1
|
Dort H, van der Bijl W, Wahlberg N, Nylin S, Wheat CW. Genome-Wide Gene Birth-Death Dynamics Are Associated with Diet Breadth Variation in Lepidoptera. Genome Biol Evol 2024; 16:evae095. [PMID: 38976568 PMCID: PMC11229701 DOI: 10.1093/gbe/evae095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2024] [Indexed: 07/10/2024] Open
Abstract
Comparative analyses of gene birth-death dynamics have the potential to reveal gene families that played an important role in the evolution of morphological, behavioral, or physiological variation. Here, we used whole genomes of 30 species of butterflies and moths to identify gene birth-death dynamics among the Lepidoptera that are associated with specialist or generalist feeding strategies. Our work advances this field using a uniform set of annotated proteins for all genomes, investigating associations while correcting for phylogeny, and assessing all gene families rather than a priori subsets. We discovered that the sizes of several important gene families (e.g. those associated with pesticide resistance, xenobiotic detoxification, and/or protein digestion) are significantly correlated with diet breadth. We also found 22 gene families showing significant shifts in gene birth-death dynamics at the butterfly (Papilionoidea) crown node, the most notable of which was a family of pheromone receptors that underwent a contraction potentially linked with a shift to visual-based mate recognition. Our findings highlight the importance of uniform annotations, phylogenetic corrections, and unbiased gene family analyses in generating a list of candidate genes that warrant further exploration.
Collapse
Affiliation(s)
- Hanna Dort
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Wouter van der Bijl
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | | | - Sören Nylin
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | | |
Collapse
|
2
|
Rueda-M N, Pardo-Diaz C, Montejo-Kovacevich G, McMillan WO, Kozak KM, Arias CF, Ready J, McCarthy S, Durbin R, Jiggins CD, Meier JI, Salazar C. Genomic evidence reveals three W-autosome fusions in Heliconius butterflies. PLoS Genet 2024; 20:e1011318. [PMID: 39024186 PMCID: PMC11257349 DOI: 10.1371/journal.pgen.1011318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/24/2024] [Indexed: 07/20/2024] Open
Abstract
Sex chromosomes are evolutionarily labile in many animals and sometimes fuse with autosomes, creating so-called neo-sex chromosomes. Fusions between sex chromosomes and autosomes have been proposed to reduce sexual conflict and to promote adaptation and reproductive isolation among species. Recently, advances in genomics have fuelled the discovery of such fusions across the tree of life. Here, we discovered multiple fusions leading to neo-sex chromosomes in the sapho subclade of the classical adaptive radiation of Heliconius butterflies. Heliconius butterflies generally have 21 chromosomes with very high synteny. However, the five Heliconius species in the sapho subclade show large variation in chromosome number ranging from 21 to 60. We find that the W chromosome is fused with chromosome 4 in all of them. Two sister species pairs show subsequent fusions between the W and chromosomes 9 or 14, respectively. These fusions between autosomes and sex chromosomes make Heliconius butterflies an ideal system for studying the role of neo-sex chromosomes in adaptive radiations and the degeneration of sex chromosomes over time. Our findings emphasize the capability of short-read resequencing to detect genomic signatures of fusion events between sex chromosomes and autosomes even when sex chromosomes are not explicitly assembled.
Collapse
Affiliation(s)
- Nicol Rueda-M
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Carolina Pardo-Diaz
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | | | | | - Krzysztof M. Kozak
- Smithsonian Tropical Research Institute, Panama City, Panama
- Museum of Vertebrate Zoology, Berkeley, California, United States of America
| | - Carlos F. Arias
- Smithsonian Tropical Research Institute, Panama City, Panama
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, Washington DC, United States of America
| | - Jonathan Ready
- Institute for Biological Sciences, Federal University of Pará - UFPA, Belém, Brazil
- Centre for Advanced Studies of Biodiversity - CEABIO, Belém, Brazil
| | - Shane McCarthy
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Richard Durbin
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Chris D. Jiggins
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Joana I. Meier
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| |
Collapse
|
3
|
Rosser N, Seixas F, Queste LM, Cama B, Mori-Pezo R, Kryvokhyzha D, Nelson M, Waite-Hudson R, Goringe M, Costa M, Elias M, Mendes Eleres de Figueiredo C, Freitas AVL, Joron M, Kozak K, Lamas G, Martins ARP, McMillan WO, Ready J, Rueda-Muñoz N, Salazar C, Salazar P, Schulz S, Shirai LT, Silva-Brandão KL, Mallet J, Dasmahapatra KK. Hybrid speciation driven by multilocus introgression of ecological traits. Nature 2024; 628:811-817. [PMID: 38632397 PMCID: PMC11041799 DOI: 10.1038/s41586-024-07263-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 03/01/2024] [Indexed: 04/19/2024]
Abstract
Hybridization allows adaptations to be shared among lineages and may trigger the evolution of new species1,2. However, convincing examples of homoploid hybrid speciation remain rare because it is challenging to demonstrate that hybridization was crucial in generating reproductive isolation3. Here we combine population genomic analysis with quantitative trait locus mapping of species-specific traits to examine a case of hybrid speciation in Heliconius butterflies. We show that Heliconius elevatus is a hybrid species that is sympatric with both parents and has persisted as an independently evolving lineage for at least 180,000 years. This is despite pervasive and ongoing gene flow with one parent, Heliconius pardalinus, which homogenizes 99% of their genomes. The remaining 1% introgressed from the other parent, Heliconius melpomene, and is scattered widely across the H. elevatus genome in islands of divergence from H. pardalinus. These islands contain multiple traits that are under disruptive selection, including colour pattern, wing shape, host plant preference, sex pheromones and mate choice. Collectively, these traits place H. elevatus on its own adaptive peak and permit coexistence with both parents. Our results show that speciation was driven by introgression of ecological traits, and that speciation with gene flow is possible with a multilocus genetic architecture.
Collapse
Affiliation(s)
- Neil Rosser
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Biology, University of York, York, UK.
| | - Fernando Seixas
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | - Bruna Cama
- Department of Biology, University of York, York, UK
| | - Ronald Mori-Pezo
- URKU Estudios Amazónicos, Tarapoto, Perú
- Universidad Nacional Autónoma de Alto Amazona, Yurimaguas, Perú
| | - Dmytro Kryvokhyzha
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
| | | | | | - Matt Goringe
- Department of Biology, University of York, York, UK
| | | | - Marianne Elias
- Institut Systématique, Evolution, Biodiversité, UMR 7205 MNHN-CNRS-EPHE-UPMC Sorbonne Universités, Muséum National d'Histoire Naturelle, Paris, France
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Clarisse Mendes Eleres de Figueiredo
- Institute for Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Centre for Advanced Studies of Biodiversity (CEABIO), Belém, Brazil
| | - André Victor Lucci Freitas
- Departamento de Biologia Animal and Museu de Diversidade Biológica, Instituto de Biologia, Universidade Estadual de Campinas, São Paulo, Brazil
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 CNRS, Université de Montpellier-Université Paul Valéry Montpellier-EPHE, Montpellier, France
| | - Krzysztof Kozak
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Gerardo Lamas
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | | | - W Owen McMillan
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Jonathan Ready
- Institute for Biological Sciences, Federal University of Pará (UFPA), Belém, Brazil
- Centre for Advanced Studies of Biodiversity (CEABIO), Belém, Brazil
| | - Nicol Rueda-Muñoz
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Patricio Salazar
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Stefan Schulz
- Institut für Organische Chemie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Leila T Shirai
- Departamento de Biologia Animal and Museu de Diversidade Biológica, Instituto de Biologia, Universidade Estadual de Campinas, São Paulo, Brazil
| | - Karina L Silva-Brandão
- Leibniz Institute for the Analysis of Biodiversity Change, Museum de Natur Hamburg Zoology, Hamburg, Germany
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Kanchon K Dasmahapatra
- Department of Biology, University of York, York, UK
- Leverhulme Centre for Anthropocene Biodiversity, Department of Biology, University of York, York, UK
| |
Collapse
|
4
|
Briscoe AD. A genetic cause of male mate preference. Science 2024; 383:1290-1291. [PMID: 38513043 DOI: 10.1126/science.ado4079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
A gene for mate preference has been shared between hybridizing butterfly species.
Collapse
Affiliation(s)
- Adriana D Briscoe
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| |
Collapse
|
5
|
Page E, Queste LM, Rosser N, Salazar PA, Nadeau NJ, Mallet J, Srygley RB, McMillan WO, Dasmahapatra KK. Pervasive mimicry in flight behavior among aposematic butterflies. Proc Natl Acad Sci U S A 2024; 121:e2300886121. [PMID: 38408213 PMCID: PMC10945825 DOI: 10.1073/pnas.2300886121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 01/10/2024] [Indexed: 02/28/2024] Open
Abstract
Flight was a key innovation in the adaptive radiation of insects. However, it is a complex trait influenced by a large number of interacting biotic and abiotic factors, making it difficult to unravel the evolutionary drivers. We investigate flight patterns in neotropical heliconiine butterflies, well known for mimicry of their aposematic wing color patterns. We quantify the flight patterns (wing beat frequency and wing angles) of 351 individuals representing 29 heliconiine and 9 ithomiine species belonging to ten color pattern mimicry groupings. For wing beat frequency and up wing angles, we show that heliconiine species group by color pattern mimicry affiliation. Convergence of down wing angles to mimicry groupings is less pronounced, indicating that distinct components of flight are under different selection pressures and constraints. The flight characteristics of the Tiger mimicry group are particularly divergent due to convergence with distantly related ithomiine species. Predator-driven selection for mimicry also explained variation in flight among subspecies, indicating that this convergence can occur over relatively short evolutionary timescales. Our results suggest that the flight convergence is driven by aposematic signaling rather than shared habitat between comimics. We demonstrate that behavioral mimicry can occur between lineages that have separated over evolutionary timescales ranging from <0.5 to 70 My.
Collapse
Affiliation(s)
- Edward Page
- Department of Biology, University of York, HeslingtonYO10 5DD, United Kingdom
| | - Lucie M. Queste
- Department of Biology, University of York, HeslingtonYO10 5DD, United Kingdom
- Division of Evolutionary Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried82152, Germany
| | - Neil Rosser
- Department of Biology, University of York, HeslingtonYO10 5DD, United Kingdom
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA02138
| | - Patricio A. Salazar
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, SheffieldS10 2TN, United Kingdom
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, CambridgeCB10 1SA, United Kingdom
| | - Nicola J. Nadeau
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, SheffieldS10 2TN, United Kingdom
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA02138
| | - Robert B. Srygley
- Smithsonian Tropical Research Institute, Apartado, Panamá0843-03092, Republic of Panama
- Pest Management Research Unit, Agricultural Research Service, United States Department of Agriculture, Sidney, MT59270
| | - W. Owen McMillan
- Smithsonian Tropical Research Institute, Apartado, Panamá0843-03092, Republic of Panama
| | | |
Collapse
|
6
|
Thawornwattana Y, Seixas F, Yang Z, Mallet J. Major patterns in the introgression history of Heliconius butterflies. eLife 2023; 12:RP90656. [PMID: 38108819 PMCID: PMC10727504 DOI: 10.7554/elife.90656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023] Open
Abstract
Gene flow between species, although usually deleterious, is an important evolutionary process that can facilitate adaptation and lead to species diversification. It also makes estimation of species relationships difficult. Here, we use the full-likelihood multispecies coalescent (MSC) approach to estimate species phylogeny and major introgression events in Heliconius butterflies from whole-genome sequence data. We obtain a robust estimate of species branching order among major clades in the genus, including the 'melpomene-silvaniform' group, which shows extensive historical and ongoing gene flow. We obtain chromosome-level estimates of key parameters in the species phylogeny, including species divergence times, present-day and ancestral population sizes, as well as the direction, timing, and intensity of gene flow. Our analysis leads to a phylogeny with introgression events that differ from those obtained in previous studies. We find that Heliconius aoede most likely represents the earliest-branching lineage of the genus and that 'silvaniform' species are paraphyletic within the melpomene-silvaniform group. Our phylogeny provides new, parsimonious histories for the origins of key traits in Heliconius, including pollen feeding and an inversion involved in wing pattern mimicry. Our results demonstrate the power and feasibility of the full-likelihood MSC approach for estimating species phylogeny and key population parameters despite extensive gene flow. The methods used here should be useful for analysis of other difficult species groups with high rates of introgression.
Collapse
Affiliation(s)
| | - Fernando Seixas
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College LondonLondonUnited Kingdom
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| |
Collapse
|
7
|
Ehlers S, Blow R, Szczerbowski D, Jiggins C, Schulz S. Variation of Clasper Scent Gland Composition of Heliconius Butterflies from a Biodiversity Hotspot. Chembiochem 2023; 24:e202300537. [PMID: 37650217 DOI: 10.1002/cbic.202300537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/01/2023]
Abstract
Male Heliconius butterflies possess two pheromone emitting structures, wing androconia and abdominal clasper scent glands. The composition of the clasper scent gland of males of 17 Heliconius and Eueides species from an overlapping area in Ecuador, comprising three mimicry groups, was investigated by GC/MS. The chemical signal serves as an anti-aphrodisiac signal that is transferred from males to females during mating, indicating the mating status of the female to prevent them from harassment by other males. In addition, the odour may also serve in predator defence. There is potential for convergence driven by mimicry, although, such convergence might be detrimental for species recognition of the butterflies within the mimicry ring, making mating more difficult. More than 500 compounds were detected, consisting of volatile, semi-volatile or non-volatile compounds, including terpenes, fatty acid esters or aromatic compounds. Several novel esters were identified by GC/MS and GC/IR data, microderivatisation and synthesis, including butyl (Z)-3-dodecenoate and other (Z)-3-alkenoates, 3-oxohexyl citronellate and 5-methylhexa-3,5-dienyl (E)-2,3-dihydrofarnesoate. The secretions were found to be species specific, potentially allowing for species differentiation. Statistical analysis of the compounds showed differentiation by phylogenetic clade and species, but not by mimicry group.
Collapse
Affiliation(s)
- Stephanie Ehlers
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany
| | - Rachel Blow
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Daiane Szczerbowski
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany
| | - Chris Jiggins
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany
| |
Collapse
|
8
|
Anton AA, Farnworth MS, Hebberecht L, Harrison CJ, Montgomery SH. A modified method to analyse cell proliferation using EdU labelling in large insect brains. PLoS One 2023; 18:e0292009. [PMID: 37796816 PMCID: PMC10553331 DOI: 10.1371/journal.pone.0292009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/11/2023] [Indexed: 10/07/2023] Open
Abstract
The study of neurogenesis is critical to understanding of the evolution of nervous systems. Within invertebrates, this process has been extensively studied in Drosophila melanogaster, which is the predominant model thanks to the availability of advanced genetic tools. However, insect nervous systems are extremely diverse, and by studying a range of taxa we can gain additional information about how nervous systems and their development evolve. One example of the high diversity of insect nervous system diversity is provided by the mushroom bodies. Mushroom bodies have critical roles in learning and memory and vary dramatically across species in relative size and the type(s) of sensory information they process. Heliconiini butterflies provide a useful snapshot of this diversity within a closely related clade. Within Heliconiini, the genus Heliconius contains species where mushroom bodies are 3-4 times larger than other closely related genera, relative to the rest of the brain. This variation in size is largely explained by increases in the number of Kenyon cells, the intrinsic neurons which form the mushroom body. Hence, variation in mushroom body size is the product of changes in cell proliferation during Kenyon cell neurogenesis. Studying this variation requires adapting labelling techniques for use in less commonly studied organisms, as methods developed for common laboratory insects often do not work. Here, we present a modified protocol for EdU staining to examine neurogenesis in large-brained insects, using Heliconiini butterflies as our primary case, but also demonstrating applicability to cockroaches, another large-brained insect.
Collapse
Affiliation(s)
- Amaia Alcalde Anton
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Max S. Farnworth
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Laura Hebberecht
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - C. Jill Harrison
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | | |
Collapse
|
9
|
Cicconardi F, Milanetti E, Pinheiro de Castro EC, Mazo-Vargas A, Van Belleghem SM, Ruggieri AA, Rastas P, Hanly J, Evans E, Jiggins CD, Owen McMillan W, Papa R, Di Marino D, Martin A, Montgomery SH. Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies. Nat Commun 2023; 14:5620. [PMID: 37699868 PMCID: PMC10497600 DOI: 10.1038/s41467-023-41412-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 08/30/2023] [Indexed: 09/14/2023] Open
Abstract
Heliconius butterflies, a speciose genus of Müllerian mimics, represent a classic example of an adaptive radiation that includes a range of derived dietary, life history, physiological and neural traits. However, key lineages within the genus, and across the broader Heliconiini tribe, lack genomic resources, limiting our understanding of how adaptive and neutral processes shaped genome evolution during their radiation. Here, we generate highly contiguous genome assemblies for nine Heliconiini, 29 additional reference-assembled genomes, and improve 10 existing assemblies. Altogether, we provide a dataset of annotated genomes for a total of 63 species, including 58 species within the Heliconiini tribe. We use this extensive dataset to generate a robust and dated heliconiine phylogeny, describe major patterns of introgression, explore the evolution of genome architecture, and the genomic basis of key innovations in this enigmatic group, including an assessment of the evolution of putative regulatory regions at the Heliconius stem. Our work illustrates how the increased resolution provided by such dense genomic sampling improves our power to generate and test gene-phenotype hypotheses, and precisely characterize how genomes evolve.
Collapse
Affiliation(s)
- Francesco Cicconardi
- School of Biological Sciences, Bristol University, Bristol, United Kingdom.
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom.
| | - Edoardo Milanetti
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy
- Center for Life Nano- & Neuro-Science, Italian Institute of Technology, Viale Regina Elena 291, 00161, Rome, Italy
| | | | - Anyi Mazo-Vargas
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Steven M Van Belleghem
- Department of Biology, University of Puerto Rico, Rio Piedras, PR, Puerto Rico
- Ecology, Evolution and Conservation Biology, Biology Department, KU Leuven, Leuven, Belgium
| | | | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Joseph Hanly
- Department of Biological Sciences, The George Washington University, Washington DC, WA, 20052, USA
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Elizabeth Evans
- Department of Biology, University of Puerto Rico, Rio Piedras, PR, Puerto Rico
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Riccardo Papa
- Department of Biology, University of Puerto Rico, Rio Piedras, PR, Puerto Rico
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan, PR, Puerto Rico
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, PR, Puerto Rico
| | - Daniele Di Marino
- Department of Life and Environmental Sciences, New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
- Neuronal Death and Neuroprotection Unit, Department of Neuroscience, Mario Negri Institute for Pharmacological Research-IRCCS, Via Mario Negri 2, 20156, Milano, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington DC, WA, 20052, USA
| | - Stephen H Montgomery
- School of Biological Sciences, Bristol University, Bristol, United Kingdom.
- Smithsonian Tropical Research Institute, Panama City, Panama.
| |
Collapse
|
10
|
Chakraborty M, Lara AG, Dang A, McCulloch KJ, Rainbow D, Carter D, Ngo LT, Solares E, Said I, Corbett-Detig RB, Gilbert LE, Emerson JJ, Briscoe AD. Sex-linked gene traffic underlies the acquisition of sexually dimorphic UV color vision in Heliconius butterflies. Proc Natl Acad Sci U S A 2023; 120:e2301411120. [PMID: 37552755 PMCID: PMC10438391 DOI: 10.1073/pnas.2301411120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 06/16/2023] [Indexed: 08/10/2023] Open
Abstract
The acquisition of novel sexually dimorphic traits poses an evolutionary puzzle: How do new traits arise and become sex-limited? Recently acquired color vision, sexually dimorphic in animals like primates and butterflies, presents a compelling model for understanding how traits become sex-biased. For example, some Heliconius butterflies uniquely possess UV (ultraviolet) color vision, which correlates with the expression of two differentially tuned UV-sensitive rhodopsins, UVRh1 and UVRh2. To discover how such traits become sexually dimorphic, we studied Heliconius charithonia, which exhibits female-specific UVRh1 expression. We demonstrate that females, but not males, discriminate different UV wavelengths. Through whole-genome shotgun sequencing and assembly of the H. charithonia genome, we discovered that UVRh1 is present on the W chromosome, making it obligately female-specific. By knocking out UVRh1, we show that UVRh1 protein expression is absent in mutant female eye tissue, as in wild-type male eyes. A PCR survey of UVRh1 sex-linkage across the genus shows that species with female-specific UVRh1 expression lack UVRh1 gDNA in males. Thus, acquisition of sex linkage is sufficient to achieve female-specific expression of UVRh1, though this does not preclude other mechanisms, like cis-regulatory evolution from also contributing. Moreover, both this event, and mutations leading to differential UV opsin sensitivity, occurred early in the history of Heliconius. These results suggest a path for acquiring sexual dimorphism distinct from existing mechanistic models. We propose a model where gene traffic to heterosomes (the W or the Y) genetically partitions a trait by sex before a phenotype shifts (spectral tuning of UV sensitivity).
Collapse
Affiliation(s)
- Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
- Department of Biology, Texas A&M University, College Station, TX77843
| | | | - Andrew Dang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
| | - Kyle J. McCulloch
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN55108
| | - Dylan Rainbow
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
| | - David Carter
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA92521
| | - Luna Thanh Ngo
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
| | - Edwin Solares
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
| | - Iskander Said
- Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, CA95064
| | - Russell B. Corbett-Detig
- Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, CA95064
| | | | - J. J. Emerson
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
| | - Adriana D. Briscoe
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
| |
Collapse
|
11
|
Hebberecht L, Wainwright JB, Thompson C, Kershenbaum S, McMillan WO, Montgomery SH. Plasticity and genetic effects contribute to different axes of neural divergence in a community of mimetic Heliconius butterflies. J Evol Biol 2023; 36:1116-1132. [PMID: 37341138 DOI: 10.1111/jeb.14188] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/12/2023] [Accepted: 04/16/2023] [Indexed: 06/22/2023]
Abstract
Changes in ecological preference, often driven by spatial and temporal variation in resource distribution, can expose populations to environments with divergent information content. This can lead to adaptive changes in the degree to which individuals invest in sensory systems and downstream processes, to optimize behavioural performance in different contexts. At the same time, environmental conditions can produce plastic responses in nervous system development and maturation, providing an alternative route to integrating neural and ecological variation. Here, we explore how these two processes play out across a community of Heliconius butterflies. Heliconius communities exhibit multiple Mullerian mimicry rings, associated with habitat partitioning across environmental gradients. These environmental differences have previously been linked to heritable divergence in brain morphology in parapatric species pairs. They also exhibit a unique dietary adaptation, known as pollen feeding, that relies heavily on learning foraging routes, or trap-lines, between resources, which implies an important environmental influence on behavioural development. By comparing brain morphology across 133 wild-caught and insectary-reared individuals from seven Heliconius species, we find strong evidence for interspecific variation in patterns of neural investment. These largely fall into two distinct patterns of variation; first, we find consistent patterns of divergence in the size of visual brain components across both wild and insectary-reared individuals, suggesting genetically encoded divergence in the visual pathway. Second, we find interspecific differences in mushroom body size, a central component of learning and memory systems, but only among wild caught individuals. The lack of this effect in common-garden individuals suggests an extensive role for developmental plasticity in interspecific variation in the wild. Finally, we illustrate the impact of relatively small-scale spatial effects on mushroom body plasticity by performing experiments altering the cage size and structure experienced by individual H. hecale. Our data provide a comprehensive survey of community level variation in brain structure, and demonstrate that genetic effects and developmental plasticity contribute to different axes of interspecific neural variation.
Collapse
Affiliation(s)
- Laura Hebberecht
- School of Biological Sciences, University of Bristol, Bristol, UK
- Department of Zoology, University of Cambridge, Cambridge, UK
- Smithsonian Tropical Research Institute, Gamboa, Panama
| | | | | | | | | | - Stephen H Montgomery
- School of Biological Sciences, University of Bristol, Bristol, UK
- Smithsonian Tropical Research Institute, Gamboa, Panama
| |
Collapse
|
12
|
Gauthier J, Meier J, Legeai F, McClure M, Whibley A, Bretaudeau A, Boulain H, Parrinello H, Mugford ST, Durbin R, Zhou C, McCarthy S, Wheat CW, Piron-Prunier F, Monsempes C, François MC, Jay P, Noûs C, Persyn E, Jacquin-Joly E, Meslin C, Montagné N, Lemaitre C, Elias M. First chromosome scale genomes of ithomiine butterflies (Nymphalidae: Ithomiini): Comparative models for mimicry genetic studies. Mol Ecol Resour 2023; 23:872-885. [PMID: 36533297 DOI: 10.1111/1755-0998.13749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
Abstract
The ithomiine butterflies (Nymphalidae: Danainae) represent the largest known radiation of Müllerian mimetic butterflies. They dominate by number the mimetic butterfly communities, which include species such as the iconic neotropical Heliconius genus. Recent studies on the ecology and genetics of speciation in Ithomiini have suggested that sexual pheromones, colour pattern and perhaps hostplant could drive reproductive isolation. However, no reference genome was available for Ithomiini, which has hindered further exploration on the genetic architecture of these candidate traits, and more generally on the genomic patterns of divergence. Here, we generated high-quality, chromosome-scale genome assemblies for two Melinaea species, M. marsaeus and M. menophilus, and a draft genome of the species Ithomia salapia. We obtained genomes with a size ranging from 396 to 503 Mb across the three species and scaffold N50 of 40.5 and 23.2 Mb for the two chromosome-scale assemblies. Using collinearity analyses we identified massive rearrangements between the two closely related Melinaea species. An annotation of transposable elements and gene content was performed, as well as a specialist annotation to target chemosensory genes, which is crucial for host plant detection and mate recognition in mimetic species. A comparative genomic approach revealed independent gene expansions in ithomiines and particularly in gustatory receptor genes. These first three genomes of ithomiine mimetic butterflies constitute a valuable addition and a welcome comparison to existing biological models such as Heliconius, and will enable further understanding of the mechanisms of adaptation in butterflies.
Collapse
Affiliation(s)
| | - Joana Meier
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Fabrice Legeai
- BIPAA, IGEPP, INRAE, Institut Agro, Univ Rennes, Rennes, France
- Univ Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Melanie McClure
- Institut Systématique Évolution Biodiversité (ISYEB), Centre National de la Recherche Scientifique, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
- Laboratoire Écologie, Évolution, Interactions des Systèmes Amazoniens (LEEISA), Université de Guyane, CNRS, IFREMER, Cayenne, France
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Anthony Bretaudeau
- BIPAA, IGEPP, INRAE, Institut Agro, Univ Rennes, Rennes, France
- Univ Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Hélène Boulain
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Hugues Parrinello
- MGX-Montpellier GenomiX, Univ. Montpellier, CNRS, INSERM, Montpellier, France
| | - Sam T Mugford
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Chenxi Zhou
- Department of Genetics, University of Cambridge, Cambridge, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Shane McCarthy
- Department of Genetics, University of Cambridge, Cambridge, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | | | - Florence Piron-Prunier
- Institut Systématique Évolution Biodiversité (ISYEB), Centre National de la Recherche Scientifique, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| | - Christelle Monsempes
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Marie-Christine François
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Paul Jay
- Ecologie Systématique Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
| | | | - Emma Persyn
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
- CIRAD, UMR PVBMT, St Pierre, France
| | - Emmanuelle Jacquin-Joly
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Camille Meslin
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Nicolas Montagné
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | | | - Marianne Elias
- Institut Systématique Évolution Biodiversité (ISYEB), Centre National de la Recherche Scientifique, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| |
Collapse
|
13
|
Hausmann AE, Freire M, Alfthan SA, Kuo CY, Linares M, McMillan O, Pardo-Diaz C, Salazar C, Merrill RM. Does sexual conflict contribute to the evolution of novel warning patterns? J Evol Biol 2023; 36:563-578. [PMID: 36702779 DOI: 10.1111/jeb.14151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 01/28/2023]
Abstract
Why warning patterns are so diverse is an enduring evolutionary puzzle. Because predators associate particular patterns with unpleasant experiences, an individual's predation risk should decrease as the local density of its warning pattern increases, promoting pattern monomorphism. Distasteful Heliconius butterflies are known for their diversity of warning patterns. Here, we explore whether interlocus sexual conflict can contribute to their diversification. Male Heliconius use warning patterns as mating cues, but mated females may suffer costs if this leads to disturbance, favouring novel patterns. Using simulations, we show that under our model conditions drift alone is unlikely to cause pattern diversification, but that sexual conflict can assist such a process. We also find that genetic architecture influences the evolution of male preferences, which track changes in warning pattern due to sexual selection. When male attraction imposes costs on females, this affects the speed at which novel pattern alleles increase. In two experiments, females laid fewer eggs with males present. However, although males in one experiment showed less interest in females with manipulated patterns, we found no evidence that female colouration mitigates sex-specific costs. Overall, male attraction to conspecific warning patterns may impose an unrecognized cost on Heliconius females, but further work is required to determine this experimentally.
Collapse
Affiliation(s)
- Alexander E Hausmann
- Division of Evolutionary Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Marília Freire
- Division of Evolutionary Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Sara A Alfthan
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Chi-Yun Kuo
- Division of Evolutionary Biology, Ludwig-Maximilians-Universität, Munich, Germany.,Smithsonian Tropical Research Institute, Panama City, Panama
| | - Mauricio Linares
- Department of Biology, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Owen McMillan
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Carolina Pardo-Diaz
- Department of Biology, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Camilo Salazar
- Department of Biology, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Richard M Merrill
- Division of Evolutionary Biology, Ludwig-Maximilians-Universität, Munich, Germany.,Smithsonian Tropical Research Institute, Panama City, Panama
| |
Collapse
|
14
|
Ruggieri AA, Livraghi L, Lewis JJ, Evans E, Cicconardi F, Hebberecht L, Ortiz-Ruiz Y, Montgomery SH, Ghezzi A, Rodriguez-Martinez JA, Jiggins CD, McMillan WO, Counterman BA, Papa R, Van Belleghem SM. A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility. Genome Res 2022; 32:1862-1875. [PMID: 36109150 PMCID: PMC9712634 DOI: 10.1101/gr.276839.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 09/13/2022] [Indexed: 01/16/2023]
Abstract
Despite insertions and deletions being the most common structural variants (SVs) found across genomes, not much is known about how much these SVs vary within populations and between closely related species, nor their significance in evolution. To address these questions, we characterized the evolution of indel SVs using genome assemblies of three closely related Heliconius butterfly species. Over the relatively short evolutionary timescales investigated, up to 18.0% of the genome was composed of indels between two haplotypes of an individual Heliconius charithonia butterfly and up to 62.7% included lineage-specific SVs between the genomes of the most distant species (11 Mya). Lineage-specific sequences were mostly characterized as transposable elements (TEs) inserted at random throughout the genome and their overall distribution was similarly affected by linked selection as single nucleotide substitutions. Using chromatin accessibility profiles (i.e., ATAC-seq) of head tissue in caterpillars to identify sequences with potential cis-regulatory function, we found that out of the 31,066 identified differences in chromatin accessibility between species, 30.4% were within lineage-specific SVs and 9.4% were characterized as TE insertions. These TE insertions were localized closer to gene transcription start sites than expected at random and were enriched for sites with significant resemblance to several transcription factor binding sites with known function in neuron development in Drosophila We also identified 24 TE insertions with head-specific chromatin accessibility. Our results show high rates of structural genome evolution that were previously overlooked in comparative genomic studies and suggest a high potential for structural variation to serve as raw material for adaptive evolution.
Collapse
Affiliation(s)
- Angelo A Ruggieri
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan PR 00931, Puerto Rico
| | - Luca Livraghi
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
- Smithsonian Tropical Research Institute, Apartado 0843-03092 Panamá, Panama
| | - James J Lewis
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Elizabeth Evans
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan PR 00931, Puerto Rico
| | - Francesco Cicconardi
- School of Biological Sciences, Bristol University, Bristol BS8 1QU, United Kingdom
| | - Laura Hebberecht
- School of Biological Sciences, Bristol University, Bristol BS8 1QU, United Kingdom
| | - Yadira Ortiz-Ruiz
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan PR 00931, Puerto Rico
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan 00926, Puerto Rico
| | - Stephen H Montgomery
- School of Biological Sciences, Bristol University, Bristol BS8 1QU, United Kingdom
| | - Alfredo Ghezzi
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan PR 00931, Puerto Rico
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Apartado 0843-03092 Panamá, Panama
| | - Brian A Counterman
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, USA
| | - Riccardo Papa
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan PR 00931, Puerto Rico
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan 00926, Puerto Rico
| | - Steven M Van Belleghem
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan PR 00931, Puerto Rico
- Ecology, Evolution and Conservation Biology, Biology Department, KU Leuven, 3000 Leuven, Belgium
| |
Collapse
|
15
|
Cong Y, Ye X, Mei Y, He K, Li F. Transposons and non-coding regions drive the intrafamily differences of genome size in insects. iScience 2022; 25:104873. [PMID: 36039293 PMCID: PMC9418806 DOI: 10.1016/j.isci.2022.104873] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/24/2022] [Accepted: 07/29/2022] [Indexed: 11/02/2022] Open
Abstract
Genome size (GS) can vary considerably between phylogenetically close species, but the landscape of GS changes in insects remain largely unclear. To better understand the specific evolutionary factors that determine GS in insects, we examined flow cytometry-based published GS data from 1,326 insect species, spanning 700 genera, 155 families, and 21 orders. Model fitting showed that GS generally followed an Ornstein-Uhlenbeck adaptive evolutionary model in Insecta overall. Ancestral reconstruction indicated a likely GS of 1,069 Mb, suggesting that most insect clades appeared to undergo massive genome expansions or contractions. Quantification of genomic components in 56 species from nine families in four insect orders revealed that the proliferation of transposable elements contributed to high variation in GS between close species, such as within Coleoptera. This study sheds lights on the pattern of GS variation in insects and provides a better understanding of insect GS evolution.
Collapse
Affiliation(s)
- Yuyang Cong
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xinhai Ye
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yang Mei
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Kang He
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fei Li
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| |
Collapse
|
16
|
Twort VG, Blande D, Duplouy A. One's trash is someone else's treasure: sequence read archives from Lepidoptera genomes provide material for genome reconstruction of their endosymbionts. BMC Microbiol 2022; 22:209. [PMID: 36042402 PMCID: PMC9426245 DOI: 10.1186/s12866-022-02602-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Maternally inherited bacterial symbionts are extremely widespread in insects. They owe their success to their ability to promote their own transmission through various manipulations of their hosts' life-histories. Many symbionts however very often go undetected. Consequently, we have only a restricted idea of the true symbiont diversity in insects, which may hinder our understanding of even bigger questions in the field such as the evolution or establishment of symbiosis. RESULTS In this study, we screened publicly available Lepidoptera genomic material for two of the most common insect endosymbionts, namely Wolbachia and Spiroplasma, in 1904 entries, encompassing 106 distinct species. We compared the performance of two screening software, Kraken2 and MetaPhlAn2, to identify the bacterial infections and using a baiting approach we reconstruct endosymbiont genome assemblies. Of the 106 species screened, 20 (19%) and nine (8.5%) were found to be infected with either Wolbachia or Spiroplasma, respectively. Construction of partial symbiotic genomes and phylogenetic analyses suggested the Wolbachia strains from the supergroup B were the most prevalent type of symbionts, while Spiroplasma infections were scarce in the Lepidoptera species screened here. CONCLUSIONS Our results indicate that many of the host-symbiont associations remain largely unexplored, with the majority of associations we identify never being recorded before. This highlights the usefulness of public databases to explore the hidden diversity of symbiotic entities, allowing the development of hypotheses regarding host-symbiont associations. The ever-expanding genomic databases provide a diverse databank from which one can characterize and explore the true diversity of symbiotic entities.
Collapse
Affiliation(s)
- Victoria G Twort
- Finnish Natural History Museum, LUOMUS, The University of Helsinki, Helsinki, Finland.
| | - Daniel Blande
- Organismal and Evolutionary Biology, The University of Helsinki, Helsinki, Finland
| | - Anne Duplouy
- Organismal and Evolutionary Biology, The University of Helsinki, Helsinki, Finland
| |
Collapse
|
17
|
Repeated genetic adaptation to altitude in two tropical butterflies. Nat Commun 2022; 13:4676. [PMID: 35945236 PMCID: PMC9363431 DOI: 10.1038/s41467-022-32316-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 07/26/2022] [Indexed: 01/02/2023] Open
Abstract
Repeated evolution can provide insight into the mechanisms that facilitate adaptation to novel or changing environments. Here we study adaptation to altitude in two tropical butterflies, Heliconius erato and H. melpomene, which have repeatedly and independently adapted to montane habitats on either side of the Andes. We sequenced 518 whole genomes from altitudinal transects and found many regions differentiated between highland (~ 1200 m) and lowland (~ 200 m) populations. We show repeated genetic differentiation across replicate populations within species, including allopatric comparisons. In contrast, there is little molecular parallelism between the two species. By sampling five close relatives, we find that a large proportion of divergent regions identified within species have arisen from standing variation and putative adaptive introgression from high-altitude specialist species. Taken together our study supports a role for both standing genetic variation and gene flow from independently adapted species in promoting parallel local adaptation to the environment. Here, the authors study adaptation to altitude in 518 whole genomes from two species of tropical butterflies. They find repeated genetic differentiation within species, little molecular parallelism between these species, and introgression from closely related species, concluding that standing genetic variation promotes parallel local adaptation.
Collapse
|
18
|
Guo R, Papanicolaou A, Fritz ML. Validation of reference-assisted assembly using existing and novel Heliothine genomes. Genomics 2022; 114:110441. [PMID: 35931274 DOI: 10.1016/j.ygeno.2022.110441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 07/19/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022]
Abstract
Chloridea subflexa and Chloridea virescens are a pair of closely related noctuid species exhibiting pheromone-based sexual isolation and divergent host plant preferences. We produced a novel Illumina short read C. subflexa genome assembly and an improved C. virescens genome assembly, which offer opportunities to study the genomic basis for evolutionarily important traits in this lepidopteran family with few genomic resources. We then examined the feasibility of reference-assisted assembly, an approach that leverages existing high quality genomic resources for genome improvement in closely related taxa and applied it to our Heliothine genomes. Our work demonstrates that reference-assisted assembly has the potential to enhance contiguity and completeness of existing insect genomic resources with minimal additional laboratory costs. We conclude by discussing both the potential and pitfalls of reference-assisted assembly according to the intended downstream assembly application.
Collapse
Affiliation(s)
- Rong Guo
- Department of Entomology, University of Maryland, College Park, MD 20742, USA; Computational Biology, Bioinformatics and Genomics Program, Department of Biological Sciences, University of Maryland, College Park, MD 20742, USA
| | - Alexie Papanicolaou
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, Australia.
| | - Megan L Fritz
- Department of Entomology, University of Maryland, College Park, MD 20742, USA; Computational Biology, Bioinformatics and Genomics Program, Department of Biological Sciences, University of Maryland, College Park, MD 20742, USA.
| |
Collapse
|
19
|
Cama B, Ehlers S, Szczerbowski D, Thomas-Oates J, Jiggins CD, Schulz S, McMillan WO, Dasmahapatra KK. Exploitation of an ancestral pheromone biosynthetic pathway contributes to diversification in Heliconius butterflies. Proc Biol Sci 2022; 289:20220474. [PMID: 35892212 PMCID: PMC9326301 DOI: 10.1098/rspb.2022.0474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
During courtship, male butterflies of many species produce androconial secretions containing male sex pheromones (MSPs) that communicate species identity and affect female choice. MSPs are thus likely candidates as reproductive barriers, yet their role in speciation remains poorly studied. Although Heliconius butterflies are a model system in speciation, their MSPs have not been investigated from a macroevolutionary perspective. We use GC/MS to characterize male androconial secretions in 33 of the 69 species in the Heliconiini tribe. We found these blends to be species-specific, consistent with a role in reproductive isolation. We detected a burst in blend diversification rate at the most speciose genus, Heliconius; a consequence of Heliconius and Eueides species using a fatty acid (FA) metabolic pathway to unlock more complex blends than basal Heliconiini species, whose secretions are dominated by plant-like metabolites. A comparison of 10 sister species pairs demonstrates a striking positive correlation between blend dissimilarity and range overlap, consistent with character displacement or reinforcement in sympatry. These results demonstrate for the first time that MSP diversification can promote reproductive isolation across this group of butterflies, showcasing how implementation of an ancestral trait, the co-option of the FA metabolic pathway for pheromone production, can facilitate rapid speciation.
Collapse
Affiliation(s)
- Bruna Cama
- Department of Biology, University of York, Heslington YO10 5DD, UK
| | - Stephanie Ehlers
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, Braunschweig 38106, Germany
| | - Daiane Szczerbowski
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, Braunschweig 38106, Germany
| | - Jane Thomas-Oates
- Department of Chemistry, University of York, Heslington YO10 5DD, UK
| | - Chris D. Jiggins
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, Braunschweig 38106, Germany
| | | | | |
Collapse
|
20
|
Farfán J, Cerdeña J, Vargas HA, Gonçalves GL, Lamas G, Moreira GRP. A peculiar new species of Dione (Agraulis) Boisduval & Le Conte (Lepidoptera, Nymphalidae, Heliconiinae) associated with Malesherbia Ruiz & Pavón (Passifloraceae) in xeric western slopes of the Andes. Zookeys 2022; 1113:199-226. [PMID: 36762230 PMCID: PMC9848672 DOI: 10.3897/zookeys.1113.85769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/17/2022] [Indexed: 11/12/2022] Open
Abstract
Butterflies associated with xerophytic environments of the Andes have been little studied, and they exhibit high levels of endemism. Herein Dione (Agraulis) dodona Lamas & Farfán, sp. nov. (Nymphalidae; Heliconiinae) is described, distributed on the western slopes of the Andes of Peru and northern Chile, between 800 and 3,000 m elevation. Adults of both sexes, and the immature stages, are described and illustrated based on light and scanning electron microscopy. The immature stages are associated with MalesherbiatenuifoliaD. Don (Passifloraceae) found in xeric environments, representing a new record of this genus as a host plant for the subfamily Heliconiinae. Conspicuous morphological differences are presented for all stages at the generic level. Based on a phylogenetic analysis of the COI barcode mitochondrial gene fragment, D. (A.) dodona Lamas & Farfán, sp. nov. is distinguished as an independent lineage within the Agraulis clade of Dione, with ca. 5% difference to congeneric species.
Collapse
Affiliation(s)
- Jackie Farfán
- PPG Biologia Animal, Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Porto Alegre, RS 91501-970, Brazil,Museo de Historia Natural, Universidad Nacional de San Agustín de Arequipa, Av. Alcides Carrión s/n, Arequipa, Peru
| | - José Cerdeña
- PPG Biologia Animal, Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Porto Alegre, RS 91501-970, Brazil,Museo de Historia Natural, Universidad Nacional de San Agustín de Arequipa, Av. Alcides Carrión s/n, Arequipa, Peru
| | - Héctor A. Vargas
- Departamento de Recursos Ambientales, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Casilla 6-D, Arica, Chile
| | - Gislene L. Gonçalves
- PPG Biologia Animal, Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Porto Alegre, RS 91501-970, Brazil,Departamento de Recursos Ambientales, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Casilla 6-D, Arica, Chile
| | - Gerardo Lamas
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, Porto Alegre RS, 91501-970, Brazil
| | - Gilson R. P. Moreira
- PPG Biologia Animal, Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Porto Alegre, RS 91501-970, Brazil
| |
Collapse
|
21
|
Hebberecht L, Melo‐Flórez L, Young FJ, McMillan WO, Montgomery SH. The evolution of adult pollen feeding did not alter postembryonic growth in Heliconius butterflies. Ecol Evol 2022; 12:e8999. [PMID: 35784071 PMCID: PMC9237422 DOI: 10.1002/ece3.8999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 11/23/2022] Open
Abstract
For many animals, the availability and provision of dietary resources can vary markedly between juvenile and adult stages, often leading to a temporal separation of nutrient acquisition and use. Juvenile developmental programs are likely limited by the energetic demands of many adult tissues and processes with early developmental origins. Enhanced dietary quality in the adult stage may, therefore, alter selection on life history and growth patterns in juvenile stages. Heliconius are unique among butterflies in actively collecting and digesting pollen grains, which provide an adult source of essential amino acids. The origin of pollen feeding has therefore previously been hypothesized to lift constraints on larval growth rates, allowing Heliconius to spend less time as larvae when they are most vulnerable to predation. By measuring larval and pupal life-history traits across three pollen-feeding and three nonpollen-feeding Heliconiini, we provide the first test of this hypothesis. Although we detect significant interspecific variation in larval and pupal development, we do not find any consistent shift associated with pollen feeding. We discuss how this result may fit with patterns of nitrogen allocation, the benefits of nitrogenous stores, and developmental limitations on growth. Our results provide a framework for studies aiming to link innovations in adult Heliconius to altered selection regimes and developmental programs in early life stages.
Collapse
Affiliation(s)
- Laura Hebberecht
- Department of ZoologyUniversity of CambridgeCambridgeUK
- School of Biological SciencesUniversity of BristolBristolUK
- Smithsonian Tropical Research InstituteGamboaPanama
| | | | - Fletcher J. Young
- Department of ZoologyUniversity of CambridgeCambridgeUK
- School of Biological SciencesUniversity of BristolBristolUK
- Smithsonian Tropical Research InstituteGamboaPanama
| | | | - Stephen H. Montgomery
- School of Biological SciencesUniversity of BristolBristolUK
- Smithsonian Tropical Research InstituteGamboaPanama
| |
Collapse
|
22
|
Brien MN, Enciso-Romero J, Lloyd VJ, Curran EV, Parnell AJ, Morochz C, Salazar PA, Rastas P, Zinn T, Nadeau NJ. The genetic basis of structural colour variation in mimetic
Heliconius
butterflies. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200505. [PMID: 35634924 PMCID: PMC9149798 DOI: 10.1098/rstb.2020.0505] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Structural colours, produced by the reflection of light from ultrastructures, have evolved multiple times in butterflies. Unlike pigmentary colours and patterns, little is known about the genetic basis of these colours. Reflective structures on wing-scale ridges are responsible for iridescent structural colour in many butterflies, including the Müllerian mimics Heliconius erato and Heliconius melpomene. Here, we quantify aspects of scale ultrastructure variation and colour in crosses between iridescent and non-iridescent subspecies of both of these species and perform quantitative trait locus (QTL) mapping. We show that iridescent structural colour has a complex genetic basis in both species, with offspring from crosses having a wide variation in blue colour (both hue and brightness) and scale structure measurements. We detect two different genomic regions in each species that explain modest amounts of this variation, with a sex-linked QTL in H. erato but not H. melpomene. We also find differences between species in the relationships between structure and colour, overall suggesting that these species have followed different evolutionary trajectories in their evolution of structural colour. We then identify genes within the QTL intervals that are differentially expressed between subspecies and/or wing regions, revealing likely candidates for genes controlling structural colour formation. This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.
Collapse
Affiliation(s)
- Melanie N. Brien
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - Juan Enciso-Romero
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Victoria J. Lloyd
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - Emma V. Curran
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - Andrew J. Parnell
- Department of Physics and Astronomy, The University of Sheffield, Hicks Building, Hounsfield Road, Sheffield S3 7RH, UK
| | | | - Patricio A. Salazar
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - Pasi Rastas
- Institute of Biotechnology, 00014 University of Helsinki, Finland
| | - Thomas Zinn
- ESRF - The European Synchrotron, 38043 Grenoble Cedex 9, France
| | - Nicola J. Nadeau
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| |
Collapse
|
23
|
Hodel RGJ, Massatti R, Knowles LL. Hybrid enrichment of adaptive variation revealed by genotype-environment associations in montane sedges. Mol Ecol 2022; 31:3722-3737. [PMID: 35560840 PMCID: PMC9327521 DOI: 10.1111/mec.16502] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 12/04/2022]
Abstract
The role of hybridization in diversification is complex and may result in many possible outcomes. Not only can hybridization produce new lineages, but those lineages may contain unique combinations of adaptive genetic variation derived from parental taxa that allow hybrid‐origin lineages to occupy unique environmental space relative to one (or both) parent(s). We document such a case of hybridization between two sedge species, Carex nova and Carex nelsonii (Cyperaceae), that occupy partially overlapping environmental space in the southern Rocky Mountains, USA. In the region hypothesized to be the origin of the hybrid lineage, one parental taxon (C. nelsonii) is at the edge of its environmental tolerance. Hybrid‐origin individuals display mixed ancestry between the parental taxa—of nearly 7000 unlinked loci sampled, almost 30% showed evidence of excess ancestry from one parental lineage—approximately half displayed a genomic background skewed towards one parent, and half skewed towards the other. To test whether excess ancestry loci may have conferred an adaptive advantage to the hybrid‐origin lineage, we conducted genotype–environment association analyses on different combinations of loci—with and without excess ancestry—and with multiple contrasts between the hybrids and parental taxa. Loci with skewed ancestry showed significant environmental associations distinguishing the hybrid lineage from one parent (C. nelsonii), whereas loci with relatively equal representation of parental ancestries showed no such environmental associations. Moreover, the overwhelming majority of candidate adaptive loci with respect to environmental gradients also had excess ancestry from a parental lineage, implying these loci have facilitated the persistence of the hybrid lineage in an environment unsuitable to at least one parent.
Collapse
Affiliation(s)
- Richard G J Hodel
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.,Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, USA
| | - Rob Massatti
- U.S. Geological Survey, Southwest Biological Science Center, Flagstaff, AZ, USA
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
24
|
McCulloch KJ, Macias-Muñoz A, Mortazavi A, Briscoe AD. Multiple mechanisms of photoreceptor spectral tuning in Heliconius butterflies. Mol Biol Evol 2022; 39:6555095. [PMID: 35348742 PMCID: PMC9048915 DOI: 10.1093/molbev/msac067] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The evolution of color vision is often studied through the lens of receptor gain relative to an ancestor with fewer spectral classes of photoreceptor. For instance, in Heliconius butterflies, a genus-specific UVRh opsin duplication led to the evolution of UV color discrimination in Heliconius erato females, a rare trait among butterflies. However, color vision evolution is not well understood in the context of loss. In Heliconius melpomene and Heliconius ismenius lineages, the UV2 receptor subtype has been lost, which limits female color vision in shorter wavelengths. Here, we compare the visual systems of butterflies that have either retained or lost the UV2 photoreceptor using intracellular recordings, ATAC-seq, and antibody staining. We identify several ways these butterflies modulate their color vision. In H. melpomene, chromatin reorganization has downregulated an otherwise intact UVRh2 gene, whereas in H. ismenius, pseudogenization has led to the truncation of UVRh2. In species that lack the UV2 receptor, the peak sensitivity of the remaining UV1 photoreceptor cell is shifted to longer wavelengths. Across Heliconius, we identify the widespread use of filtering pigments and co-expression of two opsins in the same photoreceptor cells. Multiple mechanisms of spectral tuning, including the molecular evolution of blue opsins, have led to the divergence of receptor sensitivities between species. The diversity of photoreceptor and ommatidial subtypes between species suggests that Heliconius visual systems are under varying selection pressures for color discrimination. Modulating the wavelengths of peak sensitivities of both the blue- and remaining UV-sensitive photoreceptor cells suggests that Heliconius species may have compensated for UV receptor loss.
Collapse
Affiliation(s)
- Kyle J McCulloch
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108, USA
| | - Aide Macias-Muñoz
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697, USA.,Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara CA 93106, USA.,Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Adriana D Briscoe
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697, USA
| |
Collapse
|
25
|
Thawornwattana Y, Seixas FA, Yang Z, Mallet J. OUP accepted manuscript. Syst Biol 2022; 71:1159-1177. [PMID: 35169847 PMCID: PMC9366460 DOI: 10.1093/sysbio/syac009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 02/01/2022] [Accepted: 02/08/2022] [Indexed: 11/21/2022] Open
Abstract
Introgressive hybridization plays a key role in adaptive evolution and species diversification in many groups of species. However, frequent hybridization and gene flow between species make estimation of the species phylogeny and key population parameters challenging. Here, we show that by accounting for phasing and using full-likelihood methods, introgression histories and population parameters can be estimated reliably from whole-genome sequence data. We employ the multispecies coalescent (MSC) model with and without gene flow to infer the species phylogeny and cross-species introgression events using genomic data from six members of the erato-sara clade of Heliconius butterflies. The methods naturally accommodate random fluctuations in genealogical history across the genome due to deep coalescence. To avoid heterozygote phasing errors in haploid sequences commonly produced by genome assembly methods, we process and compile unphased diploid sequence alignments and use analytical methods to average over uncertainties in heterozygote phase resolution. There is robust evidence for introgression across the genome, both among distantly related species deep in the phylogeny and between sister species in shallow parts of the tree. We obtain chromosome-specific estimates of key population parameters such as introgression directions, times and probabilities, as well as species divergence times and population sizes for modern and ancestral species. We confirm ancestral gene flow between the sara clade and an ancestral population of Heliconius telesiphe, a likely hybrid speciation origin for Heliconius hecalesia, and gene flow between the sister species Heliconius erato and Heliconius himera. Inferred introgression among ancestral species also explains the history of two chromosomal inversions deep in the phylogeny of the group. This study illustrates how a full-likelihood approach based on the MSC makes it possible to extract rich historical information of species divergence and gene flow from genomic data. [3s; bpp; gene flow; Heliconius; hybrid speciation; introgression; inversion; multispecies coalescent]
Collapse
Affiliation(s)
- Yuttapong Thawornwattana
- Correspondence to be sent to: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; E-mail: ; (Y.T. and J.M.); Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK; E-mail: (Z.Y.)
| | - Fernando A Seixas
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ziheng Yang
- Correspondence to be sent to: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; E-mail: ; (Y.T. and J.M.); Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK; E-mail: (Z.Y.)
| | - James Mallet
- Correspondence to be sent to: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; E-mail: ; (Y.T. and J.M.); Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK; E-mail: (Z.Y.)
| |
Collapse
|
26
|
Ehlers S, Szczerbowski D, Harig T, Stell M, Hötling S, Darragh K, Jiggins CD, Schulz S. Identification and Composition of Clasper Scent Gland Components of the Butterfly Heliconius erato and Its Relation to Mimicry. Chembiochem 2021; 22:3300-3313. [PMID: 34547164 PMCID: PMC9293309 DOI: 10.1002/cbic.202100372] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/20/2021] [Indexed: 12/01/2022]
Abstract
The butterfly Heliconius erato occurs in various mimetic morphs. The male clasper scent gland releases an anti‐aphrodisiac pheromone and additionally contains a complex mixture of up to 350 components, varying between individuals. In 114 samples of five different mimicry groups and their hybrids 750 different compounds were detected by gas chromatography/mass spectrometry (GC/MS). Many unknown components occurred, which were identified using their mass spectra, gas chromatography/infrared spectroscopy (GC/IR)‐analyses, derivatization, and synthesis. Key compounds proved to be various esters of 3‐oxohexan‐1‐ol and (Z)‐3‐hexen‐1‐ol with (S)‐2,3‐dihydrofarnesoic acid, accompanied by a large variety of other esters with longer terpene acids, fatty acids, and various alcohols. In addition, linear terpenes with up to seven uniformly connected isoprene units occur, e. g. farnesylfarnesol. A large number of the compounds have not been reported before from nature. Discriminant analyses of principal components of the gland contents showed that the iridescent mimicry group differs strongly from the other, mostly also separated, mimicry groups. Comparison with data from other species indicated that Heliconius recruits different biosynthetic pathways in a species‐specific manner for semiochemical formation.
Collapse
Affiliation(s)
- Stephanie Ehlers
- Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany
| | - Daiane Szczerbowski
- Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany
| | - Tim Harig
- Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany
| | - Matthew Stell
- Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany
| | - Susan Hötling
- Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany
| | - Kathy Darragh
- Department of Evolution and Ecology, Storer Hall University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Downing Street, CB2 3EJ, Cambridge, UK
| | - Stefan Schulz
- Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany
| |
Collapse
|
27
|
Ferrari G, Atmore LM, Jentoft S, Jakobsen KS, Makowiecki D, Barrett JH, Star B. An accurate assignment test for extremely low-coverage whole-genome sequence data. Mol Ecol Resour 2021; 22:1330-1344. [PMID: 34779123 DOI: 10.1111/1755-0998.13551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 11/28/2022]
Abstract
Genomic assignment tests can provide important diagnostic biological characteristics, such as population of origin or ecotype. Yet, assignment tests often rely on moderate- to high-coverage sequence data that can be difficult to obtain for fields such as molecular ecology and ancient DNA. We have developed a novel approach that efficiently assigns biologically relevant information (i.e., population identity or structural variants such as inversions) in extremely low-coverage sequence data. First, we generate databases from existing reference data using a subset of diagnostic single nucleotide polymorphisms (SNPs) associated with a biological characteristic. Low-coverage alignment files are subsequently compared to these databases to ascertain allelic state, yielding a joint probability for each association. To assess the efficacy of this approach, we assigned haplotypes and population identity in Heliconius butterflies, Atlantic herring, and Atlantic cod using chromosomal inversion sites and whole-genome data. We scored both modern and ancient specimens, including the first whole-genome sequence data recovered from ancient Atlantic herring bones. The method accurately assigns biological characteristics, including population membership, using extremely low-coverage data (as low as 0.0001x) based on genome-wide SNPs. This approach will therefore increase the number of samples in evolutionary, ecological and archaeological research for which relevant biological information can be obtained.
Collapse
Affiliation(s)
- Giada Ferrari
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Lane M Atmore
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Daniel Makowiecki
- Department of Environmental Archaeology and Human Paleoecology, Institute of Archaeology, Nicolaus Copernicus University, Torun, Poland
| | - James H Barrett
- McDonald Institute for Archaeological Research, Department of Archaeology, University of Cambridge, Cambridge, UK.,Department of Archaeology and Cultural History, NTNU University Museum, Trondheim, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| |
Collapse
|
28
|
Salisbury SJ, Ruzzante DE. Genetic Causes and Consequences of Sympatric Morph Divergence in Salmonidae: A Search for Mechanisms. Annu Rev Anim Biosci 2021; 10:81-106. [PMID: 34758272 DOI: 10.1146/annurev-animal-051021-080709] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Repeatedly and recently evolved sympatric morphs exhibiting consistent phenotypic differences provide natural experimental replicates of speciation. Because such morphs are observed frequently in Salmonidae, this clade provides a rare opportunity to uncover the genomic mechanisms underpinning speciation. Such insight is also critical for conserving salmonid diversity, the loss of which could have significant ecological and economic consequences. Our review suggests that genetic differentiation among sympatric morphs is largely nonparallel apart from a few key genes that may be critical for consistently driving morph differentiation. We discuss alternative levels of parallelism likely underlying consistent morph differentiation and identify several factors that may temper this incipient speciation between sympatric morphs, including glacial history and contemporary selective pressures. Our synthesis demonstrates that salmonids are useful for studying speciation and poses additional research questions to be answered by future study of this family. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- S J Salisbury
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada; ,
| | - D E Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada; ,
| |
Collapse
|
29
|
Rueda-M N, Salgado-Roa FC, Gantiva-Q CH, Pardo-Díaz C, Salazar C. Environmental Drivers of Diversification and Hybridization in Neotropical Butterflies. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.750703] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Studying how the environment shapes current biodiversity patterns in species rich regions is a fundamental issue in biogeography, ecology, and conservation. However, in the Neotropics, the study of the forces driving species distribution and richness, is mostly based on vertebrates and plants. In this study, we used 54,392 georeferenced records for 46 species and 1,012 georeferenced records for 38 interspecific hybrids of the Neotropical Heliconius butterflies to investigate the role of the environment in shaping their distribution and richness, as well as their geographic patterns of phylogenetic diversity and phylogenetic endemism. We also evaluated whether niche similarity promotes hybridization in Heliconius. We found that these insects display five general distribution patterns mostly explained by precipitation and isothermality, and to a lesser extent, by altitude. Interestingly, altitude plays a major role as a predictor of species richness and phylogenetic diversity, while precipitation explains patterns of phylogenetic endemism. We did not find evidence supporting the role of the environment in facilitating hybridization because hybridizing species do not necessarily share the same climatic niche despite some of them having largely overlapping geographic distributions. Overall, we confirmed that, as in other organisms, high annual temperature, a constant supply of water, and spatio-topographic complexity are the main predictors of diversity in Heliconius. However, future studies at large scale need to investigate the effect of microclimate variables and ecological interactions.
Collapse
|
30
|
Chazot N, Condamine FL, Dudas G, Peña C, Kodandaramaiah U, Matos-Maraví P, Aduse-Poku K, Elias M, Warren AD, Lohman DJ, Penz CM, DeVries P, Fric ZF, Nylin S, Müller C, Kawahara AY, Silva-Brandão KL, Lamas G, Kleckova I, Zubek A, Ortiz-Acevedo E, Vila R, Vane-Wright RI, Mullen SP, Jiggins CD, Wheat CW, Freitas AVL, Wahlberg N. Conserved ancestral tropical niche but different continental histories explain the latitudinal diversity gradient in brush-footed butterflies. Nat Commun 2021; 12:5717. [PMID: 34588433 PMCID: PMC8481491 DOI: 10.1038/s41467-021-25906-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/07/2021] [Indexed: 02/08/2023] Open
Abstract
The global increase in species richness toward the tropics across continents and taxonomic groups, referred to as the latitudinal diversity gradient, stimulated the formulation of many hypotheses to explain the underlying mechanisms of this pattern. We evaluate several of these hypotheses to explain spatial diversity patterns in a butterfly family, the Nymphalidae, by assessing the contributions of speciation, extinction, and dispersal, and also the extent to which these processes differ among regions at the same latitude. We generate a time-calibrated phylogeny containing 2,866 nymphalid species (~45% of extant diversity). Neither speciation nor extinction rate variations consistently explain the latitudinal diversity gradient among regions because temporal diversification dynamics differ greatly across longitude. The Neotropical diversity results from low extinction rates, not high speciation rates, and biotic interchanges with other regions are rare. Southeast Asia is also characterized by a low speciation rate but, unlike the Neotropics, is the main source of dispersal events through time. Our results suggest that global climate change throughout the Cenozoic, combined with tropical niche conservatism, played a major role in generating the modern latitudinal diversity gradient of nymphalid butterflies.
Collapse
Affiliation(s)
- Nicolas Chazot
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 75651, Uppsala, Sweden.
- Systematic Biology Group, Department of Biology, Lund University, Lund, Sweden.
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden.
| | - Fabien L Condamine
- CNRS, UMR 5554 Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier|CNRS|IRD|EPHE), Place Eugene Bataillon, 34095, Montpellier, France
| | - Gytis Dudas
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Carlos Peña
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Ullasa Kodandaramaiah
- IISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE), School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, India
| | - Pável Matos-Maraví
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
| | - Kwaku Aduse-Poku
- Department of Life and Earth Sciences, Perimeter College, Georgia State University, 33 Gilmer Street, Atlanta, GA, 30303, USA
| | - Marianne Elias
- ISYEB, CNRS, MNHN, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, Paris, 75005, France
| | - Andrew D Warren
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - David J Lohman
- City College of New York and Graduate Center, CUNY, New York, NY, USA
- National Museum of Natural History, Manila, Philippines
| | - Carla M Penz
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, USA
| | - Phil DeVries
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, USA
| | - Zdenek F Fric
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
| | - Soren Nylin
- Department of Zoology, Stockholm University, 10691, Stockholm, Sweden
| | - Chris Müller
- Australian Museum, 6 College Street, Sydney, NSW, 2010, Australia
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Karina L Silva-Brandão
- Universidade Estadual de Campinas, Centro de Biologia Molecular e Engenharia Genética, Av. Candido Rondom, 400, 13083-875, Campinas, SP, Brazil
| | - Gerardo Lamas
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Irena Kleckova
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
| | - Anna Zubek
- Nature Education Centre, Jagiellonian University, ul. Gronostajowa 5, 30-387, Kraków, Poland
| | - Elena Ortiz-Acevedo
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Departamento de Química y Biología, Universidad del Norte, Barranquilla, Colombia
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - Richard I Vane-Wright
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
- Durrell Institute of Conservation and Ecology (DICE), University of Kent, Canterbury, CT2 7NR, UK
| | - Sean P Mullen
- 5 Cummington Street, Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Downing St., Cambridge, CB2 3EJ, UK
- Smithsonian Tropical Research Institute, Gamboa, Panama
| | | | - Andre V L Freitas
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), 13083-862, Campinas, SP, Brazil
| | - Niklas Wahlberg
- Systematic Biology Group, Department of Biology, Lund University, Lund, Sweden
| |
Collapse
|
31
|
Piron-Prunier F, Persyn E, Legeai F, McClure M, Meslin C, Robin S, Alves-Carvalho S, Mohammad A, Blugeon C, Jacquin-Joly E, Montagné N, Elias M, Gauthier J. Comparative transcriptome analysis at the onset of speciation in a mimetic butterfly-The Ithomiini Melinaea marsaeus. J Evol Biol 2021; 34:1704-1721. [PMID: 34570954 DOI: 10.1111/jeb.13940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/16/2021] [Accepted: 09/03/2021] [Indexed: 11/28/2022]
Abstract
Ecological speciation entails divergent selection on specific traits and ultimately on the developmental pathways responsible for these traits. Selection can act on gene sequences but also on regulatory regions responsible for gene expression. Mimetic butterflies are a relevant system for speciation studies because wing colour pattern (WCP) often diverges between closely related taxa and is thought to drive speciation through assortative mating and increased predation on hybrids. Here, we generate the first transcriptomic resources for a mimetic butterfly of the tribe Ithomiini, Melinaea marsaeus, to examine patterns of differential expression between two subspecies and between tissues that express traits that likely drive reproductive isolation; WCP and chemosensory genes. We sequenced whole transcriptomes of three life stages to cover a large catalogue of transcripts, and we investigated differential expression between subspecies in pupal wing discs and antennae. Eighteen known WCP genes were expressed in wing discs and 115 chemosensory genes were expressed in antennae, with a remarkable diversity of chemosensory protein genes. Many transcripts were differentially expressed between subspecies, including two WCP genes and one odorant receptor. Our results suggest that in M. marsaeus the same genes as in other mimetic butterflies are involved in traits causing reproductive isolation, and point at possible candidates for the differences in those traits between subspecies. Differential expression analyses of other developmental stages and body organs and functional studies are needed to confirm and expand these results. Our work provides key resources for comparative genomics in mimetic butterflies, and more generally in Lepidoptera.
Collapse
Affiliation(s)
- Florence Piron-Prunier
- Institut de Systématique, Evolution, Biodiversité, MNHN, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Emma Persyn
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Fabrice Legeai
- BIPAA, IGEPP, INRAE, Institut Agro, Univ Rennes, Rennes, France.,Univ Rennes, INRIA, CNRS, IRISA, Rennes, France
| | - Melanie McClure
- Institut de Systématique, Evolution, Biodiversité, MNHN, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,Laboratoire Écologie, Évolution,Interactions des Systèmes Amazoniens (LEEISA), Université de Guyane, CNRS, IFREMER, Cayenne, France
| | - Camille Meslin
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Stéphanie Robin
- BIPAA, IGEPP, INRAE, Institut Agro, Univ Rennes, Rennes, France.,Univ Rennes, INRIA, CNRS, IRISA, Rennes, France
| | | | - Ammara Mohammad
- Département de Biologie, Genomics Core Facility, Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Corinne Blugeon
- Département de Biologie, Genomics Core Facility, Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Emmanuelle Jacquin-Joly
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Nicolas Montagné
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Marianne Elias
- Institut de Systématique, Evolution, Biodiversité, MNHN, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Jérémy Gauthier
- Univ Rennes, INRIA, CNRS, IRISA, Rennes, France.,Geneva Natural History Museum, Geneva, Switzerland
| |
Collapse
|
32
|
Cicconardi F, Lewis JJ, Martin SH, Reed RD, Danko CG, Montgomery SH. Chromosome Fusion Affects Genetic Diversity and Evolutionary Turnover of Functional Loci but Consistently Depends on Chromosome Size. Mol Biol Evol 2021; 38:4449-4462. [PMID: 34146107 PMCID: PMC8476138 DOI: 10.1093/molbev/msab185] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Major changes in chromosome number and structure are linked to a series of evolutionary phenomena, including intrinsic barriers to gene flow or suppression of recombination due to chromosomal rearrangements. However, chromosome rearrangements can also affect the fundamental dynamics of molecular evolution within populations by changing relationships between linked loci and altering rates of recombination. Here, we build chromosome-level assembly Eueides isabella and, together with a recent chromosome-level assembly of Dryas iulia, examine the evolutionary consequences of multiple chromosome fusions in Heliconius butterflies. These assemblies pinpoint fusion points on 10 of the 20 autosomal chromosomes and reveal striking differences in the characteristics of fused and unfused chromosomes. The ten smallest autosomes in D. iulia and E. isabella, which have each fused to a longer chromosome in Heliconius, have higher repeat and GC content, and longer introns than predicted by their chromosome length. When fused, these characteristics change to become more in line with chromosome length. The fusions also led to reduced diversity, which likely reflects increased background selection and selection against introgression between diverging populations, following a reduction in per-base recombination rate. We further show that chromosome size and fusion impact turnover rates of functional loci at a macroevolutionary scale. Together these results provide further evidence that chromosome fusion in Heliconius likely had dramatic effects on population level processes shaping rates of neutral and adaptive divergence. These effects may have impacted patterns of diversification in Heliconius, a classic example of an adaptive radiation.
Collapse
Affiliation(s)
- Francesco Cicconardi
- School of Biological Sciences, University of Bristol Bristol—Life Sciences Building, Bristol, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - James J Lewis
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
- Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Simon H Martin
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Robert D Reed
- Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Charles G Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Stephen H Montgomery
- School of Biological Sciences, University of Bristol Bristol—Life Sciences Building, Bristol, United Kingdom
| |
Collapse
|
33
|
Montejo-Kovacevich G, Salazar PA, Smith SH, Gavilanes K, Bacquet CN, Chan YF, Jiggins CD, Meier JI, Nadeau NJ. Genomics of altitude-associated wing shape in two tropical butterflies. Mol Ecol 2021; 30:6387-6402. [PMID: 34233044 DOI: 10.1111/mec.16067] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 07/01/2021] [Indexed: 11/30/2022]
Abstract
Understanding how organisms adapt to their local environment is central to evolution. With new whole-genome sequencing technologies and the explosion of data, deciphering the genomic basis of complex traits that are ecologically relevant is becoming increasingly feasible. Here, we studied the genomic basis of wing shape in two Neotropical butterflies that inhabit large geographical ranges. Heliconius butterflies at high elevations have been shown to generally have rounder wings than those in the lowlands. We reared over 1,100 butterflies from 71 broods of H. erato and H. melpomene in common-garden conditions and showed that wing aspect ratio, that is, elongatedness, is highly heritable in both species and that elevation-associated wing aspect ratio differences are maintained. Genome-wide associations with a published data set of 666 whole genomes from across a hybrid zone, uncovered a highly polygenic basis to wing aspect ratio variation in the wild. We identified several genes that have roles in wing morphogenesis or wing aspect ratio variation in Drosophila flies, making them promising candidates for future studies. There was little evidence for molecular parallelism in the two species, with only one shared candidate gene, nor for a role of the four known colour pattern loci, except for optix in H. erato. Thus, we present the first insights into the heritability and genomic basis of within-species wing aspect ratio in two Heliconius species, adding to a growing body of evidence that polygenic adaptation may underlie many ecologically relevant traits.
Collapse
Affiliation(s)
| | | | - Sophie H Smith
- Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | | | | | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Joana I Meier
- Department of Zoology, University of Cambridge, Cambridge, UK.,St John's College, University of Cambridge, Cambridge, UK
| | - Nicola J Nadeau
- Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| |
Collapse
|
34
|
Kozak KM, Joron M, McMillan WO, Jiggins CD. Rampant Genome-Wide Admixture across the Heliconius Radiation. Genome Biol Evol 2021; 13:evab099. [PMID: 33944917 PMCID: PMC8283734 DOI: 10.1093/gbe/evab099] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2021] [Indexed: 12/12/2022] Open
Abstract
How frequent is gene flow between species? The pattern of evolution is typically portrayed as a phylogenetic tree, yet gene flow between good species may be an important mechanism in diversification, spreading adaptive traits and leading to a complex pattern of phylogenetic incongruence. This process has thus far been studied mainly among a few closely related species, or in geographically restricted areas such as islands, but not on the scale of a continental radiation. Using a genomic representation of 40 out of 47 species in the genus, we demonstrate that admixture has played a role throughout the evolution of the charismatic Neotropical butterflies Heliconius. Modeling of phylogenetic networks based on the exome uncovers up to 13 instances of interspecific gene flow. Admixture is detected among the relatives of Heliconius erato, as well as between the ancient lineages leading to modern clades. Interspecific gene flow played a role throughout the evolution of the genus, although the process has been most frequent in the clade of Heliconius melpomene and relatives. We identify Heliconius hecalesia and relatives as putative hybrids, including new evidence for introgression at the loci controlling the mimetic wing patterns. Models accounting for interspecific gene flow yield a more complete picture of the radiation as a network, which will improve our ability to study trait evolution in a realistic comparative framework.
Collapse
Affiliation(s)
- Krzysztof M Kozak
- Smithsonian Tropical Research Institute, Panamá, Panamá
- Department of Zoology, University of Cambridge, United Kingdom
| | - Mathieu Joron
- Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, EPHE, IRD, France
| | | | - Chris D Jiggins
- Smithsonian Tropical Research Institute, Panamá, Panamá
- Department of Zoology, University of Cambridge, United Kingdom
| |
Collapse
|
35
|
Lewis JJ, Cicconardi F, Martin SH, Reed RD, Danko CG, Montgomery SH. The Dryas iulia Genome Supports Multiple Gains of a W Chromosome from a B Chromosome in Butterflies. Genome Biol Evol 2021; 13:evab128. [PMID: 34117762 PMCID: PMC8290107 DOI: 10.1093/gbe/evab128] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2021] [Indexed: 12/17/2022] Open
Abstract
In butterflies and moths, which exhibit highly variable sex determination mechanisms, the homogametic Z chromosome is deeply conserved and is featured in many genome assemblies. The evolution and origin of the female W sex chromosome, however, remains mostly unknown. Previous studies have proposed that a ZZ/Z0 sex determination system is ancestral to Lepidoptera, and that W chromosomes may originate from sex-linked B chromosomes. Here, we sequence and assemble the female Dryas iulia genome into 32 highly contiguous ordered and oriented chromosomes, including the Z and W sex chromosomes. We then use sex-specific Hi-C, ATAC-seq, PRO-seq, and whole-genome DNA sequence data sets to test if features of the D. iulia W chromosome are consistent with a hypothesized B chromosome origin. We show that the putative W chromosome displays female-associated DNA sequence, gene expression, and chromatin accessibility to confirm the sex-linked function of the W sequence. In contrast with expectations from studies of homologous sex chromosomes, highly repetitive DNA content on the W chromosome, the sole presence of domesticated repetitive elements in functional DNA, and lack of sequence homology with the Z chromosome or autosomes is most consistent with a B chromosome origin for the W, although it remains challenging to rule out extensive sequence divergence. Synteny analysis of the D. iulia W chromosome with other female lepidopteran genome assemblies shows no homology between W chromosomes and suggests multiple, independent origins of the W chromosome from a B chromosome likely occurred in butterflies.
Collapse
Affiliation(s)
- James J Lewis
- Baker Institute for Animal Health, Cornell University, Ithaca, New York, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Francesco Cicconardi
- School of Biological Sciences, University of Bristol, United Kingdom
- Department of Zoology, University of Cambridge, United Kingdom
| | - Simon H Martin
- Institute of Evolutionary Biology, University of Edinburgh, United Kingdom
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Charles G Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, New York, USA
| | | |
Collapse
|
36
|
Meier JI, Salazar PA, Kučka M, Davies RW, Dréau A, Aldás I, Box Power O, Nadeau NJ, Bridle JR, Rolian C, Barton NH, McMillan WO, Jiggins CD, Chan YF. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. Proc Natl Acad Sci U S A 2021; 118:e2015005118. [PMID: 34155138 PMCID: PMC8237668 DOI: 10.1073/pnas.2015005118] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genetic variation segregates as linked sets of variants or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. Yet, genomic data often omit haplotype information due to constraints in sequencing technologies. Here, we present "haplotagging," a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species, the geographic clines for the major wing-pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the center of the hybrid zone. We propose that shared warning signaling (Müllerian mimicry) may couple the cline shifts seen in both species and facilitate the parallel coemergence of a novel hybrid morph in both comimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations.
Collapse
Affiliation(s)
- Joana I Meier
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
- St. John's College, University of Cambridge, Cambridge CB2 1TP, United Kingdom
| | - Patricio A Salazar
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Marek Kučka
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
| | | | - Andreea Dréau
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
| | | | - Olivia Box Power
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - Nicola J Nadeau
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Jon R Bridle
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
| | - Campbell Rolian
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Nicholas H Barton
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Panamá, Apartado Postal 0843-00153, República de Panamá
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom;
- Smithsonian Tropical Research Institute, Panamá, Apartado Postal 0843-00153, República de Panamá
| | - Yingguang Frank Chan
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany;
| |
Collapse
|
37
|
Sedano-Cruz RE, Calero-Mejía H. CARACTERIZACIÓN GENÉTICA DE LA POBLACIÓN DE Heliconius sara (Nymphalidae) EN LA ISLA GORGONA, COLOMBIA. ACTA BIOLÓGICA COLOMBIANA 2021. [DOI: 10.15446/abc.v26n3.86205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
La estructura genética de poblaciones de mariposas con distribución en islas y sus pares continentales ha sido poco documentada para el neotrópico. Este estudio presenta la caracterización de una población de Heliconius sara con distribución en la Isla Gorgona, ubicada en la región del Pacífico Oriental Colombiano. Para esto se examinaron secuencias parciales de un marcador mitocondrial incluyendo información obtenida del GenBank. Se comparó la diversidad y estructura genética con sus conespecíficos continentales y también con congéneres, con los que comparte un ancestro común cercano en el clado Sapho-Sara. Para el análisis de diversidad y estructura genética se realizó un análisis molecular de varianza. Este análisis muestra que la distancia entre la población de la isla y sus pares en el continente es consistente con la variación intraespecífica observada en otras especies del género Heliconius. Para la reconstrucción de la genealogía y datación reciente en el Pleistoceno superior del grupo monofilético de secuencias de H. sara, se realizó un análisis de inferencia bayesiana, así como una de máxima verosimilitud. Del análisis demográfico se seleccionó un modelo histórico de flujo asimétrico desde la isla hacia el continente que sugiere baja resistencia de la discontinuidad geográfica a la dispersión de esta mariposa diurna desde la isla. Este es el primer estudio en examinar un posible evento de aislamiento de una población insular de mariposas en Colombia.
Collapse
|
38
|
Cox CL, Chung AK, Blackwell C, Davis MM, Gulsby M, Islam H, Miller N, Lambert C, Lewis O, Rector IV, Walsh M, Yamamoto AD, Davis Rabosky AR. Tactile stimuli induce deimatic antipredator displays in ringneck snakes. Ethology 2021. [DOI: 10.1111/eth.13152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Christian L. Cox
- Department of Biological Sciences Florida International University Miami FL USA
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
| | - Albert K. Chung
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
- Department of Ecology and Evolutionary Biology University of California Los Angeles Los Angeles CA USA
| | | | - Maura M. Davis
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
| | - Miranda Gulsby
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
- Department of Biology Kennesaw State University Kennesaw GA USA
| | - Hasib Islam
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
| | - Nathan Miller
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
- James Madison University Harrisonburg VA USA
| | - Carson Lambert
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
| | - Olivia Lewis
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
| | - Ian V. Rector
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
| | - Marleigh Walsh
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
| | - Alannah D. Yamamoto
- Mountain Lake Biological Station University of Virginia Charlottesville VA USA
- University of Maryland College Park MD USA
| | | |
Collapse
|
39
|
Seixas FA, Edelman NB, Mallet J. Synteny-Based Genome Assembly for 16 Species of Heliconius Butterflies, and an Assessment of Structural Variation across the Genus. Genome Biol Evol 2021; 13:6207971. [PMID: 33792688 PMCID: PMC8290116 DOI: 10.1093/gbe/evab069] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2021] [Indexed: 12/11/2022] Open
Abstract
Heliconius butterflies (Lepidoptera: Nymphalidae) are a group of 48 neotropical species widely studied in evolutionary research. Despite the wealth of genomic data generated in past years, chromosomal level genome assemblies currently exist for only two species, Heliconius melpomene and Heliconius erato, each a representative of one of the two major clades of the genus. Here, we use these reference genomes to improve the contiguity of previously published draft genome assemblies of 16 Heliconius species. Using a reference-assisted scaffolding approach, we place and order the scaffolds of these genomes onto chromosomes, resulting in 95.7-99.9% of their genomes anchored to chromosomes. Genome sizes are somewhat variable among species (270-422 Mb) and in one small group of species (Heliconius hecale, Heliconius elevatus, and Heliconius pardalinus) expansions in genome size are driven mainly by repetitive sequences that map to four small regions in the H. melpomene reference genome. Genes from these repeat regions show an increase in exon copy number, an absence of internal stop codons, evidence of constraint on nonsynonymous changes, and increased expression, all of which suggest that at least some of the extra copies are functional. Finally, we conducted a systematic search for inversions and identified five moderately large inversions fixed between the two major Heliconius clades. We infer that one of these inversions was transferred by introgression between the lineages leading to the erato/sara and burneyi/doris clades. These reference-guided assemblies represent a major improvement in Heliconius genomic resources that enable further genetic and evolutionary discoveries in this genus.
Collapse
Affiliation(s)
- Fernando A Seixas
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Nathaniel B Edelman
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Yale Institute for Biospheric Studies, Yale University, New Haven, Connecticut, USA
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| |
Collapse
|
40
|
Habitat generalist species constrain the diversity of mimicry rings in heterogeneous habitats. Sci Rep 2021; 11:5072. [PMID: 33658554 PMCID: PMC7930205 DOI: 10.1038/s41598-021-83867-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 02/05/2021] [Indexed: 11/08/2022] Open
Abstract
How evolution creates and maintains trait patterns in species-rich communities is still an unsolved topic in evolutionary ecology. One classical example of community-level pattern is the unexpected coexistence of different mimicry rings, each of which is a group of mimetic species with the same warning signal. The coexistence of different mimicry rings in a community seems paradoxical because selection among unpalatable species should favor convergence to a single warning pattern. We combined mathematical modeling based on network theory and numerical simulations to explore how different types of selection, such as mimetic and environmental selections, and habitat use by mimetic species influence the formation of coexisting rings. We show that when habitat and mimicry are strong sources of selection, the formation of multiple rings takes longer due to conflicting selective pressures. Moreover, habitat generalist species decrease the distinctiveness of different mimicry rings’ patterns and a few habitat generalist species can generate a “small-world effect”, preventing the formation of multiple mimicry rings. These results may explain why the coexistence of mimicry rings is more common in groups of animals that tend towards habitat specialism, such as butterflies.
Collapse
|
41
|
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] [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.
Collapse
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
| |
Collapse
|
42
|
Llaurens V, Le Poul Y, Puissant A, Blandin P, Debat V. Convergence in sympatry: Evolution of blue-banded wing pattern in Morpho butterflies. J Evol Biol 2020; 34:284-295. [PMID: 33119141 DOI: 10.1111/jeb.13726] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 10/07/2020] [Accepted: 10/13/2020] [Indexed: 11/30/2022]
Abstract
Species interactions such as mimicry can promote trait convergence but disentangling this effect from those of shared ecology, evolutionary history, and niche conservatism is often challenging. Here by focusing on wing colour pattern variation within and between three butterfly species living in sympatry in a large proportion of their range, we tested the effect of species interactions on trait diversification. These butterflies display a conspicuous iridescent blue coloration on the dorsal side of their wings and a cryptic brownish colour on the ventral side. Combined with an erratic and fast flight, these colour patterns increase the difficulty of capture by predators and contribute to the high escape abilities of these butterflies. We hypothesize that, beyond their direct contribution to predator escape, these wing patterns can be used as signals of escape abilities by predators, resulting in positive frequency-dependent selection favouring convergence in wing pattern in sympatry. To test this hypothesis, we quantified dorsal wing pattern variations of 723 butterflies from the three species sampled throughout their distribution, including sympatric and allopatric situations and compared the phenotypic distances between species, sex and localities. We detected a significant effect of localities on colour pattern, and higher inter-specific resemblance in sympatry as compared to allopatry, consistent with the hypothesis of local convergence of wing patterns. Our results provide support to the existence of escape mimicry in the wild and stress the importance of estimating trait variation within species to understand trait variation between species, and to a larger extent, trait diversification at the macro-evolutionary scale.
Collapse
Affiliation(s)
- Violaine Llaurens
- Institut de Systématique, Evolution et Biodiversité, UMR 7205 CNRS/MNHN/Sorbonne Université/EPHE, Museum National d'Histoire Naturelle, Paris, France
| | - Yann Le Poul
- Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Agathe Puissant
- Institut de Systématique, Evolution et Biodiversité, UMR 7205 CNRS/MNHN/Sorbonne Université/EPHE, Museum National d'Histoire Naturelle, Paris, France
| | - Patrick Blandin
- Institut de Systématique, Evolution et Biodiversité, UMR 7205 CNRS/MNHN/Sorbonne Université/EPHE, Museum National d'Histoire Naturelle, Paris, France
| | - Vincent Debat
- Institut de Systématique, Evolution et Biodiversité, UMR 7205 CNRS/MNHN/Sorbonne Université/EPHE, Museum National d'Histoire Naturelle, Paris, France
| |
Collapse
|
43
|
Heliconius Butterflies Host Characteristic and Phylogenetically Structured Adult-Stage Microbiomes. Appl Environ Microbiol 2020; 86:AEM.02007-20. [PMID: 33008816 DOI: 10.1128/aem.02007-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022] Open
Abstract
Lepidoptera (butterflies and moths) are diverse and ecologically important, yet we know little about how they interact with microbes as adults. Due to metamorphosis, the form and function of their adult-stage microbiomes might be very different from those of microbiomes in the larval stage (caterpillars). We studied adult-stage microbiomes of Heliconius and closely related passion-vine butterflies (Heliconiini), which are an important model system in evolutionary biology. To characterize the structure and dynamics of heliconiine microbiomes, we used field collections of wild butterflies, 16S rRNA gene sequencing, quantitative PCR, and shotgun metagenomics. We found that Heliconius butterflies harbor simple and abundant bacterial communities that are moderately consistent among conspecific individuals and over time. Heliconiine microbiomes also exhibited a strong signal of the host phylogeny, with a major distinction between Heliconius and other butterflies. These patterns were largely driven by differing relative abundances of bacterial phylotypes shared among host species and genera, as opposed to the presence or absence of host-specific phylotypes. We suggest that the phylogenetic structure in heliconiine microbiomes arises from conserved host traits that differentially filter microbes from the environment. While the relative importance of different traits remains unclear, our data indicate that pollen feeding (unique to Heliconius) is not a primary driver. Using shotgun metagenomics, we also discovered trypanosomatids and microsporidia to be prevalent in butterfly guts, raising the possibility of antagonistic interactions between eukaryotic parasites and colocalized gut bacteria. Our discovery of characteristic and phylogenetically structured microbiomes provides a foundation for tests of adult-stage microbiome function, a poorly understood aspect of lepidopteran biology.IMPORTANCE Many insects host microbiomes with important ecological functions. However, the prevalence of this phenomenon is unclear because in many insect taxa, microbiomes have been studied in only part of the life cycle, if at all. A prominent example is butterflies and moths, in which the composition and functional role of adult-stage microbiomes are largely unknown. We comprehensively characterized microbiomes in adult passion-vine butterflies. Butterfly-associated bacterial communities are generally abundant in guts, consistent within populations, and composed of taxa widely shared among hosts. More closely related butterflies harbor more similar microbiomes, with the most dramatic shift in microbiome composition occurring in tandem with a suite of ecological and life history traits unique to the genus Heliconius Butterflies are also frequently infected with previously undescribed eukaryotic parasites, which may interact with bacteria in important ways. These findings advance our understanding of butterfly biology and insect-microbe interactions generally.
Collapse
|
44
|
Young FJ, Montgomery SH. Pollen feeding in Heliconius butterflies: the singular evolution of an adaptive suite. Proc Biol Sci 2020; 287:20201304. [PMID: 33171092 PMCID: PMC7735275 DOI: 10.1098/rspb.2020.1304] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/15/2020] [Indexed: 12/21/2022] Open
Abstract
Major evolutionary transitions can be triggered by behavioural novelty, and are often associated with 'adaptive suites', which involve shifts in multiple co-adapted traits subject to complex interactions. Heliconius butterflies represent one such example, actively feeding on pollen, a behaviour unique among butterflies. Pollen feeding permits a prolonged reproductive lifespan, and co-occurs with a constellation of behavioural, neuroanatomical, life history, morphological and physiological traits that are absent in closely related, non-pollen-feeding genera. As a highly tractable system, supported by considerable ecological and genomic data, Heliconius are an excellent model for investigating how behavioural innovation can trigger a cascade of adaptive shifts in multiple diverse, but interrelated, traits. Here, we synthesize current knowledge of pollen feeding in Heliconius, and explore potential interactions between associated, putatively adaptive, traits. Currently, no physiological, morphological or molecular innovation has been explicitly linked to the origin of pollen feeding, and several hypothesized links between different aspects of Heliconius biology remain poorly tested. However, resolving these uncertainties will contribute to our understanding of how behavioural innovations evolve and subsequently alter the evolutionary trajectories of diverse traits impacting resource acquisition, life history, senescence and cognition.
Collapse
Affiliation(s)
- Fletcher J. Young
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
- School of Biological Science, University of Bristol, 24 Tyndall Avenue, Bristol UBS8 1TQ, UK
| | - Stephen H. Montgomery
- School of Biological Science, University of Bristol, 24 Tyndall Avenue, Bristol UBS8 1TQ, UK
| |
Collapse
|
45
|
Morris J, Hanly JJ, Martin SH, Van Belleghem SM, Salazar C, Jiggins CD, Dasmahapatra KK. Deep Convergence, Shared Ancestry, and Evolutionary Novelty in the Genetic Architecture of Heliconius Mimicry. Genetics 2020; 216:765-780. [PMID: 32883703 PMCID: PMC7648585 DOI: 10.1534/genetics.120.303611] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/25/2020] [Indexed: 01/31/2023] Open
Abstract
Convergent evolution can occur through different genetic mechanisms in different species. It is now clear that convergence at the genetic level is also widespread, and can be caused by either (i) parallel genetic evolution, where independently evolved convergent mutations arise in different populations or species, or (ii) collateral evolution in which shared ancestry results from either ancestral polymorphism or introgression among taxa. The adaptive radiation of Heliconius butterflies shows color pattern variation within species, as well as mimetic convergence between species. Using comparisons from across multiple hybrid zones, we use signals of shared ancestry to identify and refine multiple putative regulatory elements in Heliconius melpomene and its comimics, Heliconius elevatus and Heliconius besckei, around three known major color patterning genes: optix, WntA, and cortex While we find that convergence between H. melpomene and H. elevatus is caused by a complex history of collateral evolution via introgression in the Amazon, convergence between these species in the Guianas appears to have evolved independently. Thus, we find adaptive convergent genetic evolution to be a key driver of regulatory changes that lead to rapid phenotypic changes. Furthermore, we uncover evidence of parallel genetic evolution at some loci around optix and WntA in H. melpomene and its distant comimic Heliconius erato Ultimately, we show that all three of convergence, conservation, and novelty underlie the modular architecture of Heliconius color pattern mimicry.
Collapse
Affiliation(s)
- Jake Morris
- Department of Biology, University of York, Heslington YO10 5DD, United Kingdom
| | - Joseph J Hanly
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, United Kingdom
| | - Simon H Martin
- Institute of Evolutionary Biology, The University of Edinburgh, Ashworth Laboratories, Edinburgh EH9 3FL, United Kingdom
| | - Steven M Van Belleghem
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, United Kingdom
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá 111221, Colombia
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, United Kingdom
| | | |
Collapse
|
46
|
Phylomitogenomics provides new perspectives on the Euphasmatodea radiation (Insecta: Phasmatodea). Mol Phylogenet Evol 2020; 155:106983. [PMID: 33059069 DOI: 10.1016/j.ympev.2020.106983] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 09/11/2020] [Accepted: 10/06/2020] [Indexed: 11/20/2022]
Abstract
Phasmatodea species diversity lies almost entirely within its suborder Euphasmatodea, which exhibits a pantropical distribution and is considered to derive from a recent and rapid evolutionary radiation. To shed light on Euphasmatodea origins and diversification, we assembled the mitogenomes of 17 species from transcriptomic sequencing data and analysed them along with 22 already available Phasmatodea mitogenomes and 33 mitogenomes representing most of the Polyneoptera lineages. Maximum Likelihood and Bayesian Inference approaches retrieved consistent topologies, both showing the widespread conflict between phylogenetic approaches and traditional systematics. We performed a divergence time analysis leveraging ten fossil specimens representative of most polyneopteran lineages: the time tree obtained supports an older radiation of the clade with respect to previous hypotheses. Euphasmatodea diversification is inferred to have started ~ 187 million years ago, suggesting that the Triassic-Jurassic mass extinction and the breakup of Pangea could have contributed to the process. We also investigated Euphasmatodea mitogenomes patterns of dN, dS and dN/dS ratio throughout our time-tree, trying to characterize the selective regime which may have shaped the clade evolution.
Collapse
|
47
|
McMillan WO, Livraghi L, Concha C, Hanly JJ. From Patterning Genes to Process: Unraveling the Gene Regulatory Networks That Pattern Heliconius Wings. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00221] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
|
48
|
Van Belleghem SM, Alicea Roman PA, Carbia Gutierrez H, Counterman BA, Papa R. Perfect mimicry between Heliconius butterflies is constrained by genetics and development. Proc Biol Sci 2020; 287:20201267. [PMID: 32693728 PMCID: PMC7423669 DOI: 10.1098/rspb.2020.1267] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Müllerian mimicry strongly exemplifies the power of natural selection. However, the exact measure of such adaptive phenotypic convergence and the possible causes of its imperfection often remain unidentified. Here, we first quantify wing colour pattern differences in the forewing region of 14 co-mimetic colour pattern morphs of the butterfly species Heliconius erato and Heliconius melpomene and measure the extent to which mimicking colour pattern morphs are not perfectly identical. Next, using gene-editing CRISPR/Cas9 KO experiments of the gene WntA, which has been mapped to colour pattern diversity in these butterflies, we explore the exact areas of the wings in which WntA affects colour pattern formation differently in H. erato and H. melpomene. We find that, while the relative size of the forewing pattern is generally nearly identical between co-mimics, the CRISPR/Cas9 KO results highlight divergent boundaries in the wing that prevent the co-mimics from achieving perfect mimicry. We suggest that this mismatch may be explained by divergence in the gene regulatory network that defines wing colour patterning in both species, thus constraining morphological evolution even between closely related species.
Collapse
Affiliation(s)
| | - Paola A Alicea Roman
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico.,Department of Biology, University of Puerto Rico, Humacao, Puerto Rico
| | - Heriberto Carbia Gutierrez
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico.,Department of Mathematics, University of Puerto Rico, Rio Piedras, Puerto Rico
| | - Brian A Counterman
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Riccardo Papa
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico.,Smithsonian Tropical Research Institution, Panama, Republic of Panama.,Molecular Sciences and Research Center, University of Puerto Rico, Puerto Rico
| |
Collapse
|
49
|
de Vos JM, Augustijnen H, Bätscher L, Lucek K. Speciation through chromosomal fusion and fission in Lepidoptera. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190539. [PMID: 32654638 DOI: 10.1098/rstb.2019.0539] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Changes in chromosome numbers may strongly affect reproductive barriers, because individuals heterozygous for distinct karyotypes are typically expected to be at least partially sterile or to show reduced recombination. Therefore, several classic speciation models are based on chromosomal changes. One import mechanism generating variation in chromosome numbers is fusion and fission of existing chromosomes, which is particularly likely in species with holocentric chromosomes, i.e. chromosomes that lack a single centromere. Holocentric chromosomes evolved repeatedly across the tree of life, including in Lepidoptera. Although changes in chromosome numbers are hypothesized to be an important driver of the spectacular diversification of Lepidoptera, comparative studies across the order are lacking. We performed the first comprehensive literature survey of karyotypes for Lepidoptera species since the 1970s and tested if, and how, chromosomal variation might affect speciation. Even though a meta-analysis of karyological differences between closely related taxa did not reveal an effect on the degree of reproductive isolation, phylogenetic diversification rate analyses across the 16 best-covered genera indicated a strong, positive association of rates of chromosome number evolution and speciation. These findings suggest a macroevolutionary impact of varying chromosome numbers in Lepidoptera and likely apply to other taxonomic groups, especially to those with holocentric chromosomes. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
Collapse
Affiliation(s)
- Jurriaan M de Vos
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Hannah Augustijnen
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Livio Bätscher
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Kay Lucek
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| |
Collapse
|
50
|
Massardo D, VanKuren NW, Nallu S, Ramos RR, Ribeiro PG, Silva-Brandão KL, Brandão MM, Lion MB, Freitas AVL, Cardoso MZ, Kronforst MR. The roles of hybridization and habitat fragmentation in the evolution of Brazil's enigmatic longwing butterflies, Heliconius nattereri and H. hermathena. BMC Biol 2020; 18:84. [PMID: 32620168 PMCID: PMC7334841 DOI: 10.1186/s12915-020-00797-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 05/19/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Heliconius butterflies are widely distributed across the Neotropics and have evolved a stunning array of wing color patterns that mediate Müllerian mimicry and mating behavior. Their rapid radiation has been strongly influenced by hybridization, which has created new species and allowed sharing of color patterning alleles between mimetic species pairs. While these processes have frequently been observed in widespread species with contiguous distributions, many Heliconius species inhabit patchy or rare habitats that may strongly influence the origin and spread of species and color patterns. Here, we assess the effects of historical population fragmentation and unique biology on the origins, genetic health, and color pattern evolution of two rare and sparsely distributed Brazilian butterflies, Heliconius hermathena and Heliconius nattereri. RESULTS We assembled genomes and re-sequenced whole genomes of eight H. nattereri and 71 H. hermathena individuals. These species harbor little genetic diversity, skewed site frequency spectra, and high deleterious mutation loads consistent with recent population bottlenecks. Heliconius hermathena consists of discrete, strongly isolated populations that likely arose from a single population that dispersed after the last glacial maximum. Despite having a unique color pattern combination that suggested a hybrid origin, we found no genome-wide evidence that H. hermathena is a hybrid species. However, H. hermathena mimicry evolved via introgression, from co-mimetic Heliconius erato, of a small genomic region upstream of the color patterning gene cortex. CONCLUSIONS Heliconius hermathena and H. nattereri population fragmentation, potentially driven by historical climate change and recent deforestation, has significantly reduced the genetic health of these rare species. Our results contribute to a growing body of evidence that introgression of color patterning alleles between co-mimetic species appears to be a general feature of Heliconius evolution.
Collapse
Affiliation(s)
- Darli Massardo
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL, USA
| | - Nicholas W VanKuren
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL, USA.
| | - Sumitha Nallu
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL, USA
| | - Renato R Ramos
- Departamento de Biologia Animal e Museu de Zoologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Pedro G Ribeiro
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Karina L Silva-Brandão
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brazil
| | - Marcelo M Brandão
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Marília B Lion
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - André V L Freitas
- Departamento de Biologia Animal e Museu de Zoologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Márcio Z Cardoso
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Marcus R Kronforst
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL, USA.
| |
Collapse
|