51
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Komata S, Kajitani R, Itoh T, Fujiwara H. Genomic architecture and functional unit of mimicry supergene in female limited Batesian mimic Papilio butterflies. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210198. [PMID: 35694751 PMCID: PMC9189499 DOI: 10.1098/rstb.2021.0198] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
It has long been suggested that dimorphic female-limited Batesian mimicry of two closely related Papilio butterflies, Papilio memnon and Papilio polytes, is controlled by supergenes. Whole-genome sequencing, genome-wide association studies and functional analyses have recently identified mimicry supergenes, including the doublesex (dsx) gene. Although supergenes of both the species are composed of highly divergent regions between mimetic and non-mimetic alleles and are located at the same chromosomal locus, they show critical differences in genomic architecture, particularly with or without an inversion: P. polytes has an inversion, but P. memnon does not. This review introduces and compares the detailed genomic structure of mimicry supergenes in two Papilio species, including gene composition, repetitive sequence composition, breakpoint/boundary site structure, chromosomal inversion and linkage disequilibrium. Expression patterns and functional analyses of the respective genes within or flanking the supergene suggest that dsx and other genes are involved in mimetic traits. In addition, structural comparison of the corresponding region for the mimicry supergene among further Papilio species suggests three scenarios for the evolution of the mimicry supergene between the two Papilio species. The structural features revealed in the Papilio mimicry supergene provide insight into the formation, maintenance and evolution of supergenes. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.
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Affiliation(s)
- Shinya Komata
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Rei Kajitani
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Haruhiko Fujiwara
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
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52
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Berdan EL, Flatt T, Kozak GM, Lotterhos KE, Wielstra B. Genomic architecture of supergenes: connecting form and function. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210192. [PMID: 35694757 PMCID: PMC9189501 DOI: 10.1098/rstb.2021.0192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Supergenes are tightly linked sets of loci that are inherited together and control complex phenotypes. While classical supergenes-governing traits such as wing patterns in Heliconius butterflies or heterostyly in Primula-have been studied since the Modern Synthesis, we still understand very little about how they evolve and persist in nature. The genetic architecture of supergenes is a critical factor affecting their evolutionary fate, as it can change key parameters such as recombination rate and effective population size, potentially redirecting molecular evolution of the supergene in addition to the surrounding genomic region. To understand supergene evolution, we must link genomic architecture with evolutionary patterns and processes. This is now becoming possible with recent advances in sequencing technology and powerful forward computer simulations. The present theme issue brings together theoretical and empirical papers, as well as opinion and synthesis papers, which showcase the architectural diversity of supergenes and connect this to critical processes in supergene evolution, such as polymorphism maintenance and mutation accumulation. Here, we summarize those insights to highlight new ideas and methods that illuminate the path forward for the study of supergenes in nature. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.
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Affiliation(s)
- Emma L Berdan
- Institute of Biology Leiden, Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands.,Naturalis Biodiversity Center, PO Box 9517, 2300 RA Leiden, The Netherlands.,Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, 45296 Strömstad, Sweden
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Genevieve M Kozak
- Department of Biology, University of Massachusetts Dartmouth, 285 Old Westport Road, MA 02747, USA
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University, 430 Nahant Road, Nahant, MA 01908, USA
| | - Ben Wielstra
- Institute of Biology Leiden, Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands.,Naturalis Biodiversity Center, PO Box 9517, 2300 RA Leiden, The Netherlands
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53
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Tafreshi AG, Otto SP, Chapuisat M. Unbalanced selection: the challenge of maintaining a social polymorphism when a supergene is selfish. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210197. [PMID: 35694754 PMCID: PMC9189496 DOI: 10.1098/rstb.2021.0197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Supergenes often have multiple phenotypic effects, including unexpected detrimental ones, because recombination suppression maintains associations among co-adapted alleles but also allows the accumulation of recessive deleterious mutations and selfish genetic elements. Yet, supergenes often persist over long evolutionary periods. How are such polymorphisms maintained in the face of selection, drive and drift? We present a population genetic model that investigates the conditions necessary for a stable polymorphic equilibrium when one of the supergene haplotypes is a selfish genetic element. The model fits the characteristics of the Alpine silver ant, Formica selysi, in which a large supergene underlies colony social organization, and one haplotype distorts Mendelian transmission by killing progeny that did not inherit it. The model shows that such maternal-effect killing strongly limits the maintenance of social polymorphism. Under random mating, transmission ratio distortion prevents rare single-queen colonies from invading populations of multiple-queen colonies, regardless of the fitness of each genotype. A stable polymorphic equilibrium can, however, be reached when high rates of assortative mating are combined with large fitness differences among supergene genotypes. The model reveals that the persistence of the social polymorphism is non-trivial and expected to occur only under restrictive conditions that deserve further empirical investigation. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.
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Affiliation(s)
- Alireza G Tafreshi
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Sarah P Otto
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Michel Chapuisat
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
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54
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Finseth F, Brown K, Demaree A, Fishman L. Supergene potential of a selfish centromere. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210208. [PMID: 35694746 PMCID: PMC9189507 DOI: 10.1098/rstb.2021.0208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Selfishly evolving centromeres bias their transmission by exploiting the asymmetry of female meiosis and preferentially segregating to the egg. Such female meiotic drive systems have the potential to be supergenes, with multiple linked loci contributing to drive costs or enhancement. Here, we explore the supergene potential of a selfish centromere (D) in Mimulus guttatus, which was discovered in the Iron Mountain (IM) Oregon population. In the nearby Cone Peak population, D is still a large, non-recombining and costly haplotype that recently swept, but shorter haplotypes and mutational variation suggest a distinct population history. We detected D in five additional populations spanning more than 200 km; together, these findings suggest that selfish centromere dynamics are widespread in M. guttatus. Transcriptome comparisons reveal elevated differences in expression between driving and non-driving haplotypes within, but not outside, the drive region, suggesting large-scale cis effects of D's spread on gene expression. We use the expression data to refine linked candidates that may interact with drive, including Nuclear Autoantigenic Sperm Protein (NASPSIM3), which chaperones the centromere-defining histone CenH3 known to modify Mimulus drive. Together, our results show that selfishly evolving centromeres may exhibit supergene behaviour and lay the foundation for future genetic dissection of drive and its costs. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.
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Affiliation(s)
- Findley Finseth
- W.M. Keck Science Department, Claremont McKenna, Scripps, and Pitzer Colleges, Claremont, CA 91711, USA
| | - Keely Brown
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
| | - Andrew Demaree
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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55
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Kay T, Helleu Q, Keller L. Iterative evolution of supergene-based social polymorphism in ants. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210196. [PMID: 35694755 PMCID: PMC9189498 DOI: 10.1098/rstb.2021.0196] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/08/2022] [Indexed: 12/16/2022] Open
Abstract
Species commonly exhibit alternative morphs, with individual fate being determined during development by either genetic factors, environmental cues or a combination thereof. Ants offer an interesting case study because many species are polymorphic in their social structure. Some colonies contain one queen while others contain many queens. This variation in queen number is generally associated with a suite of phenotypic and life-history traits, including mode of colony founding, queen lifespan, queen-worker dimorphism and colony size. The basis of this social polymorphism has been studied in five ant lineages, and remarkably social morph seems to be determined by a supergene in all cases. These 'social supergenes' tend to be large, having formed through serial inversions, and to comprise hundreds of linked genes. They have persisted over long evolutionary timescales, in multiple lineages following speciation events, and have spread between closely related species via introgression. Their evolutionary dynamics are unusually complex, combining recessive lethality, spatially variable selection, selfish genetic elements and non-random mating. Here, we synthesize the five cases of supergene-based social polymorphism in ants, highlighting interesting commonalities, idiosyncrasies and implications for the evolution of polymorphisms in general. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.
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Affiliation(s)
- Tomas Kay
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Quentin Helleu
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
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56
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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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57
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Berdan EL, Blanckaert A, Butlin RK, Flatt T, Slotte T, Wielstra B. Mutation accumulation opposes polymorphism: supergenes and the curious case of balanced lethals. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210199. [PMID: 35694750 PMCID: PMC9189497 DOI: 10.1098/rstb.2021.0199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Supergenes offer spectacular examples of long-term balancing selection in nature, but their origin and maintenance remain a mystery. Reduced recombination between arrangements, a critical aspect of many supergenes, protects adaptive multi-trait phenotypes but can lead to mutation accumulation. Mutation accumulation can stabilize the system through the emergence of associative overdominance (AOD), destabilize the system, or lead to new evolutionary outcomes. One outcome is the formation of maladaptive balanced lethal systems, where only heterozygotes remain viable and reproduce. We investigated the conditions under which these different outcomes occur, assuming a scenario of introgression after divergence. We found that AOD aided the invasion of a new supergene arrangement and the establishment of a polymorphism. However, this polymorphism was easily destabilized by further mutation accumulation, which was often asymmetric, disrupting the quasi-equilibrium state. Mechanisms that accelerated degeneration tended to amplify asymmetric mutation accumulation between the supergene arrangements and vice-versa. As the evolution of balanced lethal systems requires symmetric degeneration of both arrangements, this leaves only restricted conditions for their evolution, namely small population sizes and low rates of gene conversion. The dichotomy between the persistence of polymorphism and degeneration of supergene arrangements likely underlies the rarity of balanced lethal systems in nature. This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’.
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Affiliation(s)
- Emma L Berdan
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands.,Tjarnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, 45296 Stromstad, Sweden
| | - Alexandre Blanckaert
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA.,cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Roger K Butlin
- Tjarnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, 45296 Stromstad, Sweden.,Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, 106 91 Stockholm, Sweden
| | - Ben Wielstra
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands
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58
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Migration of repetitive DNAs during evolution of the permanent translocation heterozygosity in the oyster plant (Tradescantia section Rhoeo). Chromosoma 2022; 131:163-173. [PMID: 35896680 PMCID: PMC9470650 DOI: 10.1007/s00412-022-00776-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/28/2022] [Accepted: 07/14/2022] [Indexed: 11/30/2022]
Abstract
Due to translocation heterozygosity for all chromosomes in the cell complement, the oyster plant (Tradescantia spathacea) forms a complete meiotic ring. It also shows Rabl-arrangement at interphase, featured by polar centromere clustering. We demonstrate that the pericentromeric regions of the oyster plant are homogenized in concert by three subtelomeric sequences: 45S rDNA, (TTTAGGG)n motif, and TSrepI repeat. The Rabl-based clustering of pericentromeric regions may have been an excellent device to combine the subtelomere-pericentromere sequence migration (via inversions) with the pericentromere-pericentromere DNA movement (via whole arm translocations) that altogether led to the concerted homogenization of all the pericentromeric domains by the subtelomeric sequences. We also show that the repetitive sequence landscape of interstitial chromosome regions contains many loci consisting of Arabidopsis-type telomeric sequence or of TSrepI repeat, and it is extensively heterozygous. However, the sequence arrangement on some chromosomal arms suggest segmental inversions that are fully or partially homozygous, a fact that could be explained if the inversions started to create linkages already in a bivalent-forming ancestor. Remarkably, the subterminal TSrepI loci reside exclusively on the longer arms that could be due to sharing sequences between similarly-sized chromosomal arms in the interphase nucleus. Altogether, our study spotlights the supergene system of the oyster plant as an excellent model to link complex chromosome rearrangements, evolution of repetitive sequences, and nuclear architecture.
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59
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Abstract
The rediscovery of Mendel’s work showing that the heredity of phenotypes is controlled by discrete genes was followed by the reconciliation of Mendelian genetics with evolution by natural selection in the middle of the last century with the Modern Synthesis. In the past two decades, dramatic advances in genomic methods have facilitated the identification of the loci, genes, and even individual mutations that underlie phenotypic variants that are the putative targets of natural selection. Moreover, these methods have also changed how we can study adaptation by flipping the problem around, allowing us to first examine what loci show evidence of having been under selection, and then connecting these genetic variants to phenotypic variation. As a result, we now have an expanding list of actual genetic changes that underlie potentially adaptive phenotypic variation. Here, we synthesize how considering the effects of these adaptive loci in the context of cellular environments, genomes, organisms, and populations has provided new insights to the genetic architecture of adaptation.
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60
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Maney DL, Küpper C. Supergenes on steroids. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200507. [PMID: 35634926 PMCID: PMC9149793 DOI: 10.1098/rstb.2020.0507] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/18/2021] [Indexed: 07/20/2023] Open
Abstract
At the birth of supergenes, the genomic landscape is dramatically re-organized leading to pronounced differences in phenotypes and increased intrasexual diversity. Two of the best-studied supergenes in vertebrates are arguably the inversion polymorphisms on chromosomes 2 and 11 in the white-throated sparrow (Zonotrichia albicollis) and the ruff (Calidris pugnax), respectively. In both species, regions of suppressed recombination determine plumage coloration and social behavioural phenotypes. Despite the apparent lack of gene overlap between these two supergenes, in both cases the alternative phenotypes seem to be driven largely by alterations in steroid hormone pathways. Here, we explore the interplay between genomic architecture and steroid-related genes. Due to the highly pleiotropic effects of steroid-related genes and their universal involvement in social behaviour and transcriptomic regulation, processes favouring their linkage are likely to have substantial effects on the evolution of behavioural phenotypes, individual fitness, and life-history strategies. We propose that inversion-related differentiation and regulatory changes in steroid-related genes lie at the core of phenotypic differentiation in both of these interesting species. This article is part of the theme issue 'Genetic basis of adaptation and speciation: from loci to causative mutations'.
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Affiliation(s)
- Donna L. Maney
- Department of Psychology, Emory University, Atlanta, GA 30322, USA
| | - Clemens Küpper
- Research Group of Behavioural Genetics and Evolutionary Ecology, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
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61
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Jay P, Tezenas E, Véber A, Giraud T. Sheltering of deleterious mutations explains the stepwise extension of recombination suppression on sex chromosomes and other supergenes. PLoS Biol 2022; 20:e3001698. [PMID: 35853091 PMCID: PMC9295944 DOI: 10.1371/journal.pbio.3001698] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/03/2022] [Indexed: 12/19/2022] Open
Abstract
Many organisms have sex chromosomes with large nonrecombining regions that have expanded stepwise, generating "evolutionary strata" of differentiation. The reasons for this remain poorly understood, but the principal hypotheses proposed to date are based on antagonistic selection due to differences between sexes. However, it has proved difficult to obtain empirical evidence of a role for sexually antagonistic selection in extending recombination suppression, and antagonistic selection has been shown to be unlikely to account for the evolutionary strata observed on fungal mating-type chromosomes. We show here, by mathematical modeling and stochastic simulation, that recombination suppression on sex chromosomes and around supergenes can expand under a wide range of parameter values simply because it shelters recessive deleterious mutations, which are ubiquitous in genomes. Permanently heterozygous alleles, such as the male-determining allele in XY systems, protect linked chromosomal inversions against the expression of their recessive mutation load, leading to the successive accumulation of inversions around these alleles without antagonistic selection. Similar results were obtained with models assuming recombination-suppressing mechanisms other than chromosomal inversions and for supergenes other than sex chromosomes, including those without XY-like asymmetry, such as fungal mating-type chromosomes. However, inversions capturing a permanently heterozygous allele were found to be less likely to spread when the mutation load segregating in populations was lower (e.g., under large effective population sizes or low mutation rates). This may explain why sex chromosomes remain homomorphic in some organisms but are highly divergent in others. Here, we model a simple and testable hypothesis explaining the stepwise extensions of recombination suppression on sex chromosomes, mating-type chromosomes, and supergenes in general.
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Affiliation(s)
- Paul Jay
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-sur-Yvette, France
- * E-mail:
| | - Emilie Tezenas
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-sur-Yvette, France
- Univ. Lille, CNRS, UMR 8198 –Evo-Eco-Paleo, F-59000 Lille, France
- Université Paris Cité, CNRS, MAP 5, F-75006 Paris, France
| | - Amandine Véber
- Université Paris Cité, CNRS, MAP 5, F-75006 Paris, France
| | - Tatiana Giraud
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-sur-Yvette, France
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62
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Pierce D, Sun P, Purcell J, Brelsford A. A socially polymorphic Formica ant species exhibits a novel distribution of social supergene genotypes. J Evol Biol 2022; 35:1031-1044. [PMID: 35759556 PMCID: PMC9543797 DOI: 10.1111/jeb.14038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/15/2022] [Accepted: 05/15/2022] [Indexed: 11/29/2022]
Abstract
Most supergenes discovered so far are young, occurring in one species or a few closely related species. An ancient supergene in the ant genus Formica presents an unusual opportunity to compare supergene‐associated phenotypes and the factors that influence the persistence of polymorphism in different species. We investigate the genetic architecture of social organization in Formica francoeuri, an ant species native to low‐ and mid‐elevation semiarid regions of southern California, and describe an efficient technique for estimating mode of social organization using population genomic data. Using this technique, we show that F. francoeuri exhibits polymorphism in colony social organization and that the phenotypic polymorphism is strongly associated with genotypes within the Formica social supergene region. The distribution of supergene haplotypes in F. francoeuri differs from that of related species Formica selysi in that colonies with multiple queens contain almost exclusively workers that are heterozygous for alternative supergene haplotypes. Moreover, heterozygous workers exhibit allele‐specific expression of the polygyne‐associated haplotype at the candidate gene Knockout, which is thought to influence social organization. We also report geographic population structure and variation in worker size across a large fraction of the species range. Our results suggest that, although the Formica supergene is conserved within the genus, the mechanisms that maintain the supergene and its associated polymorphisms differ among species.
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Affiliation(s)
- Daniel Pierce
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California, USA
| | - Penglin Sun
- Department of Entomology, University of California, Riverside, California, USA
| | - Jessica Purcell
- Department of Entomology, University of California, Riverside, California, USA
| | - Alan Brelsford
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California, USA
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63
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Repeated translocation of a supergene underlying rapid sex chromosome turnover in Takifugu pufferfish. Proc Natl Acad Sci U S A 2022; 119:e2121469119. [PMID: 35658077 DOI: 10.1073/pnas.2121469119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceAlthough turnover of sex chromosomes is very common in many vertebrate lineages, the transition process is still elusive. We studied the sex-determining region (SDR) of 12 congeneric fish species of Takifugu fish that compose an important model for the study of genomics and sex determination. We found that while nine species retained their ancestral SDR, three species had acquired derived SDRs. Although the derived SDRs resided in three different chromosomes, they harbored a shared supergene flanked by two putative transposable elements. The results highlight the underestimated role of a mobile supergene in turnover of sex chromosomes in vertebrates.
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64
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Liu L, Megens HJ, Crooijmans RP, Bosse M, Huang Q, Sonsbeek GBV, Groenen MA, Madsen O. The Visayan warty pig (Sus cebifrons) genome provides insight into chromosome evolution and sensory adaptation in pigs. Mol Biol Evol 2022; 39:6596366. [PMID: 35642310 PMCID: PMC9178973 DOI: 10.1093/molbev/msac110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
It is largely unknown how mammalian genomes evolve under rapid speciation and environmental adaptation. An excellent model for understanding fast evolution is provided by the genus Sus, which diverged relatively recently and lacks post-zygotic isolation. Here, we present a high-quality reference genome of the Visayan warty pig, which is specialized to a tropical island environment. Comparing the genome sequences and chromatin contact maps of the Visayan warty pig (Sus cebifrons) and domestic pig (Sus scrofa), we characterized the dynamics of chromosomal structure evolution during Sus speciation, revealing the similar chromosome conformation as the potential biological mechanism of frequent post-divergence hybridization among Suidae. We further investigated the different signatures of adaptive selection and domestication in Visayan warty pig and domestic pig with specific emphasize on the evolution of olfactory and gustatory genes, elucidating higher olfactory diversity in Visayan warty pig and positive and relaxed evolution of bitter and fat taste receptors, respectively, in domestic pig. Our comprehensive evolutionary and comparative genome analyses provide insight into the dynamics of genomes and how these change over relative short evolutionary times, as well as how these genomic differences encode for differences in the phenotypes.
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Affiliation(s)
- Langqing Liu
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands.,Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands
| | | | - Mirte Bosse
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands
| | - Qitong Huang
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands.,Center for Animal Genomics, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | | | - Martien Am Groenen
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands
| | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands
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65
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Li Q, Lindtke D, Rodríguez-Ramírez C, Kakioka R, Takahashi H, Toyoda A, Kitano J, Ehrlich RL, Chang Mell J, Yeaman S. Local Adaptation and the Evolution of Genome Architecture in Threespine Stickleback. Genome Biol Evol 2022; 14:6589818. [PMID: 35594844 PMCID: PMC9178229 DOI: 10.1093/gbe/evac075] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2022] [Indexed: 12/11/2022] Open
Abstract
Theory predicts that local adaptation should favor the evolution of a concentrated genetic architecture, where the alleles driving adaptive divergence are tightly clustered on chromosomes. Adaptation to marine versus freshwater environments in threespine stickleback has resulted in an architecture that seems consistent with this prediction: divergence among populations is mainly driven by a few genomic regions harboring multiple quantitative trait loci for environmentally adapted traits, as well as candidate genes with well-established phenotypic effects. One theory for the evolution of these "genomic islands" is that rearrangements remodel the genome to bring causal loci into tight proximity, but this has not been studied explicitly. We tested this theory using synteny analysis to identify micro- and macro-rearrangements in the stickleback genome and assess their potential involvement in the evolution of genomic islands. To identify rearrangements, we conducted a de novo assembly of the closely related tubesnout (Aulorhyncus flavidus) genome and compared this to the genomes of threespine stickleback and two other closely related species. We found that small rearrangements, within-chromosome duplications, and lineage-specific genes (LSGs) were enriched around genomic islands, and that all three chromosomes harboring large genomic islands have experienced macro-rearrangements. We also found that duplicates and micro-rearrangements are 9.9× and 2.9× more likely to involve genes differentially expressed between marine and freshwater genotypes. While not conclusive, these results are consistent with the explanation that strong divergent selection on candidate genes drove the recruitment of rearrangements to yield clusters of locally adaptive loci.
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Affiliation(s)
- Qiushi Li
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Canada T2N 1N4
| | - Dorothea Lindtke
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Canada T2N 1N4
| | - Carlos Rodríguez-Ramírez
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Ryo Kakioka
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Nakagami-gun, Okinawa 903-0213, Japan
| | - Hiroshi Takahashi
- National Fisheries University, 2-7-1 Nagata-honmachi, Shimonoseki, Yamaguchi 759-6595, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Rachel L Ehrlich
- Department of Microbiology & Immunology, Drexel University College of Medicine, Philadelphia 19102, PA, USA
| | - Joshua Chang Mell
- Department of Microbiology & Immunology, Drexel University College of Medicine, Philadelphia 19102, PA, USA
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Canada T2N 1N4
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66
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Feller AF, Seehausen O. Genetic architecture of adaptive radiation across two trophic levels. Proc Biol Sci 2022; 289:20220377. [PMID: 35506225 PMCID: PMC9065965 DOI: 10.1098/rspb.2022.0377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Evolution of trophic diversity is a hallmark of adaptive radiation. Yet, transitions between carnivory and herbivory are rare in young adaptive radiations. Haplochromine cichlid fish of the African Great Lakes are exceptional in this regard. Lake Victoria was colonized by an insectivorous generalist and in less than 20 000 years, several clades of specialized herbivores evolved. Carnivorous versus herbivorous lifestyles in cichlids require many different adaptations in functional morphology, physiology and behaviour. Ecological transitions in either direction thus require many traits to change in a concerted fashion, which could be facilitated if genomic regions underlying these traits were physically linked or pleiotropic. However, linkage/pleiotropy could also constrain evolvability. To investigate components of the genetic architecture of a suite of traits that distinguish invertivores from algae scrapers, we performed quantitative trait locus (QTL) mapping using a second-generation hybrid cross. While we found indications of linkage/pleiotropy within trait complexes, QTLs for distinct traits were distributed across several unlinked genomic regions. Thus, a mixture of independently segregating variation and some pleiotropy may underpin the rapid trophic transitions. We argue that the emergence and maintenance of associations between the different genomic regions underpinning co-adapted traits that evolved and persist against some gene flow required reproductive isolation.
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Affiliation(s)
- Anna F. Feller
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland,Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland
| | - Ole Seehausen
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland,Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland
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67
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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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68
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Huang K, Ostevik KL, Elphinstone C, Todesco M, Bercovich N, Owens GL, Rieseberg LH. Mutation load in sunflower inversions is negatively correlated with inversion heterozygosity. Mol Biol Evol 2022; 39:6583099. [PMID: 35535689 PMCID: PMC9127631 DOI: 10.1093/molbev/msac101] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recombination is critical both for accelerating adaptation and purging deleterious mutations. Chromosomal inversions can act as recombination modifiers that suppress local recombination in heterozygotes and thus, under some conditions, are predicted to accumulate such mutations. In this study, we investigated patterns of recombination, transposable element abundance and coding sequence evolution across the genomes of 1,445 individuals from three sunflower species, as well as within nine inversions segregating within species. We also analyzed the effects of inversion genotypes on 87 phenotypic traits to test for overdominance. We found significant negative correlations of long terminal repeat retrotransposon abundance and deleterious mutations with recombination rates across the genome in all three species. However, we failed to detect an increase in these features in the inversions, except for a modest increase in the proportion of stop codon mutations in several very large or rare inversions. Consistent with this finding, there was little evidence of overdominance of inversions in phenotypes that may relate to fitness. On the other hand, significantly greater load was observed for inversions in populations polymorphic for a given inversion compared to populations monomorphic for one of the arrangements, suggesting that the local state of inversion polymorphism affects deleterious load. These seemingly contradictory results can be explained by the low frequency of inversion heterozygotes in wild sunflower populations, apparently due to divergent selection and associated geographic structure. Inversions contributing to local adaptation represent ideal recombination modifiers, acting to facilitate adaptive divergence with gene flow, while largely escaping the accumulation of deleterious mutations.
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Affiliation(s)
- Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Kate L Ostevik
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.,Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - Cassandra Elphinstone
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Marco Todesco
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Natalia Bercovich
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Gregory L Owens
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.,Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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69
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Navarro-Dominguez B, Chang CH, Brand CL, Muirhead CA, Presgraves DC, Larracuente AM. Epistatic selection on a selfish Segregation Distorter supergene - drive, recombination, and genetic load. eLife 2022; 11:e78981. [PMID: 35486424 PMCID: PMC9122502 DOI: 10.7554/elife.78981] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
Meiotic drive supergenes are complexes of alleles at linked loci that together subvert Mendelian segregation resulting in preferential transmission. In males, the most common mechanism of drive involves the disruption of sperm bearing one of a pair of alternative alleles. While at least two loci are important for male drive-the driver and the target-linked modifiers can enhance drive, creating selection pressure to suppress recombination. In this work, we investigate the evolution and genomic consequences of an autosomal, multilocus, male meiotic drive system, Segregation Distorter (SD) in the fruit fly, Drosophila melanogaster. In African populations, the predominant SD chromosome variant, SD-Mal, is characterized by two overlapping, paracentric inversions on chromosome arm 2R and nearly perfect (~100%) transmission. We study the SD-Mal system in detail, exploring its components, chromosomal structure, and evolutionary history. Our findings reveal a recent chromosome-scale selective sweep mediated by strong epistatic selection for haplotypes carrying Sd, the main driving allele, and one or more factors within the double inversion. While most SD-Mal chromosomes are homozygous lethal, SD-Mal haplotypes can recombine with other, complementing haplotypes via crossing over, and with wildtype chromosomes via gene conversion. SD-Mal chromosomes have nevertheless accumulated lethal mutations, excess non-synonymous mutations, and excess transposable element insertions. Therefore, SD-Mal haplotypes evolve as a small, semi-isolated subpopulation with a history of strong selection. These results may explain the evolutionary turnover of SD haplotypes in different populations around the world and have implications for supergene evolution broadly.
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Affiliation(s)
| | - Ching-Ho Chang
- Department of Biology, University of RochesterRochesterUnited States
| | - Cara L Brand
- Department of Biology, University of RochesterRochesterUnited States
| | - Christina A Muirhead
- Department of Biology, University of RochesterRochesterUnited States
- Ronin InstituteMontclairUnited States
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70
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McGuire D, Sankovitz M, Purcell J. A novel distribution of supergene genotypes is present in the socially polymorphic ant Formica neoclara. BMC Ecol Evol 2022; 22:47. [PMID: 35418041 PMCID: PMC9006578 DOI: 10.1186/s12862-022-02001-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/28/2022] [Indexed: 11/30/2022] Open
Abstract
Background Supergenes are chromosomal regions with tightly linked clusters of alleles that control compound phenotypic traits. Supergenes have been demonstrated to contribute to the maintenance of polymorphisms within populations in traits as diverse as mimetic wing coloration in butterflies, mating strategies in birds, and malarial susceptibility in mosquitoes. A large supergene also underlies variation in social organization in Formica ants. Alternative supergene haplotypes are associated with the presence of either a single queen (monogyny) or multiple queens (polygyny) within colonies. Here, we assess the social structure and supergene status of the North American species Formica neoclara. Results We sequenced a subset of the genome in 280 individuals sampled in populations from California to northern British Columbia using ddRADseq. We determined that F. neoclara is socially polymorphic in queen number, and we show that the social polymorphism is associated with alternative haplotypes at the social supergene. Intriguingly, polygyne colonies can harbor workers that are homozygous for both haplotypes as well as heterozygotes. Conclusions This colony genetic composition contrasts with other Formica species, in which almost all individuals in polygyne colonies have the polygyne-associated haplotype. The social polymorphism is present in widely distributed and genetically subdivided populations of F. neoclara. In studying this system in F. neoclara, we expand our understanding of the functional evolution of supergene haplotypes as they diverge in different lineages. Supplementary information The online version contains supplementary material available at 10.1186/s12862-022-02001-0.
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71
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Carpentier F, Rodríguez de la Vega RC, Jay P, Duhamel M, Shykoff JA, Perlin MH, Wallen RM, Hood ME, Giraud T. Tempo of degeneration across independently evolved non-recombining regions. Mol Biol Evol 2022; 39:6553583. [PMID: 35325190 PMCID: PMC9004411 DOI: 10.1093/molbev/msac060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Recombination is beneficial over the long term, allowing more effective selection. Despite long-term advantages of recombination, local recombination suppression can evolve and lead to genomic degeneration, in particular on sex chromosomes. Here, we investigated the tempo of degeneration in nonrecombining regions, that is, the function curve for the accumulation of deleterious mutations over time, leveraging on 22 independent events of recombination suppression identified on mating-type chromosomes of anther-smut fungi, including newly identified ones. Using previously available and newly generated high-quality genome assemblies of alternative mating types of 13 Microbotryum species, we estimated degeneration levels in terms of accumulation of nonoptimal codons and nonsynonymous substitutions in nonrecombining regions. We found a reduced frequency of optimal codons in the nonrecombining regions compared with autosomes, that was not due to less frequent GC-biased gene conversion or lower ancestral expression levels compared with recombining regions. The frequency of optimal codons rapidly decreased following recombination suppression and reached an asymptote after ca. 3 Ma. The strength of purifying selection remained virtually constant at dN/dS = 0.55, that is, at an intermediate level between purifying selection and neutral evolution. Accordingly, nonsynonymous differences between mating-type chromosomes increased linearly with stratum age, at a rate of 0.015 per My. We thus develop a method for disentangling effects of reduced selection efficacy from GC-biased gene conversion in the evolution of codon usage and we quantify the tempo of degeneration in nonrecombining regions, which is important for our knowledge on genomic evolution and on the maintenance of regions without recombination.
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Affiliation(s)
- Fantin Carpentier
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
- Université de Lille, CNRS, UMR 8198-Evo-Eco-Paleo F-59000, Lille, France
| | - Ricardo C. Rodríguez de la Vega
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
- Corresponding authors: E-mails: ;
| | - Paul Jay
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
| | - Marine Duhamel
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
- Evolution der Pflanzen und Pilze, Ruhr-Universität Bochum, Universitätsstraße 150, 44780, Bochum, Germany
| | - Jacqui A. Shykoff
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
| | - Michael H. Perlin
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY 40292, USA
| | - R. Margaret Wallen
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY 40292, USA
| | | | - Tatiana Giraud
- Laboratoire Ecologie Systématique et Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France
- Corresponding authors: E-mails: ;
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72
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Giraldo-Deck LM, Loveland JL, Goymann W, Tschirren B, Burke T, Kempenaers B, Lank DB, Küpper C. Intralocus conflicts associated with a supergene. Nat Commun 2022; 13:1384. [PMID: 35296671 PMCID: PMC8927407 DOI: 10.1038/s41467-022-29033-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 02/23/2022] [Indexed: 11/12/2022] Open
Abstract
Chromosomal inversions frequently underlie major phenotypic variation maintained by divergent selection within and between sexes. Here we examine whether and how intralocus conflicts contribute to balancing selection stabilizing an autosomal inversion polymorphism in the ruff Calidris pugnax. In this lekking shorebird, three male mating morphs (Independents, Satellites and Faeders) are controlled by an inversion-based supergene. We show that in a captive population, Faeder females, who are smaller and whose inversion haplotype has not undergone recombination, have lower average reproductive success in terms of laying rate, egg size, and offspring survival than Independent females, who lack the inversion. Satellite females, who carry a recombined inversion haplotype and have intermediate body size, more closely resemble Independent than Faeder females in reproductive performance. We inferred that the lower reproductive output of Faeder females is most likely balanced by higher than average reproductive success of individual Faeder males. These findings suggest that intralocus conflicts may play a major role in the evolution and maintenance of supergene variants.
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Affiliation(s)
- Lina M Giraldo-Deck
- Research Group Behavioural Genetics and Evolutionary Ecology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Str., 82319, Seewiesen, Germany.
| | - Jasmine L Loveland
- Research Group Behavioural Genetics and Evolutionary Ecology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Str., 82319, Seewiesen, Germany
| | - Wolfgang Goymann
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Str., 82319, Seewiesen, Germany
| | - Barbara Tschirren
- Centre for Ecology and Conservation, University of Exeter, Penryn, TR10 9FE, UK
| | - Terry Burke
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Eberhard-Gwinner-Str., 82319, Seewiesen, Germany
| | - David B Lank
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
| | - Clemens Küpper
- Research Group Behavioural Genetics and Evolutionary Ecology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Str., 82319, Seewiesen, Germany.
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73
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Jaron KS, Parker DJ, Anselmetti Y, Tran Van P, Bast J, Dumas Z, Figuet E, François CM, Hayward K, Rossier V, Simion P, Robinson-Rechavi M, Galtier N, Schwander T. Convergent consequences of parthenogenesis on stick insect genomes. SCIENCE ADVANCES 2022; 8:eabg3842. [PMID: 35196080 PMCID: PMC8865771 DOI: 10.1126/sciadv.abg3842] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The shift from sexual reproduction to parthenogenesis has occurred repeatedly in animals, but how the loss of sex affects genome evolution remains poorly understood. We generated reference genomes for five independently evolved parthenogenetic species in the stick insect genus Timema and their closest sexual relatives. Using these references and population genomic data, we show that parthenogenesis results in an extreme reduction of heterozygosity and often leads to genetically uniform populations. We also find evidence for less effective positive selection in parthenogenetic species, suggesting that sex is ubiquitous in natural populations because it facilitates fast rates of adaptation. Parthenogenetic species did not show increased transposable element (TE) accumulation, likely because there is little TE activity in the genus. By using replicated sexual-parthenogenetic comparisons, our study reveals how the absence of sex affects genome evolution in natural populations, providing empirical support for the negative consequences of parthenogenesis as predicted by theory.
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Affiliation(s)
- Kamil S. Jaron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
- Corresponding author. (D.J.P.); (K.S.J.); (T.S.)
| | - Darren J. Parker
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Corresponding author. (D.J.P.); (K.S.J.); (T.S.)
| | | | - Patrick Tran Van
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jens Bast
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Zoé Dumas
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Emeric Figuet
- ISEM—Institut des Sciences de l’Evolution, Montpellier, France
| | | | - Keith Hayward
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Victor Rossier
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Paul Simion
- ISEM—Institut des Sciences de l’Evolution, Montpellier, France
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicolas Galtier
- ISEM—Institut des Sciences de l’Evolution, Montpellier, France
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Corresponding author. (D.J.P.); (K.S.J.); (T.S.)
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Matschiner M, Barth JMI, Tørresen OK, Star B, Baalsrud HT, Brieuc MSO, Pampoulie C, Bradbury I, Jakobsen KS, Jentoft S. Supergene origin and maintenance in Atlantic cod. Nat Ecol Evol 2022; 6:469-481. [PMID: 35177802 PMCID: PMC8986531 DOI: 10.1038/s41559-022-01661-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 01/10/2022] [Indexed: 12/19/2022]
Abstract
Supergenes are sets of genes that are inherited as a single marker and encode complex phenotypes through their joint action. They are identified in an increasing number of organisms, yet their origins and evolution remain enigmatic. In Atlantic cod, four megabase-scale supergenes have been identified and linked to migratory lifestyle and environmental adaptations. Here we investigate the origin and maintenance of these four supergenes through analysis of whole-genome-sequencing data, including a new long-read-based genome assembly for a non-migratory Atlantic cod individual. We corroborate the finding that chromosomal inversions underlie all four supergenes, and we show that they originated at different times between 0.40 and 1.66 million years ago. We reveal gene flux between supergene haplotypes where migratory and stationary Atlantic cod co-occur and conclude that this gene flux is driven by gene conversion, on the basis of an increase in GC content in exchanged sites. Additionally, we find evidence for double crossover between supergene haplotypes, leading to the exchange of an ~275 kilobase fragment with genes potentially involved in adaptation to low salinity in the Baltic Sea. Our results suggest that supergenes can be maintained over long timescales in the same way as hybridizing species, through the selective purging of introduced genetic variation. Atlantic cod carries four supergenes linked to migratory lifestyle and environmental adaptations. Using whole-genome sequencing, the authors show that the genome inversions that underlie the supergenes originated at different times and show gene flux between supergene haplotypes.
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Affiliation(s)
- Michael Matschiner
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway. .,Department of Palaeontology and Museum, University of Zurich, Zurich, Switzerland. .,Natural History Museum, University of Oslo, Oslo, Norway.
| | - Julia Maria Isis Barth
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Ole Kristian Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Helle Tessand Baalsrud
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Marine Servane Ono Brieuc
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Ian Bradbury
- Fisheries and Oceans Canada, St John's, Newfoundland and Labrador, Canada
| | - Kjetill Sigurd Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
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75
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Dyson CJ, Crossley HG, Ray CH, Goodisman MAD. Social structure of perennial
Vespula squamosa
wasp colonies. Ecol Evol 2022; 12:e8569. [PMID: 35169451 PMCID: PMC8831225 DOI: 10.1002/ece3.8569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/18/2021] [Accepted: 12/23/2021] [Indexed: 11/25/2022] Open
Abstract
Many social species show variation in their social structure in response to different environmental conditions. For example, colonies of the yellowjacket wasp Vespula squamosa are typically headed by a single reproductive queen and survive for only a single season. However, in warmer climates, V. squamosa colonies sometimes persist for multiple years and can grow to extremely large size. We used genetic markers to understand patterns of reproduction and recruitment within these perennial colonies. We genotyped V. squamosa workers, pre‐reproductive queens, and males from perennial colonies in the southeastern United States at 10 polymorphic microsatellite loci and one mitochondrial DNA locus. We found that V. squamosa from perennial nests were produced by multiple reproductives, in contrast to typical annual colonies. Relatedness of nestmates from perennial colonies was significantly lower than relatedness of nestmates from annual colonies. Our analyses of mitochondrial DNA indicated that most V. squamosa perennial colonies represented semiclosed systems whereby all individuals belonged to a single matriline despite the presence of multiple reproductive females. However, new queens recruited into perennial colonies apparently mated with non‐nestmate males. Notably, perennial and annual colonies did not show significant genetic differences, supporting the hypothesis that perennial colony formation represents an instance of social plasticity. Overall, our results indicate that perennial V. squamosa colonies show substantial changes to their social biology compared to typical annual colonies and demonstrate variation in social behaviors in highly social species.
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Affiliation(s)
- Carl J. Dyson
- School of Biological Sciences Georgia Institute of Technology Atlanta Georgia USA
| | - Henry G. Crossley
- School of Biological Sciences Georgia Institute of Technology Atlanta Georgia USA
| | - Charles H. Ray
- Department of Entomology and Plant Pathology Auburn University Auburn Alabama USA
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76
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Potente G, Léveillé-Bourret É, Yousefi N, Choudhury RR, Keller B, Diop SI, Duijsings D, Pirovano W, Lenhard M, Szövényi P, Conti E. Comparative genomics elucidates the origin of a supergene controlling floral heteromorphism. Mol Biol Evol 2022; 39:6526404. [PMID: 35143659 PMCID: PMC8859637 DOI: 10.1093/molbev/msac035] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Supergenes are nonrecombining genomic regions ensuring the coinheritance of multiple, coadapted genes. Despite the importance of supergenes in adaptation, little is known on how they originate. A classic example of supergene is the S locus controlling heterostyly, a floral heteromorphism occurring in 28 angiosperm families. In Primula, heterostyly is characterized by the cooccurrence of two complementary, self-incompatible floral morphs and is controlled by five genes clustered in the hemizygous, ca. 300-kb S locus. Here, we present the first chromosome-scale genome assembly of any heterostylous species, that of Primula veris (cowslip). By leveraging the high contiguity of the P. veris assembly and comparative genomic analyses, we demonstrated that the S-locus evolved via multiple, asynchronous gene duplications and independent gene translocations. Furthermore, we discovered a new whole-genome duplication in Ericales that is specific to the Primula lineage. We also propose a mechanism for the origin of S-locus hemizygosity via nonhomologous recombination involving the newly discovered two pairs of CFB genes flanking the S locus. Finally, we detected only weak signatures of degeneration in the S locus, as predicted for hemizygous supergenes. The present study provides a useful resource for future research addressing key questions on the evolution of supergenes in general and the S locus in particular: How do supergenes arise? What is the role of genome architecture in the evolution of complex adaptations? Is the molecular architecture of heterostyly supergenes across angiosperms similar to that of Primula?
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Affiliation(s)
- Giacomo Potente
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland.,BaseClear BV, Leiden, The Netherlands.,Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Étienne Léveillé-Bourret
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland.,Institut de Recherche en Biologie Végétale and Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
| | - Narjes Yousefi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Rimjhim Roy Choudhury
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Barbara Keller
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Seydina Issa Diop
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland.,BaseClear BV, Leiden, The Netherlands.,Zurich-Basel Plant Science Center, Zurich, Switzerland
| | | | | | - Michael Lenhard
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland.,Zurich-Basel Plant Science Center, Zurich, Switzerland
| | - Elena Conti
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland.,Zurich-Basel Plant Science Center, Zurich, Switzerland
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77
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Hendrickx F, De Corte Z, Sonet G, Van Belleghem SM, Köstlbacher S, Vangestel C. A masculinizing supergene underlies an exaggerated male reproductive morph in a spider. Nat Ecol Evol 2022; 6:195-206. [PMID: 34949821 DOI: 10.1038/s41559-021-01626-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 11/15/2021] [Indexed: 11/09/2022]
Abstract
In many species, individuals can develop into strikingly different morphs, which are determined by a simple Mendelian locus. How selection shapes loci that control complex phenotypic differences remains poorly understood. In the spider Oedothorax gibbosus, males develop either into a 'hunched' morph with conspicuous head structures or as a fast-developing 'flat' morph with a female-like appearance. We show that the hunched-determining allele contains a unique genomic fragment of approximately 3 megabases that is absent in the flat-determining allele. This fragment comprises dozens of genes that duplicated from genes found at the same as well as different chromosomes. All functional duplicates, including a duplicate of the key sexual differentiation regulatory gene doublesex, show male-specific expression, which illustrates their integrated role as a masculinizing supergene. Our findings demonstrate how extensive indel polymorphisms and duplications of regulatory genes may contribute to the evolution of co-adapted gene clusters, sex-limited reproductive morphs and the enigmatic evolution of exaggerated sexual traits in general.
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Affiliation(s)
- Frederik Hendrickx
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium. .,Terrestrial Ecology Unity, Biology Department, Ghent University, Gent, Belgium.
| | - Zoë De Corte
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Gontran Sonet
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Steven M Van Belleghem
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico
| | - Stephan Köstlbacher
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.,Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Carl Vangestel
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Terrestrial Ecology Unity, Biology Department, Ghent University, Gent, Belgium
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78
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Chan AW, Villwock SS, Williams AL, Jannink JL. Sexual dimorphism and the effect of wild introgressions on recombination in cassava (Manihot esculenta Crantz) breeding germplasm. G3 (BETHESDA, MD.) 2022; 12:jkab372. [PMID: 34791172 PMCID: PMC8728042 DOI: 10.1093/g3journal/jkab372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 09/29/2021] [Indexed: 01/09/2023]
Abstract
Recombination has essential functions in meiosis, evolution, and breeding. The frequency and distribution of crossovers dictate the generation of new allele combinations and can vary across species and between sexes. Here, we examine recombination landscapes across the 18 chromosomes of cassava (Manihot esculenta Crantz) with respect to male and female meioses and known introgressions from the wild relative Manihot glaziovii. We used SHAPEIT2 and duoHMM to infer crossovers from genotyping-by-sequencing data and a validated multigenerational pedigree from the International Institute of Tropical Agriculture cassava breeding germplasm consisting of 7020 informative meioses. We then constructed new genetic maps and compared them to an existing map previously constructed by the International Cassava Genetic Map Consortium. We observed higher recombination rates in females compared to males, and lower recombination rates in M. glaziovii introgression segments on chromosomes 1 and 4, with suppressed recombination along the entire length of the chromosome in the case of the chromosome 4 introgression. Finally, we discuss hypothesized mechanisms underlying our observations of heterochiasmy and crossover suppression and discuss the broader implications for plant breeding.
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Affiliation(s)
- Ariel W Chan
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Seren S Villwock
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Amy L Williams
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jean-Luc Jannink
- RW Holley Center for Agriculture and Health, United States Department of Agriculture—Agricultural Research Service, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA
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79
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Liu Z, Roesti M, Marques D, Hiltbrunner M, Saladin V, Peichel CL. Chromosomal fusions facilitate adaptation to divergent environments in threespine stickleback. Mol Biol Evol 2021; 39:6462204. [PMID: 34908155 PMCID: PMC8826639 DOI: 10.1093/molbev/msab358] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Chromosomal fusions are hypothesized to facilitate adaptation to divergent environments, both by bringing together previously unlinked adaptive alleles and by creating regions of low recombination that facilitate the linkage of adaptive alleles; but, there is little empirical evidence to support this hypothesis. Here, we address this knowledge gap by studying threespine stickleback (Gasterosteus aculeatus), in which ancestral marine fish have repeatedly adapted to freshwater across the northern hemisphere. By comparing the threespine and ninespine stickleback (Pungitius pungitius) genomes to a de novo assembly of the fourspine stickleback (Apeltes quadracus) and an outgroup species, we find two chromosomal fusion events involving the same chromosomes have occurred independently in the threespine and ninespine stickleback lineages. On the fused chromosomes in threespine stickleback, we find an enrichment of quantitative trait loci underlying traits that contribute to marine versus freshwater adaptation. By comparing whole-genome sequences of freshwater and marine threespine stickleback populations, we also find an enrichment of regions under divergent selection on these two fused chromosomes. There is elevated genetic diversity within regions under selection in the freshwater population, consistent with a simulation study showing that gene flow can increase diversity in genomic regions associated with local adaptation and our demographic models showing gene flow between the marine and freshwater populations. Integrating our results with previous studies, we propose that these fusions created regions of low recombination that enabled the formation of adaptative clusters, thereby facilitating freshwater adaptation in the face of recurrent gene flow between marine and freshwater threespine sticklebacks.
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Affiliation(s)
- Zuyao Liu
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Marius Roesti
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - David Marques
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland.,Natural History Museum Basel, Basel, Switzerland
| | - Melanie Hiltbrunner
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Verena Saladin
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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80
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Guzmán NV, Kemppainen P, Monti D, Castillo ERD, Rodriguero MS, Sánchez-Restrepo AF, Cigliano MM, Confalonieri VA. Stable inversion clines in a grasshopper species group despite complex geographical history. Mol Ecol 2021; 31:1196-1215. [PMID: 34862997 DOI: 10.1111/mec.16305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 11/24/2021] [Accepted: 11/29/2021] [Indexed: 11/27/2022]
Abstract
Chromosomal inversions are known to play roles in adaptation and differentiation in many species. They involve clusters of correlated genes (i.e., loci in linkage disequilibrium, LD) possibly associated with environmental variables. The grasshopper "species complex" Trimerotropis pallidipennis comprises several genetic lineages distributed from North to South America in arid and semi-arid high-altitude environments. The southernmost lineage, Trimerotropis sp., segregates for four to seven putative inversions that display clinal variation, possibly through adaptation to temperate environments. We analysed chromosomal, mitochondrial and genome-wide single nucleotide polymorphism data in 19 Trimerotropis sp. populations mainly distributed along two altitudinal gradients (MS and Ju). Populations across Argentina comprise two main chromosomally and genetically differentiated lineages: one distributed across the southernmost border of the "Andes Centrales," adding evidence for a differentiation hotspot in this area; and the other widely distributed in Argentina. Within the latter, network analytical approaches to LD found three clusters of correlated loci (LD-clusters), with inversion karyotypes explaining >79% of the genetic variation. Outlier loci associated with environmental variables mapped to two of these LD-clusters. Furthermore, despite the complex geographical history indicated by population genetic analyses, the clines in inversion karyotypes have remained stable for more than 20 generations, implicating their role in adaptation and differentiation within this lineage. We hypothesize that these clines could be the consequence of a coupling between extrinsic postzygotic barriers and spatially varying selection along environmental gradients resulting in a hybrid zone. These results provide a framework for future investigations about candidate genes implicated in rapid adaptation to new environments.
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Affiliation(s)
- Noelia V Guzmán
- Departamento de Ecología, Genética y Evolución, FCEyN, Universidad de Buenos Aires (UBA), IEGEBA (Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET)/UBA), Ciudad Universitaria, Buenos Aires, Argentina
| | - Petri Kemppainen
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Daniela Monti
- Departamento de Ecología, Genética y Evolución, FCEyN, Universidad de Buenos Aires (UBA), IEGEBA (Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET)/UBA), Ciudad Universitaria, Buenos Aires, Argentina
| | - Elio R D Castillo
- Laboratorio de Genética Evolutiva "Dr. Claudio J. Bidau", FCEQyN, Universidad Nacional de Misiones (UNaM), Instituto de Biología Subtropical (IBS) (CONICET/UNaM), LQH, Posadas, Misiones, Argentina
| | - Marcela S Rodriguero
- Departamento de Ecología, Genética y Evolución, FCEyN, Universidad de Buenos Aires (UBA), IEGEBA (Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET)/UBA), Ciudad Universitaria, Buenos Aires, Argentina
| | - Andrés F Sánchez-Restrepo
- Departamento de Ecología, Genética y Evolución, FCEyN, Universidad de Buenos Aires (UBA), IEGEBA (Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET)/UBA), Ciudad Universitaria, Buenos Aires, Argentina.,Fundación para el Estudio de Especies Invasivas (FuEDEI), Hurlingham, Buenos Aires, Argentina
| | - Maria Marta Cigliano
- Museo de La Plata, Centro de Estudios Parasitológicos y de Vectores (CEPAVE- CONICET/UNLP), Universidad Nacional de la Plata, Buenos Aires, Argentina
| | - Viviana A Confalonieri
- Departamento de Ecología, Genética y Evolución, FCEyN, Universidad de Buenos Aires (UBA), IEGEBA (Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET)/UBA), Ciudad Universitaria, Buenos Aires, Argentina
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81
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Li F, Rane RV, Luria V, Xiong Z, Chen J, Li Z, Catullo RA, Griffin PC, Schiffer M, Pearce S, Lee SF, McElroy K, Stocker A, Shirriffs J, Cockerell F, Coppin C, Sgrò CM, Karger A, Cain JW, Weber JA, Santpere G, Kirschner MW, Hoffmann AA, Oakeshott JG, Zhang G. Phylogenomic analyses of the genus Drosophila reveals genomic signals of climate adaptation. Mol Ecol Resour 2021; 22:1559-1581. [PMID: 34839580 PMCID: PMC9299920 DOI: 10.1111/1755-0998.13561] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/10/2021] [Indexed: 01/13/2023]
Abstract
Many Drosophila species differ widely in their distributions and climate niches, making them excellent subjects for evolutionary genomic studies. Here, we have developed a database of high‐quality assemblies for 46 Drosophila species and one closely related Zaprionus. Fifteen of the genomes were newly sequenced, and 20 were improved with additional sequencing. New or improved annotations were generated for all 47 species, assisted by new transcriptomes for 19. Phylogenomic analyses of these data resolved several previously ambiguous relationships, especially in the melanogaster species group. However, it also revealed significant phylogenetic incongruence among genes, mainly in the form of incomplete lineage sorting in the subgenus Sophophora but also including asymmetric introgression in the subgenus Drosophila. Using the phylogeny as a framework and taking into account these incongruences, we then screened the data for genome‐wide signals of adaptation to different climatic niches. First, phylostratigraphy revealed relatively high rates of recent novel gene gain in three temperate pseudoobscura and five desert‐adapted cactophilic mulleri subgroup species. Second, we found differing ratios of nonsynonymous to synonymous substitutions in several hundred orthologues between climate generalists and specialists, with trends for significantly higher ratios for those in tropical and lower ratios for those in temperate‐continental specialists respectively than those in the climate generalists. Finally, resequencing natural populations of 13 species revealed tropics‐restricted species generally had smaller population sizes, lower genome diversity and more deleterious mutations than the more widespread species. We conclude that adaptation to different climates in the genus Drosophila has been associated with large‐scale and multifaceted genomic changes.
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Affiliation(s)
- Fang Li
- BGI-Shenzhen, Shenzhen, China.,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rahul V Rane
- Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia.,Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Vic., Australia
| | - Victor Luria
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Zijun Xiong
- BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | | | - Renee A Catullo
- Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia.,Division of Ecology and Evolution, Centre for Biodiversity Analysis, The Australian National University, Acton, ACT, Australia
| | - Philippa C Griffin
- Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Vic., Australia
| | - Michele Schiffer
- Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Vic., Australia.,Daintree Rainforest Observatory, James Cook University, Cape Tribulation, Qld, Australia
| | - Stephen Pearce
- Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Siu Fai Lee
- Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia.,Applied BioSciences, Macquarie University, North Ryde, NSW, Australia
| | - Kerensa McElroy
- Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Ann Stocker
- Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Vic., Australia
| | - Jennifer Shirriffs
- Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Vic., Australia
| | - Fiona Cockerell
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Chris Coppin
- Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Carla M Sgrò
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Amir Karger
- IT - Research Computing, Harvard Medical School, Boston, Massachusetts, USA
| | - John W Cain
- Department of Mathematics, Harvard University, Cambridge, Massachusetts, USA
| | - Jessica A Weber
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Gabriel Santpere
- Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences (DCEXS), Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Ary A Hoffmann
- Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Vic., Australia
| | - John G Oakeshott
- Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia.,Applied BioSciences, Macquarie University, North Ryde, NSW, Australia
| | - Guojie Zhang
- BGI-Shenzhen, Shenzhen, China.,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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82
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Sanchez-Donoso I, Ravagni S, Rodríguez-Teijeiro JD, Christmas MJ, Huang Y, Maldonado-Linares A, Puigcerver M, Jiménez-Blasco I, Andrade P, Gonçalves D, Friis G, Roig I, Webster MT, Leonard JA, Vilà C. Massive genome inversion drives coexistence of divergent morphs in common quails. Curr Biol 2021; 32:462-469.e6. [PMID: 34847353 DOI: 10.1016/j.cub.2021.11.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/25/2021] [Accepted: 11/08/2021] [Indexed: 12/31/2022]
Abstract
The presence of population-specific phenotypes often reflects local adaptation or barriers to gene flow. The co-occurrence of phenotypic polymorphisms that are restricted within the range of a highly mobile species is more difficult to explain. An example of such polymorphisms is in the common quail Coturnix coturnix, a small migratory bird that moves widely during the breeding season in search of new mating opportunities, following ephemeral habitats,1,2 and whose females may lay successive clutches at different locations while migrating.3 In spite of this vagility, previous studies reported a higher frequency of heavier males with darker throat coloration in the southwest of the distribution (I. Jiménez-Blasco et al., 2015, Int. Union Game Biol., conference). We used population genomics and cytogenetics to explore the basis of this polymorphism and discovered a large inversion in the genome of the common quail. This inversion extends 115 Mbp in length and encompasses more than 7,000 genes (about 12% of the genome), producing two very different forms. Birds with the inversion are larger, have darker throat coloration and rounder wings, are inferred to have poorer flight efficiency, and are geographically restricted despite the high mobility of the species. Stable isotope analyses confirmed that birds carrying the inversion have shorter migratory distances or do not migrate. However, we found no evidence of pre- or post-zygotic isolation, indicating the two forms commonly interbreed and that the polymorphism remains locally restricted because of the effect on behavior. This illustrates a genomic mechanism underlying maintenance of geographically structured polymorphisms despite interbreeding with a lineage with high mobility.
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Affiliation(s)
- Ines Sanchez-Donoso
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville 41092, Spain.
| | - Sara Ravagni
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville 41092, Spain
| | - J Domingo Rodríguez-Teijeiro
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona 08028, Spain
| | - Matthew J Christmas
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 75123, Sweden
| | - Yan Huang
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Andros Maldonado-Linares
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Manel Puigcerver
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona 08028, Spain
| | - Irene Jiménez-Blasco
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona 08028, Spain
| | - Pedro Andrade
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão 4485-661, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - David Gonçalves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão 4485-661, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto 4169-007, Portugal
| | - Guillermo Friis
- Center for Genomics and Systems Biology, New York University-Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Ignasi Roig
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 75123, Sweden
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville 41092, Spain
| | - Carles Vilà
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville 41092, Spain.
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83
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Rose NH, Bay RA, Morikawa MK, Thomas L, Sheets EA, Palumbi SR. Genomic analysis of distinct bleaching tolerances among cryptic coral species. Proc Biol Sci 2021; 288:20210678. [PMID: 34641729 DOI: 10.1098/rspb.2021.0678] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Reef-building coral species are experiencing an unprecedented decline owing to increasing frequency and intensity of marine heatwaves and associated bleaching-induced mortality. Closely related species from the Acropora hyacinthus species complex differ in heat tolerance and in their association with heat-tolerant symbionts. We used low-coverage full genome sequencing of 114 colonies monitored across the 2015 bleaching event in American Samoa to determine the genetic differences among four cryptic species (termed HA, HC, HD and HE) that have diverged in these species traits. Cryptic species differed strongly at thousands of single nucleotide polymorphisms across the genome which are enriched for amino acid changes in the bleaching-resistant species HE. In addition, HE also showed two particularly divergent regions with strong signals of differentiation. One approximately 220 kb locus, HES1, contained the majority of fixed differences in HE. A second locus, HES2, was fixed in HE but polymorphic in the other cryptic species. Surprisingly, non-HE individuals with HE-like haplotypes at HES2 were more likely to bleach. At both loci, HE showed particular sequence similarity to a congener, Acropora millepora. Overall, resilience to bleaching during the third global bleaching event was strongly structured by host cryptic species, buoyed by differences in symbiont associations between these species.
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Affiliation(s)
- Noah H Rose
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
| | - Rachael A Bay
- Department of Evolution and Ecology, University of California, Davis, CA, USA.,Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
| | - Megan K Morikawa
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
| | - Luke Thomas
- The UWA Oceans Institute, The University of Western Australia, Perth, Western Australia, Australia.,Australian Institute of Marine Science, Perth, Western Australia, Australia.,Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
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84
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Nosil P, Feder JL, Gompert Z. Biodiversity, resilience and the stability of evolutionary systems. Curr Biol 2021; 31:R1149-R1153. [PMID: 34637720 DOI: 10.1016/j.cub.2021.01.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Various macro-evolutionary phenomena, such as long-term stability punctuated by bursts of evolution, are difficult to explain via the micro-evolutionary process of weak selection acting steadily on individual mutations. In contrast, bursts of change are expected if evolutionary systems are complex and balanced, with occasional disruption of balance. Such disruption represents the collapse of resilience, akin to the snapping of an elastic band. It can be driven by external factors, or by self-propagating feedback loops internal to a system. Thus, evolutionary resilience could help explain how evolution generates broader patterns of biodiversity. We outline evidence and tests for this hypothesis, which emphasizes the processes balancing evolution, as urged fifty years ago in ecological genetics and via modern results in a range of systems.
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Affiliation(s)
- Patrik Nosil
- CEFE, Univ. Montpellier, CNRS, EPHE, IRD, Univ Paul Valery Montpellier 3, Montpellier, 34293, France; Department of Biology, Utah State University, Logan, UT 84322, USA.
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
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85
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Peart CR, Williams C, Pophaly SD, Neely BA, Gulland FMD, Adams DJ, Ng BL, Cheng W, Goebel ME, Fedrigo O, Haase B, Mountcastle J, Fungtammasan A, Formenti G, Collins J, Wood J, Sims Y, Torrance J, Tracey A, Howe K, Rhie A, Hoffman JI, Johnson J, Jarvis ED, Breen M, Wolf JBW. Hi-C scaffolded short- and long-read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution. Mol Ecol Resour 2021; 21:2455-2470. [PMID: 34097816 PMCID: PMC9732816 DOI: 10.1111/1755-0998.13443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/06/2021] [Accepted: 05/26/2021] [Indexed: 12/13/2022]
Abstract
With the advent of chromatin-interaction maps, chromosome-level genome assemblies have become a reality for a wide range of organisms. Scaffolding quality is, however, difficult to judge. To explore this gap, we generated multiple chromosome-scale genome assemblies of an emerging wild animal model for carcinogenesis, the California sea lion (Zalophus californianus). Short-read assemblies were scaffolded with two independent chromatin interaction mapping data sets (Hi-C and Chicago), and long-read assemblies with three data types (Hi-C, optical maps and 10X linked reads) following the "Vertebrate Genomes Project (VGP)" pipeline. In both approaches, 18 major scaffolds recovered the karyotype (2n = 36), with scaffold N50s of 138 and 147 Mb, respectively. Synteny relationships at the chromosome level with other pinniped genomes (2n = 32-36), ferret (2n = 34), red panda (2n = 36) and domestic dog (2n = 78) were consistent across approaches and recovered known fissions and fusions. Comparative chromosome painting and multicolour chromosome tiling with a panel of 264 genome-integrated single-locus canine bacterial artificial chromosome probes provided independent evaluation of genome organization. Broad-scale discrepancies between the approaches were observed within chromosomes, most commonly in translocations centred around centromeres and telomeres, which were better resolved in the VGP assembly. Genomic and cytological approaches agreed on near-perfect synteny of the X chromosome, and in combination allowed detailed investigation of autosomal rearrangements between dog and sea lion. This study presents high-quality genomes of an emerging cancer model and highlights that even highly fragmented short-read assemblies scaffolded with Hi-C can yield reliable chromosome-level scaffolds suitable for comparative genomic analyses.
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Affiliation(s)
- Claire R. Peart
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munchen, Germany
| | - Christina Williams
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Saurabh D. Pophaly
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munchen, Germany,Max Planck institute for Plant Breeding Research, Cologne, Germany
| | - Benjamin A. Neely
- National Institute of Standards and Technology, NIST Charleston, Charleston, South Carolina, USA
| | - Frances M. D. Gulland
- Karen Dryer Wildlife Health Center, University of California Davis, Davis, California, USA
| | - David J. Adams
- Cytometry Core Facility, Wellcome Sanger Institute, Cambridge, UK
| | - Bee Ling Ng
- Cytometry Core Facility, Wellcome Sanger Institute, Cambridge, UK
| | - William Cheng
- Cytometry Core Facility, Wellcome Sanger Institute, Cambridge, UK
| | - Michael E. Goebel
- Institute of Marine Science, University of California Santa Cruz, Santa Cruz, California, USA
| | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, New York City, New York, USA
| | - Bettina Haase
- Vertebrate Genome Lab, The Rockefeller University, New York City, New York, USA
| | | | | | - Giulio Formenti
- Vertebrate Genome Lab, The Rockefeller University, New York City, New York, USA,Laboratory of Neurogenetics of Language, The Rockefeller University, New York City, New York, USA
| | - Joanna Collins
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Jonathan Wood
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Ying Sims
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - James Torrance
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Alan Tracey
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Kerstin Howe
- Tree of Life Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Joseph I. Hoffman
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany,British Antarctic Survey, Cambridge, UK
| | - Jeremy Johnson
- Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
| | - Erich D. Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York City, New York, USA,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA,Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, USA
| | - Jochen B. W. Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Munchen, Germany
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86
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Purcell J, Lagunas-Robles G, Rabeling C, Borowiec ML, Brelsford A. The maintenance of polymorphism in an ancient social supergene. Mol Ecol 2021; 30:6246-6258. [PMID: 34570409 DOI: 10.1111/mec.16196] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 09/03/2021] [Accepted: 09/15/2021] [Indexed: 12/30/2022]
Abstract
Supergenes, regions of the genome with suppressed recombination between sets of functional mutations, contribute to the evolution of complex phenotypes in diverse systems. Excluding sex chromosomes, most supergenes discovered so far appear to be young, being found in one species or a few closely related species. Here, we investigate how a chromosome harbouring an ancient supergene has evolved over about 30 million years (Ma). The Formica supergene underlies variation in colony queen number in at least five species. We expand previous analyses of sequence divergence on this chromosome to encompass about 90 species spanning the Formica phylogeny. Within the nonrecombining region, the gene knockout contains 22 single nucleotide polymorphisms (SNPs) that are consistently differentiated between two alternative supergene haplotypes in divergent European Formica species, and we show that these same SNPs are present in most Formica clades. In these clades, including an early diverging Nearctic Formica clade, individuals with alternative genotypes at knockout also have higher differentiation in other portions of this chromosome. We identify hotspots of SNPs along this chromosome that are present in multiple Formica clades to detect genes that may have contributed to the emergence and maintenance of the genetic polymorphism. Finally, we infer three gene duplications on one haplotype, based on apparent heterozygosity within these genes in the genomes of haploid males. This study strengthens the evidence that this supergene originated early in the evolution of Formica and that just a few loci in this large region of suppressed recombination retain strongly differentiated alleles across contemporary Formica lineages.
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Affiliation(s)
- Jessica Purcell
- Department of Entomology, University of California Riverside, Riverside, CA, USA
| | - German Lagunas-Robles
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, USA
| | | | - Marek L Borowiec
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID, USA
| | - Alan Brelsford
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, USA
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87
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Hale MC, Campbell MA, McKinney GJ. A candidate chromosome inversion in Arctic charr (Salvelinus alpinus) identified by population genetic analysis techniques. G3-GENES GENOMES GENETICS 2021; 11:6329827. [PMID: 34568922 PMCID: PMC8473973 DOI: 10.1093/g3journal/jkab267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 07/23/2021] [Indexed: 11/13/2022]
Abstract
The "genomics era" has allowed questions to be asked about genome organization and genome architecture of non-model species at a rate not previously seen. Analyses of these genome-wide datasets have documented many examples of novel structural variants (SVs) such as chromosomal inversions, copy number variants, and chromosomal translocations, many of which have been linked to adaptation. The salmonids are a taxonomic group with abundant genome-wide datasets due to their importance in aquaculture and fisheries. However, the number of documented SVs in salmonids is surprisingly low and is most likely due to removing loci in high linkage disequilibrium when analyzing structure and gene flow. Here we re-analyze RAD-seq data from several populations of Arctic charr (Salvelinus alpinus) and document a novel ∼1.2 MB SV at the distal end of LG12. This variant contains 15 protein-coding genes connected to a wide-range of functions including cell adhesion and signal transduction. Interestingly, we studied the frequency of this polymorphism in four disjointed populations of charr-one each from Nunavut, Newfoundland, Eastern Russia, and Scotland-and found evidence of the variant only in Nunavut, Canada, suggesting the polymorphism is novel and recently evolved.
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Affiliation(s)
- Matthew C Hale
- Department of Biology, Texas Christian University, Fort Worth, TX 76129, USA
| | - Matthew A Campbell
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA.,University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - Garrett J McKinney
- National Research Council Research Associateship Program, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98112, USA
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88
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Abstract
The repeated adaptation of oceanic threespine sticklebacks to fresh water has made it a premier organism to study parallel evolution. These small fish have multiple distinct ecotypes that display a wide range of diverse phenotypic traits. Ecotypes are easily crossed in the laboratory, and families are large and develop quickly enough for quantitative trait locus analyses, positioning the threespine stickleback as a versatile model organism to address a wide range of biological questions. Extensive genomic resources, including linkage maps, a high-quality reference genome, and developmental genetics tools have led to insights into the genomic basis of adaptation and the identification of genomic changes controlling traits in vertebrates. Recently, threespine sticklebacks have been used as a model system to identify the genomic basis of highly complex traits, such as behavior and host-microbiome and host-parasite interactions. We review the latest findings and new avenues of research that have led the threespine stickleback to be considered a supermodel of evolutionary genomics.
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Affiliation(s)
- Kerry Reid
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA;
| | - Michael A Bell
- University of California Museum of Paleontology, Berkeley, California 94720, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA;
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89
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Jeffries DL, Gerchen JF, Scharmann M, Pannell JR. A neutral model for the loss of recombination on sex chromosomes. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200096. [PMID: 34247504 PMCID: PMC8273504 DOI: 10.1098/rstb.2020.0096] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2021] [Indexed: 01/10/2023] Open
Abstract
The loss of recombination between sex chromosomes has occurred repeatedly throughout nature, with important implications for their subsequent evolution. Explanations for this remarkable convergence have generally invoked only adaptive processes (e.g. sexually antagonistic selection); however, there is still little evidence for these hypotheses. Here we propose a model in which recombination on sex chromosomes is lost due to the neutral accumulation of sequence divergence adjacent to (and thus, in linkage disequilibrium with) the sex determiner. Importantly, we include in our model the fact that sequence divergence, in any form, reduces the probability of recombination between any two sequences. Using simulations, we show that, under certain conditions, a region of suppressed recombination arises and expands outwards from the sex-determining locus, under purely neutral processes. Further, we show that the rate and pattern of recombination loss are sensitive to the pre-existing recombination landscape of the genome and to sex differences in recombination rates, with patterns consistent with evolutionary strata emerging under some conditions. We discuss the applicability of these results to natural systems. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.
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Affiliation(s)
- Daniel L. Jeffries
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jörn F. Gerchen
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Mathias Scharmann
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - John R. Pannell
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
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90
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Mérot C, Berdan EL, Cayuela H, Djambazian H, Ferchaud AL, Laporte M, Normandeau E, Ragoussis J, Wellenreuther M, Bernatchez L. Locally Adaptive Inversions Modulate Genetic Variation at Different Geographic Scales in a Seaweed Fly. Mol Biol Evol 2021; 38:3953-3971. [PMID: 33963409 PMCID: PMC8382925 DOI: 10.1093/molbev/msab143] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Across a species range, multiple sources of environmental heterogeneity, at both small and large scales, create complex landscapes of selection, which may challenge adaptation, particularly when gene flow is high. One key to multidimensional adaptation may reside in the heterogeneity of recombination along the genome. Structural variants, like chromosomal inversions, reduce recombination, increasing linkage disequilibrium among loci at a potentially massive scale. In this study, we examined how chromosomal inversions shape genetic variation across a species range and ask how their contribution to adaptation in the face of gene flow varies across geographic scales. We sampled the seaweed fly Coelopa frigida along a bioclimatic gradient stretching across 10° of latitude, a salinity gradient, and a range of heterogeneous, patchy habitats. We generated a chromosome-level genome assembly to analyze 1,446 low-coverage whole genomes collected along those gradients. We found several large nonrecombining genomic regions, including putative inversions. In contrast to the collinear regions, inversions and low-recombining regions differentiated populations more strongly, either along an ecogeographic cline or at a fine-grained scale. These genomic regions were associated with environmental factors and adaptive phenotypes, albeit with contrasting patterns. Altogether, our results highlight the importance of recombination in shaping adaptation to environmental heterogeneity at local and large scales.
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Affiliation(s)
- Claire Mérot
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Emma L Berdan
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Hugo Cayuela
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Anne-Laure Ferchaud
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Martin Laporte
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | | | - Maren Wellenreuther
- Seafood Research Unit, Plant & Food Research, Port Nelson, Nelson, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
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91
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Campbell MA, Anderson EC, Garza JC, Pearse DE. Polygenic basis and the role of genome duplication in adaptation to similar selective environments. J Hered 2021; 112:614-625. [PMID: 34420047 DOI: 10.1093/jhered/esab049] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 08/20/2021] [Indexed: 02/02/2023] Open
Abstract
Genetic changes underlying adaptation vary greatly in terms of complexity and, within the same species, genetic responses to similar selective pressures may or may not be the same. We examine both complex (supergene) and simple (SNP) genetic variants occurring in populations of rainbow trout (Oncorhynchus mykiss) independently isolated from ocean access and compared them to each other and to an anadromous below-barrier population representing their ancestral source to search for signatures of both parallel and non-parallel adaptation. All landlocked populations displayed an increased frequency of a large inversion on chromosome Omy05, while three of the four populations exhibited elevated frequencies of another inversion located on chromosome Omy20. In addition, we identified numerous regions outside these two inversions that also show significant shifts in allele frequencies consistent with adaptive evolution. However, there was little concordance among above-barrier populations in these specific genomic regions under selection. In part, the lack of concordance appears to arise from ancestral autopolyploidy in rainbow trout that provides duplicate genomic regions of similar functional composition for selection to act upon. Thus, while selection acting on landlocked populations universally favors the resident ecotype, outside of the major chromosomal inversions, the resulting genetic changes are largely distinct among populations. Our results indicate that selection on standing genetic variation is likely the primary mode of rapid adaptation, and that both supergene complexes and individual loci contribute to adaptive evolution, further highlighting the diversity of adaptive genomic variation involved in complex phenotypic evolution.
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Affiliation(s)
- Matthew A Campbell
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Eric C Anderson
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
| | - John Carlos Garza
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
| | - Devon E Pearse
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
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92
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Hartmann FE, Ament-Velásquez SL, Vogan AA, Gautier V, Le Prieur S, Berramdane M, Snirc A, Johannesson H, Grognet P, Malagnac F, Silar P, Giraud T. Size Variation of the Nonrecombining Region on the Mating-Type Chromosomes in the Fungal Podospora anserina Species Complex. Mol Biol Evol 2021; 38:2475-2492. [PMID: 33555341 PMCID: PMC8136517 DOI: 10.1093/molbev/msab040] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Sex chromosomes often carry large nonrecombining regions that can extend progressively over time, generating evolutionary strata of sequence divergence. However, some sex chromosomes display an incomplete suppression of recombination. Large genomic regions without recombination and evolutionary strata have also been documented around fungal mating-type loci, but have been studied in only a few fungal systems. In the model fungus Podospora anserina (Ascomycota, Sordariomycetes), the reference S strain lacks recombination across a 0.8-Mb region around the mating-type locus. The lack of recombination in this region ensures that nuclei of opposite mating types are packaged into a single ascospore (pseudohomothallic lifecycle). We found evidence for a lack of recombination around the mating-type locus in the genomes of ten P. anserina strains and six closely related pseudohomothallic Podospora species. Importantly, the size of the nonrecombining region differed between strains and species, as indicated by the heterozygosity levels around the mating-type locus and experimental selfing. The nonrecombining region is probably labile and polymorphic, differing in size and precise location within and between species, resulting in occasional, but infrequent, recombination at a given base pair. This view is also supported by the low divergence between mating types, and the lack of strong linkage disequilibrium, chromosomal rearrangements, transspecific polymorphism and genomic degeneration. We found a pattern suggestive of evolutionary strata in P. pseudocomata. The observed heterozygosity levels indicate low but nonnull outcrossing rates in nature in these pseudohomothallic fungi. This study adds to our understanding of mating-type chromosome evolution and its relationship to mating systems.
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Affiliation(s)
- Fanny E Hartmann
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | | | - Aaron A Vogan
- Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Valérie Gautier
- Laboratoire Interdisciplinaire des Energies de Demain, Université de Paris, Paris, France
| | - Stephanie Le Prieur
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Myriam Berramdane
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Alodie Snirc
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | | | - Pierre Grognet
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Fabienne Malagnac
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Philippe Silar
- Laboratoire Interdisciplinaire des Energies de Demain, Université de Paris, Paris, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
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93
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94
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Extreme Y chromosome polymorphism corresponds to five male reproductive morphs of a freshwater fish. Nat Ecol Evol 2021; 5:939-948. [PMID: 33958755 DOI: 10.1038/s41559-021-01452-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 03/23/2021] [Indexed: 02/02/2023]
Abstract
Loss of recombination between sex chromosomes often depletes Y chromosomes of functional content and genetic variation, which might limit their potential to generate adaptive diversity. Males of the freshwater fish Poecilia parae occur as one of five discrete morphs, all of which shoal together in natural populations where morph frequency has been stable for over 50 years. Each morph uses a different complex reproductive strategy and morphs differ dramatically in colour, body size and mating behaviour. Morph phenotype is passed perfectly from father to son, indicating there are five Y haplotypes segregating in the species, which encode the complex male morph characteristics. Here, we examine Y diversity in natural populations of P. parae. Using linked-read sequencing on multiple P. parae females and males of all five morphs, we find that the genetic architecture of the male morphs evolved on the Y chromosome after recombination suppression had occurred with the X. Comparing Y chromosomes between each of the morphs, we show that, although the Ys of the three minor morphs that differ in colour are highly similar, there are substantial amounts of unique genetic material and divergence between the Ys of the three major morphs that differ in reproductive strategy, body size and mating behaviour. Altogether, our results suggest that the Y chromosome is able to overcome the constraints of recombination loss to generate extreme diversity, resulting in five discrete Y chromosomes that control complex reproductive strategies.
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95
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Loveland JL, Lank DB, Küpper C. Gene Expression Modification by an Autosomal Inversion Associated With Three Male Mating Morphs. Front Genet 2021; 12:641620. [PMID: 34149796 PMCID: PMC8213371 DOI: 10.3389/fgene.2021.641620] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/22/2021] [Indexed: 11/22/2022] Open
Abstract
Chromosomal inversions are structural rearrangements that frequently provide genomic substrate for phenotypic diversity. In the ruff Philomachus pugnax, three distinct male reproductive morphs (Independents, Satellites and Faeders) are genetically determined by a 4.5 Mb autosomal inversion. Here we test how this stable inversion polymorphism affects gene expression in males during the lekking season. Gene expression may be altered through disruptions at the breakpoints and the accumulation of mutations due to suppressed recombination. We used quantitative PCR to measure expression of 11 candidate inversion genes across three different tissues (liver, adrenal glands and gonads) and tested for allelic imbalance in four inversion genes across 12 males of all three morphs (8 Independents, 2 Satellites, 2 Faeders). We quantified transcripts of CENPN, an essential gene disrupted by the inversion at the proximal breakpoint, at different exons distributed near and across the breakpoint region. Consistent with dosage dependent gene expression for the breakpoint gene CENPN, we found that expression in Independents was broadly similar for transcripts segments from inside and outside the inversion regions, whereas for Satellites and Faeders, transcript segments outside of the inversion showed at least twofold higher expression than those spanning over the breakpoint. Within the inversion, observed expression differences for inversion males across all four genes with allele-specific primers were consistent with allelic imbalance. We further analyzed gonadal expression of two inversion genes, HSD17B2 and SDR42E1, along with 12 non-inversion genes related to steroid metabolism and signaling in 25 males (13 Independents, 7 Satellites, 5 Faeders). Although we did not find clear morph differentiation for many individual genes, all three morphs could be separated based on gene expression differences when using linear discriminant analysis (LDA), regardless of genomic location (i.e., inside or outside of the inversion). This was robust to the removal of genes with the highest loadings. Pairwise correlations in the expression of genes showed significant correlations for 9–18 pairs of genes within morphs. However, between morphs, we only found a single association between genes SDR42E1 and AROM for Independents and Satellites. Our results suggest complex and wide-ranging changes in gene expression caused by structural variants.
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Affiliation(s)
- Jasmine L Loveland
- Research Group for Behavioural Genetics and Evolutionary Ecology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - David B Lank
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Clemens Küpper
- Research Group for Behavioural Genetics and Evolutionary Ecology, Max Planck Institute for Ornithology, Seewiesen, Germany
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96
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Villoutreix R, Ayala D, Joron M, Gompert Z, Feder JL, Nosil P. Inversion breakpoints and the evolution of supergenes. Mol Ecol 2021; 30:2738-2755. [PMID: 33786937 PMCID: PMC7614923 DOI: 10.1111/mec.15907] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 02/04/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022]
Abstract
The coexistence of discrete morphs that differ in multiple traits is common within natural populations of many taxa. Such morphs are often associated with chromosomal inversions, presumably because the recombination suppressing effects of inversions help maintain alternate adaptive combinations of alleles across the multiple loci affecting these traits. However, inversions can also harbour selected mutations at their breakpoints, leading to their rise in frequency in addition to (or independent from) their role in recombination suppression. In this review, we first describe the different ways that breakpoints can create mutations. We then critically examine the evidence for the breakpoint-mutation and recombination suppression hypotheses for explaining the existence of discrete morphs associated with chromosomal inversions. We find that the evidence that inversions are favoured due to recombination suppression is often indirect. The evidence that breakpoints harbour mutations that are adaptive is also largely indirect, with the characterization of inversion breakpoints at the sequence level being incomplete in most systems. Direct tests of the role of suppressed recombination and breakpoint mutations in inversion evolution are thus needed. Finally, we emphasize how the two hypotheses of recombination suppression and breakpoint mutation can act in conjunction, with implications for understanding the emergence of supergenes and their evolutionary dynamics. We conclude by discussing how breakpoint characterization could improve our understanding of complex, discrete phenotypic forms in nature.
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Affiliation(s)
- Romain Villoutreix
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier
3, Montpellier 34293, France
| | - Diego Ayala
- UMR MIVEGEC, Univ. Montpellier, CNRS, IRD, 34934 Montpellier, France
| | - Mathieu Joron
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier
3, Montpellier 34293, France
| | | | - Jeffrey L. Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame,
Indiana 46556, USA
| | - Patrik Nosil
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier
3, Montpellier 34293, France
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97
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Runge JN, Lindholm AK. Experiments confirm a dispersive phenotype associated with a natural gene drive system. ROYAL SOCIETY OPEN SCIENCE 2021; 8:202050. [PMID: 34040786 PMCID: PMC8113913 DOI: 10.1098/rsos.202050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
Meiotic drivers are genetic entities that increase their own probability of being transmitted to offspring, usually to the detriment of the rest of the organism, thus 'selfishly' increasing their fitness. In many meiotic drive systems, driver-carrying males are less successful in sperm competition, which occurs when females mate with multiple males in one oestrus cycle (polyandry). How do drivers respond to this selection? An observational study found that house mice carrying the t haplotype, a meiotic driver, are more likely to disperse from dense populations. This could help the t avoid detrimental sperm competition, because density is associated with the frequency of polyandry. However, no controlled experiments have been conducted to test these findings. Here, we confirm that carriers of the t haplotype are more dispersive, but we do not find this to depend on the local density. t-carriers with above-average body weight were particularly more likely to disperse than wild-type mice. t-carrying mice were also more explorative but not more active than wild-type mice. These results add experimental support to the previous observational finding that the t haplotype affects the dispersal phenotype in house mice, which supports the hypothesis that dispersal reduces the fitness costs of the t.
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Affiliation(s)
- Jan-Niklas Runge
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Anna K. Lindholm
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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98
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Fontcuberta A, De Gasperin O, Avril A, Dind S, Chapuisat M. Disentangling the mechanisms linking dispersal and sociality in supergene-mediated ant social forms. Proc Biol Sci 2021; 288:20210118. [PMID: 33906407 PMCID: PMC8080013 DOI: 10.1098/rspb.2021.0118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/31/2021] [Indexed: 12/26/2022] Open
Abstract
The coevolution between dispersal and sociality can lead to linked polymorphisms in both traits, which may favour the emergence of supergenes. Supergenes have recently been found to control social organization in several ant lineages. Whether and how these 'social supergenes' also control traits related to dispersal is yet unknown. Our goal here was to get a comprehensive view of the dispersal mechanisms associated with supergene-controlled alternative social forms in the ant Formica selysi. We measured the production and emission of young females and males by single-queen (monogyne) and multiple-queen (polygyne) colonies, the composition of mating aggregations, and the frequency of crosses within and between social forms in the wild. We found that males and females from alternative social forms did not display strong differences in their propensity to leave the nest and disperse, nor in their mating behaviour. Instead, the social forms differed substantially in sex allocation. Monogyne colonies produced 90% of the females flying to swarms, whereas 57% of the males in swarms originated from polygyne colonies. Most crosses were assortative with respect to social form. However, 20% of the monogyne females did mate with polygyne males, which is surprising as this cross has never been found in mature monogyne colonies. We suggest that the polygyny-determining haplotype free rides on monogyne females, who establish independent colonies that later become polygyne. By identifying the steps in dispersal where the social forms differ, this study sheds light on the behavioural and colony-level traits linking dispersal and sociality through supergenes.
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Affiliation(s)
- Amaranta Fontcuberta
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Ornela De Gasperin
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Amaury Avril
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Sagane Dind
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Michel Chapuisat
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
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99
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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: 37] [Impact Index Per Article: 12.3] [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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100
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Hartmann FE, Duhamel M, Carpentier F, Hood ME, Foulongne‐Oriol M, Silar P, Malagnac F, Grognet P, Giraud T. Recombination suppression and evolutionary strata around mating-type loci in fungi: documenting patterns and understanding evolutionary and mechanistic causes. THE NEW PHYTOLOGIST 2021; 229:2470-2491. [PMID: 33113229 PMCID: PMC7898863 DOI: 10.1111/nph.17039] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/03/2020] [Indexed: 05/08/2023]
Abstract
Genomic regions determining sexual compatibility often display recombination suppression, as occurs in sex chromosomes, plant self-incompatibility loci and fungal mating-type loci. Regions lacking recombination can extend beyond the genes determining sexes or mating types, by several successive steps of recombination suppression. Here we review the evidence for recombination suppression around mating-type loci in fungi, sometimes encompassing vast regions of the mating-type chromosomes. The suppression of recombination at mating-type loci in fungi has long been recognized and maintains the multiallelic combinations required for correct compatibility determination. We review more recent evidence for expansions of recombination suppression beyond mating-type genes in fungi ('evolutionary strata'), which have been little studied and may be more pervasive than commonly thought. We discuss testable hypotheses for the ultimate (evolutionary) and proximate (mechanistic) causes for such expansions of recombination suppression, including (1) antagonistic selection, (2) association of additional functions to mating-type, such as uniparental mitochondria inheritance, (3) accumulation in the margin of nonrecombining regions of various factors, including deleterious mutations or transposable elements resulting from relaxed selection, or neutral rearrangements resulting from genetic drift. The study of recombination suppression in fungi could thus contribute to our understanding of recombination suppression expansion across a broader range of organisms.
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Affiliation(s)
- Fanny E. Hartmann
- Ecologie Systematique EvolutionBatiment 360Université Paris‐SaclayCNRSAgroParisTechOrsay91400France
| | - Marine Duhamel
- Ecologie Systematique EvolutionBatiment 360Université Paris‐SaclayCNRSAgroParisTechOrsay91400France
- Ruhr‐Universität Bochum, Evolution of Plants and Fungi ‐ Gebäude ND 03/174Universitätsstraße150, 44801 BochumGermany
| | - Fantin Carpentier
- Ecologie Systematique EvolutionBatiment 360Université Paris‐SaclayCNRSAgroParisTechOrsay91400France
| | - Michael E. Hood
- Biology Department, Science CentreAmherst CollegeAmherstMA01002USA
| | | | - Philippe Silar
- Lab Interdisciplinaire Energies DemainUniv Paris DiderotSorbonne Paris CiteParis 13F‐75205France
| | - Fabienne Malagnac
- Institute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayCEACNRSGif‐sur‐Yvette91198France
| | - Pierre Grognet
- Institute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayCEACNRSGif‐sur‐Yvette91198France
| | - Tatiana Giraud
- Ecologie Systematique EvolutionBatiment 360Université Paris‐SaclayCNRSAgroParisTechOrsay91400France
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