biological Sciences, University of Bristol, United Kingdom
| | - Kate L Ciborowski
- School of Biological Sciences, University of Bristol, United KingdomInstitute of Zoology, Zoological Society of London, London, United Kingdom
| | - Elisa Casadei
- Institute of Biological and Environmental Sciences, University of Aberdeen, United Kingdom
| | - David G Hazlerigg
- Institute of Biological and Environmental Sciences, University of Aberdeen, United KingdomDepartment of Arctic and Marine Biology, Faculty of BioSciences Fisheries & Economy, University of Tromsø, Norway
| | - Sam Martin
- Institute of Biological and Environmental Sciences, University of Aberdeen, United Kingdom
| | - William C Jordan
- Institute of Zoology, Zoological Society of London, London, United Kingdom
| | - Seirian Sumner
- School of Biological Sciences, University of Bristol, United KingdomInstitute of Zoology, Zoological Society of London, London, United Kingdom
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16
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Warren IA, Vera JC, Johns A, Zinna R, Marden JH, Emlen DJ, Dworkin I, Lavine LC. Insights into the development and evolution of exaggerated traits using de novo transcriptomes of two species of horned scarab beetles. PLoS One 2014; 9:e88364. [PMID: 24586317 PMCID: PMC3930525 DOI: 10.1371/journal.pone.0088364] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 01/06/2014] [Indexed: 11/18/2022] Open
Abstract
Scarab beetles exhibit an astonishing variety of rigid exo-skeletal outgrowths, known as “horns”. These traits are often sexually dimorphic and vary dramatically across species in size, shape, location, and allometry with body size. In many species, the horn exhibits disproportionate growth resulting in an exaggerated allometric relationship with body size, as compared to other traits, such as wings, that grow proportionately with body size. Depending on the species, the smallest males either do not produce a horn at all, or they produce a disproportionately small horn for their body size. While the diversity of horn shapes and their behavioural ecology have been reasonably well studied, we know far less about the proximate mechanisms that regulate horn growth. Thus, using 454 pyrosequencing, we generated transcriptome profiles, during horn growth and development, in two different scarab beetle species: the Asian rhinoceros beetle, Trypoxylus dichotomus, and the dung beetle, Onthophagus nigriventris. We obtained over half a million reads for each species that were assembled into over 6,000 and 16,000 contigs respectively. We combined these data with previously published studies to look for signatures of molecular evolution. We found a small subset of genes with horn-biased expression showing evidence for recent positive selection, as is expected with sexual selection on horn size. We also found evidence of relaxed selection present in genes that demonstrated biased expression between horned and horn-less morphs, consistent with the theory of developmental decoupling of phenotypically plastic traits.
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Affiliation(s)
- Ian A Warren
- Department of Entomology, Washington State University, Pullman, Washington, United States of America ; School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - J Cristobal Vera
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Annika Johns
- Division of Biological Sciences, The University of Montana, Missoula, Montana, United States of America
| | - Robert Zinna
- Department of Entomology, Washington State University, Pullman, Washington, United States of America
| | - James H Marden
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Douglas J Emlen
- Division of Biological Sciences, The University of Montana, Missoula, Montana, United States of America
| | - Ian Dworkin
- Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan, United States of America ; Department of Zoology, Michigan State University, East Lansing, Michigan, United States of America
| | - Laura C Lavine
- Department of Entomology, Washington State University, Pullman, Washington, United States of America
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17
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Abstract
Sexually-selected exaggerated traits tend to be unusually reliable signals of individual condition, as their expression tends to be more sensitive to nutritional history and physiological circumstance than that of other phenotypes. As such, these traits are the foundation for many models of sexual selection and animal communication, such as "handicap" and "good genes" models. Exactly how expression of these traits is linked to the bearer's condition has been a central yet unresolved question, in part because the underlying physiological mechanisms regulating their development have remained largely unknown. Recent discoveries across animals as diverse as deer, beetles, and flies now implicate the widely conserved insulin-like signaling pathway, as a common physiological mechanism regulating condition-sensitive structures with extreme growth. This raises the exciting possibility that one highly conserved pathway may underlie the evolution of trait exaggeration in a multitude of sexually-selected signal traits across the animal kingdom.
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Affiliation(s)
- Ian A Warren
- School of Biological Sciences, University of Bristol, UK
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18
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Lavine LC, Hahn LL, Warren IA, Garczynski SF, Dworkin I, Emlen DJ. Cloning and characterization of an mRNA encoding an insulin receptor from the horned scarab beetle Onthophagus nigriventris (Coleoptera: Scarabaeidae). Arch Insect Biochem Physiol 2013; 82:43-57. [PMID: 23136112 DOI: 10.1002/arch.21072] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The insulin signaling pathway is the primary signaling pathway coupling growth with nutritional condition in all animals. Sensitivity to circulating levels of insulin has been shown to regulate the growth of specific traits in a dose-dependent manner in response to environmental conditions in a diversity of insect species. Alternative phenotypes in insects manifest in a variety of morphologies such as the sexually dimorphic and male dimorphic horned beetles. Large males of the sexually dimorphic dung beetle Onthophagus nigriventris develop a thoracic horn up to twice the length of the body whereas small males and females never develop this horn. The regulation of this dimorphism is known to be nutrition dependent for males. We focused on the insulin signaling pathway as a potential regulator of this dimorphism. We sequenced a full-length gene transcript encoding the O. nigriventris insulin receptor (OnInR), which is the receptor for circulating insulin and insulin-like peptides in animals. We show that the predicted OnInR protein is similar in overall amino acid identity to other insulin receptors (InRs) and is most closely related phylogenetically to insect InRs. Expression of the OnInR transcript was found during development of imaginal tissues in both males and females. However, expression of OnInR in the region where a horn would grow of small males and female was significantly higher than in the horn tissues of large males at the end of growth. This variation in OnInR expression between sexes and morphs indicates a role for the InR in polymorphic horn development.
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Affiliation(s)
- Laura Corley Lavine
- Department of Entomology, Washington State University, Pullman, WA 99164, USA.
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19
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Emlen DJ, Warren IA, Johns A, Dworkin I, Lavine LC. A mechanism of extreme growth and reliable signaling in sexually selected ornaments and weapons. Science 2012; 337:860-4. [PMID: 22837386 DOI: 10.1126/science.1224286] [Citation(s) in RCA: 314] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Many male animals wield ornaments or weapons of exaggerated proportions. We propose that increased cellular sensitivity to signaling through the insulin/insulin-like growth factor (IGF) pathway may be responsible for the extreme growth of these structures. We document how rhinoceros beetle horns, a sexually selected weapon, are more sensitive to nutrition and more responsive to perturbation of the insulin/IGF pathway than other body structures. We then illustrate how enhanced sensitivity to insulin/IGF signaling in a growing ornament or weapon would cause heightened condition sensitivity and increased variability in expression among individuals--critical properties of reliable signals of male quality. The possibility that reliable signaling arises as a by-product of the growth mechanism may explain why trait exaggeration has evolved so many different times in the context of sexual selection.
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Affiliation(s)
- Douglas J Emlen
- Division of Biological Sciences, The University of Montana, 104 Health Science Building, Missoula, MT 59812, USA.
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Abstract
BACKGROUND Stalk-eyed flies of the family Diopsidae have proven to be an excellent model organism for studying the evolution of ornamental sexual traits. In diopsid flies the eyes and antennae are borne at the end of lateral head projections called 'eye-stalks'. Eyespan, the distance between the eyes, and the degree of sexual dimorphism in eyespan vary considerably between species and several sexually dimorphic species show sexual selection through female mate preference for males with exaggerated eyespan. Relatively little is known about the molecular genetic basis of intra- or inter-species variation in eyespan, eye-stalk development or growth regulation in diopsids. Molecular approaches including comparative developmental analyses, EST screening and QTL mapping have identified potential candidate loci for eyespan regulation in the model species Teleopsis dalmanni. Functional analyses of these genes to confirm and fully characterise their roles in eye-stalk growth require the development of techniques such as germline transformation to manipulate gene activity in vivo. RESULTS We used in vivo excision assays to identify transposon vector systems with the activity required to mediate transgenesis in T. dalmanni. Mariner based vectors showed no detectable excision while both Minos and piggyBac were active in stalk-eyed fly embryos. Germline transformation with an overall efficiency of 4% was achieved using a Minos based vector and the 3xP3-EGFP marker construct. Chromosomal insertion of constructs was confirmed by Southern blot analysis. Both autosomal and X-linked inserts were recovered. A homozygous stock, established from one of the X-linked inserts, has maintained stable expression for eight generations. CONCLUSIONS We have performed stable germline transformation of a stalk-eyed fly, T. dalmanni. This is the first transgenic protocol to be developed in an insect species that exhibits an exaggerated male sexual trait. Transgenesis will enable the development of a range of techniques for analysing gene function in this species and so provide insight into the mechanisms underlying the development of a morphological trait subject to sexual selection. Our X-linked insertion line will permit the sex of live larvae to be determined. This will greatly facilitate the identification of genes which are differentially expressed during eye-stalk development in males and females.
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Affiliation(s)
- Ian A Warren
- Department of Genetics, Evolution & Environment, University College London, London, UK
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