1
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Lin RC, Ferreira BT, Yuan YW. The molecular basis of phenotypic evolution: beyond the usual suspects. Trends Genet 2024; 40:668-680. [PMID: 38704304 PMCID: PMC11303103 DOI: 10.1016/j.tig.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024]
Abstract
It has been well documented that mutations in coding DNA or cis-regulatory elements underlie natural phenotypic variation in many organisms. However, the development of sophisticated functional tools in recent years in a wide range of traditionally non-model systems have revealed many 'unusual suspects' in the molecular bases of phenotypic evolution, including upstream open reading frames (uORFs), cryptic splice sites, and small RNAs. Furthermore, large-scale genome sequencing, especially long-read sequencing, has identified a cornucopia of structural variation underlying phenotypic divergence and elucidated the composition of supergenes that control complex multi-trait polymorphisms. In this review article we highlight recent studies that demonstrate this great diversity of molecular mechanisms producing adaptive genetic variation and the panoply of evolutionary paths leading to the 'grandeur of life'.
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Affiliation(s)
- Rong-Chien Lin
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Bianca T Ferreira
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Yao-Wu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.
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2
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Tian S, Asano Y, Banerjee TD, Wee JLQ, Lamb A, Wang Y, Murugesan SN, Ui-Tei K, Wittkopp PJ, Monteiro A. A micro-RNA is the effector gene of a classic evolutionary hotspot locus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.09.579741. [PMID: 38659873 PMCID: PMC11042203 DOI: 10.1101/2024.02.09.579741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
In Lepidoptera (butterflies and moths), the genomic region around the gene cortex is a 'hotspot' locus, repeatedly used to generate intraspecific melanic wing color polymorphisms across 100-million-years of evolution. However, the identity of the effector gene regulating melanic wing color within this locus remains unknown. Here, we show that none of the four candidate protein-coding genes within this locus, including cortex, serve as major effectors. Instead, a micro-RNA (miRNA), mir-193, serves as the major effector across three deeply diverged lineages of butterflies, and its function is conserved in Drosophila. In Lepidoptera, mir-193 is derived from a gigantic long non-coding RNA, ivory, and it functions by directly repressing multiple pigmentation genes. We show that a miRNA can drive repeated instances of adaptive evolution in animals.
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Affiliation(s)
- Shen Tian
- Department of Biological Sciences, Faculty of Science, National University of Singapore; Singapore, 117543, Singapore
| | - Yoshimasa Asano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo; Tokyo, 113-0033, Japan
| | - Tirtha Das Banerjee
- Department of Biological Sciences, Faculty of Science, National University of Singapore; Singapore, 117543, Singapore
| | - Jocelyn Liang Qi Wee
- Department of Biological Sciences, Faculty of Science, National University of Singapore; Singapore, 117543, Singapore
| | - Abigail Lamb
- Department of Molecular, Cellular, and Developmental Biology, College of Literature, Science, and the Arts, The University of Michigan; Ann Arbor, MI 48109-1085, USA
| | - Yehan Wang
- Department of Biological Sciences, Faculty of Science, National University of Singapore; Singapore, 117543, Singapore
| | - Suriya Narayanan Murugesan
- Department of Biological Sciences, Faculty of Science, National University of Singapore; Singapore, 117543, Singapore
| | - Kumiko Ui-Tei
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo; Tokyo, 113-0033, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo; Chiba, 277-8561, Japan
| | - Patricia J. Wittkopp
- Department of Molecular, Cellular, and Developmental Biology, College of Literature, Science, and the Arts, The University of Michigan; Ann Arbor, MI 48109-1085, USA
- Department of Ecology and Evolutionary Biology, College of Literature, Science, and the Arts, The University of Michigan; Ann Arbor, MI 48109-1085, USA
| | - Antónia Monteiro
- Department of Biological Sciences, Faculty of Science, National University of Singapore; Singapore, 117543, Singapore
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3
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Jay P, Aubier TG, Joron M. The interplay of local adaptation and gene flow may lead to the formation of supergenes. Mol Ecol 2024:e17297. [PMID: 38415327 DOI: 10.1111/mec.17297] [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: 06/14/2023] [Revised: 12/28/2023] [Accepted: 01/10/2024] [Indexed: 02/29/2024]
Abstract
Supergenes are genetic architectures resulting in the segregation of alternative combinations of alleles underlying complex phenotypes. The co-segregation of alleles at linked loci is often facilitated by polymorphic chromosomal rearrangements suppressing recombination locally. Supergenes are involved in many complex polymorphisms, including sexual, colour or behavioural polymorphisms in numerous plants, fungi, mammals, fish, and insects. Despite a long history of empirical and theoretical research, the formation of supergenes remains poorly understood. Here, using a two-island population genetic model, we explore how gene flow and the evolution of overdominant chromosomal inversions may jointly lead to the formation of supergenes. We show that the evolution of inversions in differentiated populations, both under disruptive selection, leads to an increase in frequency of poorly adapted, immigrant haplotypes. Indeed, rare allelic combinations, such as immigrant haplotypes, are more frequently reshuffled by recombination than common allelic combinations, and therefore benefit from the recombination suppression generated by inversions. When an inversion capturing a locally adapted haplotype spreads but is associated with a fitness cost hampering its fixation (e.g. a recessive mutation load), the maintenance of a non-inverted haplotype in the population is enhanced; under certain conditions, the immigrant haplotype persists alongside the inverted local haplotype, while the standard local haplotype disappears. This establishes a stable, local polymorphism with two non-recombining haplotypes encoding alternative adaptive strategies, that is, a supergene. These results bring new light to the importance of local adaptation, overdominance, and gene flow in the formation of supergenes and inversion polymorphisms in general.
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Affiliation(s)
- Paul Jay
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | - Thomas G Aubier
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UT3), Toulouse, France
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
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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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VanKuren NW, Sheikh SI, Massardo D, Lu W, Kronforst MR. Supergene evolution via gain of auto-regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574839. [PMID: 38260248 PMCID: PMC10802445 DOI: 10.1101/2024.01.09.574839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The development of complex phenotypes requires the coordinated action of many genes across space and time, yet many species have evolved the ability to develop multiple discrete, alternate phenotypes1-3. Such polymorphisms are often controlled by supergenes, sets of tightly-linked mutations in one or more loci that function together to produce a complex phenotype4. Although theories of supergene evolution are well-established, the mutations that cause functional differences between supergene alleles remain essentially unknown. doublesex is the master regulator of insect sexual differentiation but functions as a supergene in multiple Papilio swallowtail butterflies, where divergent dsx alleles control development of discrete non-mimetic or mimetic female wing color patterns5-7. Here we demonstrate that the functional elements of the mimetic allele in Papilio alphenor are six new cis-regulatory elements (CREs) spread across 150 kb that are bound by DSX itself. Our findings provide experimental support to classic supergene theory and suggest that the evolution of auto-regulation may provide a simple route to supergene origination and to the co-option of pleiotropic genes into new developmental roles.
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Affiliation(s)
| | - Sofia I. Sheikh
- Department of Ecology & Evolution, The University of Chicago, Chicago IL USA
| | - Darli Massardo
- Department of Ecology & Evolution, The University of Chicago, Chicago IL USA
| | - Wei Lu
- Department of Ecology & Evolution, The University of Chicago, Chicago IL USA
| | - Marcus R. Kronforst
- Department of Ecology & Evolution, The University of Chicago, Chicago IL USA
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6
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Näsvall K, Boman J, Talla V, Backström N. Base Composition, Codon Usage, and Patterns of Gene Sequence Evolution in Butterflies. Genome Biol Evol 2023; 15:evad150. [PMID: 37565492 PMCID: PMC10462419 DOI: 10.1093/gbe/evad150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 07/17/2023] [Accepted: 08/08/2023] [Indexed: 08/12/2023] Open
Abstract
Coding sequence evolution is influenced by both natural selection and neutral evolutionary forces. In many species, the effects of mutation bias, codon usage, and GC-biased gene conversion (gBGC) on gene sequence evolution have not been detailed. Quantification of how these forces shape substitution patterns is therefore necessary to understand the strength and direction of natural selection. Here, we used comparative genomics to investigate the association between base composition and codon usage bias on gene sequence evolution in butterflies and moths (Lepidoptera), including an in-depth analysis of underlying patterns and processes in one species, Leptidea sinapis. The data revealed significant G/C to A/T substitution bias at third codon position with some variation in the strength among different butterfly lineages. However, the substitution bias was lower than expected from previously estimated mutation rate ratios, partly due to the influence of gBGC. We found that A/T-ending codons were overrepresented in most species, but there was a positive association between the magnitude of codon usage bias and GC-content in third codon positions. In addition, the tRNA-gene population in L. sinapis showed higher GC-content at third codon positions compared to coding sequences in general and less overrepresentation of A/T-ending codons. There was an inverse relationship between synonymous substitutions and codon usage bias indicating selection on synonymous sites. We conclude that the evolutionary rate in Lepidoptera is affected by a complex interaction between underlying G/C -> A/T mutation bias and partly counteracting fixation biases, predominantly conferred by overall purifying selection, gBGC, and selection on codon usage.
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Affiliation(s)
- Karin Näsvall
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala, Sweden
| | - Jesper Boman
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala, Sweden
| | - Venkat Talla
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala, Sweden
| | - Niclas Backström
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala, Sweden
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7
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Komata S, Yoda S, KonDo Y, Shinozaki S, Tamai K, Fujiwara H. Functional unit of supergene in female-limited Batesian mimicry of Papilio polytes. Genetics 2023; 223:iyac177. [PMID: 36454671 PMCID: PMC9910408 DOI: 10.1093/genetics/iyac177] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/14/2022] [Accepted: 11/14/2022] [Indexed: 12/05/2022] Open
Abstract
Supergenes are sets of genes and genetic elements that are inherited like a single gene and control complex adaptive traits, but their functional roles and units are poorly understood. In Papilio polytes, female-limited Batesian mimicry is thought to be regulated by a ∼130 kb inversion region (highly diversified region: HDR) containing 3 genes, UXT, U3X, and doublesex (dsx) which switches non-mimetic and mimetic types. To determine the functional unit, we here performed electroporation-mediated RNAi analyses (and further Crispr/Cas9 for UXT) of genes within and flanking the HDR in pupal hindwings. We first clarified that non-mimetic dsx-h had a function to form the non-mimetic trait in female and only dsx-H isoform 3 had an important function in the formation of mimetic traits. Next, we found that UXT was involved in making mimetic-type pale-yellow spots and adjacent gene sir2 in making red spots in hindwings, both of which refine more elaborate mimicry. Furthermore, downstream gene networks of dsx, U3X, and UXT screened by RNA sequencing showed that U3X upregulated dsx-H expression and repressed UXT expression. These findings demonstrate that a set of multiple genes, not only inside but also flanking HDR, can function as supergene members, which extends the definition of supergene unit than we considered before. Also, our results indicate that dsx functions as the switching gene and some other genes such as UXT and sir2 within the supergene unit work as the modifier gene.
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Affiliation(s)
- Shinya Komata
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Shinichi Yoda
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, 444-8585, Japan
| | - Yûsuke KonDo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Souta Shinozaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Kouki Tamai
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Haruhiko Fujiwara
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
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8
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Widespread chromosomal rearrangements preceded genetic divergence in a monitor lizard, Varanus acanthurus (Varanidae). Chromosome Res 2023; 31:9. [PMID: 36745262 PMCID: PMC9902428 DOI: 10.1007/s10577-023-09715-x] [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: 09/02/2022] [Revised: 11/12/2022] [Accepted: 11/28/2022] [Indexed: 02/07/2023]
Abstract
Chromosomal rearrangements are often associated with local adaptation and speciation because they suppress recombination, and as a result, rearrangements have been implicated in disrupting gene flow. Although there is strong evidence to suggest that chromosome rearrangements are a factor in genetic isolation of divergent populations, the underlying mechanism remains elusive. Here, we applied an integrative cytogenetics and genomics approach testing whether chromosomal rearrangements are the initial process, or a consequence, of population divergence in the dwarf goanna, Varanus acanthurus. Specifically, we tested whether chromosome rearrangements are indicators of genetic barriers that can be used to identify divergent populations by looking at gene flow within and between populations with rearrangements. We found that gene flow was present between individuals with chromosome rearrangements within populations, but there was no gene flow between populations that had similar chromosome rearrangements. Moreover, we identified a correlation between reduced genetic variation in populations with a higher frequency of homozygous submetacentric individuals. These findings suggest that chromosomal rearrangements were widespread prior to divergence, and because we found populations with higher frequencies of submetacentric chromosomes were associated with lower genetic diversity, this could indicate that polymorphisms within populations are early indicators of genetic drift.
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9
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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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10
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Yin N, Xiao H, Yang A, Wu C, Liu N. Genome-Wide Analysis of Odorant and Gustatory Receptors in Six Papilio Butterflies (Lepidoptera: Papilionidae). INSECTS 2022; 13:779. [PMID: 36135480 PMCID: PMC9500883 DOI: 10.3390/insects13090779] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/20/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
The chemical interactions of insects and host plants are shaping the evolution of chemosensory receptor gene families. However, the correlation between host range and chemoreceptor gene repertoire sizes is still elusive in Papilionidae. Here, we addressed the issue of whether host plant diversities are correlated with the expansions of odorant (ORs) or gustatory (GRs) receptors in six Papilio butterflies. By combining genomics, transcriptomics and bioinformatics approaches, 381 ORs and 328 GRs were annotated in the genomes of a generalist P. glaucus and five specialists, P. xuthus, P. polytes, P. memnon, P. machaon and P. dardanus. Orthologous ORs or GRs in Papilio had highly conserved gene structure. Five Papilio specialists exhibited a similar frequency of intron lengths for ORs or GRs, but which was different from those in the generalist. Phylogenetic analysis revealed 60 orthologous OR groups, 45 of which shared one-to-one relationships. Such a single gene in each butterfly also occurred in 26 GR groups. Intriguingly, bitter GRs had fewer introns than other GRs and clustered into a large clade. Focusing on the two chemoreceptor gene families in P. xuthus, most PxutORs (52/58) were expressed in antennae and 31 genes in reproductive tissues. Eleven out of 28 foretarsus-expressed PxutGRs were female-biased genes, as strong candidates for sensing oviposition stimulants. These results indicate that the host range may not shape the large-scale expansions of ORs and GRs in Papilio butterflies and identify important molecular targets involved in olfaction, oviposition or reproduction in P. xuthus.
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Affiliation(s)
| | | | | | | | - Naiyong Liu
- Correspondence: ; Tel./Fax: +86-871-63862665
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11
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Berdan EL, Flatt T, Kozak GM, Lotterhos KE, Wielstra B. Genomic architecture of supergenes: connecting form and function. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210192. [PMID: 35694757 PMCID: PMC9189501 DOI: 10.1098/rstb.2021.0192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Supergenes are tightly linked sets of loci that are inherited together and control complex phenotypes. While classical supergenes-governing traits such as wing patterns in Heliconius butterflies or heterostyly in Primula-have been studied since the Modern Synthesis, we still understand very little about how they evolve and persist in nature. The genetic architecture of supergenes is a critical factor affecting their evolutionary fate, as it can change key parameters such as recombination rate and effective population size, potentially redirecting molecular evolution of the supergene in addition to the surrounding genomic region. To understand supergene evolution, we must link genomic architecture with evolutionary patterns and processes. This is now becoming possible with recent advances in sequencing technology and powerful forward computer simulations. The present theme issue brings together theoretical and empirical papers, as well as opinion and synthesis papers, which showcase the architectural diversity of supergenes and connect this to critical processes in supergene evolution, such as polymorphism maintenance and mutation accumulation. Here, we summarize those insights to highlight new ideas and methods that illuminate the path forward for the study of supergenes in nature. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.
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Affiliation(s)
- Emma L Berdan
- Institute of Biology Leiden, Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands.,Naturalis Biodiversity Center, PO Box 9517, 2300 RA Leiden, The Netherlands.,Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, 45296 Strömstad, Sweden
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Genevieve M Kozak
- Department of Biology, University of Massachusetts Dartmouth, 285 Old Westport Road, MA 02747, USA
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University, 430 Nahant Road, Nahant, MA 01908, USA
| | - Ben Wielstra
- Institute of Biology Leiden, Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands.,Naturalis Biodiversity Center, PO Box 9517, 2300 RA Leiden, The Netherlands
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12
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Komata S, Kajitani R, Itoh T, Fujiwara H. Genomic architecture and functional unit of mimicry supergene in female limited Batesian mimic Papilio butterflies. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210198. [PMID: 35694751 PMCID: PMC9189499 DOI: 10.1098/rstb.2021.0198] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/17/2022] [Indexed: 11/12/2022] Open
Abstract
It has long been suggested that dimorphic female-limited Batesian mimicry of two closely related Papilio butterflies, Papilio memnon and Papilio polytes, is controlled by supergenes. Whole-genome sequencing, genome-wide association studies and functional analyses have recently identified mimicry supergenes, including the doublesex (dsx) gene. Although supergenes of both the species are composed of highly divergent regions between mimetic and non-mimetic alleles and are located at the same chromosomal locus, they show critical differences in genomic architecture, particularly with or without an inversion: P. polytes has an inversion, but P. memnon does not. This review introduces and compares the detailed genomic structure of mimicry supergenes in two Papilio species, including gene composition, repetitive sequence composition, breakpoint/boundary site structure, chromosomal inversion and linkage disequilibrium. Expression patterns and functional analyses of the respective genes within or flanking the supergene suggest that dsx and other genes are involved in mimetic traits. In addition, structural comparison of the corresponding region for the mimicry supergene among further Papilio species suggests three scenarios for the evolution of the mimicry supergene between the two Papilio species. The structural features revealed in the Papilio mimicry supergene provide insight into the formation, maintenance and evolution of supergenes. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.
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Affiliation(s)
- Shinya Komata
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Rei Kajitani
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Haruhiko Fujiwara
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
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13
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Kim KW, De-Kayne R, Gordon IJ, Omufwoko KS, Martins DJ, Ffrench-Constant R, Martin SH. Stepwise evolution of a butterfly supergene via duplication and inversion. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210207. [PMID: 35694743 PMCID: PMC9189502 DOI: 10.1098/rstb.2021.0207] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Supergenes maintain adaptive clusters of alleles in the face of genetic mixing. Although usually attributed to inversions, supergenes can be complex, and reconstructing the precise processes that led to recombination suppression and their timing is challenging. We investigated the origin of the BC supergene, which controls variation in warning coloration in the African monarch butterfly, Danaus chrysippus. By generating chromosome-scale assemblies for all three alleles, we identified multiple structural differences. Most strikingly, we find that a region of more than 1 million bp underwent several segmental duplications at least 7.5 Ma. The resulting duplicated fragments appear to have triggered four inversions in surrounding parts of the chromosome, resulting in stepwise growth of the region of suppressed recombination. Phylogenies for the inversions are incongruent with the species tree and suggest that structural polymorphisms have persisted for at least 4.1 Myr. In addition to the role of duplications in triggering inversions, our results suggest a previously undescribed mechanism of recombination suppression through independent losses of divergent duplicated tracts. Overall, our findings add support for a stepwise model of supergene evolution involving a variety of structural changes. This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’.
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Affiliation(s)
- Kang-Wook Kim
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Rishi De-Kayne
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Ian J Gordon
- Centre of Excellence in Biodiversity and Natural Resource Management, University of Rwanda, Huye Campus, Huye, Rwanda
| | | | - Dino J Martins
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, USA.,Mpala Research Centre, Nanyuki, Kenya
| | | | - Simon H Martin
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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14
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Komata S, Lin CP, Fujiwara H. doublesex Controls Both Hindwing and Abdominal Mimicry Traits in the Female-Limited Batesian Mimicry of Papilio memnon. FRONTIERS IN INSECT SCIENCE 2022; 2:929518. [PMID: 38468762 PMCID: PMC10926503 DOI: 10.3389/finsc.2022.929518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/20/2022] [Indexed: 03/13/2024]
Abstract
Papilio butterflies are known to possess female-limited Batesian mimicry polymorphisms. In Papilio memnon, females have mimetic and non-mimetic forms, whereas males are monomorphic and non-mimetic. Mimetic females are characterized by color patterns and tails in the hindwing and yellow abdomens. Recently, an analysis of whole-genome sequences has shown that an approximately 160 kb region of chromosome 25 is responsible for mimicry and has high diversity between mimetic (A) and non-mimetic (a) alleles (highly diversified region: HDR). The HDR includes three genes, UXT, doublesex (dsx), and Nach-like, but the functions of these genes are unknown. Here, we investigated the function of dsx, a gene involved in sexual differentiation, which is expected to be functionally important for hindwing and abdominal mimetic traits in P. memnon. Expression analysis by reverse transcription quantitative PCR (RT-qPCR) and RNA sequencing showed that mimetic dsx (dsx-A) was highly expressed in the hindwings in the early pupal stage. In the abdomen, both dsx-A and dsx-a were highly expressed during the early pupal stage. When dsx was knocked down using small interfering RNAs (siRNAs) designed in the common region of dsx-A and dsx-a, a male-like pattern appeared on the hindwings of mimetic and non-mimetic females. Similarly, when dsx was knocked down in the abdomen, the yellow scales characteristic of mimetic females changed to black. Furthermore, when dsx-a was specifically knocked down, the color pattern of the hindwings changed, as in the case of dsx knockdown in non-mimetic females but not mimetic females. These results suggest that dsx-a is involved in color pattern formation on the hindwings of non-mimetic females, whereas dsx-A is involved in hindwing and abdominal mimetic traits. dsx was involved in abdominal and hindwing mimetic traits, but dsx expression patterns in the hindwing and abdomen were different, suggesting that different regulatory mechanisms may exist. Our study is the first to show that the same gene (dsx) regulates both the hindwing and abdominal mimetic traits. This is the first functional analysis of abdominal mimicry in butterflies.
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Affiliation(s)
- Shinya Komata
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Chung-Ping Lin
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Haruhiko Fujiwara
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
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15
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Jay P, Joron M. The double game of chromosomal inversions in a neotropical butterfly. C R Biol 2022; 345:57-73. [DOI: 10.5802/crbiol.73] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 01/31/2022] [Indexed: 11/24/2022]
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16
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Londoño GA, Sandoval‐H J, Sallam MF, Allen JM. On the evolution of mimicry in avian nestlings. Ecol Evol 2022; 12:e8842. [PMID: 35449583 PMCID: PMC9013854 DOI: 10.1002/ece3.8842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/22/2022] [Accepted: 03/01/2022] [Indexed: 11/26/2022] Open
Abstract
Batesian mimicry (BM), where a nontoxic species resembles a toxic species with aposematic coloring, has been recently described for a Neotropical species of the suboscine passerine (Laniocera hypopyrra). Understanding the order and series in which these characteristics evolved is unknown and requires character information from closely related taxa. Here, we trace the origin of mimetic traits and how they evolved by examining antipredator characteristics using images and other field‐collected trait data from nest and nestlings along with data available in the literature for the Laniisominae clade and closely related taxa. We found that morphological modifications of the downy feathers appeared first in the broader clade leading to the Laniisominae clade followed by further morphological and behavioral characteristics within the Laniisominae clade leading to the full BM. Images of nestlings in the Laniisominae and closely related clades demonstrated the extent of antipredator and camouflage characteristics. We found a complex set of behavioral and morphological traits in this clade for reducing predation from hiding to camouflage to mimicry. We further propose the evolution of two distinctive mimicry strategies in the Laniisominae clade: (1) Batesian Mimicry, as described above and (2) Masquerade, resemblance to inedible objects commonly found in their local environment. This complex set of antipredator traits shed light on the diversity of antipredator characteristics in avian nestlings, particularly in neotropical areas where the avian diversity is highest. Unfortunately, there are hundreds of species in the neotropics that lack basic natural history information on nesting traits, and therefore, we are likely missing critical information on the diversity of antipredator characteristics across avian nestlings.
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Affiliation(s)
- Gustavo A. Londoño
- Facultad de Ciencias NaturalesDepartamento de Ciencias BiológicasUniversidad IcesiCaliColombia
| | - Juliana Sandoval‐H
- A.C. Red de Biodiversidad y SistemáticaInstituto de EcologíaXalapaMexico
| | | | - Julie M. Allen
- Biology DepartmentUniversity of Nevada‐RenoRenoNevadaUSA
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17
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Takahashi M, Okude G, Futahashi R, Takahashi Y, Kawata M. The effect of the doublesex gene in body colour masculinization of the damselfly Ischnura senegalensis. Biol Lett 2021; 17:20200761. [PMID: 34102071 PMCID: PMC8187028 DOI: 10.1098/rsbl.2020.0761] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 05/17/2021] [Indexed: 12/25/2022] Open
Abstract
Odonata species display a remarkable diversity of colour patterns, including intrasexual polymorphisms. In the damselfly (Ischnura senegalensis), the expression of a sex-determining transcription factor, the doublesex (Isdsx) gene is reportedly associated with female colour polymorphism (CP) (gynomorph for female-specific colour and andromorph for male-mimicking colour). Here, the function of Isdsx in thoracic coloration was investigated by electroporation-mediated RNA interference (RNAi). RNAi of the Isdsx common region in males and andromorphic females reduced melanization and thus changed the colour pattern into that of gynomorphic females, while the gynomorphic colour pattern was not affected. By contrast, RNAi against the Isdsx long isoform produced no changes, suggesting that the Isdsx short isoform is important for body colour masculinization in both males and andromorphic females. When examining the expression levels of five genes with differences between sexes and female morphs, two melanin-suppressing genes, black and ebony, were expressed at higher levels in the Isdsx RNAi body area than a control area. Therefore, the Isdsx short isoform may induce thoracic colour differentiation by suppressing black and ebony, thereby generating female CP in I. senegalensis. These findings contribute to the understanding of the molecular and evolutionary mechanisms underlying female CP in Odonata.
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Affiliation(s)
- Michihiko Takahashi
- Graduate School of Life Sciences, Tohoku University, 6-3 Aramaki, Aoba, Sendai 980-8578, Japan
| | - Genta Okude
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Tsukuba, Ibaraki 305-8566, Japan
| | - Ryo Futahashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Tsukuba, Ibaraki 305-8566, Japan
| | - Yuma Takahashi
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoi, Inage, Chiba 263-8522, Japan
| | - Masakado Kawata
- Graduate School of Life Sciences, Tohoku University, 6-3 Aramaki, Aoba, Sendai 980-8578, Japan
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18
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Evolution of sexual development and sexual dimorphism in insects. Curr Opin Genet Dev 2021; 69:129-139. [PMID: 33848958 DOI: 10.1016/j.gde.2021.02.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/19/2021] [Accepted: 02/24/2021] [Indexed: 12/18/2022]
Abstract
Most animal species consist of two distinct sexes. At the morphological, physiological, and behavioral levels the differences between males and females are numerous and dramatic, yet at the genomic level they are often slight or absent. This disconnect is overcome because simple genetic differences or environmental signals are able to direct the sex-specific expression of a shared genome. A canonical picture of how this process works in insects emerged from decades of work on Drosophila. But recent years have seen an explosion of molecular-genetic and developmental work on a broad range of insects. Drawing these studies together, we describe the evolution of sexual dimorphism from a comparative perspective and argue that insect sex determination and differentiation systems are composites of rapidly evolving and highly conserved elements.
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19
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Mullen SP, VanKuren NW, Zhang W, Nallu S, Kristiansen EB, Wuyun Q, Liu K, Hill RI, Briscoe AD, Kronforst MR. Disentangling Population History and Character Evolution among Hybridizing Lineages. Mol Biol Evol 2021; 37:1295-1305. [PMID: 31930401 DOI: 10.1093/molbev/msaa004] [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: 12/28/2022] Open
Abstract
Understanding the origin and maintenance of adaptive phenotypic novelty is a central goal of evolutionary biology. However, both hybridization and incomplete lineage sorting can lead to genealogical discordance between the regions of the genome underlying adaptive traits and the remainder of the genome, decoupling inferences about character evolution from population history. Here, to disentangle these effects, we investigated the evolutionary origins and maintenance of Batesian mimicry between North American admiral butterflies (Limenitis arthemis) and their chemically defended model (Battus philenor) using a combination of de novo genome sequencing, whole-genome resequencing, and statistical introgression mapping. Our results suggest that balancing selection, arising from geographic variation in the presence or absence of the unpalatable model, has maintained two deeply divergent color patterning haplotypes that have been repeatedly sieved among distinct mimetic and nonmimetic lineages of Limenitis via introgressive hybridization.
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Affiliation(s)
- Sean P Mullen
- Department of Biology, Boston University, Boston, MA
| | | | - Wei Zhang
- School of Life Sciences, Peking University, Beijing, P.R. China
| | - Sumitha Nallu
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
| | | | - Qiqige Wuyun
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI
| | - Kevin Liu
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI
| | - Ryan I Hill
- Department of Biological Sciences, University of the Pacific, Stockton, CA
| | - Adriana D Briscoe
- Department of Ecology and Evolutionary Biology, University of California-Irvine, Irvine, CA
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20
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Gutiérrez-Valencia J, Hughes PW, Berdan EL, Slotte T. The Genomic Architecture and Evolutionary Fates of Supergenes. Genome Biol Evol 2021; 13:6178796. [PMID: 33739390 PMCID: PMC8160319 DOI: 10.1093/gbe/evab057] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2021] [Indexed: 12/25/2022] Open
Abstract
Supergenes are genomic regions containing sets of tightly linked loci that control multi-trait phenotypic polymorphisms under balancing selection. Recent advances in genomics have uncovered significant variation in both the genomic architecture as well as the mode of origin of supergenes across diverse organismal systems. Although the role of genomic architecture for the origin of supergenes has been much discussed, differences in the genomic architecture also subsequently affect the evolutionary trajectory of supergenes and the rate of degeneration of supergene haplotypes. In this review, we synthesize recent genomic work and historical models of supergene evolution, highlighting how the genomic architecture of supergenes affects their evolutionary fate. We discuss how recent findings on classic supergenes involved in governing ant colony social form, mimicry in butterflies, and heterostyly in flowering plants relate to theoretical expectations. Furthermore, we use forward simulations to demonstrate that differences in genomic architecture affect the degeneration of supergenes. Finally, we discuss implications of the evolution of supergene haplotypes for the long-term fate of balanced polymorphisms governed by supergenes.
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Affiliation(s)
- Juanita Gutiérrez-Valencia
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Sweden
| | - P William Hughes
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Sweden
| | - Emma L Berdan
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Sweden
| | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Sweden
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21
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Sato Y, Tsurui‐Sato K, Katoh M, Kimura R, Tatsuta H, Tsuji K. Population genetic structure and evolution of Batesian mimicry in Papilio polytes from the Ryukyu Islands, Japan, analyzed by genotyping-by-sequencing. Ecol Evol 2021; 11:872-886. [PMID: 33520172 PMCID: PMC7820160 DOI: 10.1002/ece3.7092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 01/03/2023] Open
Abstract
Batesian mimicry is a striking example of Darwinian evolution, in which a mimetic species resembles toxic or unpalatable model species, thereby receiving protection from predators. In some species exhibiting Batesian mimicry, nonmimetic individuals coexist as polymorphism in the same population despite the benefits of mimicry. In a previous study, we proposed that the abundance of mimics is limited by that of the models, leading to polymorphic Batesian mimicry in the swallowtail butterfly, Papilio polytes, on the Ryukyu Islands in Japan. We found that their mimic ratios (MRs), which varied among the Islands, were explained by the model abundance of each habitat, rather than isolation by distance or phylogenetic constraint based on the mitochondrial DNA (mtDNA) analysis. In the present study, this possibility was reexamined based on hundreds of nuclear single nucleotide polymorphisms (SNPs) of 93 P. polytes individuals from five Islands of the Ryukyus. We found that the population genetic and phylogenetic structures of P. polytes largely corresponded to the geographic arrangement of the habitat Islands, and the genetic distances among island populations show significant correlation with the geographic distances, which was not evident by the mtDNA-based analysis. A partial Mantel test controlling for the present SNP-based genetic distances revealed that the MRs of P. polytes were strongly correlated with the model abundance of each island, implying that negative frequency-dependent selection interacting with model species shaped and maintained the mimetic polymorphism. Taken together, our results support the possibility that predation pressure, not isolation by distance or other neutral factors, is a major driving force of evolution of the Batesian mimicry in P. polytes from the Ryukyus.
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Affiliation(s)
- Yukuto Sato
- Center for Strategic Research ProjectUniversity of the RyukyusOkinawaJapan
| | - Kaori Tsurui‐Sato
- Center for Strategic Research ProjectUniversity of the RyukyusOkinawaJapan
| | - Mitsuho Katoh
- Department of Agro‐Environmental SciencesFaculty of AgricultureUniversity of the RyukyusOkinawaJapan
- The United Graduate School of Agricultural SciencesKagoshima UniversityKagoshimaJapan
| | - Ryosuke Kimura
- Department of Human Biology and AnatomyGraduate School of MedicineUniversity of the RyukyusOkinawaJapan
| | - Haruki Tatsuta
- Department of Agro‐Environmental SciencesFaculty of AgricultureUniversity of the RyukyusOkinawaJapan
- The United Graduate School of Agricultural SciencesKagoshima UniversityKagoshimaJapan
| | - Kazuki Tsuji
- Department of Agro‐Environmental SciencesFaculty of AgricultureUniversity of the RyukyusOkinawaJapan
- The United Graduate School of Agricultural SciencesKagoshima UniversityKagoshimaJapan
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22
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Yoda S, Sakakura K, Kitamura T, KonDo Y, Sato K, Ohnuki R, Someya I, Komata S, Kojima T, Yoshioka S, Fujiwara H. Genetic switch in UV response of mimicry-related pale-yellow colors in Batesian mimic butterfly, Papilio polytes. SCIENCE ADVANCES 2021; 7:7/2/eabd6475. [PMID: 33523992 PMCID: PMC7793577 DOI: 10.1126/sciadv.abd6475] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/18/2020] [Indexed: 05/14/2023]
Abstract
In a Batesian mimic butterfly Papilio polytes, mimetic females resemble an unpalatable model, Pachliopta aristolochiae, but exhibit a different color pattern from nonmimetic females and males. In particular, the pale-yellow region on hind wings, which correspondingly sends important putative signals for mimicry and mate preference, is different in shape and chemical features between nonmimetic and mimetic morphs. Recently, we found that mimetic-type doublesex [dsx (H)] causes mimetic traits; however, the control of dimorphic pale-yellow colors remains unclear. Here, we revealed that dsx (H) switched the pale-yellow colors from UV-excited fluorescent type (nonmimetic) to UV-reflecting type (mimetic), by repressing the papiliochrome II synthesis genes and nanostructural changes in wing scales. Photoreceptor reactivities showed that some birds and butterflies could effectively recognize mimetic and nonmimetic pale-yellow colors, suggesting that a genetic switch in the UV response of pale-yellow colors may play essential roles in establishing the dimorphic female-limited Batesian mimicry.
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Affiliation(s)
- Shinichi Yoda
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Kousuke Sakakura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Tasuku Kitamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Yûsuke KonDo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Kazuki Sato
- Department of Physics, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Japan
| | - Ryosuke Ohnuki
- Department of Physics, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Japan
| | - Itsuki Someya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Shinya Komata
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Tetsuya Kojima
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Shinya Yoshioka
- Department of Physics, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Japan
| | - Haruhiko Fujiwara
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan.
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23
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Komata S, Kitamura T, Fujiwara H. Batesian mimicry has evolved with deleterious effects of the pleiotropic gene doublesex. Sci Rep 2020; 10:21333. [PMID: 33288816 PMCID: PMC7721872 DOI: 10.1038/s41598-020-78055-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 11/18/2020] [Indexed: 11/19/2022] Open
Abstract
Dimorphic female-limited Batesian mimicry in the swallowtail butterfly Papilio polytes is regulated by the supergene locus H, harbouring the mimetic (H) and non-mimetic (h) doublesex (dsx) gene. In the present study, we demonstrated that dsx-H negatively affects the number of eggs laid, hatching rate, larval survival rate, and adult lifespan. When crossed with hh males, the number of eggs laid of mimetic females (genotype HH) was lower than that of non-mimetic females (hh). Moreover, hh and Hh females laid fewer eggs when crossed with HH males. The hatching and larval survival rates were lower when both female and male parents harboured dsx-H. The adult lifespan of HH females was shorter than that of hh females, while it was similar in males regardless of the genotype. These findings suggest the presence of a cost-benefit balance of Batesian mimicry, which is evolved to avoid predation but is accompanied by physiological deficits, in this species.
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Affiliation(s)
- Shinya Komata
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Tasuku Kitamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Haruhiko Fujiwara
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan.
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24
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Deshmukh R, Lakhe D, Kunte K. Tissue-specific developmental regulation and isoform usage underlie the role of doublesex in sex differentiation and mimicry in Papilio swallowtails. ROYAL SOCIETY OPEN SCIENCE 2020; 7:200792. [PMID: 33047041 PMCID: PMC7540742 DOI: 10.1098/rsos.200792] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
Adaptive phenotypes often arise by rewiring existing developmental networks. Co-option of transcription factors in novel contexts has facilitated the evolution of ecologically important adaptations. doublesex (dsx) governs fundamental sex differentiation during embryonic stages and has been co-opted to regulate diverse secondary sexual dimorphisms during pupal development of holometabolous insects. In Papilio polytes, dsx regulates female-limited mimetic polymorphism, resulting in mimetic and non-mimetic forms. To understand how a critical gene such as dsx regulates novel wing patterns while maintaining its basic function in sex differentiation, we traced its expression through metamorphosis in P. polytes using developmental transcriptome data. We found three key dsx expression peaks: (i) eggs in pre- and post-ovisposition stages; (ii) developing wing discs and body in final larval instar; and (iii) 3-day pupae. We identified potential dsx targets using co-expression and differential expression analysis, and found distinct, non-overlapping sets of genes-containing putative dsx-binding sites-in developing wings versus abdominal tissue and in mimetic versus non-mimetic individuals. This suggests that dsx regulates distinct downstream targets in different tissues and wing colour morphs and has perhaps acquired new, previously unknown targets, for regulating mimetic polymorphism. Additionally, we observed that the three female isoforms of dsx were differentially expressed across stages (from eggs to adults) and tissues and differed in their protein structure. This may promote differential protein-protein interactions for each isoform and facilitate sub-functionalization of dsx activity across its isoforms. Our findings suggest that dsx employs tissue-specific downstream effectors and partitions its functions across multiple isoforms to regulate primary and secondary sexual dimorphism through insect development.
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25
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Bortoluzzi C, Megens HJ, Bosse M, Derks MFL, Dibbits B, Laport K, Weigend S, Groenen MAM, Crooijmans RPMA. Parallel Genetic Origin of Foot Feathering in Birds. Mol Biol Evol 2020; 37:2465-2476. [PMID: 32344429 PMCID: PMC7475038 DOI: 10.1093/molbev/msaa092] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Understanding the genetic basis of similar phenotypes shared between lineages is a long-lasting research interest. Even though animal evolution offers many examples of parallelism, for many phenotypes little is known about the underlying genes and mutations. We here use a combination of whole-genome sequencing, expression analyses, and comparative genomics to study the parallel genetic origin of ptilopody (Pti) in chicken. Ptilopody (or foot feathering) is a polygenic trait that can be observed in domesticated and wild avian species and is characterized by the partial or complete development of feathers on the ankle and feet. In domesticated birds, ptilopody is easily selected to fixation, though extensive variation in the type and level of feather development is often observed. By means of a genome-wide association analysis, we identified two genomic regions associated with ptilopody. At one of the loci, we identified a 17-kb deletion affecting PITX1 expression, a gene known to encode a transcription regulator of hindlimb identity and development. Similarly to pigeon, at the second loci, we observed ectopic expression of TBX5, a gene involved in forelimb identity and a key determinant of foot feather development. We also observed that the trait evolved only once as foot-feathered birds share the same haplotype upstream TBX5. Our findings indicate that in chicken and pigeon ptilopody is determined by the same set of genes that affect similar molecular pathways. Our study confirms that ptilopody has evolved through parallel evolution in chicken and pigeon.
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Affiliation(s)
- Chiara Bortoluzzi
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Mirte Bosse
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Martijn F L Derks
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Bert Dibbits
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Kimberly Laport
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Steffen Weigend
- Friedrich-Loeffler-Institut (FLI), Institute of Farm Animal Genetics, Neustadt, Germany
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
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26
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Almeida P, Proux-Wera E, Churcher A, Soler L, Dainat J, Pucholt P, Nordlund J, Martin T, Rönnberg-Wästljung AC, Nystedt B, Berlin S, Mank JE. Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion. BMC Biol 2020; 18:78. [PMID: 32605573 PMCID: PMC7329446 DOI: 10.1186/s12915-020-00808-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/11/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear. RESULTS Here, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes. CONCLUSIONS Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.
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Affiliation(s)
- Pedro Almeida
- Department of Genetics, Evolution & Environment, University College London, London, UK.
| | - Estelle Proux-Wera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Allison Churcher
- Department of Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jacques Dainat
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Pascal Pucholt
- Department of Medical Sciences, Section of Rheumatology, Uppsala University, Uppsala, Sweden
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, National Genomics Infrastructure, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tom Martin
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ann-Christin Rönnberg-Wästljung
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sofia Berlin
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Judith E Mank
- Department of Genetics, Evolution & Environment, University College London, London, UK
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
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27
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Almeida P, Proux-Wera E, Churcher A, Soler L, Dainat J, Pucholt P, Nordlund J, Martin T, Rönnberg-Wästljung AC, Nystedt B, Berlin S, Mank JE. Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion. BMC Biol 2020. [PMID: 32605573 DOI: 10.1101/589804v1.full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear. RESULTS Here, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes. CONCLUSIONS Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.
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Affiliation(s)
- Pedro Almeida
- Department of Genetics, Evolution & Environment, University College London, London, UK.
| | - Estelle Proux-Wera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Allison Churcher
- Department of Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jacques Dainat
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Pascal Pucholt
- Department of Medical Sciences, Section of Rheumatology, Uppsala University, Uppsala, Sweden
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, National Genomics Infrastructure, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tom Martin
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ann-Christin Rönnberg-Wästljung
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sofia Berlin
- Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Judith E Mank
- Department of Genetics, Evolution & Environment, University College London, London, UK
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
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28
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Timmermans MJTN, Srivathsan A, Collins S, Meier R, Vogler AP. Mimicry diversification in Papilio dardanus via a genomic inversion in the regulatory region of engrailed- invected. Proc Biol Sci 2020; 287:20200443. [PMID: 32345166 DOI: 10.1098/rspb.2020.0443] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Polymorphic Batesian mimics exhibit multiple protective morphs that each mimic a different noxious model. Here, we study the genomic transitions leading to the evolution of different mimetic wing patterns in the polymorphic Mocker Swallowtail Papilio dardanus. We generated a draft genome (231 Mb over 30 chromosomes) and re-sequenced individuals of three morphs. Genome-wide single nucleotide polymorphism (SNP) analysis revealed elevated linkage disequilibrium and divergence between morphs in the regulatory region of engrailed, a developmental gene previously implicated in the mimicry switch. The diverged region exhibits a discrete chromosomal inversion (of 40 kb) relative to the ancestral orientation that is associated with the cenea morph, but not with the bottom-recessive hippocoonides morph or with non-mimetic allopatric populations. The functional role of this inversion in the expression of the novel phenotype is currently unknown, but by preventing recombination, it allows the stable inheritance of divergent alleles enabling geographic spread and local coexistence of multiple adaptive morphs.
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Affiliation(s)
- Martijn J T N Timmermans
- Department of Life Sciences, Natural History Museum, London, UK.,Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, UK.,Department of Natural Sciences, Middlesex University, London, UK
| | - Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Steve Collins
- African Butterfly Research Institute, Nairobi, Kenya
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore.,Lee Kong Chian Natural History Museum, National University of Singapore, Singapore
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK.,Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, UK
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29
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Orteu A, Jiggins CD. The genomics of coloration provides insights into adaptive evolution. Nat Rev Genet 2020; 21:461-475. [PMID: 32382123 DOI: 10.1038/s41576-020-0234-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2020] [Indexed: 01/31/2023]
Abstract
Coloration is an easily quantifiable visual trait that has proven to be a highly tractable system for genetic analysis and for studying adaptive evolution. The application of genomic approaches to evolutionary studies of coloration is providing new insight into the genetic architectures underlying colour traits, including the importance of large-effect mutations and supergenes, the role of development in shaping genetic variation and the origins of adaptive variation, which often involves adaptive introgression. Improved knowledge of the genetic basis of traits can facilitate field studies of natural selection and sexual selection, making it possible for strong selection and its influence on the genome to be demonstrated in wild populations.
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Affiliation(s)
- Anna Orteu
- Department of Zoology, University of Cambridge, Cambridge, UK.
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK.
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30
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Yoda S, Otaguro E, Nobuta M, Fujiwara H. Molecular Mechanisms Underlying Pupal Protective Color Switch in Papilio polytes Butterflies. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00051] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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31
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VanKuren NW, Massardo D, Nallu S, Kronforst MR. Butterfly Mimicry Polymorphisms Highlight Phylogenetic Limits of Gene Reuse in the Evolution of Diverse Adaptations. Mol Biol Evol 2020; 36:2842-2853. [PMID: 31504750 DOI: 10.1093/molbev/msz194] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Some genes have repeatedly been found to control diverse adaptations in a wide variety of organisms. Such gene reuse reveals not only the diversity of phenotypes these unique genes control but also the composition of developmental gene networks and the genetic routes available to and taken by organisms during adaptation. However, the causes of gene reuse remain unclear. A small number of large-effect Mendelian loci control a huge diversity of mimetic butterfly wing color patterns, but reasons for their reuse are difficult to identify because the genetic basis of mimicry has primarily been studied in two systems with correlated factors: female-limited Batesian mimicry in Papilio swallowtails (Papilionidae) and non-sex-limited Müllerian mimicry in Heliconius longwings (Nymphalidae). Here, we break the correlation between phylogenetic relationship and sex-limited mimicry by identifying loci controlling female-limited mimicry polymorphism Hypolimnas misippus (Nymphalidae) and non-sex-limited mimicry polymorphism in Papilio clytia (Papilionidae). The Papilio clytia polymorphism is controlled by the genome region containing the gene cortex, the classic P supergene in Heliconius numata, and loci controlling color pattern variation across Lepidoptera. In contrast, female-limited mimicry polymorphism in Hypolimnas misippus is associated with a locus not previously implicated in color patterning. Thus, although many species repeatedly converged on cortex and its neighboring genes over 120 My of evolution of diverse color patterns, female-limited mimicry polymorphisms each evolved using a different gene. Our results support conclusions that gene reuse occurs mainly within ∼10 My and highlight the puzzling diversity of genes controlling seemingly complex female-limited mimicry polymorphisms.
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Affiliation(s)
| | - Darli Massardo
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL
| | - Sumitha Nallu
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL
| | - Marcus R Kronforst
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL
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32
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Palmer DH, Kronforst MR. A shared genetic basis of mimicry across swallowtail butterflies points to ancestral co-option of doublesex. Nat Commun 2020; 11:6. [PMID: 31900419 PMCID: PMC6941989 DOI: 10.1038/s41467-019-13859-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 12/03/2019] [Indexed: 11/09/2022] Open
Abstract
Uncovering whether convergent adaptations share a genetic basis is consequential for understanding the evolution of phenotypic diversity. This information can help us understand the extent to which shared ancestry or independent evolution shape adaptive phenotypes. In this study, we first ask whether the same genes underlie polymorphic mimicry in Papilio swallowtail butterflies. By comparing signatures of genetic variation between polymorphic and monomorphic species, we then investigate how ancestral variation, hybridization, and independent evolution contributed to wing pattern diversity in this group. We report that a single gene, doublesex (dsx), controls mimicry across multiple taxa, but with species-specific patterns of genetic differentiation and linkage disequilibrium. In contrast to widespread examples of phenotypic evolution driven by introgression, our analyses reveal distinct mimicry alleles. We conclude that mimicry evolution in this group was likely facilitated by ancestral polymorphism resulting from early co-option of dsx as a mimicry locus, and that evolutionary turnover of dsx alleles may underlie the wing pattern diversity of extant polymorphic and monomorphic lineages.
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Affiliation(s)
- Daniela H Palmer
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL, 60637, USA. .,Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA. .,Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| | - Marcus R Kronforst
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL, 60637, USA.,Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA
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33
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An Ancient and Eroded Social Supergene Is Widespread across Formica Ants. Curr Biol 2020; 30:304-311.e4. [PMID: 31902719 DOI: 10.1016/j.cub.2019.11.032] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 08/10/2019] [Accepted: 11/11/2019] [Indexed: 12/25/2022]
Abstract
Supergenes, clusters of tightly linked genes, play a key role in the evolution of complex adaptive variation [1, 2]. Although supergenes have been identified in many species, we lack an understanding of their origin, evolution, and persistence [3]. Here, we uncover 20-40 Ma of evolutionary history of a supergene associated with polymorphic social organization in Formica ants [4]. We show that five Formica species exhibit homologous divergent haplotypes spanning 11 Mbp on chromosome 3. Despite the supergene's size, only 142 single nucleotide polymorphisms (SNPs) consistently distinguish alternative supergene haplotypes across all five species. These conserved trans-species SNPs are localized in a small number of disjunct clusters distributed across the supergene. This unexpected pattern of divergence indicates that the Formica supergene does not follow standard models of sex chromosome evolution, in which distinct evolutionary strata reflect an expanding region of suppressed recombination [5]. We propose an alternative "eroded strata model" in which clusters of conserved trans-species SNPs represent functionally important areas maintained by selection in the face of rare recombination between ancestral haplotypes. The comparison of whole-genome sequences across 10 additional Formica species reveals that the most conserved region of the supergene contains a transcription factor essential for motor neuron development in Drosophila [6]. The discovery that a very small portion of this large and ancient supergene harbors conserved trans-species SNPs linked to colony social organization suggests that the ancestral haplotypes have been eroded by recombination, with selection preserving differentiation at one or a few genes generating alternative social organization.
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34
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Hines HM, Rahman SR. Evolutionary genetics in insect phenotypic radiations: the value of a comparative genomic approach. CURRENT OPINION IN INSECT SCIENCE 2019; 36:90-95. [PMID: 31541856 DOI: 10.1016/j.cois.2019.08.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 08/22/2019] [Accepted: 08/26/2019] [Indexed: 06/10/2023]
Abstract
Expanding genome sequencing and transgenic technologies are enabling the discovery of genes driving phenotypic diversity across insect taxa. Limitations in downstream functional genetic approaches, however, have been an obstacle for developing non-model systems for evolutionary genetics. Phenotypically diverse radiations, such as those exhibiting convergence and divergence as a result of mimicry, are ideal for evolutionary genetics as they can lead to insights using comparative genomic approaches alone. The varied and repeated instances of phenotypes in highly polymorphic systems allow assessment of whether similar loci are repeatedly targeted by selection and can inform how alleles sort across lineages. Comparative genomics of these taxa can be used to decipher components of gene regulatory networks, dissect regulatory regions, and validate genes.
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Affiliation(s)
- Heather M Hines
- Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA.
| | - Sarthok Rasique Rahman
- Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
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35
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Lu S, Yang J, Dai X, Xie F, He J, Dong Z, Mao J, Liu G, Chang Z, Zhao R, Wan W, Zhang R, Li Y, Wang W, Li X. Chromosomal-level reference genome of Chinese peacock butterfly (Papilio bianor) based on third-generation DNA sequencing and Hi-C analysis. Gigascience 2019; 8:giz128. [PMID: 31682256 PMCID: PMC6827417 DOI: 10.1093/gigascience/giz128] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 08/18/2019] [Accepted: 10/04/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Papilio bianor Cramer, 1777 (commonly known as the Chinese peacock butterfly) (Insecta, Lepidoptera, Papilionidae) is a widely distributed swallowtail butterfly with a wide number of geographic populations ranging from the southeast of Russia to China, Japan, India, Vietnam, Myanmar, and Thailand. Its wing color consists of both pigmentary colored scales (black, reddish) and structural colored scales (iridescent blue or green dust). A high-quality reference genome of P. bianor is an important foundation for investigating iridescent color evolution, phylogeography, and the evolution of swallowtail butterflies. FINDINGS We obtained a chromosome-level de novo genome assembly of the highly heterozygous P. bianor using long Pacific Biosciences sequencing reads and high-throughput chromosome conformation capture technology. The final assembly is 421.52 Mb on 30 chromosomes (29 autosomes and 1 Z sex chromosome) with 13.12 Mb scaffold N50. In total, 15,375 protein-coding genes and 233.09 Mb of repetitive sequences were identified. Phylogenetic analyses indicated that P. bianor separated from a common ancestor of swallowtails ∼23.69-36.04 million years ago. Demographic history suggested that the population expansion of this species from the last interglacial period to the last glacial maximum possibly resulted from its decreased natural enemies and its adaptation to climate change during the glacial period. CONCLUSIONS We present a high-quality chromosome-level reference genome of P. bianor using long-read single-molecule sequencing and Hi-C-based chromatin interaction maps. Our results lay the foundation for exploring the genetic basis of special biological features of P. bianor and also provide a useful data source for comparative genomics and phylogenomics among butterflies and moths.
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Affiliation(s)
- Sihan Lu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, No.1 Dongxiang Road, Chang'an District, Xi'an, Shaanxi 710129, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No.32 Jiaochang Raod, Kunming, Yunnan 650223, China
| | - Jie Yang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, No.1 Dongxiang Road, Chang'an District, Xi'an, Shaanxi 710129, China
| | - Xuelei Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No.22 Xinong Road,Yangling, Shaanxi 712100, China
| | - Feiang Xie
- School of Marine Science and Technology, Zhejiang Ocean University, No.1 Haida South Road, Lincheng Changzhi Island, Zhoushan, Zhejiang 316022, China
| | - Jinwu He
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, No.1 Dongxiang Road, Chang'an District, Xi'an, Shaanxi 710129, China
| | - Zhiwei Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No.32 Jiaochang Raod, Kunming, Yunnan 650223, China
| | - Junlai Mao
- School of Marine Science and Technology, Zhejiang Ocean University, No.1 Haida South Road, Lincheng Changzhi Island, Zhoushan, Zhejiang 316022, China
| | - Guichun Liu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, No.1 Dongxiang Road, Chang'an District, Xi'an, Shaanxi 710129, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No.32 Jiaochang Raod, Kunming, Yunnan 650223, China
| | - Zhou Chang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No.32 Jiaochang Raod, Kunming, Yunnan 650223, China
| | - Ruoping Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No.32 Jiaochang Raod, Kunming, Yunnan 650223, China
| | - Wenting Wan
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, No.1 Dongxiang Road, Chang'an District, Xi'an, Shaanxi 710129, China
| | - Ru Zhang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, No.1 Dongxiang Road, Chang'an District, Xi'an, Shaanxi 710129, China
| | - Yuan Li
- Nextomics Biosciences Institute, No.666 Gaoxin Road, Wuhan, Hubei 430000, China
| | - Wen Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, No.1 Dongxiang Road, Chang'an District, Xi'an, Shaanxi 710129, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No.32 Jiaochang Raod, Kunming, Yunnan 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, No.32 Jiaochang Raod, Kunming, Yunnan 650223, China
| | - Xueyan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No.32 Jiaochang Raod, Kunming, Yunnan 650223, China
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36
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Ye CY, Tang W, Wu D, Jia L, Qiu J, Chen M, Mao L, Lin F, Xu H, Yu X, Lu Y, Wang Y, Olsen KM, Timko MP, Fan L. Genomic evidence of human selection on Vavilovian mimicry. Nat Ecol Evol 2019; 3:1474-1482. [PMID: 31527731 DOI: 10.1038/s41559-019-0976-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/05/2019] [Indexed: 01/25/2023]
Abstract
Vavilovian mimicry is an evolutionary process by which weeds evolve to resemble domesticated crop plants and is thought to be the result of unintentional selection by humans. Unravelling its molecular mechanisms will extend our knowledge of mimicry and contribute to our understanding of the origin and evolution of agricultural weeds, an important component of crop biology. To this end, we compared mimetic and non-mimetic populations of Echinochloa crus-galli from the Yangtze River basin phenotypically and by genome resequencing, and we show that this weed in rice paddies has evolved a small tiller angle, allowing it to phenocopy cultivated rice at the seedling stage. We demonstrate that mimetic lines evolved from the non-mimetic population as recently as 1,000 yr ago and were subject to a genetic bottleneck, and that genomic regions containing 87 putative plant architecture-related genes (including LAZY1, a key gene controlling plant tiller angle) were under selection during the mimicry process. Our data provide genome-level evidence for the action of human selection on Vavilovian mimicry.
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Affiliation(s)
- Chu-Yu Ye
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Wei Tang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Dongya Wu
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Lei Jia
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jie Qiu
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Meihong Chen
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Lingfeng Mao
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Feng Lin
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Haiming Xu
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiaoyue Yu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yongliang Lu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yonghong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Longjiang Fan
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
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37
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Hanly JJ, Wallbank RWR, McMillan WO, Jiggins CD. Conservation and flexibility in the gene regulatory landscape of heliconiine butterfly wings. EvoDevo 2019; 10:15. [PMID: 31341608 PMCID: PMC6631869 DOI: 10.1186/s13227-019-0127-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 06/21/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Many traits evolve by cis-regulatory modification, by which changes to noncoding sequences affect the binding affinity for available transcription factors and thus modify the expression profile of genes. Multiple examples of cis-regulatory evolution have been described at pattern switch genes responsible for butterfly wing pattern polymorphism, including in the diverse neotropical genus Heliconius, but the identities of the factors that can regulate these switch genes have not been identified. RESULTS We investigated the spatial transcriptomic landscape across the wings of three closely related butterfly species, two of which have a convergently evolved co-mimetic pattern and the other having a divergent pattern. We identified candidate factors for regulating the expression of wing patterning genes, including transcription factors with a conserved expression profile in all three species, and others, including both transcription factors and Wnt pathway genes, with markedly different profiles in each of the three species. We verified the conserved expression profile of the transcription factor homothorax by immunofluorescence and showed that its expression profile strongly correlates with that of the selector gene optix in butterflies with the Amazonian forewing pattern element 'dennis.' CONCLUSION Here we show that, in addition to factors with conserved expression profiles like homothorax, there are also a variety of transcription factors and signaling pathway components that appear to vary in their expression profiles between closely related butterfly species, highlighting the importance of genome-wide regulatory evolution between species.
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Affiliation(s)
- Joseph J. Hanly
- Department of Zoology, University of Cambridge, Downing St., Cambridge, CB2 3EJ UK
- Smithsonian Tropical Research Institute, Gamboa, Panama
- Biological Sciences, The George Washington University, Washington, DC 20052 USA
| | - Richard W. R. Wallbank
- Department of Zoology, University of Cambridge, Downing St., Cambridge, CB2 3EJ UK
- Smithsonian Tropical Research Institute, Gamboa, Panama
| | | | - Chris D. Jiggins
- Department of Zoology, University of Cambridge, Downing St., Cambridge, CB2 3EJ UK
- Smithsonian Tropical Research Institute, Gamboa, Panama
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Iijima T, Yoda S, Fujiwara H. The mimetic wing pattern of Papilio polytes butterflies is regulated by a doublesex-orchestrated gene network. Commun Biol 2019; 2:257. [PMID: 31312726 PMCID: PMC6620351 DOI: 10.1038/s42003-019-0510-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 06/18/2019] [Indexed: 12/27/2022] Open
Abstract
The swallowtail butterfly Papilio polytes is sexually dimorphic and exhibits female-limited Batesian mimicry. This species also has two female forms, a non-mimetic form with male-like wing patterns, and a mimetic form resembling an unpalatable model, Pachliopta aristolochiae. The mimicry locus H constitutes a dimorphic Mendelian 'supergene', including a transcription factor gene doublesex (dsx). However, how the mimetic-type dsx (dsx-H) orchestrates the downstream gene network and causes the mimetic traits remains unclear. Here we performed RNA-seq-based gene screening and found that Wnt1 and Wnt6 are up-regulated by dsx-H during the early pupal stage and are involved in the red/white pigmentation and patterning of mimetic female wings. In contrast, a homeobox gene abdominal-A is repressed by dsx-H and involved in the non-mimetic colouration pattern. These findings suggest that dual regulation by dsx-H, induction of mimetic gene networks and repression of non-mimetic gene networks, is essential for the switch from non-mimetic to mimetic pattern in mimetic female wings.
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Affiliation(s)
- Takuro Iijima
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562 Japan
| | - Shinichi Yoda
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562 Japan
| | - Haruhiko Fujiwara
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562 Japan
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Baral S, Arumugam G, Deshmukh R, Kunte K. Genetic architecture and sex-specific selection govern modular, male-biased evolution of doublesex. SCIENCE ADVANCES 2019; 5:eaau3753. [PMID: 31086812 PMCID: PMC6506240 DOI: 10.1126/sciadv.aau3753] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 03/29/2019] [Indexed: 06/09/2023]
Abstract
doublesex regulates early embryonic sex differentiation in holometabolous insects, along with the development of species-, sex-, and morph-specific adaptations during pupal stages. How does a highly conserved gene with a critical developmental role also remain functionally dynamic enough to gain ecologically important adaptations that are divergent in sister species? We analyzed patterns of exon-level molecular evolution and protein structural homology of doublesex from 145 species of four insect orders representing 350 million years of divergence. This analysis revealed that evolution of doublesex was governed by a modular architecture: Functional domains and female-specific regions were highly conserved, whereas male-specific sequences and protein structures evolved up to thousand-fold faster, with sites under pervasive and/or episodic positive selection. This pattern of sex bias was reversed in Hymenoptera. Thus, highly conserved yet dynamic master regulators such as doublesex may partition specific conserved and novel functions in different genic modules at deep evolutionary time scales.
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