1
|
Errbii M, Gadau J, Becker K, Schrader L, Oettler J. Causes and consequences of a complex recombinational landscape in the ant Cardiocondyla obscurior. Genome Res 2024; 34:863-876. [PMID: 38839375 DOI: 10.1101/gr.278392.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 05/30/2024] [Indexed: 06/07/2024]
Abstract
Eusocial Hymenoptera have the highest recombination rates among all multicellular animals studied so far, but it is unclear why this is and how this affects the biology of individual species. A high-resolution linkage map for the ant Cardiocondyla obscurior corroborates genome-wide high recombination rates reported for ants (8.1 cM/Mb). However, recombination is locally suppressed in regions that are enriched with TEs, that have strong haplotype divergence, or that show signatures of epistatic selection in C. obscurior The results do not support the hypotheses that high recombination rates are linked to phenotypic plasticity or to modulating selection efficiency. Instead, genetic diversity and the frequency of structural variants correlate positively with local recombination rates, potentially compensating for the low levels of genetic variation expected in haplodiploid social Hymenoptera with low effective population size. Ultimately, the data show that recombination contributes to within-population polymorphism and to the divergence of the lineages within C. obscurior.
Collapse
Affiliation(s)
- Mohammed Errbii
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Jürgen Gadau
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Kerstin Becker
- Cologne Center for Genomics (CCG), Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Lukas Schrader
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany;
| | - Jan Oettler
- Lehrstuhl für Zoologie/Evolutionsbiologie, University Regensburg, 93053 Regensburg, Germany
| |
Collapse
|
2
|
De Gasperin O, Blacher P, Sarton-Lohéac S, Grasso G, Corliss MK, Nicole S, Chérasse S, Aron S, Chapuisat M. A supergene-controlling social structure in Alpine ants also affects the dispersal ability and fecundity of each sex. Proc Biol Sci 2024; 291:20240494. [PMID: 38864332 DOI: 10.1098/rspb.2024.0494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 04/18/2024] [Indexed: 06/13/2024] Open
Abstract
Social organization, dispersal and fecundity coevolve, but whether they are genetically linked remains little known. Supergenes are prime candidates for coupling adaptive traits and mediating sex-specific trade-offs. Here, we test whether a supergene that controls social structure in Formica selysi also influences dispersal-related traits and fecundity within each sex. In this ant species, single-queen colonies contain only the ancestral supergene haplotype M and produce MM queens and M males, while multi-queen colonies contain the derived haplotype P and produce MP queens, PP queens and P males. By combining multiple experiments, we show that the M haplotype induces phenotypes with higher dispersal potential and higher fecundity in both sexes. Specifically, MM queens, MP queens and M males are more aerodynamic and more fecund than PP queens and P males, respectively. Differences between MP and PP queens from the same colonies reveal a direct genetic effect of the supergene on dispersal-related traits and fecundity. The derived haplotype P, associated with multi-queen colonies, produces queens and males with reduced dispersal abilities and lower fecundity. More broadly, similarities between the Formica and Solenopsis systems reveal that supergenes play a major role in linking behavioural, morphological and physiological traits associated with intraspecific social polymorphisms.
Collapse
Affiliation(s)
- Ornela De Gasperin
- Department of Ecology and Evolution, University of Lausanne , Lausanne 1015, Switzerland
- Red de Ecoetología, Instituto de Ecología, A. C. , Xalapa, Veracruz 91073, Mexico
| | - Pierre Blacher
- Department of Ecology and Evolution, University of Lausanne , Lausanne 1015, Switzerland
| | - Solenn Sarton-Lohéac
- Department of Ecology and Evolution, University of Lausanne , Lausanne 1015, Switzerland
| | - Guglielmo Grasso
- Department of Ecology and Evolution, University of Lausanne , Lausanne 1015, Switzerland
- University of Manchester , Manchester M13 9PL, UK
| | - Mia Kotur Corliss
- Department of Ecology and Evolution, University of Lausanne , Lausanne 1015, Switzerland
| | - Sidonie Nicole
- Department of Ecology and Evolution, University of Lausanne , Lausanne 1015, Switzerland
| | | | - Serge Aron
- Universite libre de Bruxelles , Brussels 1050, Belgium
| | - Michel Chapuisat
- Department of Ecology and Evolution, University of Lausanne , Lausanne 1015, Switzerland
| |
Collapse
|
3
|
Errbii M, Ernst UR, Lajmi A, Privman E, Gadau J, Schrader L. Evolutionary genomics of socially polymorphic populations of Pogonomyrmex californicus. BMC Biol 2024; 22:109. [PMID: 38735942 PMCID: PMC11089791 DOI: 10.1186/s12915-024-01907-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 04/30/2024] [Indexed: 05/14/2024] Open
Abstract
BACKGROUND Social insects vary considerably in their social organization both between and within species. In the California harvester ant, Pogonomyrmex californicus (Buckley 1867), colonies are commonly founded and headed by a single queen (haplometrosis, primary monogyny). However, in some populations in California (USA), unrelated queens cooperate not only during founding (pleometrosis) but also throughout the life of the colony (primary polygyny). The genetic architecture and evolutionary dynamics of this complex social niche polymorphism (haplometrosis vs pleometrosis) have remained unknown. RESULTS We provide a first analysis of its genomic basis and evolutionary history using population genomics comparing individuals from a haplometrotic population to those from a pleometrotic population. We discovered a recently evolved (< 200 k years), 8-Mb non-recombining region segregating with the observed social niche polymorphism. This region shares several characteristics with supergenes underlying social polymorphisms in other socially polymorphic ant species. However, we also find remarkable differences from previously described social supergenes. Particularly, four additional genomic regions not in linkage with the supergene show signatures of a selective sweep in the pleometrotic population. Within these regions, we find for example genes crucial for epigenetic regulation via histone modification (chameau) and DNA methylation (Dnmt1). CONCLUSIONS Altogether, our results suggest that social morph in this species is a polygenic trait involving a potential young supergene. Further studies targeting haplo- and pleometrotic individuals from a single population are however required to conclusively resolve whether these genetic differences underlie the alternative social phenotypes or have emerged through genetic drift.
Collapse
Affiliation(s)
- Mohammed Errbii
- Molecular Evolution and Sociobiology Group, Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, Münster, DE-48149, Germany
| | - Ulrich R Ernst
- Molecular Evolution and Sociobiology Group, Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, Münster, DE-48149, Germany
- Present Address: Apicultural State Institute, University of Hohenheim, Erna-Hruschka-Weg 6, Stuttgart, DE-70599, Germany
- Center for Biodiversity and Integrative Taxonomy (KomBioTa), University of Hohenheim, Stuttgart, DE-70599, Germany
| | - Aparna Lajmi
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Eyal Privman
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Jürgen Gadau
- Molecular Evolution and Sociobiology Group, Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, Münster, DE-48149, Germany.
| | - Lukas Schrader
- Molecular Evolution and Sociobiology Group, Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, Münster, DE-48149, Germany.
| |
Collapse
|
4
|
Groh JS, Vik DC, Stevens KA, Brown PJ, Langley CH, Coop G. Distinct ancient structural polymorphisms control heterodichogamy in walnuts and hickories. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.23.573205. [PMID: 38187547 PMCID: PMC10769452 DOI: 10.1101/2023.12.23.573205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The maintenance of stable mating type polymorphisms is a classic example of balancing selection, underlying the nearly ubiquitous 50/50 sex ratio in species with separate sexes. One lesser known but intriguing example of a balanced mating polymorphism in angiosperms is heterodichogamy - polymorphism for opposing directions of dichogamy (temporal separation of male and female function in hermaphrodites) within a flowering season. This mating system is common throughout Juglandaceae, the family that includes globally important and iconic nut and timber crops - walnuts (Juglans), as well as pecan and other hickories (Carya). In both genera, heterodichogamy is controlled by a single dominant allele. We fine-map the locus in each genus, and find two ancient (>50 Mya) structural variants involving different genes that both segregate as genus-wide trans-species polymorphisms. The Juglans locus maps to a ca. 20 kb structural variant adjacent to a probable trehalose phosphate phosphatase (TPPD-1), homologs of which regulate floral development in model systems. TPPD-1 is differentially expressed between morphs in developing male flowers, with increased allele-specific expression of the dominant haplotype copy. Across species, the dominant haplotype contains a tandem array of duplicated sequence motifs, part of which is an inverted copy of the TPPD-1 3' UTR. These repeats generate various distinct small RNAs matching sequences within the 3' UTR and further downstream. In contrast to the single-gene Juglans locus, the Carya heterodichogamy locus maps to a ca. 200-450 kb cluster of tightly linked polymorphisms across 20 genes, some of which have known roles in flowering and are differentially expressed between morphs in developing flowers. The dominant haplotype in pecan, which is nearly always heterozygous and appears to rarely recombine, shows markedly reduced genetic diversity and is over twice as long as its recessive counterpart due to accumulation of various types of transposable elements. We did not detect either genetic system in other heterodichogamous genera within Juglandaceae, suggesting that additional genetic systems for heterodichogamy may yet remain undiscovered.
Collapse
Affiliation(s)
- Jeffrey S Groh
- Department of Evolution and Ecology, University of California, Davis
- Center for Population Biology, University of California, Davis
| | - Diane C Vik
- Department of Evolution and Ecology, University of California, Davis
| | - Kristian A Stevens
- Department of Evolution and Ecology, University of California, Davis
- Department of Computer Science, University of California, Davis
| | - Patrick J Brown
- Department of Plant Sciences, University of California, Davis
| | - Charles H Langley
- Department of Evolution and Ecology, University of California, Davis
- Center for Population Biology, University of California, Davis
| | - Graham Coop
- Department of Evolution and Ecology, University of California, Davis
- Center for Population Biology, University of California, Davis
| |
Collapse
|
5
|
Nunez JCB, Lenhart BA, Bangerter A, Murray CS, Mazzeo GR, Yu Y, Nystrom TL, Tern C, Erickson PA, Bergland AO. A cosmopolitan inversion facilitates seasonal adaptation in overwintering Drosophila. Genetics 2024; 226:iyad207. [PMID: 38051996 PMCID: PMC10847723 DOI: 10.1093/genetics/iyad207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 11/28/2023] [Indexed: 12/07/2023] Open
Abstract
Fluctuations in the strength and direction of natural selection through time are a ubiquitous feature of life on Earth. One evolutionary outcome of such fluctuations is adaptive tracking, wherein populations rapidly adapt from standing genetic variation. In certain circumstances, adaptive tracking can lead to the long-term maintenance of functional polymorphism despite allele frequency change due to selection. Although adaptive tracking is likely a common process, we still have a limited understanding of aspects of its genetic architecture and its strength relative to other evolutionary forces such as drift. Drosophila melanogaster living in temperate regions evolve to track seasonal fluctuations and are an excellent system to tackle these gaps in knowledge. By sequencing orchard populations collected across multiple years, we characterized the genomic signal of seasonal demography and identified that the cosmopolitan inversion In(2L)t facilitates seasonal adaptive tracking and shows molecular footprints of selection. A meta-analysis of phenotypic studies shows that seasonal loci within In(2L)t are associated with behavior, life history, physiology, and morphological traits. We identify candidate loci and experimentally link them to phenotype. Our work contributes to our general understanding of fluctuating selection and highlights the evolutionary outcome and dynamics of contemporary selection on inversions.
Collapse
Affiliation(s)
- Joaquin C B Nunez
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
- Department of Biology, University of Vermont, 109 Carrigan Drive, Burlington, VT 05405, USA
| | - Benedict A Lenhart
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Alyssa Bangerter
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Connor S Murray
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Giovanni R Mazzeo
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Yang Yu
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Taylor L Nystrom
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Courtney Tern
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Priscilla A Erickson
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
- Department of Biology, University of Richmond, 138 UR Drive, Richmond, VA 23173, USA
| | - Alan O Bergland
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| |
Collapse
|
6
|
Yang J, Xue H, Li Z, Zhang Y, Shi T, He X, Barrett SCH, Wang Q, Chen J. Haplotype-resolved genome assembly provides insights into the evolution of S-locus supergene in distylous Nymphoides indica. THE NEW PHYTOLOGIST 2023; 240:2058-2071. [PMID: 37717220 DOI: 10.1111/nph.19264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/30/2023] [Indexed: 09/19/2023]
Abstract
Distyly has evolved independently in numerous animal-pollinated angiosperm lineages. Understanding of its molecular basis has been restricted to a few species, primarily Primula. Here, we investigate the genetic architecture of the single diallelic locus (S-locus) supergene, a linkage group of functionally associated genes, and explore how it may have evolved in distylous Nymphoides indica, a lineage of flowering plants not previously investigated. We assembled haplotype-resolved genomes, used read-coverage-based genome-wide association study (rb-GWAS) to locate the S-locus supergene, co-expression network analysis to explore gene networks underpinning the development of distyly, and comparative genomic analyses to investigate the origins of the S-locus supergene. We identified three linked candidate S-locus genes - NinBAS1, NinKHZ2, and NinS1 - that were only evident in the short-styled morph and were hemizygous. Co-expression network analysis suggested that brassinosteroids contribute to dimorphic sex organs in the short-styled morph. Comparative genomic analyses indicated that the S-locus supergene likely evolved via stepwise duplications and has been affected by transposable element activities. Our study provides novel insight into the structure, regulation, and evolution of the supergene governing distyly in N. indica. It also provides high-quality genomic resources for future research on the molecular mechanisms underlying the striking evolutionary convergence in form and function across heterostylous taxa.
Collapse
Affiliation(s)
- Jingshan Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haoran Xue
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St, Toronto, ON, M5S 3B2, Canada
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam-Golm, Germany
| | - Zhizhong Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Yue Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Tao Shi
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Xiangyan He
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St, Toronto, ON, M5S 3B2, Canada
| | - Qingfeng Wang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Jinming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| |
Collapse
|
7
|
Enge S, Mérot C, Mozūraitis R, Apšegaitė V, Bernatchez L, Martens GA, Radžiutė S, Pavia H, Berdan EL. A supergene in seaweed flies modulates male traits and female perception. Proc Biol Sci 2023; 290:20231494. [PMID: 37817592 PMCID: PMC10565388 DOI: 10.1098/rspb.2023.1494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/18/2023] [Indexed: 10/12/2023] Open
Abstract
Supergenes, tightly linked sets of alleles, offer some of the most spectacular examples of polymorphism persisting under long-term balancing selection. However, we still do not understand their evolution and persistence, especially in the face of accumulation of deleterious elements. Here, we show that an overdominant supergene in seaweed flies, Coelopa frigida, modulates male traits, potentially facilitating disassortative mating and promoting intraspecific polymorphism. Across two continents, the Cf-Inv(1) supergene strongly affected the composition of male cuticular hydrocarbons (CHCs) but only weakly affected CHC composition in females. Using gas chromatography-electroantennographic detection, we show that females can sense male CHCs and that there may be differential perception between genotypes. Combining our phenotypic results with RNA-seq data, we show that candidate genes for CHC biosynthesis primarily show differential expression for Cf-Inv(1) in males but not females. Conversely, candidate genes for odorant detection were differentially expressed in both sexes but showed high levels of divergence between supergene haplotypes. We suggest that the reduced recombination between supergene haplotypes may have led to rapid divergence in mate preferences as well as increasing linkage between male traits, and overdominant loci. Together this probably helped to maintain the polymorphism despite deleterious effects in homozygotes.
Collapse
Affiliation(s)
- Swantje Enge
- Department of Marine Sciences, University of Gothenburg, Tjärnö, Sweden
| | - Claire Mérot
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- CNRS UMR 6553 Ecobio, Université de Rennes, OSUR, Rennes, France
| | - Raimondas Mozūraitis
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Laboratory of Chemical and Behavioural Ecology, Institute of Ecology, Nature Research Centre, Vilnius, Lithuania
| | - Violeta Apšegaitė
- Laboratory of Chemical and Behavioural Ecology, Institute of Ecology, Nature Research Centre, Vilnius, Lithuania
| | - Louis Bernatchez
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Gerrit A. Martens
- Institute of Cell and Systems Biology of Animals, University of Hamburg, Hamburg, Germany
| | - Sandra Radžiutė
- Laboratory of Chemical and Behavioural Ecology, Institute of Ecology, Nature Research Centre, Vilnius, Lithuania
| | - Henrik Pavia
- Department of Marine Sciences, University of Gothenburg, Tjärnö, Sweden
| | - Emma L. Berdan
- Department of Marine Sciences, University of Gothenburg, Tjärnö, Sweden
| |
Collapse
|
8
|
Cauret CMS, Jordan DC, Kukoly LM, Burton SR, Anele EU, Kwiecien JM, Gansauge MT, Senthillmohan S, Greenbaum E, Meyer M, Horb ME, Evans BJ. Functional dissection and assembly of a small, newly evolved, W chromosome-specific genomic region of the African clawed frog Xenopus laevis. PLoS Genet 2023; 19:e1010990. [PMID: 37792893 PMCID: PMC10578606 DOI: 10.1371/journal.pgen.1010990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 10/16/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023] Open
Abstract
Genetic triggers for sex determination are frequently co-inherited with other linked genes that may also influence one or more sex-specific phenotypes. To better understand how sex-limited regions evolve and function, we studied a small W chromosome-specific region of the frog Xenopus laevis that contains only three genes (dm-w, scan-w, ccdc69-w) and that drives female differentiation. Using gene editing, we found that the sex-determining function of this region requires dm-w but that scan-w and ccdc69-w are not essential for viability, female development, or fertility. Analysis of mesonephros+gonad transcriptomes during sexual differentiation illustrates masculinization of the dm-w knockout transcriptome, and identifies mostly non-overlapping sets of differentially expressed genes in separate knockout lines for each of these three W-specific gene compared to wildtype sisters. Capture sequencing of almost all Xenopus species and PCR surveys indicate that the female-determining function of dm-w is present in only a subset of species that carry this gene. These findings map out a dynamic evolutionary history of a newly evolved W chromosome-specific genomic region, whose components have distinctive functions that frequently degraded during Xenopus diversification, and evidence the evolutionary consequences of recombination suppression.
Collapse
Affiliation(s)
- Caroline M. S. Cauret
- Biology Department, McMaster University, Hamilton, Ontario, Canada
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Danielle C. Jordan
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, Massachusetts United States of America
- The School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | | | - Sarah R. Burton
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, Massachusetts United States of America
| | - Emmanuela U. Anele
- Biology Department, McMaster University, Hamilton, Ontario, Canada
- Department Zoology, Ahmadu Bello University, Zaria, Nigeria
| | - Jacek M. Kwiecien
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Marie-Theres Gansauge
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Eli Greenbaum
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, Texas, United States of America
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marko E. Horb
- Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, Massachusetts United States of America
| | - Ben J. Evans
- Biology Department, McMaster University, Hamilton, Ontario, Canada
| |
Collapse
|
9
|
Zhang L, Li P, Zhang X, Li J. Two floral forms in the same species-distyly. PLANTA 2023; 258:72. [PMID: 37656285 DOI: 10.1007/s00425-023-04229-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 08/23/2023] [Indexed: 09/02/2023]
Abstract
MAIN CONCLUSION This paper reviews the progress of research on the morphology, physiology and molecular biology of distyly in plants. It will help to elucidate the mysteries of distyly in plants. Distyly is a unique representative type of heterostyly in plants, primarily characterized by the presence of long style and short style within the flowers of the same species. This interesting trait has always fascinated researchers. With the rapid development of molecular biology, the molecular mechanism for the production of dimorphic styles in plants is also gaining ground. Researchers have been studying plant dimorphic styles from various perspectives. The researchers are gradually unravelling the mechanisms by which plants produce distyly traits. This paper reviews advances in the study of plant dimorphic style characteristics, mainly in terms of the morphology, physiology and molecular biology of plants with dimorphic styles. The aim is to provide a theoretical basis for the study of the mechanism of distyly formation in plants.
Collapse
Affiliation(s)
- Lu Zhang
- College of Landscape and Tourism, Hebei Agricultural University, No. 289 Lingyusi Street, P. O. Box 28, Baoding, 071000, Hebei, China
| | - Ping Li
- College of Landscape and Tourism, Hebei Agricultural University, No. 289 Lingyusi Street, P. O. Box 28, Baoding, 071000, Hebei, China.
| | - Xiaoman Zhang
- College of Landscape and Tourism, Hebei Agricultural University, No. 289 Lingyusi Street, P. O. Box 28, Baoding, 071000, Hebei, China.
| | - Jinfeng Li
- College of Landscape and Tourism, Hebei Agricultural University, No. 289 Lingyusi Street, P. O. Box 28, Baoding, 071000, Hebei, China
| |
Collapse
|
10
|
Kikuchi DW, Allen WL, Arbuckle K, Aubier TG, Briolat ES, Burdfield-Steel ER, Cheney KL, Daňková K, Elias M, Hämäläinen L, Herberstein ME, Hossie TJ, Joron M, Kunte K, Leavell BC, Lindstedt C, Lorioux-Chevalier U, McClure M, McLellan CF, Medina I, Nawge V, Páez E, Pal A, Pekár S, Penacchio O, Raška J, Reader T, Rojas B, Rönkä KH, Rößler DC, Rowe C, Rowland HM, Roy A, Schaal KA, Sherratt TN, Skelhorn J, Smart HR, Stankowich T, Stefan AM, Summers K, Taylor CH, Thorogood R, Umbers K, Winters AE, Yeager J, Exnerová A. The evolution and ecology of multiple antipredator defences. J Evol Biol 2023; 36:975-991. [PMID: 37363877 DOI: 10.1111/jeb.14192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/03/2023] [Accepted: 05/07/2023] [Indexed: 06/28/2023]
Abstract
Prey seldom rely on a single type of antipredator defence, often using multiple defences to avoid predation. In many cases, selection in different contexts may favour the evolution of multiple defences in a prey. However, a prey may use multiple defences to protect itself during a single predator encounter. Such "defence portfolios" that defend prey against a single instance of predation are distributed across and within successive stages of the predation sequence (encounter, detection, identification, approach (attack), subjugation and consumption). We contend that at present, our understanding of defence portfolio evolution is incomplete, and seen from the fragmentary perspective of specific sensory systems (e.g., visual) or specific types of defences (especially aposematism). In this review, we aim to build a comprehensive framework for conceptualizing the evolution of multiple prey defences, beginning with hypotheses for the evolution of multiple defences in general, and defence portfolios in particular. We then examine idealized models of resource trade-offs and functional interactions between traits, along with evidence supporting them. We find that defence portfolios are constrained by resource allocation to other aspects of life history, as well as functional incompatibilities between different defences. We also find that selection is likely to favour combinations of defences that have synergistic effects on predator behaviour and prey survival. Next, we examine specific aspects of prey ecology, genetics and development, and predator cognition that modify the predictions of current hypotheses or introduce competing hypotheses. We outline schema for gathering data on the distribution of prey defences across species and geography, determining how multiple defences are produced, and testing the proximate mechanisms by which multiple prey defences impact predator behaviour. Adopting these approaches will strengthen our understanding of multiple defensive strategies.
Collapse
Affiliation(s)
- David W Kikuchi
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA
- Evolutionary Biology, Universität Bielefeld, Bielefeld, Germany
| | | | - Kevin Arbuckle
- Department of Biosciences, Swansea University, Swansea, UK
| | - Thomas G Aubier
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier Toulouse III, UMR 5174, CNRS/IRD, Toulouse, France
| | | | - Emily R Burdfield-Steel
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Karen L Cheney
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Klára Daňková
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Marianne Elias
- Institut de Systématique, Evolution, Biodiversité, CNRS, MNHN, Sorbonne Université, EPHE, Université des Antilles, Paris, France
- Smithsonian Tropical Research Institute, Gamboa, Panama
| | - Liisa Hämäläinen
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Marie E Herberstein
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Thomas J Hossie
- Department of Biology, Trent University, Peterborough, Ontario, Canada
| | - Mathieu Joron
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Krushnamegh Kunte
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Brian C Leavell
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Carita Lindstedt
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Ugo Lorioux-Chevalier
- Laboratoire Écologie, Évolution, Interactions des Systèmes Amazoniens (LEEISA), Université de Guyane, CNRS, IFREMER, Cayenne, France
| | - Melanie McClure
- Laboratoire Écologie, Évolution, Interactions des Systèmes Amazoniens (LEEISA), Université de Guyane, CNRS, IFREMER, Cayenne, France
| | | | - Iliana Medina
- School of BioSciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Viraj Nawge
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Erika Páez
- Institut de Systématique, Evolution, Biodiversité, CNRS, MNHN, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Arka Pal
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Olivier Penacchio
- School of Psychology and Neuroscience, University of St Andrews, St Andrews, UK
- Computer Vision Center, Computer Science Department, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jan Raška
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tom Reader
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Bibiana Rojas
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
- Department of Biology and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Katja H Rönkä
- HiLIFE Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Daniela C Rößler
- Zukunftskolleg, University of Konstanz, Konstanz, Germany
- Department of Collective Behavior, Max Planck Institute of Animal Behavior, Konstanz, Germany
| | - Candy Rowe
- Institute of Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Hannah M Rowland
- Max Planck Research Group Predators and Toxic Prey, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Arlety Roy
- Laboratoire Écologie, Évolution, Interactions des Systèmes Amazoniens (LEEISA), Université de Guyane, CNRS, IFREMER, Cayenne, France
| | - Kaitlin A Schaal
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | | | - John Skelhorn
- Institute of Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Hannah R Smart
- Hawkesbury Institute of the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Ted Stankowich
- Department of Biological Sciences, California State University, Long Beach, California, USA
| | - Amanda M Stefan
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Kyle Summers
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
| | | | - Rose Thorogood
- HiLIFE Helsinki Institute of Life Sciences, University of Helsinki, Helsinki, Finland
- Research Programme in Organismal & Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Kate Umbers
- Hawkesbury Institute of the Environment, Western Sydney University, Penrith, New South Wales, Australia
- School of Science Western Sydney University, Penrith, New South Wales, Australia
| | - Anne E Winters
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Justin Yeager
- Grupo de Biodiversidad Medio Ambiente y Salud, Universidad de Las Américas, Quito, Ecuador
| | - Alice Exnerová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| |
Collapse
|
11
|
Kapun M, Mitchell ED, Kawecki TJ, Schmidt P, Flatt T. An Ancestral Balanced Inversion Polymorphism Confers Global Adaptation. Mol Biol Evol 2023; 40:msad118. [PMID: 37220650 PMCID: PMC10234209 DOI: 10.1093/molbev/msad118] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/17/2023] [Accepted: 05/19/2023] [Indexed: 05/25/2023] Open
Abstract
Since the pioneering work of Dobzhansky in the 1930s and 1940s, many chromosomal inversions have been identified, but how they contribute to adaptation remains poorly understood. In Drosophila melanogaster, the widespread inversion polymorphism In(3R)Payne underpins latitudinal clines in fitness traits on multiple continents. Here, we use single-individual whole-genome sequencing, transcriptomics, and published sequencing data to study the population genomics of this inversion on four continents: in its ancestral African range and in derived populations in Europe, North America, and Australia. Our results confirm that this inversion originated in sub-Saharan Africa and subsequently became cosmopolitan; we observe marked monophyletic divergence of inverted and noninverted karyotypes, with some substructure among inverted chromosomes between continents. Despite divergent evolution of this inversion since its out-of-Africa migration, derived non-African populations exhibit similar patterns of long-range linkage disequilibrium between the inversion breakpoints and major peaks of divergence in its center, consistent with balancing selection and suggesting that the inversion harbors alleles that are maintained by selection on several continents. Using RNA-sequencing, we identify overlap between inversion-linked single-nucleotide polymorphisms and loci that are differentially expressed between inverted and noninverted chromosomes. Expression levels are higher for inverted chromosomes at low temperature, suggesting loss of buffering or compensatory plasticity and consistent with higher inversion frequency in warm climates. Our results suggest that this ancestrally tropical balanced polymorphism spread around the world and became latitudinally assorted along similar but independent climatic gradients, always being frequent in subtropical/tropical areas but rare or absent in temperate climates.
Collapse
Affiliation(s)
- Martin Kapun
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Division of Cell and Developmental Biology, Medical University of Vienna, Vienna, Austria
- Natural History Museum Vienna, Zentrale Forschungslaboratorien, Vienna, Austria
| | - Esra Durmaz Mitchell
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Tadeusz J Kawecki
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Paul Schmidt
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Thomas Flatt
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| |
Collapse
|
12
|
Blacher P, De Gasperin O, Grasso G, Sarton-Lohéac S, Allemann R, Chapuisat M. Cryptic recessive lethality of a supergene controlling social organization in ants. Mol Ecol 2023; 32:1062-1072. [PMID: 36504171 DOI: 10.1111/mec.16821] [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: 09/09/2022] [Revised: 11/23/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
Supergenes are clusters of linked loci that control complex phenotypes, such as alternative forms of social organization in ants. Explaining the long-term maintenance of supergenes is challenging, particularly when the derived haplotype lacks homozygous lethality and causes gene drive. In the Alpine silver ant, Formica selysi, a large and ancient social supergene with two haplotypes, M and P, controls colony social organization. Single-queen colonies only contain MM females, while multiqueen colonies contain MP and PP females. The derived P haplotype, found only in multiqueen colonies, selfishly enhances its transmission through maternal effect killing, which could have led to its fixation. A population genetic model showed that a stable social polymorphism can only be maintained under a narrow set of conditions, which includes partial assortative mating by social form (which is known to occur in the wild), and low fitness of PP queens. With a combination of field and laboratory experiments, we show that the P haplotype has deleterious effects on female fitness. The survival rate of PP queens and workers was around half that of other genotypes. Moreover, P-carrying queens had lower fertility and fecundity compared to other queens. We discuss how cryptic lethal effects of the P haplotype help stabilize this ancient polymorphism.
Collapse
Affiliation(s)
- Pierre Blacher
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Ornela De Gasperin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Red de Ecoetología, Instituto de Ecología A. C., Veracruz, Mexico
| | - Guglielmo Grasso
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,University of Manchester, Manchester, UK
| | - Solenn Sarton-Lohéac
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Roxane Allemann
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Michel Chapuisat
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
13
|
Vittorelli N, Rodríguez de la Vega RC, Snirc A, Levert E, Gautier V, Lalanne C, De Filippo E, Gladieux P, Guillou S, Zhang Y, Tejomurthula S, Grigoriev IV, Debuchy R, Silar P, Giraud T, Hartmann FE. Stepwise recombination suppression around the mating-type locus in an ascomycete fungus with self-fertile spores. PLoS Genet 2023; 19:e1010347. [PMID: 36763677 PMCID: PMC9949647 DOI: 10.1371/journal.pgen.1010347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 02/23/2023] [Accepted: 01/17/2023] [Indexed: 02/12/2023] Open
Abstract
Recombination is often suppressed at sex-determining loci in plants and animals, and at self-incompatibility or mating-type loci in plants and fungi. In fungal ascomycetes, recombination suppression around the mating-type locus is associated with pseudo-homothallism, i.e. the production of self-fertile dikaryotic sexual spores carrying the two opposite mating types. This has been well studied in two species complexes from different families of Sordariales: Podospora anserina and Neurospora tetrasperma. However, it is unclear whether this intriguing association holds in other species. We show here that Schizothecium tetrasporum, a fungus from a third family in the order Sordariales, also produces mostly self-fertile dikaryotic spores carrying the two opposite mating types. This was due to a high frequency of second meiotic division segregation at the mating-type locus, indicating the occurrence of a single and systematic crossing-over event between the mating-type locus and the centromere, as in P. anserina. The mating-type locus has the typical Sordariales organization, plus a MAT1-1-1 pseudogene in the MAT1-2 haplotype. High-quality genome assemblies of opposite mating types and segregation analyses revealed a suppression of recombination in a region of 1.47 Mb around the mating-type locus. We detected three evolutionary strata, indicating a stepwise extension of recombination suppression. The three strata displayed no rearrangement or transposable element accumulation but gene losses and gene disruptions were present, and precisely at the strata margins. Our findings indicate a convergent evolution of self-fertile dikaryotic sexual spores across multiple ascomycete fungi. The particular pattern of meiotic segregation at the mating-type locus was associated with recombination suppression around this locus, that had extended stepwise. This association between pseudo-homothallism and recombination suppression across lineages and the presence of gene disruption at the strata limits are consistent with a recently proposed mechanism of sheltering deleterious alleles to explain stepwise recombination suppression.
Collapse
Affiliation(s)
- Nina Vittorelli
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
- Département de Biologie, École Normale Supérieure, PSL Université Paris, Paris, France
| | | | - Alodie Snirc
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Emilie Levert
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Valérie Gautier
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Christophe Lalanne
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Elsa De Filippo
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Sonia Guillou
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Yu Zhang
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Sravanthi Tejomurthula
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Robert Debuchy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Philippe Silar
- Laboratoire Interdisciplinaire des Energies de Demain, Université Paris Cité, Paris, France
| | - Tatiana Giraud
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Fanny E. Hartmann
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
- * E-mail:
| |
Collapse
|
14
|
Komata S, Yoda S, KonDo Y, Shinozaki S, Tamai K, Fujiwara H. Functional unit of supergene in female-limited Batesian mimicry of Papilio polytes. Genetics 2023; 223:iyac177. [PMID: 36454671 PMCID: PMC9910408 DOI: 10.1093/genetics/iyac177] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/14/2022] [Accepted: 11/14/2022] [Indexed: 12/05/2022] Open
Abstract
Supergenes are sets of genes and genetic elements that are inherited like a single gene and control complex adaptive traits, but their functional roles and units are poorly understood. In Papilio polytes, female-limited Batesian mimicry is thought to be regulated by a ∼130 kb inversion region (highly diversified region: HDR) containing 3 genes, UXT, U3X, and doublesex (dsx) which switches non-mimetic and mimetic types. To determine the functional unit, we here performed electroporation-mediated RNAi analyses (and further Crispr/Cas9 for UXT) of genes within and flanking the HDR in pupal hindwings. We first clarified that non-mimetic dsx-h had a function to form the non-mimetic trait in female and only dsx-H isoform 3 had an important function in the formation of mimetic traits. Next, we found that UXT was involved in making mimetic-type pale-yellow spots and adjacent gene sir2 in making red spots in hindwings, both of which refine more elaborate mimicry. Furthermore, downstream gene networks of dsx, U3X, and UXT screened by RNA sequencing showed that U3X upregulated dsx-H expression and repressed UXT expression. These findings demonstrate that a set of multiple genes, not only inside but also flanking HDR, can function as supergene members, which extends the definition of supergene unit than we considered before. Also, our results indicate that dsx functions as the switching gene and some other genes such as UXT and sir2 within the supergene unit work as the modifier gene.
Collapse
Affiliation(s)
- Shinya Komata
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Shinichi Yoda
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, 444-8585, Japan
| | - Yûsuke KonDo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Souta Shinozaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Kouki Tamai
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Haruhiko Fujiwara
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| |
Collapse
|
15
|
Jeong H, Baran NM, Sun D, Chatterjee P, Layman TS, Balakrishnan CN, Maney DL, Yi SV. Dynamic molecular evolution of a supergene with suppressed recombination in white-throated sparrows. eLife 2022; 11:79387. [PMID: 36040313 PMCID: PMC9427109 DOI: 10.7554/elife.79387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 08/17/2022] [Indexed: 12/11/2022] Open
Abstract
In white-throated sparrows, two alternative morphs differing in plumage and behavior segregate with a large chromosomal rearrangement. As with sex chromosomes such as the mammalian Y, the rearranged version of chromosome two (ZAL2m) is in a near-constant state of heterozygosity, offering opportunities to investigate both degenerative and selective processes during the early evolutionary stages of 'supergenes.' Here, we generated, synthesized, and analyzed extensive genome-scale data to better understand the forces shaping the evolution of the ZAL2 and ZAL2m chromosomes in this species. We found that features of ZAL2m are consistent with substantially reduced recombination and low levels of degeneration. We also found evidence that selective sweeps took place both on ZAL2m and its standard counterpart, ZAL2, after the rearrangement event. Signatures of positive selection were associated with allelic bias in gene expression, suggesting that antagonistic selection has operated on gene regulation. Finally, we discovered a region exhibiting long-range haplotypes inside the rearrangement on ZAL2m. These haplotypes appear to have been maintained by balancing selection, retaining genetic diversity within the supergene. Together, our analyses illuminate mechanisms contributing to the evolution of a young chromosomal polymorphism, revealing complex selective processes acting concurrently with genetic degeneration to drive the evolution of supergenes.
Collapse
Affiliation(s)
- Hyeonsoo Jeong
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, United States
| | - Nicole M Baran
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, United States.,Department of Psychology, Emory University, Atlanta, United States.,Department of Ecology, Evolution, Marine Biology, University of California, Santa Barbara, Santa Barbara, United States
| | - Dan Sun
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, United States.,Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Paramita Chatterjee
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, United States
| | - Thomas S Layman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, United States
| | | | - Donna L Maney
- Department of Psychology, Emory University, Atlanta, United States
| | - Soojin V Yi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, United States.,Department of Ecology, Evolution, Marine Biology, University of California, Santa Barbara, Santa Barbara, United States
| |
Collapse
|
16
|
Hearn KE, Koch EL, Stankowski S, Butlin RK, Faria R, Johannesson K, Westram AM. Differing associations between sex determination and sex‐linked inversions in two ecotypes of
Littorina saxatilis. Evol Lett 2022; 6:358-374. [PMID: 36254259 PMCID: PMC9554762 DOI: 10.1002/evl3.295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 07/07/2022] [Accepted: 07/20/2022] [Indexed: 12/14/2022] Open
Abstract
Sexual antagonism is a common hypothesis for driving the evolution of sex chromosomes, whereby recombination suppression is favored between sexually antagonistic loci and the sex‐determining locus to maintain beneficial combinations of alleles. This results in the formation of a sex‐determining region. Chromosomal inversions may contribute to recombination suppression but their precise role in sex chromosome evolution remains unclear. Because local adaptation is frequently facilitated through the suppression of recombination between adaptive loci by chromosomal inversions, there is potential for inversions that cover sex‐determining regions to be involved in local adaptation as well, particularly if habitat variation creates environment‐dependent sexual antagonism. With these processes in mind, we investigated sex determination in a well‐studied example of local adaptation within a species: the intertidal snail, Littorina saxatilis. Using SNP data from a Swedish hybrid zone, we find novel evidence for a female‐heterogametic sex determination system that is restricted to one ecotype. Our results suggest that four putative chromosomal inversions, two previously described and two newly discovered, span the putative sex chromosome pair. We determine their differing associations with sex, which suggest distinct strata of differing ages. The same inversions are found in the second ecotype but do not show any sex association. The striking disparity in inversion‐sex associations between ecotypes that are connected by gene flow across a habitat transition that is just a few meters wide indicates a difference in selective regime that has produced a distinct barrier to the spread of the newly discovered sex‐determining region between ecotypes. Such sex chromosome‐environment interactions have not previously been uncovered in L. saxatilis and are known in few other organisms. A combination of both sex‐specific selection and divergent natural selection is required to explain these highly unusual patterns.
Collapse
Affiliation(s)
- Katherine E. Hearn
- Ecology and Evolutionary Biology, School of Biosciences University of Sheffield Sheffield S10 2TN United Kingdom
| | - Eva L. Koch
- Ecology and Evolutionary Biology, School of Biosciences University of Sheffield Sheffield S10 2TN United Kingdom
- Department of Zoology University of Cambridge Cambridge CB2 3EJ United Kingdom
| | - Sean Stankowski
- Ecology and Evolutionary Biology, School of Biosciences University of Sheffield Sheffield S10 2TN United Kingdom
- ISTA (Institute of Science and Technology Austria) Klosterneuburg 3400 Austria
| | - Roger K. Butlin
- Ecology and Evolutionary Biology, School of Biosciences University of Sheffield Sheffield S10 2TN United Kingdom
- Department of Marine Sciences University of Gothenburg Strömstad SE‐45296 Sweden
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado Campus de Vairão, Universidade do Porto Vairão 4485‐661 Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO Campus de Vairão, Universidade do Porto Vairão 4485‐661 Portugal
| | - Kerstin Johannesson
- Department of Marine Sciences University of Gothenburg Strömstad SE‐45296 Sweden
| | - Anja M. Westram
- ISTA (Institute of Science and Technology Austria) Klosterneuburg 3400 Austria
- Faculty of Biosciences and Aquaculture Nord University Bodø 8026 Norway
| |
Collapse
|
17
|
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'.
Collapse
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
| |
Collapse
|
18
|
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'.
Collapse
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
| |
Collapse
|
19
|
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'.
Collapse
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
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
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: 13] [Impact Index Per Article: 6.5] [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.
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Salina E, Muterko A, Kiseleva A, Liu Z, Korol A. Dissection of Structural Reorganization of Wheat 5B Chromosome Associated With Interspecies Recombination Suppression. FRONTIERS IN PLANT SCIENCE 2022; 13:884632. [PMID: 36340334 PMCID: PMC9629394 DOI: 10.3389/fpls.2022.884632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/08/2022] [Indexed: 06/16/2023]
Abstract
Chromosomal rearrangements that lead to recombination suppression can have a significant impact on speciation, and they are also important for breeding. The regions of recombination suppression in wheat chromosome 5B were identified based on comparisons of the 5B map of a cross between the Chinese Spring (CS) variety of hexaploid wheat and CS-5Bdic (genotype CS with 5B substituted with its homologue from tetraploid Triticum dicoccoides) with several 5B maps of tetraploid and hexaploid wheat. In total, two regions were selected in which recombination suppression occurred in cross CS × CS-5Bdic when compared with other maps: one on the short arm, 5BS_RS, limited by markers BS00009810/BS00022336, and the second on the long arm, 5BL_RS, between markers Ra_c10633_2155 and BS00087043. The regions marked as 5BS_RS and 5BL_RS, with lengths of 5 Mb and 3.6 Mb, respectively, were mined from the 5B pseudomolecule of CS and compared to the homoeologous regions (7.6 and 3.8 Mb, respectively) of the 5B pseudomolecule of Zavitan (T. dicoccoides). It was shown that, in the case of 5BS_RS, the local heterochromatin islands determined by the satellite DNA (119.2) and transposable element arrays, as well as the dissimilarity caused by large insertions/deletions (chromosome rearrangements) between 5BSs aestivum/dicoccoides, are likely the key determinants of recombination suppression in the region. Two major and two minor segments with significant loss of similarity were recognized within the 5BL_RS region. It was shown that the loss of similarity, which can lead to suppression of recombination in the 5BL_RS region, is caused by chromosomal rearrangements, driven by the activity of mobile genetic elements (both DNA transposons and long terminal repeat retrotransposons) and their divergence during evolution. It was noted that the regions marked as 5BS_RS and 5BL_RS are associated with chromosomal rearrangements identified earlier by С-banding analysis of intraspecific polymorphism of tetraploid emmer wheat. The revealed divergence in 5BS_RS and 5BL_RS may be a consequence of interspecific hybridization, plant genetic adaptation, or both.
Collapse
Affiliation(s)
- Elena Salina
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
- Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - Alexander Muterko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Antonina Kiseleva
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
- Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - Zhiyong Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Abraham Korol
- Institute of Evolution, University of Haifa, Haifa, Israel
| |
Collapse
|
24
|
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.
Collapse
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
| | | | | |
Collapse
|
25
|
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.
Collapse
|
26
|
Holland PWH, Jiggins CD, Liedvogel M, Warren G, Wurm Y. Functional genomics of supergene-controlled behavior in the white-throated sparrow. Fac Rev 2022; 10:75. [PMID: 35146495 DOI: 10.12703/r-01-000003] [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: 11/15/2022] Open
Abstract
Supergenes are regions of suppressed recombination that may span hundreds of genes and can control variation in key ecological phenotypes. Since genetic analysis is made impossible by the absence of recombination between genes, it has been difficult to establish how individual genes within these regions contribute to supergene-controlled phenotypes. The white-throated sparrow is a classic example in which a supergene controls behavioral differences as well as distinct coloration that determines mate choice. A landmark study now demonstrates that differences between supergene variants in the promoter sequences of a hormone receptor gene change its expression and control changes in behavior. To unambiguously establish the link between genotype and phenotype, the authors used antisense oligonucleotides to alter the level of gene expression in a focal brain region targeted through a cannula. The study showcases a powerful approach to the functional genomic manipulation of a wild vertebrate species.
Collapse
Affiliation(s)
| | | | - Miriam Liedvogel
- Institute of Avian Research 'Vogelwarte Helgoland'; Max Planck Institute for Evolutionary Biology
| | | | - Yannick Wurm
- Queen Mary University of London; Alan Turing Institute
| |
Collapse
|
27
|
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?
Collapse
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
| |
Collapse
|
28
|
Whiteman NK. Evolution in small steps and giant leaps. Evolution 2022; 76:67-77. [PMID: 35040122 PMCID: PMC9387839 DOI: 10.1111/evo.14432] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/28/2021] [Accepted: 01/03/2022] [Indexed: 02/03/2023]
Abstract
The first Editor of Evolution was Ernst Mayr. His foreword to the first issue of Evolution published in 1947 framed evolution as a "problem of interaction" that was just beginning to be studied in this broad context. First, I explore progress and prospects on understanding the subsidiary interactions identified by Mayr, including interactions between parts of organisms, between individuals and populations, between species, and between the organism and its abiotic environment. Mayr's overall "problem of interaction" framework is examined in the context of coevolution within and among levels of biological organization. This leads to a comparison in the relative roles of biotic versus abiotic agents of selection and fluctuating versus directional selection, followed by stabilizing selection in shaping the genomic architecture of adaptation. Oligogenic architectures may be typical for traits shaped more by fluctuating selection and biotic selection. Conversely, polygenic architectures may be typical for traits shaped more by directional followed by stabilizing selection and abiotic selection. The distribution of effect sizes and turnover dynamics of adaptive alleles in these scenarios deserves further study. Second, I review two case studies on the evolution of acquired toxicity in animals, one involving cardiac glycosides obtained from plants and one involving bacterial virulence factors horizontally transferred to animals. The approaches used in these studies and the results gained directly flow from Mayr's vision of an evolutionary biology that revolves around the "problem of interaction."
Collapse
Affiliation(s)
- Noah K. Whiteman
- Department of Integrative Biology, University of California, Berkeley, California 94720,Department of Molecular and Cell Biology, University of California, Berkeley, California 94720,
| |
Collapse
|
29
|
Supergenes, supergenomes, and complex social traits. Proc Natl Acad Sci U S A 2022; 119:2118971118. [PMID: 34987104 PMCID: PMC8764664 DOI: 10.1073/pnas.2118971118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
Ranavat S, Becher H, Newman MF, Gowda V, Twyford AD. A Draft Genome of the Ginger Species Alpinia nigra and New Insights into the Genetic Basis of Flexistyly. Genes (Basel) 2021; 12:1297. [PMID: 34573279 PMCID: PMC8468202 DOI: 10.3390/genes12091297] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 11/17/2022] Open
Abstract
Angiosperms possess various strategies to ensure reproductive success, such as stylar polymorphisms that encourage outcrossing. Here, we investigate the genetic basis of one such dimorphism that combines both temporal and spatial separation of sexual function, termed flexistyly. It is a floral strategy characterised by the presence of two morphs that differ in the timing of stylar movement. We performed a de novo assembly of the genome of Alpinia nigra using high-depth genomic sequencing. We then used Pool-seq to identify candidate regions for flexistyly based on allele frequency or coverage differences between pools of anaflexistylous and cataflexistylous morphs. The final genome assembly size was 2 Gb, and showed no evidence of recent polyploidy. The Pool-seq did not reveal large regions with high FST values, suggesting large structural chromosomal polymorphisms are unlikely to underlie differences between morphs. Similarly, no region had a 1:2 mapping depth ratio which would be indicative of hemizygosity. We propose that flexistyly is governed by a small genomic region that might be difficult to detect with Pool-seq, or a complex genomic region that proved difficult to assemble. Our genome will be a valuable resource for future studies of gingers, and provides the first steps towards characterising this complex floral phenotype.
Collapse
Affiliation(s)
- Surabhi Ranavat
- Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; (H.B.); (A.D.T.)
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK;
| | - Hannes Becher
- Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; (H.B.); (A.D.T.)
| | - Mark F. Newman
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK;
| | - Vinita Gowda
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462 066, Madhya Pradesh, India;
| | - Alex D. Twyford
- Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK; (H.B.); (A.D.T.)
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK;
| |
Collapse
|
32
|
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.
Collapse
|
33
|
Curlis JD, Davis Rabosky AR, Holmes IA, Renney TJ, Cox CL. Genetic mechanisms and correlational selection structure trait variation in a coral snake mimic. Proc Biol Sci 2021; 288:20210003. [PMID: 33726595 PMCID: PMC8059570 DOI: 10.1098/rspb.2021.0003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Covariation among traits shapes both phenotypic evolution and ecological interactions across space and time. However, rampant geographical variation in the strength and direction of such correlations can be particularly difficult to explain through generalized mechanisms. By integrating population genomics, surveys of natural history collections and spatially explicit analyses, we tested multiple drivers of trait correlations in a coral snake mimic that exhibits remarkable polymorphism in mimetic and non-mimetic colour traits. We found that although such traits co-occur extensively across space, correlations were best explained by a mixture of genetic architecture and correlational selection, rather than by any single mechanism. Our findings suggest that spatially complex trait distributions may be driven more by the simple interaction between multiple processes than by complex variation in one mechanism alone. These interactions are particularly important in mimicry systems, which frequently generate striking geographical variation and genetic correlations among colour pattern traits.
Collapse
Affiliation(s)
- John David Curlis
- Department of Biology, Georgia Southern University, Statesboro, GA, USA,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA,University of Michigan Museum of Zoology, Ann Arbor, MI, USA
| | - Alison R. Davis Rabosky
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA,University of Michigan Museum of Zoology, Ann Arbor, MI, USA
| | - Iris A. Holmes
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA,University of Michigan Museum of Zoology, Ann Arbor, MI, USA,Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY, USA
| | - Timothy J. Renney
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Christian L. Cox
- Department of Biology, Georgia Southern University, Statesboro, GA, USA,Department of Biological Sciences and Institute of Environment, Florida International University, Miami, FL, USA
| |
Collapse
|
34
|
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.
Collapse
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
| |
Collapse
|
35
|
Charlesworth D. When and how do sex-linked regions become sex chromosomes? Evolution 2021; 75:569-581. [PMID: 33592115 DOI: 10.1111/evo.14196] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 12/22/2022]
Abstract
The attention given to heteromorphism and genetic degeneration of "classical sex chromosomes" (Y chromosomes in XY systems, and the W in ZW systems that were studied first and are best described) has perhaps created the impression that the absence of recombination between sex chromosomes is inevitable. I here argue that continued recombination is often to be expected, that absence of recombination is surprising and demands further study, and that the involvement of selection in reduced recombination is not yet well understood. Despite a long history of investigations of sex chromosome pairs, there is a need for more quantitative approaches to studying sex-linked regions. I describe a scheme to help understand the relationships between different properties of sex-linked regions. Specifically, I focus on their sizes (differentiating between small regions and extensive fully sex-linked ones), the times when they evolved, and their differentiation, and review studies using DNA sequencing in nonmodel organisms that are providing information about the processes causing these properties.
Collapse
Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, United Kingdom
| |
Collapse
|
36
|
Wright SI. Deborah Charlesworth, winner of the society for the study of evolution's inaugural lifetime achievement award: Evolutionary biology for the genomics era. Evolution 2021; 75:566-568. [PMID: 33592116 DOI: 10.1111/evo.14195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 11/29/2022]
Affiliation(s)
- Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
| |
Collapse
|
37
|
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.
Collapse
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
| |
Collapse
|
38
|
Liao Q, Du R, Gou J, Guo L, Shen H, Liu H, Nguyen JK, Ming R, Yin T, Huang S, Yan J. The genomic architecture of the sex-determining region and sex-related metabolic variation in Ginkgobiloba. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1399-1409. [PMID: 33015884 DOI: 10.1111/tpj.15009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 08/14/2020] [Accepted: 09/01/2020] [Indexed: 06/11/2023]
Abstract
Sex differences and evolutionary differences are critical biological issues. Ginkgo is an ancient lineage of dioecious gymnosperms with special value for studying the mechanism of sex determination in plants. However, the major genetic basic underlying sex chromosomes remains to be uncovered. In this study, we identify the sex-determining region of Ginkgo and locate it to the area from megabases 48 to 75 on chromosome 2. We find that the male sex-determining region of Ginkgo contains more than 200 genes, including four MADS-box genes, demonstrating that the Ginkgo sex determination system is of the XY type. We also find that genetic sex differences result in specialized flavonoid metabolism and regulation in each sex. These findings establish a foundation for revealing the molecular mechanism of sexual dimorphism and promoting the development of the Ginkgo industry.
Collapse
Affiliation(s)
- Qinggang Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Ran Du
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Junbo Gou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Lvjun Guo
- Center for Synthetic and Systems Biology, MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - He Shen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Hailin Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- Key Laboratory for Cultivar Innovation and Germplasm Improvement for Salicaceae Species, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Julie K Nguyen
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tongming Yin
- Key Laboratory for Cultivar Innovation and Germplasm Improvement for Salicaceae Species, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Jianbin Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| |
Collapse
|
39
|
Wessinger CA, Hileman LC. Parallelism in Flower Evolution and Development. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-011720-124511] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Flower evolution is characterized by widespread repetition, with adaptations to pollinator environment evolving in parallel. Recent studies have expanded our understanding of the developmental basis of adaptive floral novelties—petal fusion, bilateral symmetry, heterostyly, and floral dimensions. In this article, we describe patterns of trait evolution and review developmental genetic mechanisms underlying floral novelties. We discuss the diversity of mechanisms for parallel adaptation, the evidence for constraints on these mechanisms, and how constraints help explain observed macroevolutionary patterns. We describe parallel evolution resulting from similarities at multiple hierarchical levels—genetic, developmental, morphological, functional—which indicate general principles in floral evolution, including the central role of hormone signaling. An emerging pattern is mutational bias that may contribute to rapid patterns of parallel evolution, especially if the derived trait can result from simple degenerative mutations. We argue that such mutational bias may be less likely to govern the evolution of novelties patterned by complex developmental pathways.
Collapse
Affiliation(s)
- Carolyn A. Wessinger
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
| | - Lena C. Hileman
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, USA
| |
Collapse
|
40
|
Balfour VL, Black D, Shuker DM. A single pleiotropic locus influences the rate of hybridization between two sibling species of Lygaeus bugs. Ecol Evol 2020; 10:12224-12232. [PMID: 33209283 PMCID: PMC7663077 DOI: 10.1002/ece3.6853] [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: 04/07/2020] [Accepted: 09/08/2020] [Indexed: 11/21/2022] Open
Abstract
The evolution of reproductive isolation lies at the heart of understanding the process of speciation. Of particular interest is the relationship between pre- and postzygotic reproductive isolation, and the genetic architecture of traits that contribute to one or both forms of reproductive isolation. The sibling species of seed bug Lygaeus equestris and L. simulans show a classic pattern of asymmetric prezygotic reproductive isolation, with female L. equestris hybridizing with male L. simulans, but with no hybridization in the reciprocal direction. We have recently described a mutant pale color form of L. simulans, that inherits as a single Mendelian locus and is pleiotropic for a number of other life history and behavioral traits. Here, we tested whether this locus also influences pre- and postzygotic reproductive isolation. Two sets of experimental crosses revealed that behavioral isolation varied with mutant versus wild-type phenotype for male L. simulans, with the pale form less successful at mating with female L. equestris. In terms of trying to assess postzygotic isolation, levels of hybrid offspring production were uniformly low across the experiments. However, we did obtain, for the first time, hybrid offspring from a pairing between a female L. simulans and a male L. equestris. In this instance, the female was of the pale mutant genotype. Together with evidence for heterozygote advantage in terms of nymph survival, we consider our results in terms of possible mechanisms of reproductive isolation between this species pair, the role of the pale mutation, and the possible genetic architectures underlying the mutation, from a single gene to a supergene.
Collapse
|
41
|
Supergene evolution via stepwise duplications and neofunctionalization of a floral-organ identity gene. Proc Natl Acad Sci U S A 2020; 117:23148-23157. [PMID: 32868445 DOI: 10.1073/pnas.2006296117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Heterostyly represents a fascinating adaptation to promote outbreeding in plants that evolved multiple times independently. While l-morph individuals form flowers with long styles, short anthers, and small pollen grains, S-morph individuals have flowers with short styles, long anthers, and large pollen grains. The difference between the morphs is controlled by an S-locus "supergene" consisting of several distinct genes that determine different traits of the syndrome and are held together, because recombination between them is suppressed. In Primula, the S locus is a roughly 300-kb hemizygous region containing five predicted genes. However, with one exception, their roles remain unclear, as does the evolutionary buildup of the S locus. Here we demonstrate that the MADS-box GLOBOSA2 (GLO2) gene at the S locus determines anther position. In Primula forbesii S-morph plants, GLO2 promotes growth by cell expansion in the fused tube of petals and stamen filaments beneath the anther insertion point; by contrast, neither pollen size nor male incompatibility is affected by GLO2 activity. The paralogue GLO1, from which GLO2 arose by duplication, has maintained the ancestral B-class function in specifying petal and stamen identity, indicating that GLO2 underwent neofunctionalization, likely at the level of the encoded protein. Genetic mapping and phylogenetic analysis indicate that the duplications giving rise to the style-length-determining gene CYP734A50 and to GLO2 occurred sequentially, with the CYP734A50 duplication likely the first. Together these results provide the most detailed insight into the assembly of a plant supergene yet and have important implications for the evolution of heterostyly.
Collapse
|
42
|
Martinez-Ruiz C, Pracana R, Stolle E, Paris CI, Nichols RA, Wurm Y. Genomic architecture and evolutionary antagonism drive allelic expression bias in the social supergene of red fire ants. eLife 2020; 9:55862. [PMID: 32773032 PMCID: PMC7476760 DOI: 10.7554/elife.55862] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 08/07/2020] [Indexed: 11/17/2022] Open
Abstract
Supergene regions maintain alleles of multiple genes in tight linkage through suppressed recombination. Despite their importance in determining complex phenotypes, our empirical understanding of early supergene evolution is limited. Here we focus on the young ‘social’ supergene of fire ants, a powerful system for disentangling the effects of evolutionary antagonism and suppressed recombination. We hypothesize that gene degeneration and social antagonism shaped the evolution of the fire ant supergene, resulting in distinct patterns of gene expression. We test these ideas by identifying allelic differences between supergene variants, characterizing allelic expression across populations, castes and body parts, and contrasting allelic expression biases with differences in expression between social forms. We find strong signatures of gene degeneration and gene-specific dosage compensation. On this background, a small portion of the genes has the signature of adaptive responses to evolutionary antagonism between social forms. Red fire ants (Solenopsis invicta) are native to South America, but the species has spread to North America, Australia and New Zealand where it can be an invasive pest. A reason for this species’ invasiveness types of colonies : one with a single egg-laying queen and another with several queens. However, it is not possible to simply add more queens to a colony with one queen. Instead, the number of queens in a colony is controlled genetically, by a chromosome known as the ‘social chromosome’. Like many other animals, red fire ants are diploid: their cells have two copies of each chromosome, which can carry two different versions of each gene. The social chromosome is no different, and it comes in two variants, SB and Sb. Each ant can therefore have either two SB chromosomes, leading to a colony with a single queen; or one SB chromosome and one Sb chromosome, leading to a colony with multiple queens. Ants with two copies of the Sb variant die when they are young, so the Sb version is inherited in a similar way to how the Y chromosome is passed on in humans. However, the social chromosome in red fire ants appeared less than one million years ago, making it much younger than the human Y chromosome, which is 180 million years old. This makes the social chromosome a good candidate for examining the early evolution of special chromosome variants that are only inherited. How differences between the SB and the Sb chromosomes are evolving is an open question, however. Perhaps each version of the social chromosome has been optimised through natural selection to one colony type. Another suggestion is that the Sb chromosome has degenerated over time because its genes cannot be ‘reshuffled’ as they would be on normal chromosomes. Martinez-Ruiz et al. compared genetic variants on the SB and Sb chromosomes, along with their expression in different types of ant colonies. The analysis showed that the Sb variant is in fact breaking down because of the lack of gene shuffling. This loss is compensated by intact copies of the same genes found on the SB variant, which explains why ants with the Sb variant can only survive if they also carry the SB version. Only a handful of genes on the social chromosomes appear to have been optimised by natural selection. Therefore Martinez-Ruiz et al. concluded the differences between the two chromosomes that lead to different colony types are collateral effects of Sb’s inability to reshuffle its genes. This work reveals how a special chromosome similar to the Y chromosome in humans evolved. It also shows how multiple complex evolutionary forces can shape a species’ genetic makeup and social forms.
Collapse
Affiliation(s)
- Carlos Martinez-Ruiz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Rodrigo Pracana
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Eckart Stolle
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Carolina Ivon Paris
- Departamento Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires, Argentina
| | - Richard A Nichols
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Yannick Wurm
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.,Alan Turing Institute, London, United Kingdom
| |
Collapse
|
43
|
Henning PM, Shore JS, McCubbin AG. Transcriptome and Network Analyses of Heterostyly in Turnera subulata Provide Mechanistic Insights: Are S-Loci a Red-Light for Pistil Elongation? PLANTS 2020; 9:plants9060713. [PMID: 32503265 PMCID: PMC7356734 DOI: 10.3390/plants9060713] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/21/2020] [Accepted: 05/29/2020] [Indexed: 12/19/2022]
Abstract
Heterostyly employs distinct hermaphroditic floral morphs to enforce outbreeding. Morphs differ structurally in stigma/anther positioning, promoting cross-pollination, and physiologically blocking self-fertilization. Heterostyly is controlled by a self-incompatibility (S)-locus of a small number of linked S-genes specific to short-styled morph genomes. Turnera possesses three S-genes, namely TsBAHD (controlling pistil characters), TsYUC6, and TsSPH1 (controlling stamen characters). Here, we compare pistil and stamen transcriptomes of floral morphs of T. subulata to investigate hypothesized S-gene function(s) and whether hormonal differences might contribute to physiological incompatibility. We then use network analyses to identify genetic networks underpinning heterostyly. We found a depletion of brassinosteroid-regulated genes in short styled (S)-morph pistils, consistent with hypothesized brassinosteroid-inactivating activity of TsBAHD. In S-morph anthers, auxin-regulated genes were enriched, consistent with hypothesized auxin biosynthesis activity of TsYUC6. Evidence was found for auxin elevation and brassinosteroid reduction in both pistils and stamens of S- relative to long styled (L)-morph flowers, consistent with reciprocal hormonal differences contributing to physiological incompatibility. Additional hormone pathways were also affected, however, suggesting S-gene activities intersect with a signaling hub. Interestingly, distinct S-genes controlling pistil length, from three species with independently evolved heterostyly, potentially intersect with phytochrome interacting factor (PIF) network hubs which mediate red/far-red light signaling. We propose that modification of the activities of PIF hubs by the S-locus could be a common theme in the evolution of heterostyly.
Collapse
Affiliation(s)
- Paige M. Henning
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA 99164-4236, USA;
| | - Joel S. Shore
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J1P3, Canada;
| | - Andrew G. McCubbin
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA 99164-4236, USA;
- Correspondence:
| |
Collapse
|
44
|
Parisod C, Badaeva ED. Chromosome restructuring among hybridizing wild wheats. THE NEW PHYTOLOGIST 2020; 226:1263-1273. [PMID: 31913521 DOI: 10.1111/nph.16415] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/29/2019] [Indexed: 06/10/2023]
Abstract
The wheat group offers an outstanding system to address the interplay between hybridization, chromosomal evolution and biological diversification. Most diploid wild wheats originated following hybridization between the A-genome lineage and the B-genome lineage some 4 Myr ago, resulting in an admixed D-genome lineage that presented dramatic radiation accompanied by considerable changes in genome size and chromosomal rearrangements. Comparative profiling of low-copy genes, repeated sequences and transposable elements among those divergent species characterized by different karyotypes highlights high genome dynamics and sheds new light on the processes underlying chromosomal evolution in wild wheats. One of the hybrid clades presents upsizing of metacentric chromosomes going along with the proliferation of specific repeats (i.e. 'genomic obesity'), whereas other species show stable genome size associated with increasing chromosomal asymmetry. Genetic and ecological variation in those specialized species suggest that genome restructuring was coupled with adaptive processes to support the evolution of a majority of acrocentric chromosomes. This synthesis of current knowledge on genome restructuring across the diversity of wild wheats paves the way towards surveys based on latest sequencing technologies to characterize valuable resources and address the significance of chromosomal evolution in species with complex genomes.
Collapse
Affiliation(s)
- Christian Parisod
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, 3013, Switzerland
| | - Ekaterina D Badaeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin St. 3, Moscow, 119991, Russia
| |
Collapse
|
45
|
Timmermans MJTN, Srivathsan A, Collins S, Meier R, Vogler AP. Mimicry diversification in Papilio dardanus via a genomic inversion in the regulatory region of engrailed- invected. Proc Biol Sci 2020; 287:20200443. [PMID: 32345166 DOI: 10.1098/rspb.2020.0443] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Polymorphic Batesian mimics exhibit multiple protective morphs that each mimic a different noxious model. Here, we study the genomic transitions leading to the evolution of different mimetic wing patterns in the polymorphic Mocker Swallowtail Papilio dardanus. We generated a draft genome (231 Mb over 30 chromosomes) and re-sequenced individuals of three morphs. Genome-wide single nucleotide polymorphism (SNP) analysis revealed elevated linkage disequilibrium and divergence between morphs in the regulatory region of engrailed, a developmental gene previously implicated in the mimicry switch. The diverged region exhibits a discrete chromosomal inversion (of 40 kb) relative to the ancestral orientation that is associated with the cenea morph, but not with the bottom-recessive hippocoonides morph or with non-mimetic allopatric populations. The functional role of this inversion in the expression of the novel phenotype is currently unknown, but by preventing recombination, it allows the stable inheritance of divergent alleles enabling geographic spread and local coexistence of multiple adaptive morphs.
Collapse
Affiliation(s)
- Martijn J T N Timmermans
- Department of Life Sciences, Natural History Museum, London, UK.,Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, UK.,Department of Natural Sciences, Middlesex University, London, UK
| | - Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Steve Collins
- African Butterfly Research Institute, Nairobi, Kenya
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore.,Lee Kong Chian Natural History Museum, National University of Singapore, Singapore
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK.,Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, UK
| |
Collapse
|
46
|
Xia Y, Yuan X, Luo W, Yuan S, Zeng X. The Origin and Evolution of Chromosomal Reciprocal Translocation in Quasipaa boulengeri (Anura, Dicroglossidae). Front Genet 2020; 10:1364. [PMID: 32038718 PMCID: PMC6985567 DOI: 10.3389/fgene.2019.01364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/12/2019] [Indexed: 11/28/2022] Open
Abstract
Chromosomal rearrangements have long fascinated evolutionary biologists for being widely implicated in causing genetic differentiation. Suppressed recombination has been demonstrated in various species with inversion; however, there is controversy over whether such recombination suppression would facilitate divergence in reciprocal translocation with reduced fitness. In this study, we used the spiny frog, Quasipaa boulengeri, whose western Sichuan Basin populations exhibit translocation polymorphisms, to test whether the genetic markers on translocated (rearranged) or normal chromosomes have driven this genetic differentiation. We also investigated its overall genetic structure and the possibility of chromosomal fixation. Whole-chromosome painting and genetic structure clustering suggested a single origin of the translocation polymorphisms, and high-throughput sequencing of rearranged chromosomes isolated many markers with known localizations on chromosomes. Using these markers, distinct patterns of gene flow were found between rearranged and normal chromosomes. Genetic differentiation was only found in the translocated chromosomes, not in normal chromosomes or the mitochondrial genome. Hybrid unfitness cannot explain the genetic differentiation, as then the differentiation would be observed throughout the whole genome. Our results suggest that suppressed recombination drives genetic differentiation into a balanced chromosomal polymorphism. Mapping to a reference genome, we found that the region of genetic differentiation covered a wide range of translocated chromosomes, not only in the vicinity of chromosomal breakpoints. Our results imply that the suppressed recombination region could be extended by accumulation of repetitive sequences or capture of alleles that are adapted to the local environment, following the spread and/or fixation of chromosomal rearrangement.
Collapse
Affiliation(s)
- Yun Xia
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xiuyun Yuan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,College of Computer Science, Sichuan University, Chengdu, China
| | - Wei Luo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Siqi Yuan
- College of Bioengineering, Sichuan University of Science & Engineering, Zigong, China
| | - Xiaomao Zeng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| |
Collapse
|
47
|
Martin SH, Singh KS, Gordon IJ, Omufwoko KS, Collins S, Warren IA, Munby H, Brattström O, Traut W, Martins DJ, Smith DAS, Jiggins CD, Bass C, ffrench-Constant RH. Whole-chromosome hitchhiking driven by a male-killing endosymbiont. PLoS Biol 2020; 18:e3000610. [PMID: 32108180 PMCID: PMC7046192 DOI: 10.1371/journal.pbio.3000610] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/23/2020] [Indexed: 12/30/2022] Open
Abstract
Neo-sex chromosomes are found in many taxa, but the forces driving their emergence and spread are poorly understood. The female-specific neo-W chromosome of the African monarch (or queen) butterfly Danaus chrysippus presents an intriguing case study because it is restricted to a single 'contact zone' population, involves a putative colour patterning supergene, and co-occurs with infection by the male-killing endosymbiont Spiroplasma. We investigated the origin and evolution of this system using whole genome sequencing. We first identify the 'BC supergene', a broad region of suppressed recombination across nearly half a chromosome, which links two colour patterning loci. Association analysis suggests that the genes yellow and arrow in this region control the forewing colour pattern differences between D. chrysippus subspecies. We then show that the same chromosome has recently formed a neo-W that has spread through the contact zone within approximately 2,200 years. We also assembled the genome of the male-killing Spiroplasma, and find that it shows perfect genealogical congruence with the neo-W, suggesting that the neo-W has hitchhiked to high frequency as the male-killer has spread through the population. The complete absence of female crossing-over in the Lepidoptera causes whole-chromosome hitchhiking of a single neo-W haplotype, carrying a single allele of the BC supergene and dragging multiple non-synonymous mutations to high frequency. This has created a population of infected females that all carry the same recessive colour patterning allele, making the phenotypes of each successive generation highly dependent on uninfected male immigrants. Our findings show how hitchhiking can occur between the physically unlinked genomes of host and endosymbiont, with dramatic consequences.
Collapse
Affiliation(s)
- Simon H. Martin
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Kumar Saurabh Singh
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, United Kingdom
| | - Ian J. Gordon
- Center of Excellence in Biodiversity and Natural Resource Management, University of Rwanda, Huye, Rwanda
| | - Kennedy Saitoti Omufwoko
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States of America
- Mpala Research Centre, Nanyuki, Kenya
| | - Steve Collins
- African Butterfly Research Institute, Nairobi, Kenya
| | - Ian A. Warren
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Hannah Munby
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Oskar Brattström
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Walther Traut
- Institut für Biologie, Universität Lübeck, Lübeck, Germany
| | - Dino J. Martins
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, United States of America
- Mpala Research Centre, Nanyuki, Kenya
| | | | - Chris D. Jiggins
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Chris Bass
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, United Kingdom
| | | |
Collapse
|
48
|
Yan Z, Martin SH, Gotzek D, Arsenault SV, Duchen P, Helleu Q, Riba-Grognuz O, Hunt BG, Salamin N, Shoemaker D, Ross KG, Keller L. Evolution of a supergene that regulates a trans-species social polymorphism. Nat Ecol Evol 2020; 4:240-249. [PMID: 31959939 DOI: 10.1038/s41559-019-1081-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/04/2019] [Indexed: 11/09/2022]
Abstract
Supergenes are clusters of linked genetic loci that jointly affect the expression of complex phenotypes, such as social organization. Little is known about the origin and evolution of these intriguing genomic elements. Here we analyse whole-genome sequences of males from native populations of six fire ant species and show that variation in social organization is under the control of a novel supergene haplotype (termed Sb), which evolved by sequential incorporation of three inversions spanning half of a 'social chromosome'. Two of the inversions interrupt protein-coding genes, resulting in the increased expression of one gene and modest truncation in the primary protein structure of another. All six socially polymorphic species studied harbour the same three inversions, with the single origin of the supergene in their common ancestor inferred by phylogenomic analyses to have occurred half a million years ago. The persistence of Sb along with the ancestral SB haplotype through multiple speciation events provides a striking example of a functionally important trans-species social polymorphism presumably maintained by balancing selection. We found that while recombination between the Sb and SB haplotypes is severely restricted in all species, a low level of gene flux between the haplotypes has occurred following the appearance of the inversions, potentially mitigating the evolutionary degeneration expected at genomic regions that cannot freely recombine. These results provide a detailed picture of the structural genomic innovations involved in the formation of a supergene controlling a complex social phenotype.
Collapse
Affiliation(s)
- Zheng Yan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Simon H Martin
- Institute of Evolutionary Biology, the University of Edinburgh, Edinburgh, UK
| | - Dietrich Gotzek
- Department of Entomology and Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | | | - Pablo Duchen
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Quentin Helleu
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Oksana Riba-Grognuz
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Brendan G Hunt
- Department of Entomology, University of Georgia, Athens, GA, USA
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - DeWayne Shoemaker
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Kenneth G Ross
- Department of Entomology, University of Georgia, Athens, GA, USA.
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
| |
Collapse
|
49
|
An Ancient and Eroded Social Supergene Is Widespread across Formica Ants. Curr Biol 2020; 30:304-311.e4. [PMID: 31902719 DOI: 10.1016/j.cub.2019.11.032] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 08/10/2019] [Accepted: 11/11/2019] [Indexed: 12/25/2022]
Abstract
Supergenes, clusters of tightly linked genes, play a key role in the evolution of complex adaptive variation [1, 2]. Although supergenes have been identified in many species, we lack an understanding of their origin, evolution, and persistence [3]. Here, we uncover 20-40 Ma of evolutionary history of a supergene associated with polymorphic social organization in Formica ants [4]. We show that five Formica species exhibit homologous divergent haplotypes spanning 11 Mbp on chromosome 3. Despite the supergene's size, only 142 single nucleotide polymorphisms (SNPs) consistently distinguish alternative supergene haplotypes across all five species. These conserved trans-species SNPs are localized in a small number of disjunct clusters distributed across the supergene. This unexpected pattern of divergence indicates that the Formica supergene does not follow standard models of sex chromosome evolution, in which distinct evolutionary strata reflect an expanding region of suppressed recombination [5]. We propose an alternative "eroded strata model" in which clusters of conserved trans-species SNPs represent functionally important areas maintained by selection in the face of rare recombination between ancestral haplotypes. The comparison of whole-genome sequences across 10 additional Formica species reveals that the most conserved region of the supergene contains a transcription factor essential for motor neuron development in Drosophila [6]. The discovery that a very small portion of this large and ancient supergene harbors conserved trans-species SNPs linked to colony social organization suggests that the ancestral haplotypes have been eroded by recombination, with selection preserving differentiation at one or a few genes generating alternative social organization.
Collapse
|
50
|
Shore JS, Hamam HJ, Chafe PDJ, Labonne JDJ, Henning PM, McCubbin AG. The long and short of the S-locus in Turnera (Passifloraceae). THE NEW PHYTOLOGIST 2019; 224:1316-1329. [PMID: 31144315 DOI: 10.1111/nph.15970] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/23/2019] [Indexed: 06/09/2023]
Abstract
Distyly is an intriguing floral adaptation that increases pollen transfer precision and restricts inbreeding. It has been a model system in evolutionary biology since Darwin. Although the S-locus determines the long- and short-styled morphs, the genes were unknown in Turnera. We have now identified these genes. We used deletion mapping to identify, and then sequence, BAC clones and genome scaffolds to construct S/s haplotypes. We investigated candidate gene expression, hemizygosity, and used mutants, to explore gene function. The s-haplotype possessed 21 genes collinear with a region of chromosome 7 of grape. The S-haplotype possessed three additional genes and two inversions. TsSPH1 was expressed in filaments and anthers, TsYUC6 in anthers and TsBAHD in pistils. Long-homostyle mutants did not possess TsBAHD and a short-homostyle mutant did not express TsSPH1. Three hemizygous genes appear to determine S-morph characteristics in T. subulata. Hemizygosity is common to all distylous species investigated, yet the genes differ. The pistil candidate gene, TsBAHD, differs from that of Primula, but both may inactivate brassinosteroids causing short styles. TsYUC6 is involved in auxin synthesis and likely determines pollen characteristics. TsSPH1 is likely involved in filament elongation. We propose an incompatibility mechanism involving TsYUC6 and TsBAHD.
Collapse
Affiliation(s)
- Joel S Shore
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Hasan J Hamam
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Paul D J Chafe
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Jonathan D J Labonne
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Paige M Henning
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA, 99164-4236, USA
| | - Andrew G McCubbin
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA, 99164-4236, USA
| |
Collapse
|