1
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McAllester CS, Pool JE. Inversions Can Accumulate Balanced Sexual Antagonism: Evidence from Simulations and Drosophila Experiments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.02.560529. [PMID: 37873205 PMCID: PMC10592935 DOI: 10.1101/2023.10.02.560529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Chromosomal inversion polymorphisms can be common, but the causes of their persistence are often unclear. We propose a model for the maintenance of inversion polymorphism, which requires that some variants contribute antagonistically to two phenotypes, one of which has negative frequency-dependent fitness. These conditions yield a form of frequency-dependent disruptive selection, favoring two predominant haplotypes segregating alleles that favor opposing antagonistic phenotypes. An inversion associated with one haplotype can reduce the fitness load incurred by generating recombinant offspring, reinforcing its linkage to the haplotype and enabling both haplotypes to accumulate more antagonistic variants than expected otherwise. We develop and apply a forward simulator to examine these dynamics under a tradeoff between survival and male display. These simulations indeed generate inversion-associated haplotypes with opposing sex-specific fitness effects. Antagonism strengthens with time, and can ultimately yield karyotypes at surprisingly predictable frequencies, with striking genotype frequency differences between sexes and between developmental stages. To test whether this model may contribute to well-studied yet enigmatic inversion polymorphisms in Drosophila melanogaster, we track inversion frequencies in laboratory crosses to test whether they influence male reproductive success or survival. We find that two of the four tested inversions show significant evidence for the tradeoff examined, with In(3R)K favoring survival and In(3L)Ok favoring male reproduction. In line with the apparent sex-specific fitness effects implied for both of those inversions, In(3L)Ok was also found to be less costly to the viability and/or longevity of males than females, whereas In(3R)K was more beneficial to female survival. Based on this work, we expect that balancing selection on antagonistically pleiotropic traits may provide a significant and underappreciated contribution to the maintenance of natural inversion polymorphism.
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Affiliation(s)
| | - John E. Pool
- Laboratory of Genetics, University of Wisconsin – Madison, USA
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2
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Grieshop K, Ho EKH, Kasimatis KR. Dominance reversals: the resolution of genetic conflict and maintenance of genetic variation. Proc Biol Sci 2024; 291:20232816. [PMID: 38471544 DOI: 10.1098/rspb.2023.2816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 02/05/2024] [Indexed: 03/14/2024] Open
Abstract
Beneficial reversals of dominance reduce the costs of genetic trade-offs and can enable selection to maintain genetic variation for fitness. Beneficial dominance reversals are characterized by the beneficial allele for a given context (e.g. habitat, developmental stage, trait or sex) being dominant in that context but recessive where deleterious. This context dependence at least partially mitigates the fitness consequence of heterozygotes carrying one non-beneficial allele for their context and can result in balancing selection that maintains alternative alleles. Dominance reversals are theoretically plausible and are supported by mounting empirical evidence. Here, we highlight the importance of beneficial dominance reversals as a mechanism for the mitigation of genetic conflict and review the theory and empirical evidence for them. We identify some areas in need of further research and development and outline three methods that could facilitate the identification of antagonistic genetic variation (dominance ordination, allele-specific expression and allele-specific ATAC-Seq (assay for transposase-accessible chromatin with sequencing)). There is ample scope for the development of new empirical methods as well as reanalysis of existing data through the lens of dominance reversals. A greater focus on this topic will expand our understanding of the mechanisms that resolve genetic conflict and whether they maintain genetic variation.
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Affiliation(s)
- Karl Grieshop
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada M5S 1A1
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Eddie K H Ho
- Department of Biology, Reed College, 3203 SE Woodstock Blvd, Portland, OR 97202, USA
| | - Katja R Kasimatis
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada M5S 1A1
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
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3
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Demircioğlu A. The effect of data resampling methods in radiomics. Sci Rep 2024; 14:2858. [PMID: 38310165 PMCID: PMC10838284 DOI: 10.1038/s41598-024-53491-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/01/2024] [Indexed: 02/05/2024] Open
Abstract
Radiomic datasets can be class-imbalanced, for instance, when the prevalence of diseases varies notably, meaning that the number of positive samples is much smaller than that of negative samples. In these cases, the majority class may dominate the model's training and thus negatively affect the model's predictive performance, leading to bias. Therefore, resampling methods are often utilized to class-balance the data. However, several resampling methods exist, and neither their relative predictive performance nor their impact on feature selection has been systematically analyzed. In this study, we aimed to measure the impact of nine resampling methods on radiomic models utilizing a set of fifteen publicly available datasets regarding their predictive performance. Furthermore, we evaluated the agreement and similarity of the set of selected features. Our results show that applying resampling methods did not improve the predictive performance on average. On specific datasets, slight improvements in predictive performance (+ 0.015 in AUC) could be seen. A considerable disagreement on the set of selected features was seen (only 28.7% of features agreed), which strongly impedes feature interpretability. However, selected features are similar when considering their correlation (82.9% of features correlated on average).
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Affiliation(s)
- Aydin Demircioğlu
- Institute of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, Hufelandstraße 55, 45147, Essen, Germany.
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4
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Ffrench-Constant RH, Bennie J, Gordon IJ, Depew L, Smith DAS. Penetrance interactions of colour pattern loci in the African Monarch and their implications for the evolution of dominance. Ecol Evol 2024; 14:e11024. [PMID: 38414566 PMCID: PMC10898957 DOI: 10.1002/ece3.11024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 02/29/2024] Open
Abstract
Scoring the penetrance of heterozygotes in complex phenotypes, like colour pattern, is difficult and complicates the analysis of systems in which dominance is incomplete or evolving. The African Monarch (Danaus chrysippus) represents an example where colour pattern heterozygotes, formed in the contact zone between the different subspecies, show such intermediate dominance. Colour pattern in this aposematic butterfly is controlled by three loci A, B and C. The B and C loci are closely linked in a B/C supergene and significant interaction of B and C phenotypes is therefore expected via linkage alone. The A locus, however, is not linked to B/C and is found on a different chromosome. To study interactions between these loci we generated colour pattern heterozygotes by crossing males and females bearing different A and B/C genotypes, collected from different parts of Africa. We derived a novel scoring system for the expressivity of the heterozygotes and, as predicted, we found significant interactions between the genotypes of the closely linked B and C loci. Surprisingly, however, we also found highly significant interactions between C and the unlinked A locus, modifications that generally increased the resemblance of heterozygotes to homozygous ancestors. In contrast, we found no difference in the penetrance of any of the corresponding heterozygotes from crosses conducted either in allopatry or sympatry, in reciprocal crosses of males and females, or in the presence or absence of endosymbiont mediated male-killing or its associated neoW mediated sex-linkage of colour pattern. Together, this data supports the idea that the different colour morphs of the African Monarch meet transiently in the East African contact zone and that genetic modifiers act to mask inappropriate expression of colour patterns in the incorrect environments.
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Affiliation(s)
| | - Jonathan Bennie
- Centre for Geography and Environmental Science University of Exeter Penryn UK
| | - Ian J Gordon
- Department of Biology, College of Science and Technology University of Rwanda Kigali Rwanda
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5
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Coulmance F, Akkaynak D, Le Poul Y, Höppner MP, McMillan WO, Puebla O. Phenotypic and genomic dissection of colour pattern variation in a reef fish radiation. Mol Ecol 2024; 33:e17047. [PMID: 37337919 DOI: 10.1111/mec.17047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 05/04/2023] [Accepted: 05/30/2023] [Indexed: 06/21/2023]
Abstract
Coral reefs rank among the most diverse species assemblages on Earth. A particularly striking aspect of coral reef communities is the variety of colour patterns displayed by reef fishes. Colour pattern is known to play a central role in the ecology and evolution of reef fishes through, for example, signalling or camouflage. Nevertheless, colour pattern is a complex trait in reef fishes-actually a collection of traits-that is difficult to analyse in a quantitative and standardized way. This is the challenge that we address in this study using the hamlets (Hypoplectrus spp., Serranidae) as a model system. Our approach involves a custom underwater camera system to take orientation- and size-standardized photographs in situ, colour correction, alignment of the fish images with a combination of landmarks and Bézier curves, and principal component analysis on the colour value of each pixel of each aligned fish. This approach identifies the major colour pattern elements that contribute to phenotypic variation in the group. Furthermore, we complement the image analysis with whole-genome sequencing to run a multivariate genome-wide association study for colour pattern variation. This second layer of analysis reveals sharp association peaks along the hamlet genome for each colour pattern element and allows to characterize the phenotypic effect of the single nucleotide polymorphisms that are most strongly associated with colour pattern variation at each association peak. Our results suggest that the diversity of colour patterns displayed by the hamlets is generated by a modular genomic and phenotypic architecture.
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Affiliation(s)
- Floriane Coulmance
- Leibniz Center for Tropical Marine Research, Bremen, Germany
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany
- Smithsonian Tropical Research Institute (STRI), Panama, Republic of Panama
| | - Derya Akkaynak
- Hatter Department of Marine Technologies, University of Haifa, Haifa, Israel
- Interuniversity Institute of Marine Sciences, Eilat, Israel
| | - Yann Le Poul
- Ludwig-Maximilians-Universität München, Munich, Germany
| | - Marc P Höppner
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - W Owen McMillan
- Smithsonian Tropical Research Institute (STRI), Panama, Republic of Panama
| | - Oscar Puebla
- Leibniz Center for Tropical Marine Research, Bremen, Germany
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany
- Smithsonian Tropical Research Institute (STRI), Panama, Republic of Panama
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6
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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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7
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Thawornwattana Y, Seixas F, Yang Z, Mallet J. Major patterns in the introgression history of Heliconius butterflies. eLife 2023; 12:RP90656. [PMID: 38108819 PMCID: PMC10727504 DOI: 10.7554/elife.90656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023] Open
Abstract
Gene flow between species, although usually deleterious, is an important evolutionary process that can facilitate adaptation and lead to species diversification. It also makes estimation of species relationships difficult. Here, we use the full-likelihood multispecies coalescent (MSC) approach to estimate species phylogeny and major introgression events in Heliconius butterflies from whole-genome sequence data. We obtain a robust estimate of species branching order among major clades in the genus, including the 'melpomene-silvaniform' group, which shows extensive historical and ongoing gene flow. We obtain chromosome-level estimates of key parameters in the species phylogeny, including species divergence times, present-day and ancestral population sizes, as well as the direction, timing, and intensity of gene flow. Our analysis leads to a phylogeny with introgression events that differ from those obtained in previous studies. We find that Heliconius aoede most likely represents the earliest-branching lineage of the genus and that 'silvaniform' species are paraphyletic within the melpomene-silvaniform group. Our phylogeny provides new, parsimonious histories for the origins of key traits in Heliconius, including pollen feeding and an inversion involved in wing pattern mimicry. Our results demonstrate the power and feasibility of the full-likelihood MSC approach for estimating species phylogeny and key population parameters despite extensive gene flow. The methods used here should be useful for analysis of other difficult species groups with high rates of introgression.
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Affiliation(s)
| | - Fernando Seixas
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College LondonLondonUnited Kingdom
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
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8
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Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel CL, Rafajlović M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. How chromosomal inversions reorient the evolutionary process. J Evol Biol 2023; 36:1761-1782. [PMID: 37942504 DOI: 10.1111/jeb.14242] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/13/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.
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Affiliation(s)
- Emma L Berdan
- Bioinformatics Core, Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Nicholas H Barton
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Roger Butlin
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
- Ecology and Evolutionary Biology, School of Bioscience, The University of Sheffield, Sheffield, UK
| | - Brian Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Rui Faria
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Inês Fragata
- CHANGE - Global Change and Sustainability Institute/Animal Biology Department, cE3c - Center for Ecology, Evolution and Environmental Changes, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | | | - Paul Jay
- Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | - Martin Kapun
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
- Central Research Laboratories, Natural History Museum of Vienna, Vienna, Austria
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University, Boston, Massachusetts, USA
| | - Claire Mérot
- UMR 6553 Ecobio, Université de Rennes, OSUR, CNRS, Rennes, France
| | - Esra Durmaz Mitchell
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Functional Genomics & Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Marina Rafajlović
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
- Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anja M Westram
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Stephen W Schaeffer
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Kerstin Johannesson
- Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
- Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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9
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Haberkorn C, David J, Henri H, Delpuech J, Lasseur R, Vavre F, Varaldi J. A major 6 Mb superlocus is involved in pyrethroid resistance in the common bed bug Cimex lectularius. Evol Appl 2023; 16:1012-1028. [PMID: 37216030 PMCID: PMC10197226 DOI: 10.1111/eva.13550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/23/2023] [Accepted: 04/04/2023] [Indexed: 05/24/2023] Open
Abstract
In the last few years, the bed bug Cimex lectularius has been an increasing problem worldwide, mainly due to the development of insecticide resistance to pyrethroids. The characterization of resistance alleles is a prerequisite to improve surveillance and resistance management. To identify genomic variants associated with pyrethroid resistance in Cimex lectularius, we compared the genetic composition of two recent and resistant populations with that of two ancient-susceptible strains using a genome-wide pool-seq design. We identified a large 6 Mb "superlocus" showing particularly high genetic differentiation and association with the resistance phenotype. This superlocus contained several clustered resistance genes and was also characterized by a high density of structural variants (inversions, duplications). The possibility that this superlocus constitutes a resistance "supergene" that evolved after the clustering of alleles adapted to insecticide and after reduction in recombination is discussed.
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Affiliation(s)
- Chloé Haberkorn
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
- IZInovationLyonFrance
| | - Jean‐Philippe David
- Laboratoire d'Écologie AlpineUMR UGA‐USMB‐CNRS 5553 Université Grenoble Alpes CS 40700Grenoble cedex 9France
| | - Hélène Henri
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
| | - Jean‐Marie Delpuech
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
| | | | - Fabrice Vavre
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
| | - Julien Varaldi
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
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10
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Villoutreix R, de Carvalho CF, Feder JL, Gompert Z, Nosil P. Disruptive selection and the evolution of discrete color morphs in Timema stick insects. SCIENCE ADVANCES 2023; 9:eabm8157. [PMID: 37000882 PMCID: PMC10065444 DOI: 10.1126/sciadv.abm8157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
A major unresolved issue in biology is why phenotypic and genetic variation is sometimes continuous, yet other times packaged into discrete units of diversity, such as morphs, ecotypes, and species. In theory, ecological discontinuities can impose strong disruptive selection that promotes the evolution of discrete forms, but direct tests of this hypothesis are lacking. Here, we show that Timema stick insects exhibit genetically determined color morphs that range from weakly to strongly discontinuous. Color data from nature and a manipulative field experiment demonstrate that greater morph differentiation is associated with shifts from host plants exhibiting more continuous color variation to those exhibiting greater coloration distance between green leaves and brown stems, the latter of which generates strong disruptive selection. Our results show how ecological factors can promote discrete variation, and we further present results on how this can have variable effects on the genetic differentiation that promotes speciation.
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Affiliation(s)
| | - Clarissa F. de Carvalho
- CEFE, Université Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Departamento de Ecologia e Biologia Evolutiva, UNIFESP, Diadema 09972-270, Brazil
| | - Jeffrey L. Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | | | - Patrik Nosil
- CEFE, Université Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Department of Biology, Utah State University, Logan, UT 84322, USA
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11
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Bastide H, Saenko SV, Chouteau M, Joron M, Llaurens V. Dominance mechanisms in supergene alleles controlling butterfly wing pattern variation: insights from gene expression in Heliconius numata. Heredity (Edinb) 2023; 130:92-98. [PMID: 36522413 PMCID: PMC9905084 DOI: 10.1038/s41437-022-00583-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Loci under balancing selection, where multiple alleles are maintained, offer a relevant opportunity to investigate the role of natural selection in shaping genetic dominance: the high frequency of heterozygotes at these loci has been shown to enable the evolution of dominance among alleles. In the butterfly Heliconius numata, mimetic wing color variations are controlled by an inversion polymorphism of a circa 2 Mb genomic region (supergene P), with strong dominance between sympatric alleles. To test how differences in dominance observed on wing patterns correlate with variations in expression levels throughout the supergene region, we sequenced the complete transcriptome of heterozygotes at the prepupal stage and compared it to corresponding homozygotes. By defining dominance based on non-overlapping ranges of transcript expression between genotypes, we found contrasting patterns of dominance between the supergene and the rest of the genome; the patterns of transcript expression in the heterozygotes were more similar to the expression observed in the dominant homozygotes in the supergene region. Dominance also differed among the three subinversions of the supergene, suggesting possible epistatic interactions among their gene contents underlying dominance evolution. We found the expression pattern of the melanization gene cortex located in the P-region to predict wing pattern phenotype in the heterozygote. We also identify new candidate genes that are potentially involved in mimetic color pattern variations highlighting the relevance of transcriptomic analyses in heterozygotes to pinpoint candidate genes in non-recombining regions.
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Affiliation(s)
- Héloïse Bastide
- Institut de Systématique, Evolution et Biodiversité (UMR 7205 CNRS, MNHN, Sorbonne Université, Université des Antilles) Muséum National d'Histoire Naturelle - CP50, 57 rue Cuvier, 75005, Paris, France.
- Laboratoire Évolution, Génomes, Comportement et Écologie, CNRS, IRD, Université Paris-Saclay - Institut Diversité, Écologie et Évolution (IDEEV), 12 route 128, 91190, Gif-sur-Yvette, France.
| | - Suzanne V Saenko
- Institut de Systématique, Evolution et Biodiversité (UMR 7205 CNRS, MNHN, Sorbonne Université, Université des Antilles) Muséum National d'Histoire Naturelle - CP50, 57 rue Cuvier, 75005, Paris, France
| | - Mathieu Chouteau
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Laboratoire Ecologie, Evolution, Interactions Des Systèmes Amazoniens (LEEISA), USR 3456, Université De Guyane, CNRS Guyane, 275 route de Montabo, 97334, Cayenne, French Guiana
| | - Mathieu Joron
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Violaine Llaurens
- Institut de Systématique, Evolution et Biodiversité (UMR 7205 CNRS, MNHN, Sorbonne Université, Université des Antilles) Muséum National d'Histoire Naturelle - CP50, 57 rue Cuvier, 75005, Paris, France
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12
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Helleu Q, Roux C, Ross KG, Keller L. Radiation and hybridization underpin the spread of the fire ant social supergene. Proc Natl Acad Sci U S A 2022; 119:e2201040119. [PMID: 35969752 PMCID: PMC9407637 DOI: 10.1073/pnas.2201040119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/04/2022] [Indexed: 11/18/2022] Open
Abstract
Supergenes are clusters of tightly linked genes that jointly produce complex phenotypes. Although widespread in nature, how such genomic elements are formed and how they spread are in most cases unclear. In the fire ant Solenopsis invicta and closely related species, a "social supergene controls whether a colony maintains one or multiple queens. Here, we show that the three inversions constituting the Social b (Sb) supergene emerged sequentially during the separation of the ancestral lineages of S. invicta and Solenopsis richteri. The two first inversions arose in the ancestral population of both species, while the third one arose in the S. richteri lineage. Once completely assembled in the S. richteri lineage, the supergene first introgressed into S. invicta, and from there into the other species of the socially polymorphic group of South American fire ant species. Surprisingly, the introgression of this large and important genomic element occurred despite recent hybridization being uncommon between several of the species. These results highlight how supergenes can readily move across species boundaries, possibly because of fitness benefits they provide and/or expression of selfish properties favoring their transmission.
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Affiliation(s)
- Quentin Helleu
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Camille Roux
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Kenneth G. Ross
- Department of Entomology, University of Georgia, Athens, GA 30605
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
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13
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Jay P, Leroy M, Le Poul Y, Whibley A, Arias M, Chouteau M, Joron M. Association mapping of colour variation in a butterfly provides evidence that a supergene locks together a cluster of adaptive loci. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210193. [PMID: 35694756 PMCID: PMC9189503 DOI: 10.1098/rstb.2021.0193] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Supergenes are genetic architectures associated with discrete and concerted variation in multiple traits. It has long been suggested that supergenes control these complex polymorphisms by suppressing recombination between sets of coadapted genes. However, because recombination suppression hinders the dissociation of the individual effects of genes within supergenes, there is still little evidence that supergenes evolve by tightening linkage between coadapted genes. Here, combining a landmark-free phenotyping algorithm with multivariate genome-wide association studies, we dissected the genetic basis of wing pattern variation in the butterfly Heliconius numata. We show that the supergene controlling the striking wing pattern polymorphism displayed by this species contains several independent loci associated with different features of wing patterns. The three chromosomal inversions of this supergene suppress recombination between these loci, supporting the hypothesis that they may have evolved because they captured beneficial combinations of alleles. Some of these loci are, however, associated with colour variations only in a subset of morphs where the phenotype is controlled by derived inversion forms, indicating that they were recruited after the formation of the inversions. Our study shows that supergenes and clusters of adaptive loci in general may form via the evolution of chromosomal rearrangements suppressing recombination between co-adapted loci but also via the subsequent recruitment of linked adaptive mutations. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.
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Affiliation(s)
- Paul Jay
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier cedex 5, France
| | - Manon Leroy
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier cedex 5, France
| | - Yann Le Poul
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier cedex 5, France
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Mónica Arias
- CIRAD, UMR PHIM, F-34398 Montpellier, France.,PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, CEDEX 5, 34398 Montpellier, France
| | - Mathieu Chouteau
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier cedex 5, France.,LEEISA, USR 63456, Université de Guyane, CNRS, IFREMER, 275 route de Montabo, 797334 Cayenne, French Guiana
| | - Mathieu Joron
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier cedex 5, France
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14
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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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15
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Big spots in a small population: Analyzing characteristics and temporality of coat patterns in Croatian lynx population. ZOOL ANZ 2022. [DOI: 10.1016/j.jcz.2022.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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16
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O’Connor TK, Sandoval MC, Wang J, Hans JC, Takenaka R, Child M, Whiteman NK. Ecological basis and genetic architecture of crypsis polymorphism in the desert clicker grasshopper (Ligurotettix coquilletti). Evolution 2021; 75:2441-2459. [PMID: 34370317 PMCID: PMC8932956 DOI: 10.1111/evo.14321] [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: 04/30/2021] [Revised: 07/09/2021] [Accepted: 07/20/2021] [Indexed: 11/28/2022]
Abstract
Color polymorphic species can offer exceptional insight into the ecology and genetics of adaptation. Although the genetic architecture of animal coloration is diverse, many color polymorphisms are associated with large structural variants and maintained by biotic interactions. Grasshoppers are notably polymorphic in both color and karyotype, which makes them excellent models for understanding the ecological drivers and genetic underpinnings of color variation. Banded and uniform morphs of the desert clicker grasshopper (Ligurotettix coquilletti) are found across the western deserts of North America. To address the hypothesis that predation maintains local color polymorphism and shapes regional crypsis variation, we surveyed morph frequencies and tested for covariation with two predation environments. Morphs coexisted at intermediate frequencies at most sites, consistent with local balancing selection. Morph frequencies covaried with the appearance of desert substrate-an environment used only by females-suggesting that ground-foraging predators are major agents of selection on crypsis. We next addressed the hypothesized link between morph variation and genome structure. To do so, we designed an approach for detecting inversions and indels using only RADseq data. The banded morph was perfectly correlated with a large putative indel. Remarkably, indel dominance differed among populations, a rare example of dominance evolution in nature.
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Affiliation(s)
- Timothy K. O’Connor
- Department of Integrative Biology, University of California, Berkeley, CA 94720
- Current address: Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637
| | - Marissa C. Sandoval
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Jiarui Wang
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Jacob C. Hans
- Department of Entomology, University of California, Riverside, CA 92521
| | - Risa Takenaka
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Myron Child
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Noah K. Whiteman
- Department of Integrative Biology, University of California, Berkeley, CA 94720
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17
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Cozzolino S, Scopece G, Lussu M, Cortis P, Schiestl FP. Do floral and ecogeographic isolation allow the co-occurrence of two ecotypes of Anacamptis papilionacea (Orchidaceae)? Ecol Evol 2021; 11:9917-9931. [PMID: 34367549 PMCID: PMC8328454 DOI: 10.1002/ece3.7432] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/10/2021] [Accepted: 02/18/2021] [Indexed: 11/08/2022] Open
Abstract
Ecotypes are relatively frequent in flowering plants and considered central in ecological speciation as local adaptation can promote the insurgence of reproductive isolation. Without geographic isolation, gene flow usually homogenizes the allopatrically generated phenotypic and ecological divergences, unless other forms of reproductive isolation keep them separated. Here, we investigated two orchid ecotypes with marked phenotypic floral divergence that coexist in contact zones. We found that the two ecotypes show different ecological habitat preferences with one being more climatically restricted than the other. The ecotypes remain clearly morphologically differentiated both in allopatry and in sympatry and differed in diverse floral traits. Despite only slightly different flowering times, the two ecotypes achieved floral isolation thanks to different pollination strategies. We found that both ecotypes attract a wide range of insects, but the ratio of male/female attracted by the two ecotypes was significantly different, with one ecotype mainly attracts male pollinators, while the other mainly attracts female pollinators. As a potential consequence, the two ecotypes show different pollen transfer efficiency. Experimental plots with pollen staining showed a higher proportion of intra- than interecotype movements confirming floral isolation between ecotypes in sympatry while crossing experiments excluded evident postmating barriers. Even if not completely halting the interecotypes pollen flow in sympatry, such incipient switch in pollination strategy between ecotypes may represent a first step on the path toward evolution of sexual mimicry in Orchidinae.
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Affiliation(s)
| | - Giovanni Scopece
- Department of BiologyUniversity Federico II of NaplesNapoliItaly
| | - Michele Lussu
- Department of Life and Environmental SciencesUniversity of CagliariCagliariItaly
- Istituto Regionale per la Floricoltura (IRF)SanremoItaly
| | - Pierluigi Cortis
- Department of Life and Environmental SciencesUniversity of CagliariCagliariItaly
| | - Florian P. Schiestl
- Department of Systematic and Evolutionary Botany and Botanical GardensUniversity of ZurichZurichSwitzerland
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18
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Teng D, Li F, Zhang W. Using comprehensive machine-learning models to classify complex morphological characters. Ecol Evol 2021; 11:10421-10431. [PMID: 34367585 PMCID: PMC8328437 DOI: 10.1002/ece3.7845] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/06/2021] [Accepted: 06/08/2021] [Indexed: 11/11/2022] Open
Abstract
Recognizing and classifying multiple morphological features, such as patterns, sizes, and textures, can provide a comprehensive understanding of their variability and phenotypic evolution. Yet, quantitatively measuring complex morphological characters remains challenging.We provide a machine learning-based pipeline (SVMorph) to consider and classify complex morphological characters in multiple organisms that have either small or large datasets.Our pipeline integrates two descriptors, histogram of oriented gradient and local binary pattern, to meet various classification needs. We also optimized feature extraction by adding image data augmentation to improve model generalizability.We tested SVMorph on two real-world examples to demonstrate that it can be used with small training datasets and limited computational resources. Comparing with multiple CNN-based methods and traditional techniques, we show that SVMorph is reliable and fast in texture-based individual classification. Thus, SVMorph can be used to efficiently classify multiple morphological characters in distinct nonmodel organisms.
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Affiliation(s)
- Dequn Teng
- State Key Laboratory of Protein and Plant Gene ResearchSchool of Life SciencesPeking UniversityBeijingChina
| | - Fengyuan Li
- State Key Laboratory of Protein and Plant Gene ResearchSchool of Life SciencesPeking UniversityBeijingChina
| | - Wei Zhang
- State Key Laboratory of Protein and Plant Gene ResearchSchool of Life SciencesPeking UniversityBeijingChina
- Peking‐Tsinghua Center for Life SciencesAcademy for Advanced Interdisciplinary StudiesPeking UniversityBeijingChina
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19
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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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20
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Mutation load at a mimicry supergene sheds new light on the evolution of inversion polymorphisms. Nat Genet 2021; 53:288-293. [PMID: 33495598 DOI: 10.1038/s41588-020-00771-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 12/21/2020] [Indexed: 01/30/2023]
Abstract
Chromosomal inversions are ubiquitous in genomes and often coordinate complex phenotypes, such as the covariation of behavior and morphology in many birds, fishes, insects or mammals1-11. However, why and how inversions become associated with polymorphic traits remains obscure. Here we show that despite a strong selective advantage when they form, inversions accumulate recessive deleterious mutations that generate frequency-dependent selection and promote their maintenance at intermediate frequency. Combining genomics and in vivo fitness analyses in a model butterfly for wing-pattern polymorphism, Heliconius numata, we reveal that three ecologically advantageous inversions have built up a heavy mutational load from the sequential accumulation of deleterious mutations and transposable elements. Inversions associate with sharply reduced viability when homozygous, which prevents them from replacing ancestral chromosome arrangements. Our results suggest that other complex polymorphisms, rather than representing adaptations to competing ecological optima, could evolve because chromosomal rearrangements are intrinsically prone to carrying recessive harmful mutations.
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21
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Maisonneuve L, Chouteau M, Joron M, Llaurens V. Evolution and genetic architecture of disassortative mating at a locus under heterozygote advantage. Evolution 2020; 75:149-165. [PMID: 33210282 DOI: 10.1111/evo.14129] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/04/2020] [Indexed: 02/02/2023]
Abstract
The evolution of mate choice is a major topic in evolutionary biology because it is thought to be a key factor in trait and species diversification. Here, we aim at uncovering the ecological conditions and genetic architecture enabling the puzzling evolution of disassortative mating based on adaptive traits. This rare form of mate choice is observed for some polymorphic traits but theoretical predictions on the emergence and persistence of this behavior are largely lacking. Thus, we developed a mathematical model to specifically understand the evolution of disassortative mating based on mimetic color pattern in the polymorphic butterfly Heliconius numata. We confirm that heterozygote advantage favors the evolution of disassortative mating and show that disassortative mating is more likely to emerge if at least one allele at the trait locus is free from any recessive deleterious mutations. We modeled different possible genetic architectures underlying mate choice behavior, such as self-referencing alleles, or specific preference or rejection alleles. Our results showed that self-referencing or rejection alleles linked to the color pattern locus enable the emergence of disassortative mating. However, rejection alleles allow the emergence of disassortative mating only when the color pattern and preference loci are tightly linked.
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Affiliation(s)
- Ludovic Maisonneuve
- Institut de Systematique, Evolution, Biodiversité (UMR7205), Museum National d'Histoire Naturelle, CNRS, Sorbonne-Université, EPHE, Université des Antilles, CP50, 57 rue Cuvier, Paris, 75005, France
| | - Mathieu Chouteau
- Laboratoire Ecologie, Evolution, Interactions Des Systèmes Amazoniens (LEEISA), USR 3456, Université De Guyane, IFREMER, CNRS Guyane, 275 route de Montabo, 97334 Cayenne, French Guiana
| | - Mathieu Joron
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Violaine Llaurens
- Institut de Systematique, Evolution, Biodiversité (UMR7205), Museum National d'Histoire Naturelle, CNRS, Sorbonne-Université, EPHE, Université des Antilles, CP50, 57 rue Cuvier, Paris, 75005, France
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22
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Llaurens V, Le Poul Y, Puissant A, Blandin P, Debat V. Convergence in sympatry: Evolution of blue-banded wing pattern in Morpho butterflies. J Evol Biol 2020; 34:284-295. [PMID: 33119141 DOI: 10.1111/jeb.13726] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 10/07/2020] [Accepted: 10/13/2020] [Indexed: 11/30/2022]
Abstract
Species interactions such as mimicry can promote trait convergence but disentangling this effect from those of shared ecology, evolutionary history, and niche conservatism is often challenging. Here by focusing on wing colour pattern variation within and between three butterfly species living in sympatry in a large proportion of their range, we tested the effect of species interactions on trait diversification. These butterflies display a conspicuous iridescent blue coloration on the dorsal side of their wings and a cryptic brownish colour on the ventral side. Combined with an erratic and fast flight, these colour patterns increase the difficulty of capture by predators and contribute to the high escape abilities of these butterflies. We hypothesize that, beyond their direct contribution to predator escape, these wing patterns can be used as signals of escape abilities by predators, resulting in positive frequency-dependent selection favouring convergence in wing pattern in sympatry. To test this hypothesis, we quantified dorsal wing pattern variations of 723 butterflies from the three species sampled throughout their distribution, including sympatric and allopatric situations and compared the phenotypic distances between species, sex and localities. We detected a significant effect of localities on colour pattern, and higher inter-specific resemblance in sympatry as compared to allopatry, consistent with the hypothesis of local convergence of wing patterns. Our results provide support to the existence of escape mimicry in the wild and stress the importance of estimating trait variation within species to understand trait variation between species, and to a larger extent, trait diversification at the macro-evolutionary scale.
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Affiliation(s)
- Violaine Llaurens
- Institut de Systématique, Evolution et Biodiversité, UMR 7205 CNRS/MNHN/Sorbonne Université/EPHE, Museum National d'Histoire Naturelle, Paris, France
| | - Yann Le Poul
- Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Agathe Puissant
- Institut de Systématique, Evolution et Biodiversité, UMR 7205 CNRS/MNHN/Sorbonne Université/EPHE, Museum National d'Histoire Naturelle, Paris, France
| | - Patrick Blandin
- Institut de Systématique, Evolution et Biodiversité, UMR 7205 CNRS/MNHN/Sorbonne Université/EPHE, Museum National d'Histoire Naturelle, Paris, France
| | - Vincent Debat
- Institut de Systématique, Evolution et Biodiversité, UMR 7205 CNRS/MNHN/Sorbonne Université/EPHE, Museum National d'Histoire Naturelle, Paris, France
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23
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Katoh M, Tatsuta H, Tsuji K. Mimicry genes reduce pre-adult survival rate in Papilio polytes: A possible new mechanism for maintaining female-limited polymorphism in Batesian mimicry. J Evol Biol 2020; 33:1487-1494. [PMID: 32841468 DOI: 10.1111/jeb.13686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/22/2020] [Accepted: 07/26/2020] [Indexed: 11/28/2022]
Abstract
Batesian mimicry, in which harmless organisms resemble unpalatable or harmful species, is a well-studied adaptation for predation avoidance. The females of some Batesian mimic species comprise mimetic and nonmimetic individuals. Mimetic females of such polymorphic species clearly have a selective advantage due to decreased predation pressure, but the selective forces that maintain nonmimetic females in a population remain unclear. In the swallowtail butterfly, Papilio polytes, female polymorphism is controlled by the H (mimetic) and h (nonmimetic) alleles at a single autosomal locus. Here, we examined whether the dominant H allele has a deleterious effect on the pre-adult survival rate (egg-to-adult emergence rate). We repeated an assortative mating-like treatment-that is breeding of males and females whose mothers had the same phenotype (mimetic or nonmimetic)-for three consecutive generations, while avoiding inbreeding. Results showed that pre-adult survival rate decreased over generations only in lines derived from mothers with the mimetic phenotype (hereafter, mimetic-assorted lines). This lowered survival was due to an increased mortality at the final instar larval stage and the pupal stages. Interestingly, the pre-adult mortality in the mimetic-assorted lines seemed to be associated with a male-biased sex ratio at adult emergence. These results suggest that the dominant H allele displays a mildly deleterious effect that is expressed more strongly in females and homozygous individuals than in heterozygous individuals. We propose that this cost of mimicry in larval and pupal stages contributes to the maintenance of female-limited polymorphism in P. polytes.
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Affiliation(s)
- Mitsuho Katoh
- Department of Agro-Environmental Sciences, Faculty of Agriculture, University of the Ryukyus, Okinawa, Japan
| | - Haruki Tatsuta
- Department of Agro-Environmental Sciences, Faculty of Agriculture, University of the Ryukyus, Okinawa, Japan.,The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | - Kazuki Tsuji
- Department of Agro-Environmental Sciences, Faculty of Agriculture, University of the Ryukyus, Okinawa, Japan.,The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
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24
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McMillan WO, Livraghi L, Concha C, Hanly JJ. From Patterning Genes to Process: Unraveling the Gene Regulatory Networks That Pattern Heliconius Wings. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00221] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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25
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Mérot C, Debat V, Le Poul Y, Merrill RM, Naisbit RE, Tholance A, Jiggins CD, Joron M. Hybridization and transgressive exploration of colour pattern and wing morphology in Heliconius butterflies. J Evol Biol 2020; 33:942-956. [PMID: 32255231 DOI: 10.1111/jeb.13626] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/21/2020] [Accepted: 03/24/2020] [Indexed: 12/19/2022]
Abstract
Hybridization can generate novel phenotypes distinct from those of parental lineages, a phenomenon known as transgressive trait variation. Transgressive phenotypes might negatively or positively affect hybrid fitness, and increase available variation. Closely related species of Heliconius butterflies regularly produce hybrids in nature, and hybridization is thought to play a role in the diversification of novel wing colour patterns despite strong stabilizing selection due to interspecific mimicry. Here, we studied wing phenotypes in first- and second-generation hybrids produced by controlled crosses between either two co-mimetic species of Heliconius or between two nonmimetic species. We quantified wing size, shape and colour pattern variation and asked whether hybrids displayed transgressive wing phenotypes. Discrete traits underlain by major-effect loci, such as the presence or absence of colour patches, generate novel phenotypes. For quantitative traits, such as wing shape or subtle colour pattern characters, hybrids only exceed the parental range in specific dimensions of the morphological space. Overall, our study addresses some of the challenges in defining and measuring phenotypic transgression for multivariate traits and our data suggest that the extent to which transgressive trait variation in hybrids contributes to phenotypic diversity depends on the complexity and the genetic architecture of the traits.
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Affiliation(s)
- Claire Mérot
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,IBIS, Université Laval, Québec, QC, Canada
| | - Vincent Debat
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Yann Le Poul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,Division of Evolutionary Biology, Ludwig-Maximilians-Universität, München, Germany
| | - Richard M Merrill
- Division of Evolutionary Biology, Ludwig-Maximilians-Universität, München, Germany.,Department of Zoology, University of Cambridge, Cambridge, UK.,Smithsonian Tropical Research Institute, Panama City, Panama
| | - Russell E Naisbit
- Smithsonian Tropical Research Institute, Panama City, Panama.,Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Adélie Tholance
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK.,Smithsonian Tropical Research Institute, Panama City, Panama
| | - Mathieu Joron
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,UMR 5175, CNRS-Centre d'Ecologie Fonctionnelle et Evolutive, Montpellier, France
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26
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Gauthier J, de Silva DL, Gompert Z, Whibley A, Houssin C, Le Poul Y, McClure M, Lemaitre C, Legeai F, Mallet J, Elias M. Contrasting genomic and phenotypic outcomes of hybridization between pairs of mimetic butterfly taxa across a suture zone. Mol Ecol 2020; 29:1328-1343. [PMID: 32145112 DOI: 10.1111/mec.15403] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 02/03/2020] [Accepted: 02/21/2020] [Indexed: 11/28/2022]
Abstract
Hybrid zones, whereby divergent lineages come into contact and eventually hybridize, can provide insights on the mechanisms involved in population differentiation and reproductive isolation, and ultimately speciation. Suture zones offer the opportunity to compare these processes across multiple species. In this paper we use reduced-complexity genomic data to compare the genetic and phenotypic structure and hybridization patterns of two mimetic butterfly species, Ithomia salapia and Oleria onega (Nymphalidae: Ithomiini), each consisting of a pair of lineages differentiated for their wing colour pattern and that come into contact in the Andean foothills of Peru. Despite similarities in their life history, we highlight major differences, both at the genomic and phenotypic level, between the two species. These differences include the presence of hybrids, variations in wing phenotype, and genomic patterns of introgression and differentiation. In I. salapia, the two lineages appear to hybridize only rarely, whereas in O. onega the hybrids are not only more common, but also genetically and phenotypically more variable. We also detected loci statistically associated with wing colour pattern variation, but in both species these loci were not over-represented among the candidate barrier loci, suggesting that traits other than wing colour pattern may be important for reproductive isolation. Our results contrast with the genomic patterns observed between hybridizing lineages in the mimetic Heliconius butterflies, and call for a broader investigation into the genomics of speciation in Ithomiini - the largest radiation of mimetic butterflies.
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Affiliation(s)
- Jérémy Gauthier
- Inria, CNRS, IRISA, University Rennes, Rennes, France.,Geneva Natural History Museum, Geneva, Switzerland
| | - Donna Lisa de Silva
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| | | | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Céline Houssin
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| | - Yann Le Poul
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France.,Fakultat für Biologie, Biozentrum, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Melanie McClure
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
| | | | | | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Marianne Elias
- Institut de Systématique, Évolution, Biodiversité, CNRS, MNHN, EPHE, Sorbonne Université, Université des Antilles, Paris, France
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Sculfort O, de Castro ECP, Kozak KM, Bak S, Elias M, Nay B, Llaurens V. Variation of chemical compounds in wild Heliconiini reveals ecological factors involved in the evolution of chemical defenses in mimetic butterflies. Ecol Evol 2020; 10:2677-2694. [PMID: 32185010 PMCID: PMC7069300 DOI: 10.1002/ece3.6044] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 01/08/2023] Open
Abstract
Evolutionary convergence of color pattern in mimetic species is tightly linked with the evolution of chemical defenses. Yet, the evolutionary forces involved in natural variations of chemical defenses in aposematic species are still understudied. Herein, we focus on the evolution of chemical defenses in the butterfly tribe Heliconiini. These neotropical butterflies contain large concentrations of cyanogenic glucosides, cyanide-releasing compounds acting as predator deterrent. These compounds are either de novo synthesized or sequestered from their Passiflora host plant, so that their concentrations may depend on host plant specialization and host plant availability. We sampled 375 wild Heliconiini butterflies across Central and South America, covering 43% species of this clade, and quantify individual variations in the different CGs using liquid chromatography coupled with tandem mass spectrometry. We detected new compounds and important variations in chemical defenses both within and among species. Based on the most recent and well-studied phylogeny of Heliconiini, we show that ecological factors such as mimetic interactions and host plant specialization have a significant association with chemical profiles, but these effects are largely explained by phylogenetic relationships. Our results therefore suggest that shared ancestries largely contribute to chemical defense variation, pointing out at the interaction between historical and ecological factors in the evolution of Müllerian mimicry.
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Affiliation(s)
- Ombeline Sculfort
- Institut de Systématique, Evolution, Biodiversité (ISYEB)Muséum National d'Histoire NaturelleCNRSSorbonne‐UniversitéEPHEUniversité des AntillesParisFrance
- Unité Molécules de Communication et Adaptations des Micro‐organismes (MCAM)Muséum National d'Histoire NaturelleCNRSParisFrance
| | | | | | - Søren Bak
- Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
| | - Marianne Elias
- Institut de Systématique, Evolution, Biodiversité (ISYEB)Muséum National d'Histoire NaturelleCNRSSorbonne‐UniversitéEPHEUniversité des AntillesParisFrance
| | - Bastien Nay
- Unité Molécules de Communication et Adaptations des Micro‐organismes (MCAM)Muséum National d'Histoire NaturelleCNRSParisFrance
- Laboratoire de Synthèse OrganiqueEcole PolytechniqueCNRSENSTAInstitut Polytechnique de ParisPalaiseau CedexFrance
| | - Violaine Llaurens
- Institut de Systématique, Evolution, Biodiversité (ISYEB)Muséum National d'Histoire NaturelleCNRSSorbonne‐UniversitéEPHEUniversité des AntillesParisFrance
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28
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Arias M, Davey JW, Martin S, Jiggins C, Nadeau N, Joron M, Llaurens V. How do predators generalize warning signals in simple and complex prey communities? Insights from a videogame. Proc Biol Sci 2020; 287:20200014. [PMID: 32070260 DOI: 10.1098/rspb.2020.0014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The persistence of distinct warning signals within and between sympatric mimetic communities is a puzzling evolutionary question because selection favours convergence of colour patterns among toxic species. Such convergence is partly shaped by predators' reaction to similar but not identical stimulus (i.e. generalization behaviour), and generalization by predators is likely to be shaped by the diversity of local prey. However, studying generalization behaviour is generally limited to simple variations of prey colour patterns. Here, we used a computer game played by humans as surrogate predators to investigate generalization behaviours in simple (4 morphs) and complex (10 morphs) communities of unprofitable (associated with a penalty) and profitable butterflies. Colour patterns used in the game are observed in the natural populations of unprofitable butterfly species such as Heliconius numata. Analyses of 449 game participants' behaviours show that players avoided unprofitable prey more readily in simple than in complex communities. However, generalization was observed only in players that faced complex communities, enhancing the protection of profitable prey that looked similar to at least one unprofitable morph. Additionally, similarity among unprofitable prey also reduced attack rates only in complex communities. These results are consistent with previous studies using avian predators but artificial colour patterns and suggest that mimicry is more likely to evolve in complex communities where increases in similarity are more likely to be advantageous.
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Affiliation(s)
- Mónica Arias
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles CP 50, 57 rue Cuvier, 75005 Paris, France.,Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 CNRS-Université de Montpellier, École Pratique des Hautes Études, Université Paul Valéry, 34293 Montpellier 5, France
| | - John W Davey
- Bioscience Technology Facility, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK.,Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Simon Martin
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Chris Jiggins
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Nicola Nadeau
- Molecular Ecology Lab, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 CNRS-Université de Montpellier, École Pratique des Hautes Études, Université Paul Valéry, 34293 Montpellier 5, France
| | - Violaine Llaurens
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles CP 50, 57 rue Cuvier, 75005 Paris, France
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29
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Nattero J, Carbajal de la Fuente AL, Piccinali RV, Cardozo M, Rodríguez CS, Crocco LB. Characterization of melanic and non-melanic forms in domestic and peridomestic populations of Triatoma infestans (Hemiptera: Reduviidae). Parasit Vectors 2020; 13:47. [PMID: 32014037 PMCID: PMC6998255 DOI: 10.1186/s13071-020-3912-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/21/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Melanic (dark) morphs have been barely reported in peridomestic and sylvatic conditions for Triatoma infestans, the most important vector of Chagas disease in the Southern Cone of South America. Adults with dark and small yellow markings on the connexivum were collected after manual searches conducted by technical personnel in 62 domiciliary units in Cruz del Eje, Córdoba Province, Argentina. The last community-wide insecticide spraying campaign before the study had been conducted three years earlier. We investigated if there was a measurable color morph variation (melanic and non-melanic) in wings and connexivum; we determined infestation, distribution of melanic and non-melanic forms, and correspondence of colorimetric variation with variations in morphology (wing size and shape and body length), development (wing fluctuating asymmetry), physiology (nutritional status) or behaviour (flight initiation). RESULTS Forty-nine females, 54 males and 217 nymphs were collected in 24 domiciliary units. House infestation and colonization were 53% and 47%, respectively. Most of the T. infestans individuals (83.2%) were collected in chicken coops; intradomicile infestation was recorded in only one case. The chromatic cluster analysis showed two well-defined groups: melanic and non-melanic. The melanic group included 17 (35%) females and 25 (46%) males. Peridomestic infestation was lower for melanic than for non-melanic adults. Melanic morphs were collected in houses from several localities. Sexual dimorphisms were confirmed by morphometric measurements. Body length was large in melanic adults (P < 0.01 only for males). Differences between groups were significant for wing size and shape, but not for weight or weight/body length ratio. Melanic females and males showed significantly higher fluctuating asymmetry (FA) indices than their non-melanic counterparts. CONCLUSIONS This is the second report of melanic forms of T. infestans in domestic and peridomestic habitats in the Dry Chaco region of Argentina. Although non-melanic adults exhibited a higher infestation rate, melanic adults were widespread in the area and were collected in the infested domicile and in most types of peridomestic annexes. Differences in morphometric variables between groups might be due to different ecological adaptations. The higher FA levels observed in melanic individuals suggest a higher developmental instability and a selective advantage of non-melanic individuals in domestic and peridomestic habitats.
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Affiliation(s)
- Julieta Nattero
- Departamento de Ecología, Genética y Evolución/Laboratorio de Eco-Epidemiología, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina. .,Instituto de Ecología, Genética y Evolución (CONICET-IEGEBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - Ana Laura Carbajal de la Fuente
- Departamento de Ecología, Genética y Evolución/Laboratorio de Eco-Epidemiología, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Ecología, Genética y Evolución (CONICET-IEGEBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Romina Valeria Piccinali
- Departamento de Ecología, Genética y Evolución/Laboratorio de Eco-Epidemiología, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Ecología, Genética y Evolución (CONICET-IEGEBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Miriam Cardozo
- Cátedra de Introducción a la Biología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba. Instituto de Investigaciones Biológicas y Tecnológicas (IIBYT-CONICET), Avda. Vélez Sarsfield 299, piso 5, X5000JJC, Córdoba, Argentina
| | - Claudia Susana Rodríguez
- Cátedra de Introducción a la Biología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba. Instituto de Investigaciones Biológicas y Tecnológicas (IIBYT-CONICET), Avda. Vélez Sarsfield 299, piso 5, X5000JJC, Córdoba, Argentina
| | - Liliana Beatriz Crocco
- Cátedra de Introducción a la Biología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba. Instituto de Investigaciones Biológicas y Tecnológicas (IIBYT-CONICET), Avda. Vélez Sarsfield 299, piso 5, X5000JJC, Córdoba, Argentina
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30
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Mérot C, Llaurens V, Normandeau E, Bernatchez L, Wellenreuther M. Balancing selection via life-history trade-offs maintains an inversion polymorphism in a seaweed fly. Nat Commun 2020; 11:670. [PMID: 32015341 PMCID: PMC6997199 DOI: 10.1038/s41467-020-14479-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 01/08/2020] [Indexed: 12/22/2022] Open
Abstract
How natural diversity is maintained is an evolutionary puzzle. Genetic variation can be eroded by drift and directional selection but some polymorphisms persist for long time periods, implicating a role for balancing selection. Here, we investigate the maintenance of a chromosomal inversion polymorphism in the seaweed fly Coelopa frigida. Using experimental evolution and quantifying fitness, we show that the inversion underlies a life-history trade-off, whereby each haplotype has opposing effects on larval survival and adult reproduction. Numerical simulations confirm that such antagonistic pleiotropy can maintain polymorphism. Our results also highlight the importance of sex-specific effects, dominance and environmental heterogeneity, whose interaction enhances the maintenance of polymorphism through antagonistic pleiotropy. Overall, our findings directly demonstrate how overdominance and sexual antagonism can emerge from a life-history trade-off, inviting reconsideration of antagonistic pleiotropy as a key part of multi-headed balancing selection processes that enable the persistence of genetic variation. Few studies empirically pinpoint how balanced polymorphisms are maintained. “Mérot et al”. identify an inversion polymorphism that is maintained in seaweed fly populations because of antagonistic pleiotropy that mediates a classic life history tradeoff between larval survival and adult reproduction.
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Affiliation(s)
- Claire Mérot
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Avenue de la Médecine, G1V 0A6, Quebec, Canada.
| | - Violaine Llaurens
- Institut de Systématique, Evolution et Biodiversité (UMR 7205 CNRS/MNHN/SU/EPHE), Museum National d'Histoire Naturelle, CP50, 57 rue Cuvier, 75005, Paris, France
| | - Eric Normandeau
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Avenue de la Médecine, G1V 0A6, Quebec, Canada
| | - Louis Bernatchez
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 Avenue de la Médecine, G1V 0A6, Quebec, Canada
| | - Maren Wellenreuther
- The New Zealand Institute for Plant & Food Research Ltd, PO Box 5114, Port Nelson, Nelson, 7043, New Zealand.,School of Biological Sciences, University of Auckland, 5 Symonds St, 1010, Auckland, New Zealand
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31
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Wolfe MD, Bauchet GJ, Chan AW, Lozano R, Ramu P, Egesi C, Kawuki R, Kulakow P, Rabbi I, Jannink JL. Historical Introgressions from a Wild Relative of Modern Cassava Improved Important Traits and May Be Under Balancing Selection. Genetics 2019; 213:1237-1253. [PMID: 31624088 PMCID: PMC6893375 DOI: 10.1534/genetics.119.302757] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 10/15/2019] [Indexed: 12/23/2022] Open
Abstract
Introgression of alleles from wild relatives has often been adaptive in plant breeding. However, the significance of historical hybridization events in modern breeding is often not clear. Cassava (Manihot esculenta) is among the most important staple foods in the world, sustaining hundreds of millions of people in the tropics, especially in sub-Saharan Africa. Widespread genotyping makes cassava a model for clonally propagated root and tuber crops in the developing world, and provides an opportunity to study the modern benefits and consequences of historical introgression. We detected large introgressed Manihot glaziovii genome-segments in a collection of 2742 modern cassava landraces and elite germplasm, the legacy of a 1930s era breeding to combat disease epidemics. African landraces and improved varieties were, on average, 3.8% (max 13.6%) introgressed. Introgressions accounted for a significant (mean 20%, max 56%) portion of the heritability of tested traits. M. glaziovii alleles on the distal 10 Mb of chr. 1 increased dry matter and root number. On chr. 4, introgressions in a 20 Mb region improved harvest index and brown streak disease tolerance. We observed the introgression frequency on chr. 1 double over three cycles of selection, and that later stage trials selectively excluded homozygotes from consideration as varieties. This indicates a heterozygous advantage of introgressions. However, we also found that maintaining large recombination-suppressed introgressions in the heterozygous state allowed the accumulation of deleterious mutations. We conclude that targeted recombination of introgressions would increase the efficiency of cassava breeding by allowing simultaneous fixation of beneficial alleles and purging of genetic load.
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Affiliation(s)
- Marnin D Wolfe
- Section on Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, New York 14850
| | | | - Ariel W Chan
- Section on Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, New York 14850
| | - Roberto Lozano
- Section on Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, New York 14850
| | - Punna Ramu
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14850
| | - Chiedozie Egesi
- International Programs, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York 14850
- National Root Crops Research Institute (NRCRI), Umudike, Umuahia, 440221, Nigeria
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria
| | - Robert Kawuki
- National Root Crops Resources Research Institute, Namulonge, Uganda
| | - Peter Kulakow
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria
| | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria
| | - Jean-Luc Jannink
- Section on Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, New York 14850
- United States Department of Agriculture - Agriculture Research Service, Ithaca, New York 14850
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32
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Pearse DE, Barson NJ, Nome T, Gao G, Campbell MA, Abadía-Cardoso A, Anderson EC, Rundio DE, Williams TH, Naish KA, Moen T, Liu S, Kent M, Moser M, Minkley DR, Rondeau EB, Brieuc MSO, Sandve SR, Miller MR, Cedillo L, Baruch K, Hernandez AG, Ben-Zvi G, Shem-Tov D, Barad O, Kuzishchin K, Garza JC, Lindley ST, Koop BF, Thorgaard GH, Palti Y, Lien S. Sex-dependent dominance maintains migration supergene in rainbow trout. Nat Ecol Evol 2019; 3:1731-1742. [DOI: 10.1038/s41559-019-1044-6] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/18/2019] [Indexed: 11/09/2022]
Abstract
AbstractMales and females often differ in their fitness optima for shared traits that have a shared genetic basis, leading to sexual conflict. Morphologically differentiated sex chromosomes can resolve this conflict and protect sexually antagonistic variation, but they accumulate deleterious mutations. However, how sexual conflict is resolved in species that lack differentiated sex chromosomes is largely unknown. Here we present a chromosome-anchored genome assembly for rainbow trout (Oncorhynchus mykiss) and characterize a 55-Mb double-inversion supergene that mediates sex-specific migratory tendency through sex-dependent dominance reversal, an alternative mechanism for resolving sexual conflict. The double inversion contains key photosensory, circadian rhythm, adiposity and sex-related genes and displays a latitudinal frequency cline, indicating environmentally dependent selection. Our results show sex-dependent dominance reversal across a large autosomal supergene, a mechanism for sexual conflict resolution capable of protecting sexually antagonistic variation while avoiding the homozygous lethality and deleterious mutations associated with typical heteromorphic sex chromosomes.
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33
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Hoyal Cuthill JF, Guttenberg N, Ledger S, Crowther R, Huertas B. Deep learning on butterfly phenotypes tests evolution's oldest mathematical model. SCIENCE ADVANCES 2019; 5:eaaw4967. [PMID: 31453326 PMCID: PMC6693915 DOI: 10.1126/sciadv.aaw4967] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 07/08/2019] [Indexed: 05/09/2023]
Abstract
Traditional anatomical analyses captured only a fraction of real phenomic information. Here, we apply deep learning to quantify total phenotypic similarity across 2468 butterfly photographs, covering 38 subspecies from the polymorphic mimicry complex of Heliconius erato and Heliconius melpomene. Euclidean phenotypic distances, calculated using a deep convolutional triplet network, demonstrate significant convergence between interspecies co-mimics. This quantitatively validates a key prediction of Müllerian mimicry theory, evolutionary biology's oldest mathematical model. Phenotypic neighbor-joining trees are significantly correlated with wing pattern gene phylogenies, demonstrating objective, phylogenetically informative phenome capture. Comparative analyses indicate frequency-dependent mutual convergence with coevolutionary exchange of wing pattern features. Therefore, phenotypic analysis supports reciprocal coevolution, predicted by classical mimicry theory but since disputed, and reveals mutual convergence as an intrinsic generator for the unexpected diversity of Müllerian mimicry. This demonstrates that deep learning can generate phenomic spatial embeddings, which enable quantitative tests of evolutionary hypotheses previously only testable subjectively.
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Affiliation(s)
- Jennifer F. Hoyal Cuthill
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
- Department of Earth Sciences, University of Cambridge, Cambridge CB2 3EQ, UK
- Institute of Analytics and Data Science and School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Nicholas Guttenberg
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Sophie Ledger
- Department of Entomology, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Robyn Crowther
- Department of Entomology, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Blanca Huertas
- Department of Entomology, Natural History Museum, Cromwell Road, London SW7 5BD, UK
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34
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McClure M, Mahrouche L, Houssin C, Monllor M, Le Poul Y, Frérot B, Furtos A, Elias M. Does divergent selection predict the evolution of mate preference and reproductive isolation in the tropical butterfly genus
Melinaea
(Nymphalidae: Ithomiini)? J Anim Ecol 2019; 88:940-952. [DOI: 10.1111/1365-2656.12975] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 01/25/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Melanie McClure
- Institut Systématique Évolution Biodiversité (ISYEB) Centre National de la Recherche Scientifique MNHN EPHE Sorbonne Université Université des Antilles Paris France
| | - Louiza Mahrouche
- Centre Régional de Spectrométrie de Masse Département de Chimie Université de Montréal Montréal Quebec Canada
| | - Céline Houssin
- Institut Systématique Évolution Biodiversité (ISYEB) Centre National de la Recherche Scientifique MNHN EPHE Sorbonne Université Université des Antilles Paris France
| | - Monica Monllor
- Institut Systématique Évolution Biodiversité (ISYEB) Centre National de la Recherche Scientifique MNHN EPHE Sorbonne Université Université des Antilles Paris France
| | - Yann Le Poul
- Faculty of Biology LMU Munich Planegg‐Martinsried Germany
| | - Brigitte Frérot
- Institut d’Écologie et des Sciences de l'Environnement IEES – INRA UMR 1392 Versailles Cedex France
| | - Alexandra Furtos
- Centre Régional de Spectrométrie de Masse Département de Chimie Université de Montréal Montréal Quebec Canada
| | - Marianne Elias
- Institut Systématique Évolution Biodiversité (ISYEB) Centre National de la Recherche Scientifique MNHN EPHE Sorbonne Université Université des Antilles Paris France
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35
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Fuller ZL, Koury SA, Phadnis N, Schaeffer SW. How chromosomal rearrangements shape adaptation and speciation: Case studies in Drosophila pseudoobscura and its sibling species Drosophila persimilis. Mol Ecol 2019; 28:1283-1301. [PMID: 30402909 PMCID: PMC6475473 DOI: 10.1111/mec.14923] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/30/2018] [Accepted: 10/09/2018] [Indexed: 01/01/2023]
Abstract
The gene arrangements of Drosophila have played a prominent role in the history of evolutionary biology from the original quantification of genetic diversity to current studies of the mechanisms for the origin and establishment of new inversion mutations within populations and their subsequent fixation between species supporting reproductive barriers. This review examines the genetic causes and consequences of inversions as recombination suppressors and the role that recombination suppression plays in establishing inversions in populations as they are involved in adaptation within heterogeneous environments. This often results in the formation of clines of gene arrangement frequencies among populations. Recombination suppression leads to the differentiation of the gene arrangements which may accelerate the accumulation of fixed genetic differences among populations. If these fixed mutations cause incompatibilities, then inversions pose important reproductive barriers between species. This review uses the evolution of inversions in Drosophila pseudoobscura and D. persimilis as a case study for how inversions originate, establish and contribute to the evolution of reproductive isolation.
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Affiliation(s)
- Zachary L. Fuller
- Department of Biology, The Pennsylvania State University, 208 Erwin W. Mueller Laboratory, University Park, PA 16802-5301
| | - Spencer A. Koury
- Department of Biology, University of Utah, Salt Lake City, Utah 84112
| | - Nitin Phadnis
- Department of Biology, University of Utah, Salt Lake City, Utah 84112
| | - Stephen W. Schaeffer
- Department of Biology, The Pennsylvania State University, 208 Erwin W. Mueller Laboratory, University Park, PA 16802-5301
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36
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Gautier M, Yamaguchi J, Foucaud J, Loiseau A, Ausset A, Facon B, Gschloessl B, Lagnel J, Loire E, Parrinello H, Severac D, Lopez-Roques C, Donnadieu C, Manno M, Berges H, Gharbi K, Lawson-Handley L, Zang LS, Vogel H, Estoup A, Prud'homme B. The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird. Curr Biol 2018; 28:3296-3302.e7. [PMID: 30146156 PMCID: PMC6203698 DOI: 10.1016/j.cub.2018.08.023] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 07/25/2018] [Accepted: 08/07/2018] [Indexed: 12/02/2022]
Abstract
Many animal species comprise discrete phenotypic forms. A common example in natural populations of insects is the occurrence of different color patterns, which has motivated a rich body of ecological and genetic research [1-6]. The occurrence of dark, i.e., melanic, forms displaying discrete color patterns is found across multiple taxa, but the underlying genomic basis remains poorly characterized. In numerous ladybird species (Coccinellidae), the spatial arrangement of black and red patches on adult elytra varies wildly within species, forming strikingly different complex color patterns [7, 8]. In the harlequin ladybird, Harmonia axyridis, more than 200 distinct color forms have been described, which classic genetic studies suggest result from allelic variation at a single, unknown, locus [9, 10]. Here, we combined whole-genome sequencing, population-based genome-wide association studies, gene expression, and functional analyses to establish that the transcription factor Pannier controls melanic pattern polymorphism in H. axyridis. We show that pannier is necessary for the formation of melanic elements on the elytra. Allelic variation in pannier leads to protein expression in distinct domains on the elytra and thus determines the distinct color patterns in H. axyridis. Recombination between pannier alleles may be reduced by a highly divergent sequence of ∼170 kb in the cis-regulatory regions of pannier, with a 50 kb inversion between color forms. This most likely helps maintain the distinct alleles found in natural populations. Thus, we propose that highly variable discrete color forms can arise in natural populations through cis-regulatory allelic variation of a single gene.
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Affiliation(s)
- Mathieu Gautier
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | | | - Julien Foucaud
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Anne Loiseau
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Aurélien Ausset
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Benoit Facon
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Bernhard Gschloessl
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Jacques Lagnel
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Etienne Loire
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Hugues Parrinello
- MGX, Biocampus Montpellier, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Dany Severac
- MGX, Biocampus Montpellier, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | | | | | - Maxime Manno
- INRA, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Helene Berges
- INRA, Centre National de Ressources Génomiques Végétales, 31326 Castanet-Tolosan, France
| | - Karim Gharbi
- Edinburgh Genomics, University of Edinburgh, Edinburgh, UK
| | - Lori Lawson-Handley
- Evolutionary and Environmental Genomics Group, School of Environmental Sciences, University of Hull, Hull HU6 7RX, UK
| | - Lian-Sheng Zang
- Institute of Biological Control, Jilin Agricultural University, Changchun, China
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Arnaud Estoup
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France.
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37
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Lee DE, Cavener DR, Bond ML. Seeing spots: quantifying mother-offspring similarity and assessing fitness consequences of coat pattern traits in a wild population of giraffes ( Giraffa camelopardalis). PeerJ 2018; 6:e5690. [PMID: 30310743 PMCID: PMC6173159 DOI: 10.7717/peerj.5690] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/04/2018] [Indexed: 12/21/2022] Open
Abstract
Polymorphic phenotypes of mammalian coat coloration have been important to the study of genetics and evolution, but less is known about the inheritance and fitness consequences of individual variation in complex coat pattern traits such as spots and stripes. Giraffe coat markings are highly complex and variable and it has been hypothesized that variation in coat patterns most likely affects fitness by camouflaging neonates against visually hunting predators. We quantified complex coat pattern traits of wild Masai giraffes using image analysis software, determined the similarity of spot pattern traits between mother and offspring, and assessed whether variation in spot pattern traits was related to fitness as measured by juvenile survival. The methods we described could comprise a framework for objective quantification of complex mammal coat pattern traits based on photographic coat pattern data. We demonstrated that some characteristics of giraffe coat spot shape were likely to be heritable, as measured by mother-offspring regression. We found significant variation in juvenile survival among phenotypic groups of neonates defined by multivariate clustering based on spot trait measurement variables. We also found significant variation in neonatal survival associated with spot size and shape covariates. Larger spots (smaller number of spots) and irregularly shaped or rounder spots (smaller aspect ratio) were correlated with increased survival. These findings will inform investigations into developmental and genetic architecture of complex mammal coat patterns and their adaptive value.
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Affiliation(s)
- Derek E Lee
- Wild Nature Institute, Concord, NH, United States of America.,Department of Biology, Pennsylvania State University, University Park, United States of America
| | - Douglas R Cavener
- Department of Biology, Pennsylvania State University, University Park, United States of America
| | - Monica L Bond
- Wild Nature Institute, Concord, NH, United States of America.,Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
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38
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Supergene Evolution Triggered by the Introgression of a Chromosomal Inversion. Curr Biol 2018; 28:1839-1845.e3. [DOI: 10.1016/j.cub.2018.04.072] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/29/2018] [Accepted: 04/18/2018] [Indexed: 12/30/2022]
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39
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The Colorful Sex Chromosomes of Teleost Fish. Genes (Basel) 2018; 9:genes9050233. [PMID: 29751562 PMCID: PMC5977173 DOI: 10.3390/genes9050233] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 04/24/2018] [Accepted: 04/24/2018] [Indexed: 12/14/2022] Open
Abstract
Teleost fish provide some of the most intriguing examples of sexually dimorphic coloration, which is often advantageous for only one of the sexes. Mapping studies demonstrated that the genetic loci underlying such color patterns are frequently in tight linkage to the sex-determining locus of a species, ensuring sex-specific expression of the corresponding trait. Several genes affecting color synthesis and pigment cell development have been previously described, but the color loci on the sex chromosomes have mostly remained elusive as yet. Here, we summarize the current knowledge about the genetics of such color loci in teleosts, mainly from studies on poeciliids and cichlids. Further studies on these color loci will certainly provide important insights into the evolution of sex chromosomes.
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40
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Rönkä K, Mappes J, Michalis C, Kiviö R, Salokannas J, Rojas B. Can multiple-model mimicry explain warning signal polymorphism in the wood tiger moth, Arctia plantaginis (Lepidoptera: Erebidae)? Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- K Rönkä
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, FI, Finland
| | - J Mappes
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, FI, Finland
| | - C Michalis
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - R Kiviö
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, FI, Finland
| | - J Salokannas
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, FI, Finland
| | - B Rojas
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, FI, Finland
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41
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Yu J, Wang Y, Mou L, Fang D, Chen S, Zhang S. Nature-Inspired 2D-Mosaic 3D-Gradient Mesoporous Framework: Bimetal Oxide Dual-Composite Strategy toward Ultrastable and High-Capacity Lithium Storage. ACS NANO 2018; 12:2035-2047. [PMID: 29425020 DOI: 10.1021/acsnano.8b00168] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In allusion to traditional transition-metal oxide (TMO) anodes for lithium-ion batteries, which face severe volume variation and poor conductivity, herein a bimetal oxide dual-composite strategy based on two-dimensional (2D)-mosaic three-dimensional (3D)-gradient design is proposed. Inspired by natural mosaic dominance phenomena, Zn1-xCoxO/ZnCo2O4 2D-mosaic-hybrid mesoporous ultrathin nanosheets serve as building blocks to assemble into a 3D Zn-Co hierarchical framework. Moreover, a series of derivative frameworks with high evolution are controllably synthesized, based on which a facile one-pot synthesis process can be developed. From a component-composite perspective, both Zn1-xCoxO and ZnCo2O4 provide superior conductivity due to bimetal doping effect, which is verified by density functional theory calculations. From a structure-composite perspective, 2D-mosaic-hybrid mode gives rise to ladder-type buffering and electrochemical synergistic effect, thus realizing mutual stabilization and activation between the mosaic pair, especially for Zn1-xCoxO with higher capacity yet higher expansion. Moreover, the inside-out Zn-Co concentration gradient in 3D framework and rich oxygen vacancies further greatly enhance Li storage capability and stability. As a result, a high reversible capacity (1010 mA h g-1) and areal capacity (1.48 mA h cm-2) are attained, while ultrastable cyclability is obtained during high-rate and long-term cycles, rending great potential of our 2D-mosaic 3D-gradient design together with facile synthesis.
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Affiliation(s)
- Jia Yu
- Beijing Key Laboratory of Ionic Liquid Clean Process, Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Yanlei Wang
- Beijing Key Laboratory of Ionic Liquid Clean Process, Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences , Beijing 100190, China
| | - Lihui Mou
- Beijing Key Laboratory of Ionic Liquid Clean Process, Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Daliang Fang
- Beijing Key Laboratory of Ionic Liquid Clean Process, Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Shimou Chen
- Beijing Key Laboratory of Ionic Liquid Clean Process, Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Suojiang Zhang
- Beijing Key Laboratory of Ionic Liquid Clean Process, Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences , Beijing 100190, China
- University of Chinese Academy of Sciences , Beijing 100049, China
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42
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Kappel C, Huu CN, Lenhard M. A short story gets longer: recent insights into the molecular basis of heterostyly. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5719-5730. [PMID: 29099983 DOI: 10.1093/jxb/erx387] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/09/2017] [Indexed: 06/07/2023]
Abstract
Heterostyly is a fascinating adaptation to promote outbreeding and a classical paradigm of botany. In the most common type of heterostyly, plants either form flowers with long styles and short stamens, or short styles and long stamens. This reciprocal organ positioning reduces pollen wastage and promotes cross-pollination, thus increasing male fitness. In addition, in many heterostylous species selfing and the generation of unfit progeny due to inbreeding depression is limited by a self-incompatibility system, thus promoting female fitness. The two floral forms are genetically determined by the S locus as a complex supergene, namely a chromosomal region containing several individual genes that control the different traits, such as style or stamen length, and are held together by very tight linkage due to suppressed recombination. Recent molecular-genetic studies in several systems, including Turnera, Fagopyrum, Linum, and Primula have begun to identify and characterize the causal heterostyly genes residing at the S locus. An emerging theme from several families is that the dominant S haplotype represents a hemizygous region not present on the recessive s haplotype. This provides an explanation for the suppressed recombination and suggests a scenario for the chromosomal evolution of the S locus. In this review, we discuss the results from recent molecular-genetic analyses in light of the classical models on the genetics and evolution of heterostyly.
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Affiliation(s)
- Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Germany
| | - Cuong Nguyen Huu
- Institute for Biochemistry and Biology, University of Potsdam, Germany
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43
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Lindtke D, Lucek K, Soria-Carrasco V, Villoutreix R, Farkas TE, Riesch R, Dennis SR, Gompert Z, Nosil P. Long-term balancing selection on chromosomal variants associated with crypsis in a stick insect. Mol Ecol 2017; 26:6189-6205. [DOI: 10.1111/mec.14280] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 07/12/2017] [Accepted: 07/24/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Dorothea Lindtke
- Department of Biological Sciences; University of Calgary; Calgary AB Canada
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
| | - Kay Lucek
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
- Department of Environmental Sciences; University of Basel; Basel Switzerland
| | | | - Romain Villoutreix
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
| | - Timothy E. Farkas
- Department of Ecology and Evolutionary Biology; University of Connecticut; Storrs CT USA
| | - Rüdiger Riesch
- School of Biological Sciences; Royal Holloway; University of London; Egham UK
| | - Stuart R. Dennis
- Department of Aquatic Ecology; Eawag: Swiss Federal Institute of Aquatic Science and Technology; Dübendorf Switzerland
| | - Zach Gompert
- Department of Biology; Utah State University; Logan UT USA
| | - Patrik Nosil
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield UK
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44
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Van Belleghem SM, Papa R, Ortiz-Zuazaga H, Hendrickx F, Jiggins CD, McMillan WO, Counterman BA. patternize: An R package for quantifying colour pattern variation. Methods Ecol Evol 2017; 9:390-398. [PMID: 29755717 DOI: 10.1111/2041-210x.12853] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The use of image data to quantify, study and compare variation in the colors and patterns of organisms requires the alignment of images to establish homology, followed by color-based segmentation of images. Here we describe an R package for image alignment and segmentation that has applications to quantify color patterns in a wide range of organisms. patternize is an R package that quantifies variation in color patterns obtained from image data. patternize first defines homology between pattern positions across specimens either through manually placed homologous landmarks or automated image registration. Pattern identification is performed by categorizing the distribution of colors using an RGB threshold, k-means clustering or watershed transformation.We demonstrate that patternize can be used for quantification of the color patterns in a variety of organisms by analyzing image data for butterflies, guppies, spiders and salamanders. Image data can be compared between sets of specimens, visualized as heatmaps and analyzed using principal component analysis (PCA). patternize has potential applications for fine scale quantification of color pattern phenotypes in population comparisons, genetic association studies and investigating the basis of color pattern variation across a wide range of organisms.
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Affiliation(s)
- Steven M Van Belleghem
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom.,Department of Biology, Center for Applied Tropical Ecology and Conservation, University of Puerto Rico, Rio Piedras Campus, Puerto Rico.,Department of Biological Sciences, Mississippi State University, 295 Lee Boulevard, Mississippi State, MS 39762, USA
| | - Riccardo Papa
- Department of Biology, Center for Applied Tropical Ecology and Conservation, University of Puerto Rico, Rio Piedras Campus, Puerto Rico.,Molecular Sciences and Research Center, University of Puerto Rico, San Juan, 00926, Puerto Rico
| | - Humberto Ortiz-Zuazaga
- Department of Computer Science, University of Puerto Rico, Rio Piedras Campus, Puerto Rico
| | - Frederik Hendrickx
- Terrestrial Ecology Unit, Biology Department, Ghent University, Gent, Belgium.,Royal Belgian Institute of Natural Sciences, Brussel, Belgium
| | - 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, Mississippi State University, 295 Lee Boulevard, Mississippi State, MS 39762, USA
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45
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Llaurens V, Whibley A, Joron M. Genetic architecture and balancing selection: the life and death of differentiated variants. Mol Ecol 2017; 26:2430-2448. [PMID: 28173627 DOI: 10.1111/mec.14051] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 12/15/2016] [Accepted: 12/19/2016] [Indexed: 01/02/2023]
Abstract
Balancing selection describes any form of natural selection, which results in the persistence of multiple variants of a trait at intermediate frequencies within populations. By offering up a snapshot of multiple co-occurring functional variants and their interactions, systems under balancing selection can reveal the evolutionary mechanisms favouring the emergence and persistence of adaptive variation in natural populations. We here focus on the mechanisms by which several functional variants for a given trait can arise, a process typically requiring multiple epistatic mutations. We highlight how balancing selection can favour specific features in the genetic architecture and review the evolutionary and molecular mechanisms shaping this architecture. First, balancing selection affects the number of loci underlying differentiated traits and their respective effects. Control by one or few loci favours the persistence of differentiated functional variants by limiting intergenic recombination, or its impact, and may sometimes lead to the evolution of supergenes. Chromosomal rearrangements, particularly inversions, preventing adaptive combinations from being dissociated are increasingly being noted as features of such systems. Similarly, due to the frequency of heterozygotes maintained by balancing selection, dominance may be a key property of adaptive variants. High heterozygosity and limited recombination also influence associated genetic load, as linked recessive deleterious mutations may be sheltered. The capture of deleterious elements in a locus under balancing selection may reinforce polymorphism by further promoting heterozygotes. Finally, according to recent genomewide scans, balanced polymorphism might be more pervasive than generally thought. We stress the need for both functional and ecological studies to characterize the evolutionary mechanisms operating in these systems.
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Affiliation(s)
- Violaine Llaurens
- Institut de Systématique Evolution et Biodiversité (UMR 7205 CNRS, MNHN, UPMC, EPHE), Muséum National d'Histoire Naturelle - CP50, 45 rue Buffon, 75005, Paris, France
| | - Annabel Whibley
- Cell and Developmental Biology, John Innes Centre, Norwich, Norfolk, NR4 7UH, UK
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive (UMR 5175 CNRS, Université de Montpellier, Université Paul Valéry Montpellier, EPHE), 1919 route de Mende, 34293, Montpellier, France
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46
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Ayala D, Acevedo P, Pombi M, Dia I, Boccolini D, Costantini C, Simard F, Fontenille D. Chromosome inversions and ecological plasticity in the main African malaria mosquitoes. Evolution 2017; 71:686-701. [PMID: 28071788 DOI: 10.1111/evo.13176] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/22/2016] [Indexed: 01/30/2023]
Abstract
Chromosome inversions have fascinated the scientific community, mainly because of their role in the rapid adaption of different taxa to changing environments. However, the ecological traits linked to chromosome inversions have been poorly studied. Here, we investigated the roles played by 23 chromosome inversions in the adaptation of the four major African malaria mosquitoes to local environments in Africa. We studied their distribution patterns by using spatially explicit modeling and characterized the ecogeographical determinants of each inversion range. We then performed hierarchical clustering and constrained ordination analyses to assess the spatial and ecological similarities among inversions. Our results show that most inversions are environmentally structured, suggesting that they are actively involved in processes of local adaptation. Some inversions exhibited similar geographical patterns and ecological requirements among the four mosquito species, providing evidence for parallel evolution. Conversely, common inversion polymorphisms between sibling species displayed divergent ecological patterns, suggesting that they might have a different adaptive role in each species. These results are in agreement with the finding that chromosomal inversions play a role in Anopheles ecotypic adaptation. This study establishes a strong ecological basis for future genome-based analyses to elucidate the genetic mechanisms of local adaptation in these four mosquitoes.
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Affiliation(s)
- Diego Ayala
- UMR 224 MIVEGEC/ESV, IRD, Montpellier, 34394, France.,CIRMF, BP 769, Franceville, Gabon
| | - Pelayo Acevedo
- SaBio, Instituto de Investigación en Recursos Cinegéticos (IREC), CSIC-UCLM-JCCM, Ciudad Real, 13005, Spain
| | - Marco Pombi
- Sezione di Parassitologia, Dipartimento di Scienze di Sanità Pubblica, Università di Roma "La Sapienza,", Rome, 00185, Italy
| | - Ibrahima Dia
- Medical Entomology Unit, Institut Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Daniela Boccolini
- Department MIPI, Unit Vector-Borne Diseases and International Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | | | | | - Didier Fontenille
- UMR 224 MIVEGEC/ESV, IRD, Montpellier, 34394, France.,Current Address: Institut Pasteur du Cambodge, BP 983, Phnom Penh, Cambodia
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47
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Abstract
Species co-occurrence in ecological communities is thought to be influenced by multiple ecological and evolutionary processes, especially colonization and competition. However, effects of other interspecific interactions and evolutionary relationships are less explored. We examined evolutionary histories of community members and roles of mutualistic and parasitic interactions (Müllerian and Batesian mimicry, respectively) in the assembly of mimetic butterfly communities called mimicry rings in tropical forests of the Western Ghats, India. We found that Müllerian mimics were phylogenetically clustered, sharing aposematic signals due to common ancestry. On the other hand, Batesian mimics joined mimicry rings through convergent evolution and random phylogenetic assembly. Since the Western Ghats are a habitat island, we compared species diversity and composition in its mimicry rings with those of habitat mainland to test effects of biogeographic connectivity. The Western Ghats consisted of fewer mimicry rings and an overall smaller number of aposematic species and mimics compared to habitat mainland. The depauperate mimicry rings in the Western Ghats could have resulted from stochastic processes, reflecting their long temporal and spatial isolation and trickling colonization by the mimetic butterfly communities. These results highlight how evolutionary history, biogeographic isolation, and stochastic colonization influence the evolutionary assembly and diversity of ecological communities.
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48
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Arias M, le Poul Y, Chouteau M, Boisseau R, Rosser N, Théry M, Llaurens V. Crossing fitness valleys: empirical estimation of a fitness landscape associated with polymorphic mimicry. Proc Biol Sci 2017; 283:rspb.2016.0391. [PMID: 27122560 PMCID: PMC4855388 DOI: 10.1098/rspb.2016.0391] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/05/2016] [Indexed: 12/20/2022] Open
Abstract
Characterizing fitness landscapes associated with polymorphic adaptive traits enables investigation of mechanisms allowing transitions between fitness peaks. Here, we explore how natural selection can promote genetic mechanisms preventing heterozygous phenotypes from falling into non-adaptive valleys. Polymorphic mimicry is an ideal system to investigate such fitness landscapes, because the direction of selection acting on complex mimetic colour patterns can be predicted by the local mimetic community composition. Using more than 5000 artificial butterflies displaying colour patterns exhibited by the polymorphic Müllerian mimic Heliconius numata, we directly tested the role of wild predators in shaping fitness landscapes. We compared predation rates on mimetic phenotypes (homozygotes at the supergene controlling colour pattern), intermediate phenotypes (heterozygotes), exotic morphs (absent from the local community) and palatable cryptic phenotypes. Exotic morphs were significantly more attacked than local morphs, highlighting predators' discriminatory capacities. Overall, intermediates were attacked twice as much as local homozygotes, suggesting the existence of deep fitness valleys promoting strict dominance and reduced recombination between supergene alleles. By including information on predators' colour perception, we also showed that protection on intermediates strongly depends on their phenotypic similarity to homozygous phenotypes and that ridges exist between similar phenotypes, which may facilitate divergence in colour patterns.
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Affiliation(s)
- Mónica Arias
- Institut Systématique, Evolution, Biodiversité, UMR 7205 MNHN-CNRS-EPHE-UPMC- Sorbonne universités, Muséum National d'Histoire Naturelle, Bâtiment d'entomologie, CP050, 57, rue Cuvier, 75005 Paris, France UMR CNRS 7179, CNRS-MNHN MECADEV, Muséum National d'Histoire Naturelle, 1, avenue du petit château, 91800 Brunoy, France
| | - Yann le Poul
- Institut Systématique, Evolution, Biodiversité, UMR 7205 MNHN-CNRS-EPHE-UPMC- Sorbonne universités, Muséum National d'Histoire Naturelle, Bâtiment d'entomologie, CP050, 57, rue Cuvier, 75005 Paris, France
| | - Mathieu Chouteau
- Institut Systématique, Evolution, Biodiversité, UMR 7205 MNHN-CNRS-EPHE-UPMC- Sorbonne universités, Muséum National d'Histoire Naturelle, Bâtiment d'entomologie, CP050, 57, rue Cuvier, 75005 Paris, France
| | - Romain Boisseau
- Institut Systématique, Evolution, Biodiversité, UMR 7205 MNHN-CNRS-EPHE-UPMC- Sorbonne universités, Muséum National d'Histoire Naturelle, Bâtiment d'entomologie, CP050, 57, rue Cuvier, 75005 Paris, France Département de Biologie, Ecole Normale supérieure, 75 005 Paris, France
| | - Neil Rosser
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Marc Théry
- UMR CNRS 7179, CNRS-MNHN MECADEV, Muséum National d'Histoire Naturelle, 1, avenue du petit château, 91800 Brunoy, France
| | - Violaine Llaurens
- Institut Systématique, Evolution, Biodiversité, UMR 7205 MNHN-CNRS-EPHE-UPMC- Sorbonne universités, Muséum National d'Histoire Naturelle, Bâtiment d'entomologie, CP050, 57, rue Cuvier, 75005 Paris, France
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49
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Bybee S, Córdoba-Aguilar A, Duryea MC, Futahashi R, Hansson B, Lorenzo-Carballa MO, Schilder R, Stoks R, Suvorov A, Svensson EI, Swaegers J, Takahashi Y, Watts PC, Wellenreuther M. Odonata (dragonflies and damselflies) as a bridge between ecology and evolutionary genomics. Front Zool 2016; 13:46. [PMID: 27766110 PMCID: PMC5057408 DOI: 10.1186/s12983-016-0176-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 09/16/2016] [Indexed: 12/21/2022] Open
Abstract
Odonata (dragonflies and damselflies) present an unparalleled insect model to integrate evolutionary genomics with ecology for the study of insect evolution. Key features of Odonata include their ancient phylogenetic position, extensive phenotypic and ecological diversity, several unique evolutionary innovations, ease of study in the wild and usefulness as bioindicators for freshwater ecosystems worldwide. In this review, we synthesize studies on the evolution, ecology and physiology of odonates, highlighting those areas where the integration of ecology with genomics would yield significant insights into the evolutionary processes that would not be gained easily by working on other animal groups. We argue that the unique features of this group combined with their complex life cycle, flight behaviour, diversity in ecological niches and their sensitivity to anthropogenic change make odonates a promising and fruitful taxon for genomics focused research. Future areas of research that deserve increased attention are also briefly outlined.
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Affiliation(s)
- Seth Bybee
- Brigham Young University, Provo, UT 84606 USA
| | - Alex Córdoba-Aguilar
- Departmento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Apdo, Postal 70-275, Ciudad Universitaria, 04510 Mexico City, Mexico
| | - M. Catherine Duryea
- Evolutionary Ecology Unit, Department of Biology, Lund University, 223 62 Lund, Sweden
| | - Ryo Futahashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, Tsukuba, Ibaraki 305-8566 Japan
| | - Bengt Hansson
- Evolutionary Ecology Unit, Department of Biology, Lund University, 223 62 Lund, Sweden
| | - M. Olalla Lorenzo-Carballa
- Institute of Integrative Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool, L69 7ZB UK
| | - Ruud Schilder
- Departments of Entomology and Biology, Pennsylvania State University, University Park, PA 16802 USA
| | - Robby Stoks
- Laboratory of Aquatic Ecology, Evolution and Conservation, Department of Biology, University of Leuven, 3000 Leuven, Belgium
| | - Anton Suvorov
- Department of Biology, Brigham Young University, LSB 4102, Provo, UT 84602 USA
| | - Erik I. Svensson
- Evolutionary Ecology Unit, Department of Biology, Lund University, 223 62 Lund, Sweden
| | - Janne Swaegers
- Laboratory of Aquatic Ecology, Evolution and Conservation, Department of Biology, University of Leuven, 3000 Leuven, Belgium
| | - Yuma Takahashi
- Division of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba, Sendai, Miyagi 980-8578 Japan
| | | | - Maren Wellenreuther
- Evolutionary Ecology Unit, Department of Biology, Lund University, 223 62 Lund, Sweden
- Plant and Food Research Limited, Nelson, 7010 New Zealand
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Fujiwara H, Nishikawa H. Functional analysis of genes involved in color pattern formation in Lepidoptera. CURRENT OPINION IN INSECT SCIENCE 2016; 17:16-23. [PMID: 27720069 DOI: 10.1016/j.cois.2016.05.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 05/20/2016] [Accepted: 05/20/2016] [Indexed: 05/22/2023]
Abstract
In addition to the genome editing technology, novel functional analyses using electroporation are powerful tools to reveal the gene function in the color pattern formation. Using these methods, several genes involved in various larval color pattern formation are clarified in the silkworm Bombyx mori and some Papilio species. Furthermore, the coloration pattern mechanism underlying the longtime mystery of female-limited Batesian mimicry of Papilio polytes has been recently revealed. This review presents the recent progress on the molecular mechanisms and evolutionary process of coloration patterns contributing to various mimicry in Lepidoptera, especially focusing on the gene function in the silkworm and Papilio species.
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Affiliation(s)
- Haruhiko Fujiwara
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan.
| | - Hideki Nishikawa
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan
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