1
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He AY, Danko CG. Dissection of core promoter syntax through single nucleotide resolution modeling of transcription initiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.583868. [PMID: 38559255 PMCID: PMC10979970 DOI: 10.1101/2024.03.13.583868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Our understanding of how the DNA sequences of cis-regulatory elements encode transcription initiation patterns remains limited. Here we introduce CLIPNET, a deep learning model trained on population-scale PRO-cap data that accurately predicts the position and quantity of transcription initiation with single nucleotide resolution from DNA sequence. Interpretation of CLIPNET revealed a complex regulatory syntax consisting of DNA-protein interactions in five major positions between -200 and +50 bp relative to the transcription start site, as well as more subtle positional preferences among different transcriptional activators. Transcriptional activator and core promoter motifs occupy different positions and play distinct roles in regulating initiation, with the former driving initiation quantity and the latter initiation position. We identified core promoter motifs that explain initiation patterns in the majority of promoters and enhancers, including DPR motifs and AT-rich TBP binding sequences in TATA-less promoters. Our results provide insights into the sequence architecture governing transcription initiation.
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Affiliation(s)
- Adam Y. He
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University
- Graduate Field of Computational Biology, Cornell University
| | - Charles G. Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University
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2
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Rossi M, Hausmann AE, Alcami P, Moest M, Roussou R, Van Belleghem SM, Wright DS, Kuo CY, Lozano-Urrego D, Maulana A, Melo-Flórez L, Rueda-Muñoz G, McMahon S, Linares M, Osman C, McMillan WO, Pardo-Diaz C, Salazar C, Merrill RM. Adaptive introgression of a visual preference gene. Science 2024; 383:1368-1373. [PMID: 38513020 DOI: 10.1126/science.adj9201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/30/2024] [Indexed: 03/23/2024]
Abstract
Visual preferences are important drivers of mate choice and sexual selection, but little is known of how they evolve at the genetic level. In this study, we took advantage of the diversity of bright warning patterns displayed by Heliconius butterflies, which are also used during mate choice. Combining behavioral, population genomic, and expression analyses, we show that two Heliconius species have evolved the same preferences for red patterns by exchanging genetic material through hybridization. Neural expression of regucalcin1 correlates with visual preference across populations, and disruption of regucalcin1 with CRISPR-Cas9 impairs courtship toward conspecific females, providing a direct link between gene and behavior. Our results support a role for hybridization during behavioral evolution and show how visually guided behaviors contributing to adaptation and speciation are encoded within the genome.
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Affiliation(s)
- Matteo Rossi
- Faculty of Biology, LMU, Munich, Germany
- Smithsonian Tropical Research Institute, Gamboa, Panama
| | | | | | - Markus Moest
- Department of Ecology and Research Department for Limnology, Mondsee, University of Innsbruck, Innsbruck, Austria
| | | | | | | | - Chi-Yun Kuo
- Faculty of Biology, LMU, Munich, Germany
- Smithsonian Tropical Research Institute, Gamboa, Panama
| | - Daniela Lozano-Urrego
- Faculty of Biology, LMU, Munich, Germany
- Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | | | - Lina Melo-Flórez
- Faculty of Biology, LMU, Munich, Germany
- Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Geraldine Rueda-Muñoz
- Faculty of Biology, LMU, Munich, Germany
- Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | | | - Mauricio Linares
- Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | | | | | | | - Camilo Salazar
- Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Richard M Merrill
- Faculty of Biology, LMU, Munich, Germany
- Smithsonian Tropical Research Institute, Gamboa, Panama
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3
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Orteu A, Kucka M, Gordon IJ, Ng’iru I, van der Heijden ESM, Talavera G, Warren IA, Collins S, ffrench-Constant RH, Martins DJ, Chan YF, Jiggins CD, Martin SH. Transposable Element Insertions Are Associated with Batesian Mimicry in the Pantropical Butterfly Hypolimnas misippus. Mol Biol Evol 2024; 41:msae041. [PMID: 38401262 PMCID: PMC10924252 DOI: 10.1093/molbev/msae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/26/2024] Open
Abstract
Hypolimnas misippus is a Batesian mimic of the toxic African Queen butterfly (Danaus chrysippus). Female H. misippus butterflies use two major wing patterning loci (M and A) to imitate three color morphs of D. chrysippus found in different regions of Africa. In this study, we examine the evolution of the M locus and identify it as an example of adaptive atavism. This phenomenon involves a morphological reversion to an ancestral character that results in an adaptive phenotype. We show that H. misippus has re-evolved an ancestral wing pattern present in other Hypolimnas species, repurposing it for Batesian mimicry of a D. chrysippus morph. Using haplotagging, a linked-read sequencing technology, and our new analytical tool, Wrath, we discover two large transposable element insertions located at the M locus and establish that these insertions are present in the dominant allele responsible for producing mimetic phenotype. By conducting a comparative analysis involving additional Hypolimnas species, we demonstrate that the dominant allele is derived. This suggests that, in the derived allele, the transposable elements disrupt a cis-regulatory element, leading to the reversion to an ancestral phenotype that is then utilized for Batesian mimicry of a distinct model, a different morph of D. chrysippus. Our findings present a compelling instance of convergent evolution and adaptive atavism, in which the same pattern element has independently evolved multiple times in Hypolimnas butterflies, repeatedly playing a role in Batesian mimicry of diverse model species.
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Affiliation(s)
- Anna Orteu
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Marek Kucka
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Ian J Gordon
- Centre of Excellence in Biodiversity, University of Rwanda, Huye, Rwanda
| | - Ivy Ng’iru
- Mpala Research Centre, Nanyuki 10400, Laikipia, Kenya
- School of Biosciences, Cardiff University, Cardiff CF 10 3AX, UK
- UK Centre for Ecology and Hydrology, Wallingford OX10 8BB, UK
| | - Eva S M van der Heijden
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, Barcelona, Catalonia, Spain
| | - Ian A Warren
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Steve Collins
- African Butterfly Research Institute, Nairobi, Kenya
| | | | - Dino J Martins
- Turkana Basin Institute, Stony Brook University, Stony Brook, NY 11794, USA
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Simon H Martin
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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4
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Teng D, Zhang W. The diversification of butterfly wing patterns: progress and prospects. CURRENT OPINION IN INSECT SCIENCE 2024; 61:101137. [PMID: 37922984 DOI: 10.1016/j.cois.2023.101137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023]
Abstract
Butterfly wings display rich phenotypic diversity and are associated with complex biological functions, thus serving as an important evolutionary system to address the genetic basis and evolution of phenotypic diversification. We review recent butterfly studies that revealed complex functions underlying diversified wing patterns and describe the genetic and environmental factors involved in wing pattern determinations. These factors lead to inter-specific divergence, genetic polymorphism, and phenotypic plasticity, which in many cases are decided by several key genes. We also summarize the research advances on gene co-option as an important origin of functional complexity and evolutionary novelty. These findings reveal a pattern of evolutionary innovation within a constrained developmental framework during butterfly wing morphogenesis, but further research is required to gain a systematic and comprehensive understanding.
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Affiliation(s)
- Dequn Teng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wei Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Medog Biodiversity Observation and Research Station of Tibet Autonomous Region, Nyingchi 860711, China.
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5
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Merrill RM, Arenas-Castro H, Feller AF, Harenčár J, Rossi M, Streisfeld MA, Kay KM. Genetics and the Evolution of Prezygotic Isolation. Cold Spring Harb Perspect Biol 2024; 16:a041439. [PMID: 37848246 PMCID: PMC10835618 DOI: 10.1101/cshperspect.a041439] [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: 10/19/2023]
Abstract
The significance of prezygotic isolation for speciation has been recognized at least since the Modern Synthesis. However, fundamental questions remain. For example, how are genetic associations between traits that contribute to prezygotic isolation maintained? What is the source of genetic variation underlying the evolution of these traits? And how do prezygotic barriers affect patterns of gene flow? We address these questions by reviewing genetic features shared across plants and animals that influence prezygotic isolation. Emerging technologies increasingly enable the identification and functional characterization of the genes involved, allowing us to test established theoretical expectations. Embedding these genes in their developmental context will allow further predictions about what constrains the evolution of prezygotic isolation. Ongoing improvements in statistical and computational tools will reveal how pre- and postzygotic isolation may differ in how they influence gene flow across the genome. Finally, we highlight opportunities for progress by combining theory with appropriate data.
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Affiliation(s)
- Richard M Merrill
- Faculty of Biology, Division of Evolutionary Biology, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Henry Arenas-Castro
- School of Biological Sciences, University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Anna F Feller
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Arnold Arboretum of Harvard University, Boston, Massachusetts 02131, USA
| | - Julia Harenčár
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - Matteo Rossi
- Faculty of Biology, Division of Evolutionary Biology, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Matthew A Streisfeld
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403-5289, USA
| | - Kathleen M Kay
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, California 95060, USA
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6
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Loffet EA, Durel JF, Nerurkar NL. Evo-Devo Mechanobiology: The Missing Link. Integr Comp Biol 2023; 63:1455-1473. [PMID: 37193661 DOI: 10.1093/icb/icad033] [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: 03/16/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/18/2023] Open
Abstract
While the modern framework of evolutionary development (evo-devo) has been decidedly genetic, historic analyses have also considered the importance of mechanics in the evolution of form. With the aid of recent technological advancements in both quantifying and perturbing changes in the molecular and mechanical effectors of organismal shape, how molecular and genetic cues regulate the biophysical aspects of morphogenesis is becoming increasingly well studied. As a result, this is an opportune time to consider how the tissue-scale mechanics that underlie morphogenesis are acted upon through evolution to establish morphological diversity. Such a focus will enable a field of evo-devo mechanobiology that will serve to better elucidate the opaque relations between genes and forms by articulating intermediary physical mechanisms. Here, we review how the evolution of shape is measured and related to genetics, how recent strides have been made in the dissection of developmental tissue mechanics, and how we expect these areas to coalesce in evo-devo studies in the future.
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Affiliation(s)
- Elise A Loffet
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
| | - John F Durel
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
| | - Nandan L Nerurkar
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
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7
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Yang W, Cui J, Chen Y, Wang C, Yin Y, Zhang W, Liu S, Sun C, Li H, Duan Y, Song F, Cai W, Hines HM, Tian L. Genetic Modification of a Hox Locus Drives Mimetic Color Pattern Variation in a Highly Polymorphic Bumble Bee. Mol Biol Evol 2023; 40:msad261. [PMID: 38039153 PMCID: PMC10724181 DOI: 10.1093/molbev/msad261] [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: 09/01/2023] [Revised: 11/11/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023] Open
Abstract
Müllerian mimicry provides natural replicates ideal for exploring mechanisms underlying adaptive phenotypic divergence and convergence, yet the genetic mechanisms underlying mimetic variation remain largely unknown. The current study investigates the genetic basis of mimetic color pattern variation in a highly polymorphic bumble bee, Bombus breviceps (Hymenoptera, Apidae). In South Asia, this species and multiple comimetic species converge onto local Müllerian mimicry patterns by shifting the abdominal setal color from orange to black. Genetic crossing between the orange and black phenotypes suggested the color dimorphism being controlled by a single Mendelian locus, with the orange allele being dominant over black. Genome-wide association suggests that a locus at the intergenic region between 2 abdominal fate-determining Hox genes, abd-A and Abd-B, is associated with the color change. This locus is therefore in the same intergenic region but not the same exact locus as found to drive red black midabdominal variation in a distantly related bumble bee species, Bombus melanopygus. Gene expression analysis and RNA interferences suggest that differential expression of an intergenic long noncoding RNA between abd-A and Abd-B at the onset setal color differentiation may drive the orange black color variation by causing a homeotic shift late in development. Analysis of this same color locus in comimetic species reveals no sequence association with the same color shift, suggesting that mimetic convergence is achieved through distinct genetic routes. Our study establishes Hox regions as genomic hotspots for color pattern evolution in bumble bees and demonstrates how pleiotropic developmental loci can drive adaptive radiations in nature.
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Affiliation(s)
- Wanhu Yang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Jixiang Cui
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yuxin Chen
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Chao Wang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yuanzhi Yin
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wei Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Shanlin Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Cheng Sun
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yuange Duan
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Heather M Hines
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Li Tian
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
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8
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Kratochwil CF, Mallarino R. Mechanisms Underlying the Formation and Evolution of Vertebrate Color Patterns. Annu Rev Genet 2023; 57:135-156. [PMID: 37487589 PMCID: PMC10805968 DOI: 10.1146/annurev-genet-031423-120918] [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: 07/26/2023]
Abstract
Vertebrates exhibit a wide range of color patterns, which play critical roles in mediating intra- and interspecific communication. Because of their diversity and visual accessibility, color patterns offer a unique and fascinating window into the processes underlying biological organization. In this review, we focus on describing many of the general principles governing the formation and evolution of color patterns in different vertebrate groups. We characterize the types of patterns, review the molecular and developmental mechanisms by which they originate, and discuss their role in constraining or facilitating evolutionary change. Lastly, we outline outstanding questions in the field and discuss different approaches that can be used to address them. Overall, we provide a unifying conceptual framework among vertebrate systems that may guide research into naturally evolved mechanisms underlying color pattern formation and evolution.
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Affiliation(s)
| | - Ricardo Mallarino
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA;
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9
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Murugesan SN, Monteiro A. Butterfly eyespots exhibit unique patterns of open chromatin. F1000Res 2023; 12:1428. [PMID: 38778811 PMCID: PMC11109672 DOI: 10.12688/f1000research.133789.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/02/2023] [Indexed: 05/25/2024] Open
Abstract
Background: How the precise spatial regulation of genes is correlated with spatial variation in chromatin accessibilities is not yet clear. Previous studies that analysed chromatin from homogenates of whole-body parts of insects found little variation in chromatin accessibility across those parts, but single-cell studies of Drosophila brains showed extensive spatial variation in chromatin accessibility across that organ. In this work we studied the chromatin accessibility of butterfly wing tissue fated to differentiate distinct colors and patterns in pupal wings of Bicyclus anynana. Methods: We dissected small eyespot and adjacent control tissues from 3h pupae and performed ATAC-Seq to identify the chromatin accessibility differences between different sections of the wings. Results: We observed that three dissected wing regions showed unique chromatin accessibilities. Open chromatin regions specific to eyespot color patterns were highly enriched for binding motifs recognized by Suppressor of Hairless (Su(H)), Krüppel (Kr), Buttonhead (Btd) and Nubbin (Nub) transcription factors. Genes in the vicinity of the eyespot-specific open chromatin regions included those involved in wound healing and SMAD signal transduction pathways, previously proposed to be involved in eyespot development. Conclusions: We conclude that eyespot and non-eyespot tissue samples taken from the same wing have distinct patterns of chromatin accessibility, possibly driven by the eyespot-restricted expression of potential pioneer factors, such as Kr.
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Affiliation(s)
| | - Antónia Monteiro
- Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
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10
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Yan H, Hu Z, Thomas GWC, Edwards SV, Sackton TB, Liu JS. PhyloAcc-GT: A Bayesian Method for Inferring Patterns of Substitution Rate Shifts on Targeted Lineages Accounting for Gene Tree Discordance. Mol Biol Evol 2023; 40:msad195. [PMID: 37665177 PMCID: PMC10540510 DOI: 10.1093/molbev/msad195] [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: 12/23/2022] [Revised: 08/15/2023] [Accepted: 09/01/2023] [Indexed: 09/05/2023] Open
Abstract
An important goal of evolutionary genomics is to identify genomic regions whose substitution rates differ among lineages. For example, genomic regions experiencing accelerated molecular evolution in some lineages may provide insight into links between genotype and phenotype. Several comparative genomics methods have been developed to identify genomic accelerations between species, including a Bayesian method called PhyloAcc, which models shifts in substitution rate in multiple target lineages on a phylogeny. However, few methods consider the possibility of discordance between the trees of individual loci and the species tree due to incomplete lineage sorting, which might cause false positives. Here, we present PhyloAcc-GT, which extends PhyloAcc by modeling gene tree heterogeneity. Given a species tree, we adopt the multispecies coalescent model as the prior distribution of gene trees, use Markov chain Monte Carlo (MCMC) for inference, and design novel MCMC moves to sample gene trees efficiently. Through extensive simulations, we show that PhyloAcc-GT outperforms PhyloAcc and other methods in identifying target lineage-specific accelerations and detecting complex patterns of rate shifts, and is robust to specification of population size parameters. PhyloAcc-GT is usually more conservative than PhyloAcc in calling convergent rate shifts because it identifies more accelerations on ancestral than on terminal branches. We apply PhyloAcc-GT to two examples of convergent evolution: flightlessness in ratites and marine mammal adaptations, and show that PhyloAcc-GT is a robust tool to identify shifts in substitution rate associated with specific target lineages while accounting for incomplete lineage sorting.
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Affiliation(s)
- Han Yan
- Department of Statistics, Harvard University, Cambridge, MA, USA
| | - Zhirui Hu
- Department of Statistics, Harvard University, Cambridge, MA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | | | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | - Jun S Liu
- Department of Statistics, Harvard University, Cambridge, MA, USA
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11
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Méndez-González ID, Williams TM, Rebeiz M. Changes in locus wide repression underlie the evolution of Drosophila abdominal pigmentation. PLoS Genet 2023; 19:e1010722. [PMID: 37134121 PMCID: PMC10184908 DOI: 10.1371/journal.pgen.1010722] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 05/15/2023] [Accepted: 03/28/2023] [Indexed: 05/04/2023] Open
Abstract
Changes in gene regulation represent an important path to generate developmental differences affecting anatomical traits. Interspecific divergence in gene expression often results from changes in transcription-stimulating enhancer elements. While gene repression is crucial for precise spatiotemporal expression patterns, the relative contribution of repressive transcriptional silencers to regulatory evolution remains to be addressed. Here, we show that the Drosophila pigmentation gene ebony has mainly evolved through changes in the spatial domains of silencers patterning its abdominal expression. By precisely editing the endogenous ebony locus of D. melanogaster, we demonstrate the requirement of two redundant abdominal enhancers and three silencers that repress the redundant enhancers in a patterned manner. We observe a role for changes in these silencers in every case of ebony evolution observed to date. Our findings suggest that negative regulation by silencers likely has an under-appreciated role in gene regulatory evolution.
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Affiliation(s)
- Iván D Méndez-González
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Thomas M Williams
- Department of Biology, University of Dayton, Dayton, Ohio, United States of America
| | - Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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12
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Tunström K, Woronik A, Hanly JJ, Rastas P, Chichvarkhin A, Warren AD, Kawahara AY, Schoville SD, Ficarrotta V, Porter AH, Watt WB, Martin A, Wheat CW. Evidence for a single, ancient origin of a genus-wide alternative life history strategy. SCIENCE ADVANCES 2023; 9:eabq3713. [PMID: 36947619 PMCID: PMC10032607 DOI: 10.1126/sciadv.abq3713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Understanding the evolutionary origins and factors maintaining alternative life history strategies (ALHS) within species is a major goal of evolutionary research. While alternative alleles causing discrete ALHS are expected to purge or fix over time, one-third of the ~90 species of Colias butterflies are polymorphic for a female-limited ALHS called Alba. Whether Alba arose once, evolved in parallel, or has been exchanged among taxa is currently unknown. Using comparative genome-wide association study (GWAS) and population genomic analyses, we placed the genetic basis of Alba in time-calibrated phylogenomic framework, revealing that Alba evolved once near the base of the genus and has been subsequently maintained via introgression and balancing selection. CRISPR-Cas9 mutagenesis was then used to verify a putative cis-regulatory region of Alba, which we identified using phylogenetic foot printing. We hypothesize that this cis-regulatory region acts as a modular enhancer for the induction of the Alba ALHS, which has likely facilitated its long evolutionary persistence.
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Affiliation(s)
- Kalle Tunström
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Alyssa Woronik
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Department of Biology, Sacred Heart University, Fairfield, CT, USA
| | - Joseph J. Hanly
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Anton Chichvarkhin
- National Scientific Center of Marine Biology, Far Eastern Branch of Russian Academy of Sciences, Palchevskogo 17, Vladivostok 690022, Russia
| | - Andrew D. Warren
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Akito Y. Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Sean D. Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
| | - Vincent Ficarrotta
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Adam H. Porter
- Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Ward B. Watt
- Department of Biology, University of South Carolina, Columbia, SC 29208, USA
- Rocky Mountain Biological Laboratory, Crested Butte, CO 81224, USA
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
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13
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Van Belleghem SM, Ruggieri AA, Concha C, Livraghi L, Hebberecht L, Rivera ES, Ogilvie JG, Hanly JJ, Warren IA, Planas S, Ortiz-Ruiz Y, Reed R, Lewis JJ, Jiggins CD, Counterman BA, McMillan WO, Papa R. High level of novelty under the hood of convergent evolution. Science 2023; 379:1043-1049. [PMID: 36893249 PMCID: PMC11000492 DOI: 10.1126/science.ade0004] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 02/08/2023] [Indexed: 03/11/2023]
Abstract
Little is known about the extent to which species use homologous regulatory architectures to achieve phenotypic convergence. By characterizing chromatin accessibility and gene expression in developing wing tissues, we compared the regulatory architecture of convergence between a pair of mimetic butterfly species. Although a handful of color pattern genes are known to be involved in their convergence, our data suggest that different mutational paths underlie the integration of these genes into wing pattern development. This is supported by a large fraction of accessible chromatin being exclusive to each species, including the de novo lineage-specific evolution of a modular optix enhancer. These findings may be explained by a high level of developmental drift and evolutionary contingency that occurs during the independent evolution of mimicry.
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Affiliation(s)
- Steven M. Van Belleghem
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico
- Ecology, Evolution and Conservation Biology, Biology Department, KU Leuven, Leuven, Belgium
| | - Angelo A. Ruggieri
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico
| | - Carolina Concha
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
| | - Luca Livraghi
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Laura Hebberecht
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- School of Biological Sciences, Bristol University, Bristol, UK
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Edgardo Santiago Rivera
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Department of Biomaterials, Universität Bayreuth, Bayreuth, Germany
| | - James G. Ogilvie
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Joseph J. Hanly
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Ian A. Warren
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Silvia Planas
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Yadira Ortiz-Ruiz
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Robert Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - James J. Lewis
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
| | | | | | - W. Owen McMillan
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
| | - Riccardo Papa
- Department of Biology, University of Puerto Rico, Rio Piedras, Puerto Rico
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan, Puerto Rico
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, Puerto Rico
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14
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Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. Mol Ecol 2023; 32:1441-1457. [PMID: 36433653 PMCID: PMC10946714 DOI: 10.1111/mec.16793] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 11/27/2022]
Abstract
The term "haplotype block" is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a "hard" selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies.
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Affiliation(s)
- Daria Shipilina
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala, Sweden
- Institute of Science and Technology Austria, Klosterneuburg, Austria
- Swedish Collegium for Advanced Study, Uppsala, Sweden
| | - Arka Pal
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Sean Stankowski
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | | | - Nicholas H Barton
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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15
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Murugesan SN, Monteiro A. Evolution of modular and pleiotropic enhancers. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:105-115. [PMID: 35334158 DOI: 10.1002/jez.b.23131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 01/14/2022] [Accepted: 02/28/2022] [Indexed: 11/05/2022]
Abstract
Cis-regulatory elements (CREs), or enhancers, are segments of noncoding DNA that regulate the spatial and temporal expression of nearby genes. Sometimes, genes are expressed in more than one tissue, and this can be driven by two main types of CREs: tissue-specific "modular" CREs, where different CREs drive expression of the gene in the different tissues, or by "pleiotropic" CREs, where the same CRE drives expression in the different tissues. In this perspective, we will discuss some of the ways (i) modular and pleiotropic CREs might originate; (ii) propose that modular CREs might derive from pleiotropic CREs via a process of duplication, degeneration, and complementation (the CRE-DDC model); and (iii) propose that hotspot loci of evolution are associated with the origin of modular CREs belonging to any gene in a regulatory network.
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Affiliation(s)
- Suriya N Murugesan
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Antónia Monteiro
- Department of Biological Sciences, National University of Singapore, Singapore.,Division of Science, Yale-NUS College, Singapore
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16
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Can changes in 3D genome architecture create new regulatory landscapes that contribute to phenotypic evolution? Essays Biochem 2022; 66:745-752. [PMID: 36250960 DOI: 10.1042/ebc20220057] [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: 07/27/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 12/13/2022]
Abstract
Animal genomes are compartmentalized into insulated regulatory units named topology-associated domains (TADs). TADs insulate gene promoters from enhancers that occupy neighboring TADs. Chromosomal rearrangements that disrupt TAD structure can generate new regulatory interactions between enhancers and promoters that were once separated into different TADs, which might lead to new gene expression patterns. On the one hand, TAD rearrangements are known to cause deleterious phenotypes, but, on the other hand, rearrangements can also create novel expression patterns that may be selected during evolution because they generate advantageous phenotypes. Here, we review recent studies that explore the effects of chromosomal rearrangements and genetic perturbations on TAD structure and gene regulation in the context of development and evolution. We discuss the possible contribution of evolutionary breakpoints (EBRs) that affect TAD structure to the evolution of gene regulation and the phenotype.
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17
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Functional genomic tools for emerging model species. Trends Ecol Evol 2022; 37:1104-1115. [PMID: 35914975 DOI: 10.1016/j.tree.2022.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 01/12/2023]
Abstract
Most studies in the field of ecology and evolution aiming to connect genotype to phenotype rarely validate identified loci using functional tools. Recent developments in RNA interference (RNAi) and clustered regularly interspaced palindromic repeats (CRISPR)-Cas genome editing have dramatically increased the feasibility of functional validation. However, these methods come with specific challenges when applied to emerging model organisms, including limited spatial control of gene silencing, low knock-in efficiencies, and low throughput of functional validation. Moreover, many functional studies to date do not recapitulate ecologically relevant variation, and this limits their scope for deeper insights into evolutionary processes. We therefore argue that increased use of gene editing by allelic replacement through homology-directed repair (HDR) would greatly benefit the field of ecology and evolution.
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18
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Chan WP, Rabideau Childers R, Ashe S, Tsai CC, Elson C, Keleher KJ, Sipe RLH, Maier CA, Sourakov A, Gall LF, Bernard GD, Soucy ER, Yu N, Pierce NE. A high-throughput multispectral imaging system for museum specimens. Commun Biol 2022; 5:1318. [PMID: 36456867 PMCID: PMC9715708 DOI: 10.1038/s42003-022-04282-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/18/2022] [Indexed: 12/05/2022] Open
Abstract
We present an economical imaging system with integrated hardware and software to capture multispectral images of Lepidoptera with high efficiency. This method facilitates the comparison of colors and shapes among species at fine and broad taxonomic scales and may be adapted for other insect orders with greater three-dimensionality. Our system can image both the dorsal and ventral sides of pinned specimens. Together with our processing pipeline, the descriptive data can be used to systematically investigate multispectral colors and shapes based on full-wing reconstruction and a universally applicable ground plan that objectively quantifies wing patterns for species with different wing shapes (including tails) and venation systems. Basic morphological measurements, such as body length, thorax width, and antenna size are automatically generated. This system can increase exponentially the amount and quality of trait data extracted from museum specimens.
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Affiliation(s)
- Wei-Ping Chan
- grid.38142.3c000000041936754XDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA ,grid.38142.3c000000041936754XMuseum of Comparative Zoology, Harvard University, Cambridge, MA USA
| | - Richard Rabideau Childers
- grid.38142.3c000000041936754XDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA ,grid.38142.3c000000041936754XMuseum of Comparative Zoology, Harvard University, Cambridge, MA USA
| | - Sorcha Ashe
- grid.38142.3c000000041936754XDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Cheng-Chia Tsai
- grid.21729.3f0000000419368729Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY USA
| | - Caroline Elson
- grid.38142.3c000000041936754XDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Kirsten J. Keleher
- grid.40803.3f0000 0001 2173 6074Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC USA ,grid.5386.8000000041936877XDepartment of Neurobiology and Behavior, Cornell University, Ithaca, NY USA
| | - Rachel L. Hawkins Sipe
- grid.38142.3c000000041936754XMuseum of Comparative Zoology, Harvard University, Cambridge, MA USA
| | - Crystal A. Maier
- grid.38142.3c000000041936754XMuseum of Comparative Zoology, Harvard University, Cambridge, MA USA
| | - Andrei Sourakov
- grid.15276.370000 0004 1936 8091McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL USA
| | - Lawrence F. Gall
- grid.47100.320000000419368710Computer Systems Office & Division of Entomology, Peabody Museum of Natural History, Yale University, New Haven, CT USA
| | - Gary D. Bernard
- grid.34477.330000000122986657Department of Electrical and Computer Engineering, University of Washington, Seattle, WA USA
| | - Edward R. Soucy
- grid.38142.3c000000041936754XCenter for Brain Science, Harvard University, Cambridge, MA USA
| | - Nanfang Yu
- grid.21729.3f0000000419368729Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY USA
| | - Naomi E. Pierce
- grid.38142.3c000000041936754XDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA ,grid.38142.3c000000041936754XMuseum of Comparative Zoology, Harvard University, Cambridge, MA USA
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19
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Espeland M, Podsiadlowski L. How butterfly wings got their pattern. Science 2022; 378:249-250. [PMID: 36264812 DOI: 10.1126/science.ade5689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Gene regulatory elements play a crucial role in the pattern formation of butterfly wings.
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Affiliation(s)
- Marianne Espeland
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
| | - Lars Podsiadlowski
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany
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20
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Mazo-Vargas A, Langmüller AM, Wilder A, van der Burg KRL, Lewis JJ, Messer PW, Zhang L, Martin A, Reed RD. Deep cis-regulatory homology of the butterfly wing pattern ground plan. Science 2022; 378:304-308. [PMID: 36264807 DOI: 10.1126/science.abi9407] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Butterfly wing patterns derive from a deeply conserved developmental ground plan yet are diverse and evolve rapidly. It is poorly understood how gene regulatory architectures can accommodate both deep homology and adaptive change. To address this, we characterized the cis-regulatory evolution of the color pattern gene WntA in nymphalid butterflies. Comparative assay for transposase-accessible chromatin using sequencing (ATAC-seq) and in vivo deletions spanning 46 cis-regulatory elements across five species revealed deep homology of ground plan-determining sequences, except in monarch butterflies. Furthermore, noncoding deletions displayed both positive and negative regulatory effects that were often broad in nature. Our results provide little support for models predicting rapid enhancer turnover and suggest that deeply ancestral, multifunctional noncoding elements can underlie rapidly evolving trait systems.
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Affiliation(s)
- Anyi Mazo-Vargas
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.,Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Anna M Langmüller
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Alexis Wilder
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | | | - James J Lewis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.,Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Philipp W Messer
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Linlin Zhang
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.,CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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21
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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.
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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
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22
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Wan WT, Hu P, Chang Z, Ren YD, Dong ZW, Yang J, Pan XY, He JW, Liu W, Liu GC, Zhao RP, Mao CY, Li J, Wang W, Li XY. Genome-wide survey of open chromatin regions in two swallowtail butterflies Papilio machaon and P. bianor. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2022; 111:e21952. [PMID: 35909310 DOI: 10.1002/arch.21952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/20/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Papilio machaon was assigned as the type species for all butterflies by Linnaeus and P. bianor is a congener but exhibits a great difference in morphology (especially larva and adult color pattern) and larval host plants from P. machaon. Thus, they are the ideal models to investigate genetic mechanisms underlying morphology and plasticity between congeners. The reference genomes of both species were dissected in our previous studies, but little is known about their regulatory genome and the epigenetic regulation of gene expression throughout developmental stages. Here, we profiled the chromatin accessibility and gene expression of three developmental stages (the 4th instar larva [L4], the 5th instar larva [L5], and pupa [P]) using transposase accessible chromatin sequencing (ATAC-seq) and RNA-seq. Results showed that many accessible chromatin peaks were identified at three developmental stages (peak number, P. machaon: 44,977 [L4], 36,919 [L5], 47,147 [P]; P. bianor: 20,341 [L4], 44,668 [L5], 62,249 [P]). Moreover, the number of differentially accessible peaks and differentially expressed genes between larval stages of each butterfly species are significantly fewer than that between larval and pupal stages, suggesting a higher similarity within larvae and a significant difference between larvae and pupae. This study added the annotated information of chromatin accessibility genome-wide of the two papilionid species and will promote the investigation of gene regulation in butterfly evolution.
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Affiliation(s)
- Wen-Ting Wan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Ping Hu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhou Chang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yan-Dong Ren
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Zhi-Wei Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jie Yang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Xiang-Yu Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Jin-Wu He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Wei Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Gui-Chun Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ruo-Ping Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chu-Yang Mao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jun Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi, China
- Center for Excellence in Animal Evolution and Genetics, Kunming, Yunnan, China
| | - Xue-Yan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
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23
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Abstract
The rediscovery of Mendel’s work showing that the heredity of phenotypes is controlled by discrete genes was followed by the reconciliation of Mendelian genetics with evolution by natural selection in the middle of the last century with the Modern Synthesis. In the past two decades, dramatic advances in genomic methods have facilitated the identification of the loci, genes, and even individual mutations that underlie phenotypic variants that are the putative targets of natural selection. Moreover, these methods have also changed how we can study adaptation by flipping the problem around, allowing us to first examine what loci show evidence of having been under selection, and then connecting these genetic variants to phenotypic variation. As a result, we now have an expanding list of actual genetic changes that underlie potentially adaptive phenotypic variation. Here, we synthesize how considering the effects of these adaptive loci in the context of cellular environments, genomes, organisms, and populations has provided new insights to the genetic architecture of adaptation.
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24
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An enhancer of Agouti contributes to parallel evolution of cryptically colored beach mice. Proc Natl Acad Sci U S A 2022; 119:e2202862119. [PMID: 35776547 PMCID: PMC9271204 DOI: 10.1073/pnas.2202862119] [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] [Indexed: 12/24/2022] Open
Abstract
Identifying the genetic basis of repeatedly evolved traits provides a way to reconstruct their evolutionary history and ultimately investigate the predictability of evolution. Here, we focus on the oldfield mouse (Peromyscus polionotus), which occurs in the southeastern United States, where it exhibits considerable color variation. Dorsal coats range from dark brown in mainland mice to near white in mice inhabiting sandy beaches; this light pelage has evolved independently on Florida's Gulf and Atlantic coasts as camouflage from predators. To facilitate genomic analyses, we first generated a chromosome-level genome assembly of Peromyscus polionotus subgriseus. Next, in a uniquely variable mainland population (Peromyscus polionotus albifrons), we scored 23 pigment traits and performed targeted resequencing in 168 mice. We find that pigment variation is strongly associated with an ∼2-kb region ∼5 kb upstream of the Agouti signaling protein coding region. Using a reporter-gene assay, we demonstrate that this regulatory region contains an enhancer that drives expression in the dermis of mouse embryos during the establishment of pigment prepatterns. Moreover, extended tracts of homozygosity in this Agouti region indicate that the light allele experienced recent and strong positive selection. Notably, this same light allele appears fixed in both Gulf and Atlantic coast beach mice, despite these populations being separated by >1,000 km. Together, our results suggest that this identified Agouti enhancer allele has been maintained in mainland populations as standing genetic variation and from there, has spread to and been selected in two independent beach mouse lineages, thereby facilitating their rapid and parallel evolution.
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25
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Kennerley JA, Somveille M, Hauber ME, Richardson NM, Manica A, Feeney WE. The overlooked complexity of avian brood parasite-host relationships. Ecol Lett 2022; 25:1889-1904. [PMID: 35763605 PMCID: PMC9543277 DOI: 10.1111/ele.14062] [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: 11/29/2021] [Revised: 05/13/2022] [Accepted: 05/28/2022] [Indexed: 11/27/2022]
Abstract
The relationships between avian brood parasites and their hosts are widely recognised as model systems for studying coevolution. However, while most brood parasites are known to parasitise multiple species of host and hosts are often subject to parasitism by multiple brood parasite species, the examination of multispecies interactions remains rare. Here, we compile data on all known brood parasite-host relationships and find that complex brood parasite-host systems, where multiple species of brood parasites and hosts coexist and interact, are globally commonplace. By examining patterns of past research, we outline the disparity between patterns of network complexity and past research emphases and discuss factors that may be associated with these patterns. Drawing on insights gained from other systems that have embraced a multispecies framework, we highlight the potential benefits of considering brood parasite-host interactions as ecological networks and brood parasitism as a model system for studying multispecies interactions. Overall, our results provide new insights into the diversity of these relationships, highlight the stark mismatch between past research efforts and global patterns of network complexity, and draw attention to the opportunities that more complex arrangements offer for examining how species interactions shape global patterns of biodiversity.
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Affiliation(s)
| | - Marius Somveille
- Centre for Biodiversity and Environment Research, University College London, London, UK
| | - Mark E Hauber
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | | | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - William E Feeney
- Department of Biosciences, Durham University, Durham, UK.,Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Starnberg, Germany
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26
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Laiker I, Frankel N. Pleiotropic enhancers are ubiquitous regulatory elements in the human genome. Genome Biol Evol 2022; 14:6585219. [PMID: 35552697 PMCID: PMC9156028 DOI: 10.1093/gbe/evac071] [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] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
Enhancers are regulatory elements of genomes that determine spatio-temporal patterns of gene expression. The human genome contains a vast number of enhancers, which largely outnumber protein-coding genes. Historically, enhancers have been regarded as highly tissue-specific. However, recent evidence has demonstrated that many enhancers are pleiotropic, with activity in multiple developmental contexts. Yet, the extent and impact of pleiotropy remain largely unexplored. In this study we analyzed active enhancers across human organs based on the analysis of both eRNA transcription (FANTOM5 consortium data sets) and chromatin architecture (ENCODE consortium data sets). We show that pleiotropic enhancers are pervasive in the human genome and that most enhancers active in a particular organ are also active in other organs. In addition, our analysis suggests that the proportion of context-specific enhancers of a given organ is explained, at least in part, by the proportion of context-specific genes in that same organ. The notion that such a high proportion of human enhancers can be pleiotropic suggests that small regions of regulatory DNA contain abundant regulatory information and that these regions evolve under important evolutionary constraints.
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Affiliation(s)
- Ian Laiker
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) y Universidad de Buenos Aires (UBA), Buenos Aires 1428, Argentina
| | - Nicolas Frankel
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) y Universidad de Buenos Aires (UBA), Buenos Aires 1428, Argentina.,Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires (UBA), Buenos Aires 1428, Argentina
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27
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McDonald JMC, Reed RD. Patterns of selection across gene regulatory networks. Semin Cell Dev Biol 2022; 145:60-67. [PMID: 35474149 DOI: 10.1016/j.semcdb.2022.03.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 01/31/2022] [Accepted: 03/23/2022] [Indexed: 12/29/2022]
Abstract
Gene regulatory networks (GRNs) are the core engine of organismal development. If we would like to understand the origin and diversification of phenotypes, it is necessary to consider the structure of GRNs in order to reconstruct the links between genetic mutations and phenotypic change. Much of the progress in evolutionary developmental biology, however, has occurred without a nuanced consideration of the evolution of functional relationships between genes, especially in the context of their broader network interactions. Characterizing and comparing GRNs across traits and species in a more detailed way will allow us to determine how network position influences what genes drive adaptive evolution. In this perspective paper, we consider the architecture of developmental GRNs and how positive selection strength may vary across a GRN. We then propose several testable models for these patterns of selection and experimental approaches to test these models.
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Affiliation(s)
- Jeanne M C McDonald
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States.
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States.
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28
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Hanly JJ, Livraghi L, Heryanto C, McMillan WO, Jiggins CD, Gilbert LE, Martin A. A large deletion at the cortex locus eliminates butterfly wing patterning. G3 GENES|GENOMES|GENETICS 2022; 12:6517782. [PMID: 35099556 PMCID: PMC8982378 DOI: 10.1093/g3journal/jkac021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 01/21/2022] [Indexed: 11/21/2022]
Abstract
As the genetic basis of natural and domesticated variation has been described in recent years, a number of hotspot genes have been repeatedly identified as the targets of selection, Heliconius butterflies display a spectacular diversity of pattern variants in the wild and the genetic basis of these patterns has been well-described. Here, we sought to identify the mechanism behind an unusual pattern variant that is instead found in captivity, the ivory mutant, in which all scales on both the wings and body become white or yellow. Using a combination of autozygosity mapping and coverage analysis from 37 captive individuals, we identify a 78-kb deletion at the cortex wing patterning locus, a gene which has been associated with wing pattern evolution in H. melpomene and 10 divergent lepidopteran species. This deletion is undetected among 458 wild Heliconius genomes samples, and its dosage explains both homozygous and heterozygous ivory phenotypes found in captivity. The deletion spans a large 5′ region of the cortex gene that includes a facultative 5′UTR exon detected in larval wing disk transcriptomes. CRISPR mutagenesis of this exon replicates the wing phenotypes from coding knock-outs of cortex, consistent with a functional role of ivory-deleted elements in establishing scale color fate. Population demographics reveal that the stock giving rise to the ivory mutant has a mixed origin from across the wild range of H. melpomene, and supports a scenario where the ivory mutation occurred after the introduction of cortex haplotypes from Ecuador. Homozygotes for the ivory deletion are inviable while heterozygotes are the targets of artificial selection, joining 40 other examples of allelic variants that provide heterozygous advantage in animal populations under artificial selection by fanciers and breeders. Finally, our results highlight the promise of autozygosity and association mapping for identifying the genetic basis of aberrant mutations in captive insect populations.
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Affiliation(s)
- Joseph J Hanly
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
- Smithsonian Tropical Research Institute, Panama 0843-03092, Republic of Panama
| | - Luca Livraghi
- Smithsonian Tropical Research Institute, Panama 0843-03092, Republic of Panama
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Christa Heryanto
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Panama 0843-03092, Republic of Panama
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Lawrence E Gilbert
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
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29
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Butterfly eyespots evolved via cooption of an ancestral gene-regulatory network that also patterns antennae, legs, and wings. Proc Natl Acad Sci U S A 2022; 119:2108661119. [PMID: 35169073 PMCID: PMC8872758 DOI: 10.1073/pnas.2108661119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2022] [Indexed: 12/13/2022] Open
Abstract
Where do butterfly eyespots come from? One of the long-standing questions in the field of evolution concerns addressing where novel complex traits come from. Here we show that butterfly eyespots, a novel complex trait, likely originated from the redeployment of a preexisting gene-regulatory network regulating antennae, legs, and wings, to novel locations on the wing. Butterfly eyespots are beautiful novel traits with an unknown developmental origin. Here we show that eyespots likely originated via cooption of parts of an ancestral appendage gene-regulatory network (GRN) to novel locations on the wing. Using comparative transcriptome analysis, we show that eyespots cluster most closely with antennae, relative to multiple other tissues. Furthermore, three genes essential for eyespot development, Distal-less (Dll), spalt (sal), and Antennapedia (Antp), share similar regulatory connections as those observed in the antennal GRN. CRISPR knockout of cis-regulatory elements (CREs) for Dll and sal led to the loss of eyespots, antennae, legs, and also wings, demonstrating that these CREs are highly pleiotropic. We conclude that eyespots likely reused an ancient GRN for their development, a network also previously implicated in the development of antennae, legs, and wings.
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30
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Abstract
Epigenetic mechanisms such as DNA methylation, histone modifications and non-coding RNAs are increasingly targeted in studies of natural populations. Here, I review some of the insights gained from this research, examine some of the methods currently in use and discuss some of the challenges that researchers working on natural populations are likely to face when probing epigenetic mechanisms. While studies supporting the involvement of epigenetic mechanisms in generating phenotypic variation in natural populations are amassing, many of these studies are currently correlative in nature. Thus, while empirical data point to widespread contributions of epigenetic mechanisms in generating phenotypic variation, there are still concerns as to whether epigenetic variation is instead ultimately controlled by genetic variation. Disentangling these two sources of variation will be a key to resolving the debate about the importance of epigenetic mechanisms, and studies on natural populations that partition the relative contribution of genetic and epigenetic factors to phenotypic variation can play an important role in this debate.
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Affiliation(s)
- Arild Husby
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden.,Centre for Biodiversity Dynamics, Norwegian University for Science and Technology, Trondheim, Norway
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31
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Schmitz RJ, Grotewold E, Stam M. Cis-regulatory sequences in plants: Their importance, discovery, and future challenges. THE PLANT CELL 2022; 34:718-741. [PMID: 34918159 PMCID: PMC8824567 DOI: 10.1093/plcell/koab281] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/20/2021] [Indexed: 05/19/2023]
Abstract
The identification and characterization of cis-regulatory DNA sequences and how they function to coordinate responses to developmental and environmental cues is of paramount importance to plant biology. Key to these regulatory processes are cis-regulatory modules (CRMs), which include enhancers and silencers. Despite the extraordinary advances in high-quality sequence assemblies and genome annotations, the identification and understanding of CRMs, and how they regulate gene expression, lag significantly behind. This is especially true for their distinguishing characteristics and activity states. Here, we review the current knowledge on CRMs and breakthrough technologies enabling identification, characterization, and validation of CRMs; we compare the genomic distributions of CRMs with respect to their target genes between different plant species, and discuss the role of transposable elements harboring CRMs in the evolution of gene expression. This is an exciting time to study cis-regulomes in plants; however, significant existing challenges need to be overcome to fully understand and appreciate the role of CRMs in plant biology and in crop improvement.
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Affiliation(s)
- Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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32
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Common Themes and Future Challenges in Understanding Gene Regulatory Network Evolution. Cells 2022; 11:cells11030510. [PMID: 35159319 PMCID: PMC8834487 DOI: 10.3390/cells11030510] [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] [Received: 12/23/2021] [Revised: 01/26/2022] [Accepted: 01/29/2022] [Indexed: 12/18/2022] Open
Abstract
A major driving force behind the evolution of species-specific traits and novel structures is alterations in gene regulatory networks (GRNs). Comprehending evolution therefore requires an understanding of the nature of changes in GRN structure and the responsible mechanisms. Here, we review two insect pigmentation GRNs in order to examine common themes in GRN evolution and to reveal some of the challenges associated with investigating changes in GRNs across different evolutionary distances at the molecular level. The pigmentation GRN in Drosophila melanogaster and other drosophilids is a well-defined network for which studies from closely related species illuminate the different ways co-option of regulators can occur. The pigmentation GRN for butterflies of the Heliconius species group is less fully detailed but it is emerging as a useful model for exploring important questions about redundancy and modularity in cis-regulatory systems. Both GRNs serve to highlight the ways in which redeployment of trans-acting factors can lead to GRN rewiring and network co-option. To gain insight into GRN evolution, we discuss the importance of defining GRN architecture at multiple levels both within and between species and of utilizing a range of complementary approaches.
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33
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Rennison DJ, Peichel CL. Pleiotropy facilitates parallel adaptation in sticklebacks. Mol Ecol 2022; 31:1476-1486. [PMID: 34997980 PMCID: PMC9306781 DOI: 10.1111/mec.16335] [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: 06/14/2021] [Revised: 10/27/2021] [Accepted: 12/20/2021] [Indexed: 11/27/2022]
Abstract
Highly pleiotropic genes are predicted to be used less often during adaptation, as mutations in these loci are more likely to have negative fitness consequences. Following this logic, we tested whether pleiotropy impacts the probability that a locus will be used repeatedly in adaptation. We used two proxies to estimate pleiotropy: number of phenotypic traits affected by a given genomic region and gene connectivity. We first surveyed 16 independent stream‐lake and three independent benthic‐limnetic ecotype pairs of threespine stickleback to estimate genome‐wide patterns in parallel genomic differentiation. Our analysis revealed parallel divergence across the genome; 30%–37% of outlier regions were shared between at least two independent pairs in either the stream‐lake or benthic‐limnetic comparisons. We then tested whether parallel genomic regions are less pleiotropic than nonparallel regions. Counter to our a priori prediction, parallel genomic regions contained genes with significantly more pleiotropy; that is, influencing a greater number of traits and more highly connected. The increased pleiotropy of parallel regions could not be explained by other genomic factors, as there was no significant difference in mean gene count, mutation or recombination rates between parallel and nonparallel regions. Interestingly, although nonparallel regions contained genes that were less connected and influenced fewer mapped traits on average than parallel regions, they also tended to contain the genes that were predicted to be the most pleiotropic. Taken together, our findings are consistent with the idea that pleiotropy only becomes constraining at high levels and that low or intermediate levels of pleiotropy may be beneficial for adaptation.
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Affiliation(s)
- Diana J Rennison
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland
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34
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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: 35] [Impact Index Per Article: 11.7] [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.
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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
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35
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O'Connor TK, Sandoval MC, Wang J, Hans JC, Takenaka R, Child M, Whiteman NK. Ecological basis and genetic architecture of crypsis polymorphism in the desert clicker grasshopper (Ligurotettix coquilletti). Evolution 2021; 75:2441-2459. [PMID: 34370317 DOI: 10.1111/evo.14321] [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: 04/30/2021] [Revised: 07/09/2021] [Accepted: 07/20/2021] [Indexed: 11/28/2022]
Abstract
Color polymorphic species can offer exceptional insight into the ecology and genetics of adaptation. Although the genetic architecture of animal coloration is diverse, many color polymorphisms are associated with large structural variants and maintained by biotic interactions. Grasshoppers are notably polymorphic in both color and karyotype, which makes them excellent models for understanding the ecological drivers and genetic underpinnings of color variation. Banded and uniform morphs of the desert clicker grasshopper (Ligurotettix coquilletti) are found across the western deserts of North America. To address the hypothesis that predation maintains local color polymorphism and shapes regional crypsis variation, we surveyed morph frequencies and tested for covariation with two predation environments. Morphs coexisted at intermediate frequencies at most sites, consistent with local balancing selection. Morph frequencies covaried with the appearance of desert substrate-an environment used only by females-suggesting that ground-foraging predators are major agents of selection on crypsis. We next addressed the hypothesized link between morph variation and genome structure. To do so, we designed an approach for detecting inversions and indels using only RADseq data. The banded morph was perfectly correlated with a large putative indel. Remarkably, indel dominance differed among populations, a rare example of dominance evolution in nature.
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Affiliation(s)
- Timothy K O'Connor
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, 94720.,Current Address: Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, 60637
| | - Marissa C Sandoval
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, 94720
| | - Jiarui Wang
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, 94720
| | - Jacob C Hans
- Department of Entomology, University of California, Riverside, Riverside, California, 92521
| | - Risa Takenaka
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, 98195.,Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109
| | - Myron Child
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, 84112
| | - Noah K Whiteman
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, 94720
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36
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Livraghi L, Hanly JJ, Van Bellghem SM, Montejo-Kovacevich G, van der Heijden ESM, Loh LS, Ren A, Warren IA, Lewis JJ, Concha C, Hebberecht L, Wright CJ, Walker JM, Foley J, Goldberg ZH, Arenas-Castro H, Salazar C, Perry MW, Papa R, Martin A, McMillan WO, Jiggins CD. Cortex cis-regulatory switches establish scale colour identity and pattern diversity in Heliconius. eLife 2021; 10:e68549. [PMID: 34280087 PMCID: PMC8289415 DOI: 10.7554/elife.68549] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/14/2021] [Indexed: 12/14/2022] Open
Abstract
In Heliconius butterflies, wing colour pattern diversity and scale types are controlled by a few genes of large effect that regulate colour pattern switches between morphs and species across a large mimetic radiation. One of these genes, cortex, has been repeatedly associated with colour pattern evolution in butterflies. Here we carried out CRISPR knockouts in multiple Heliconius species and show that cortex is a major determinant of scale cell identity. Chromatin accessibility profiling and introgression scans identified cis-regulatory regions associated with discrete phenotypic switches. CRISPR perturbation of these regions in black hindwing genotypes recreated a yellow bar, revealing their spatially limited activity. In the H. melpomene/timareta lineage, the candidate CRE from yellow-barred phenotype morphs is interrupted by a transposable element, suggesting that cis-regulatory structural variation underlies these mimetic adaptations. Our work shows that cortex functionally controls scale colour fate and that its cis-regulatory regions control a phenotypic switch in a modular and pattern-specific fashion.
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Affiliation(s)
- Luca Livraghi
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
| | - Joseph J Hanly
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
- The George Washington University Department of Biological Sciences, Science and Engineering HallWashingtonUnited States
| | - Steven M Van Bellghem
- Department of Biology, Centre for Applied Tropical Ecology and Conservation, University of Puerto RicoRio PiedrasPuerto Rico
| | | | - Eva SM van der Heijden
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
| | - Ling Sheng Loh
- The George Washington University Department of Biological Sciences, Science and Engineering HallWashingtonUnited States
| | - Anna Ren
- The George Washington University Department of Biological Sciences, Science and Engineering HallWashingtonUnited States
| | - Ian A Warren
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
| | - James J Lewis
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell UniversityIthacaUnited States
| | | | - Laura Hebberecht
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
| | - Charlotte J Wright
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
| | - Jonah M Walker
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
| | | | - Zachary H Goldberg
- Cell & Developmental Biology, Division of Biological Sciences, UC San DiegoLa JollaUnited States
| | | | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences, Universidad del RosarioBogotáColombia
| | - Michael W Perry
- Cell & Developmental Biology, Division of Biological Sciences, UC San DiegoLa JollaUnited States
| | - Riccardo Papa
- Department of Biology, Centre for Applied Tropical Ecology and Conservation, University of Puerto RicoRio PiedrasPuerto Rico
| | - Arnaud Martin
- The George Washington University Department of Biological Sciences, Science and Engineering HallWashingtonUnited States
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
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37
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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.
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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
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38
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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.
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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
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Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. Proc Natl Acad Sci U S A 2021; 118:2015005118. [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A defining goal in genetics is linking variation in DNA sequence to trait evolution between populations and, ultimately, species. Genome sequencing efficiently captures such variation but typically in millions of tiny fragments that omit haplotype or linkage information. We present “haplotagging,” a simple, rapid linked-read sequencing technique that allows high-throughput sequencing without sacrificing haplotype information. We validated this affordable approach for whole-genome haplotyping in large populations. We used haplotagging to investigate the rise of a novel hybrid morph in parallel hybrid zones of two comimetic Heliconius butterfly species in Ecuador. Our results reveal that strikingly parallel divergences in their genomes produced coordinated shifts in haplotype frequencies across the hybrid zone, giving rise to comimetic hybrid morphs in each species. 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.
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40
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Waters JM, McCulloch GA. Reinventing the wheel? Reassessing the roles of gene flow, sorting and convergence in repeated evolution. Mol Ecol 2021; 30:4162-4172. [PMID: 34133810 DOI: 10.1111/mec.16018] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 12/31/2022]
Abstract
Biologists have long been intrigued by apparently predictable and repetitive evolutionary trajectories inferred across a variety of lineages and systems. In recent years, high-throughput sequencing analyses have started to transform our understanding of such repetitive shifts. While researchers have traditionally categorized such shifts as either "convergent" or "parallel," based on relatedness of the lineages involved, emerging genomic insights provide an opportunity to better describe the actual evolutionary mechanisms at play. A synthesis of recent genomic analyses confirms that convergence is the predominant driver of repetitive evolution among species, whereas repeated sorting of standing variation is the major driver of repeated shifts within species. However, emerging data reveal numerous notable exceptions to these expectations, with recent examples of de novo mutations underpinning convergent shifts among even very closely related lineages, while repetitive sorting processes have occurred among even deeply divergent taxa, sometimes via introgression. A number of very recent analyses have found evidence for both processes occurring on different scales within taxa. We suggest that the relative importance of convergent versus sorting processes depends on the interplay between gene flow among populations, and phylogenetic relatedness of the lineages involved.
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41
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Hanly JJ, Robertson ECN, Corning OBWH, Martin A. Porcupine/Wntless-dependent trafficking of the conserved WntA ligand in butterflies. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 336:470-481. [PMID: 34010515 DOI: 10.1002/jez.b.23046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/30/2021] [Accepted: 04/30/2021] [Indexed: 11/11/2022]
Abstract
Wnt ligands are key signaling molecules in animals, but little is known about the evolutionary dynamics and mode of action of the WntA orthologs, which are not present in the vertebrates or in Drosophila. Here we show that the WntA subfamily evolved at the base of the Bilateria + Cnidaria clade, and conserved the thumb region and Ser209 acylation site present in most other Wnts, suggesting WntA requires the core Wnt secretory pathway. WntA proteins are distinguishable from other Wnts by a synapomorphic Iso/Val/Ala216 amino-acid residue that replaces the otherwise ubiquitous Thr216 position. WntA embryonic expression is conserved between beetles and butterflies, suggesting functionality, but the WntA gene was lost three times within arthropods, in podoplean copepods, in the cyclorrhaphan fly radiation, and in ensiferan crickets and katydids. Finally, CRISPR mosaic knockouts (KOs) of porcupine and wntless phenocopied the pattern-specific effects of WntA KOs in the wings of Vanessa cardui butterflies. These results highlight the molecular conservation of the WntA protein across invertebrates, and imply it functions as a typical Wnt ligand that is acylated and secreted through the Porcupine/Wntless secretory pathway.
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Affiliation(s)
- Joseph J Hanly
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia, USA
| | - Erica C N Robertson
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia, USA
| | - Olaf B W H Corning
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia, USA
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, District of Columbia, USA
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Earl C, Belitz MW, Laffan SW, Barve V, Barve N, Soltis DE, Allen JM, Soltis PS, Mishler BD, Kawahara AY, Guralnick R. Spatial phylogenetics of butterflies in relation to environmental drivers and angiosperm diversity across North America. iScience 2021; 24:102239. [PMID: 33997666 PMCID: PMC8101049 DOI: 10.1016/j.isci.2021.102239] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/13/2020] [Accepted: 02/23/2021] [Indexed: 11/25/2022] Open
Abstract
Broad-scale, quantitative assessments of insect biodiversity and the factors shaping it remain particularly poorly explored. Here we undertook a spatial phylogenetic analysis of North American butterflies to test whether climate stability and temperature gradients have shaped their diversity and endemism. We also performed the first quantitative comparisons of spatial phylogenetic patterns between butterflies and flowering plants. We expected concordance between the two groups based on shared historical environmental drivers and presumed strong butterfly-host plant specializations. We instead found that biodiversity patterns in butterflies are strikingly different from flowering plants, especially warm deserts. In particular, butterflies show different patterns of phylogenetic clustering compared with flowering plants, suggesting differences in habitat conservation between the two groups. These results suggest that shared biogeographic histories and trophic associations do not necessarily assure similar diversity outcomes. The work has applied value in conservation planning, documenting warm deserts as a North American butterfly biodiversity hotspot.
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Affiliation(s)
- Chandra Earl
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Michael W. Belitz
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
| | - Shawn W. Laffan
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Vijay Barve
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Narayani Barve
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Douglas E. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
| | - Julie M. Allen
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, USA
| | - Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
| | - Brent D. Mishler
- University of Jepson Herbaria, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Akito Y. Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Robert Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
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43
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van der Burg KR, Reed RD. Seasonal plasticity: how do butterfly wing pattern traits evolve environmental responsiveness? Curr Opin Genet Dev 2021; 69:82-87. [PMID: 33740694 DOI: 10.1016/j.gde.2021.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/03/2021] [Accepted: 02/09/2021] [Indexed: 01/28/2023]
Abstract
Phenotypic plasticity in response to environmental cues is common in butterflies, and is a major driver of butterfly wing pattern diversity. The endocrine signal ecdysone has been revealed as a major modulator of plasticity in butterflies. External cues such as day length or temperature are translated internally into variation in ecdysone titers, which in turn lead to alternate phenotypes such as seasonal wing patterns. Here we review the evidence showing that ecdysone-mediated plasticity of different wing pattern features such as wing color and eyespot size can evolve independently. Recent studies show that ecdysone regulates gene expression in Drosophila melanogaster via a chromatin remodeling mechanism. We thus propose that environmentally responsive ecdysone titers in butterflies may also function via chromatin regulation to promote different seasonal phenotypes. We present a model of ecdysone response evolution that integrates both gene regulatory architecture and organismal development, and propose a set of testable mechanistic hypotheses for how plastic response profiles of specific genes can evolve.
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Affiliation(s)
- Karin Rl van der Burg
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States.
| | - Robert D Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States.
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44
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Van Belleghem SM, Lewis JJ, Rivera ES, Papa R. Heliconius butterflies: a window into the evolution and development of diversity. Curr Opin Genet Dev 2021; 69:72-81. [PMID: 33714874 DOI: 10.1016/j.gde.2021.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/14/2021] [Accepted: 01/25/2021] [Indexed: 10/21/2022]
Abstract
Butterflies have become prominent models for studying the evolution and development of phenotypic variation. In Heliconius, extraordinary within species divergence and between species convergence in wing color patterns has driven decades of comparative genetic studies. However, connecting genetic patterns of diversification to the molecular mechanisms of adaptation has remained elusive. Recent studies are bridging this gap between genome and function and have driven substantial advances in deciphering the genetic architecture of diversification in Heliconius. While only a handful of large-effect genes were initially identified in the diversification of Heliconius color patterns, recent experiments have begun to unravel the underlying gene regulatory networks and how these have evolved. These results reveal an evolutionary story of many interacting loci and partly independent genetic architectures that underlie convergent evolution.
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Affiliation(s)
| | - James J Lewis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA; Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Edgardo S Rivera
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan, Puerto Rico; Chairs of Biomaterials, University of Bayreuth, Bayreuth, Bayern, Germany
| | - Riccardo Papa
- Department of Biology, University of Puerto Rico-Rio Piedras, San Juan, Puerto Rico; Molecular Sciences and Research Center, University of Puerto Rico, San Juan, Puerto Rico.
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45
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Kittelmann S, Preger-Ben Noon E, McGregor AP, Frankel N. A complex gene regulatory architecture underlies the development and evolution of cuticle morphology in Drosophila. Curr Opin Genet Dev 2021; 69:21-27. [PMID: 33529925 DOI: 10.1016/j.gde.2021.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/18/2020] [Accepted: 01/05/2021] [Indexed: 10/22/2022]
Abstract
The cuticle of insects is decorated with non-sensory hairs called trichomes. A few Drosophila species independently lost most of the dorso-lateral trichomes on first instar larvae. Genetic experiments revealed that this naked cuticle phenotype was caused by the evolution of enhancer function at the ovo/shavenbaby (ovo/svb) locus. Here we explore how this discovery catalyzed major new insights into morphological evolution in different developmental contexts, enhancer pleiotropy in gene regulation and the functionality and evolution of the Svb gene regulatory network (GRN). Taken together this highlights the importance of understanding the architecture and evolution of gene regulatory networks in detail and the great potential for further study of the Svb GRN.
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Affiliation(s)
- Sebastian Kittelmann
- Centre for Functional Genomics, Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, United Kingdom
| | - Ella Preger-Ben Noon
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion - Israel Institute of Technology, Haifa 3109601, Israel
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, United Kingdom
| | - Nicolás Frankel
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE, CONICET-UBA), Buenos Aires 1428, Argentina; Departamento de Ecología, Genética y Evolución (FCEyN, UBA), Buenos Aires 1428, Argentina.
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46
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Niederhuber MJ, McKay DJ. Mechanisms underlying the control of dynamic regulatory element activity and chromatin accessibility during metamorphosis. CURRENT OPINION IN INSECT SCIENCE 2021; 43:21-28. [PMID: 32979530 PMCID: PMC7985040 DOI: 10.1016/j.cois.2020.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/25/2020] [Indexed: 05/10/2023]
Abstract
Cis-regulatory modules of metazoan genomes determine the when and where of gene expression during development. Here we discuss insights into the genetic and molecular mechanisms behind cis-regulatory module usage that have come from recent application of genomics assays to insect metamorphosis. Assays including FAIRE-seq, ATAC-seq, and CUT&RUN indicate that sequential changes in chromatin accessibility play a key role in mediating stage-specific cis-regulatory module activity and gene expression. We review the current understanding of what controls precisely coordinated changes in chromatin accessibility during metamorphosis and describe evidence that points to systemic hormone signaling as a primary signal to trigger genome-wide shifts in accessibility patterns and cis-regulatory module usage.
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Affiliation(s)
- Matthew J Niederhuber
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States; Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States; Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Daniel J McKay
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States; Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States.
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47
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Urban S, Nater A, Meyer A, Kratochwil CF. Different Sources of Allelic Variation Drove Repeated Color Pattern Divergence in Cichlid Fishes. Mol Biol Evol 2021; 38:465-477. [PMID: 32941629 PMCID: PMC7826197 DOI: 10.1093/molbev/msaa237] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The adaptive radiations of East African cichlid fish in the Great Lakes Victoria, Malawi, and Tanganyika are well known for their diversity and repeatedly evolved phenotypes. Convergent evolution of melanic horizontal stripes has been linked to a single locus harboring the gene agouti-related peptide 2 (agrp2). However, where and when the causal variants underlying this trait evolved and how they drove phenotypic divergence remained unknown. To test the alternative hypotheses of standing genetic variation versus de novo mutations (independently originating in each radiation), we searched for shared signals of genomic divergence at the agrp2 locus. Although we discovered similar signatures of differentiation at the locus level, the haplotypes associated with stripe patterns are surprisingly different. In Lake Malawi, the highest associated alleles are located within and close to the 5' untranslated region of agrp2 and likely evolved through recent de novo mutations. In the younger Lake Victoria radiation, stripes are associated with two intronic regions overlapping with a previously reported cis-regulatory interval. The origin of these segregating haplotypes predates the Lake Victoria radiation because they are also found in more basal riverine and Lake Kivu species. This suggests that both segregating haplotypes were present as standing genetic variation at the onset of the Lake Victoria adaptive radiation with its more than 500 species and drove phenotypic divergence within the species flock. Therefore, both new (Lake Malawi) and ancient (Lake Victoria) allelic variation at the same locus fueled rapid and convergent phenotypic evolution.
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Affiliation(s)
- Sabine Urban
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Alexander Nater
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
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48
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Ruttenberg DM, VanKuren NW, Nallu S, Yen SH, Peggie D, Lohman DJ, Kronforst MR. The evolution and genetics of sexually dimorphic 'dual' mimicry in the butterfly Elymnias hypermnestra. Proc Biol Sci 2021; 288:20202192. [PMID: 33434461 DOI: 10.1098/rspb.2020.2192] [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] [Indexed: 12/14/2022] Open
Abstract
Sexual dimorphism is a major component of morphological variation across the tree of life, but the mechanisms underlying phenotypic differences between sexes of a single species are poorly understood. We examined the population genomics and biogeography of the common palmfly Elymnias hypermnestra, a dual mimic in which female wing colour patterns are either dark brown (melanic) or bright orange, mimicking toxic Euploea and Danaus species, respectively. As males always have a melanic wing colour pattern, this makes E. hypermnestra a fascinating model organism in which populations vary in sexual dimorphism. Population structure analysis revealed that there were three genetically distinct E. hypermnestra populations, which we further validated by creating a phylogenomic species tree and inferring historical barriers to gene flow. This species tree demonstrated that multiple lineages with orange females do not form a monophyletic group, and the same is true of clades with melanic females. We identified two single nucleotide polymorphisms (SNPs) near the colour patterning gene WntA that were significantly associated with the female colour pattern polymorphism, suggesting that this gene affects sexual dimorphism. Given WntA's role in colour patterning across Nymphalidae, E. hypermnestra females demonstrate the repeatability of the evolution of sexual dimorphism.
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Affiliation(s)
- Dee M Ruttenberg
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
| | - Nicholas W VanKuren
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
| | - Sumitha Nallu
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
| | - Shen-Horn Yen
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
| | - Djunijanti Peggie
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong-Bogor 16911, Indonesia
| | - David J Lohman
- Biology Department, City College of New York, City University of New York, New York, NY 10031, USA.,PhD Program in Biology, Graduate Center, City University of New York, New York, NY 10016, USA.,Entomology Section, National Museum of Natural History, Manila 1000, Philippines
| | - Marcus R Kronforst
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
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49
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van der Burg KRL, Lewis JJ, Brack BJ, Fandino RA, Mazo-Vargas A, Reed RD. Genomic architecture of a genetically assimilated seasonal color pattern. Science 2020; 370:721-725. [DOI: 10.1126/science.aaz3017] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 06/16/2020] [Accepted: 10/01/2020] [Indexed: 12/31/2022]
Affiliation(s)
| | - James J. Lewis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Benjamin J. Brack
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Richard A. Fandino
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Anyi Mazo-Vargas
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Robert D. Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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50
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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.
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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
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