1
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Hale MC, Pearse DE, Campbell MA. Characterization and distribution of a 14-Mb chromosomal inversion in native populations of rainbow trout (Oncorhynchus mykiss). G3 (BETHESDA, MD.) 2024:jkae100. [PMID: 38885060 DOI: 10.1093/g3journal/jkae100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/10/2024] [Indexed: 06/20/2024]
Abstract
Multiple studies in a range of taxa have found links between structural variants and the development of ecologically important traits. Such variants are becoming easier to find due, in large part, to the increase in the amount of genome-wide sequence data in nonmodel organisms. The salmonids (salmon, trout, and charr) are a taxonomic group with abundant genome-wide datasets due to their importance in aquaculture, fisheries, and variation in multiple ecologically important life-history traits. Previous research on rainbow trout (Oncorhynchus mykiss) has documented a large pericentric (∼55 Mb) chromosomal inversion (CI) on chromosome 5 (Omy05) and a second smaller (∼14 Mb) chromosome inversion on Omy20. While the Omy05 inversion appears to be associated with multiple adaptive traits, the inversion on Omy20 has received far less attention. In this study, we re-analyze RAD-seq and amplicon data from several populations of rainbow trout (O. mykiss) to better document the structure and geographic distribution of variation in the Omy20 CI. Moreover, we utilize phylogenomic techniques to characterize both the age- and the protein-coding gene content of the Omy20 CI. We find that the age of the Omy20 inversion dates to the early stages of O. mykiss speciation and predates the Omy05 inversion by ∼450,000 years. The 2 CIs differ further in terms of the frequency of the homokaryotypes. While both forms of the Omy05 CI are found across the eastern Pacific, the ancestral version of the Omy20 CI is restricted to the southern portion of the species range in California. Furthermore, the Omy20 inverted haplotype is comparable in genetic diversity to the ancestral form, whereas derived CIs typically show substantially reduced genetic diversity. These data contribute to our understanding of the age and distribution of a large CI in rainbow trout and provide a framework for researchers looking to document CIs in other nonmodel species.
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Affiliation(s)
- Matthew C Hale
- Department of Biology, Texas Christian University, Fort Worth, TX 76109, USA
| | - Devon E Pearse
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Santa Cruz, CA 95064, USA
| | - Matthew A Campbell
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA
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2
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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.
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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
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3
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Portnoy DS, O'Leary SJ, Fields AT, Hollenbeck CM, Grubbs RD, Peterson CT, Gardiner JM, Adams DH, Falterman B, Drymon JM, Higgs JM, Pulster EL, Wiley TR, Murawski SA. Complex patterns of genetic population structure in the mouthbrooding marine catfish, Bagre marinus, in the Gulf of Mexico and U.S. Atlantic. Ecol Evol 2024; 14:e11514. [PMID: 38859886 PMCID: PMC11163162 DOI: 10.1002/ece3.11514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 06/12/2024] Open
Abstract
Patterns of genetic variation reflect interactions among microevolutionary forces that vary in strength with changing demography. Here, patterns of variation within and among samples of the mouthbrooding gafftopsail catfish (Bagre marinus, Family Ariidae) captured in the U.S. Atlantic and throughout the Gulf of Mexico were analyzed using genomics to generate neutral and non-neutral SNP data sets. Because genomic resources are lacking for ariids, linkage disequilibrium network analysis was used to examine patterns of putatively adaptive variation. Finally, historical demographic parameters were estimated from site frequency spectra. The results show four differentiated groups, corresponding to the (1) U.S. Atlantic, and the (2) northeastern, (3) northwestern, and (4) southern Gulf of Mexico. The non-neutral data presented two contrasting signals of structure, one due to increases in diversity moving west to east and north to south, and another to increased heterozygosity in the Atlantic. Demographic analysis suggested that recently reduced long-term effective population size in the Atlantic is likely an important driver of patterns of genetic variation and is consistent with a known reduction in population size potentially due to an epizootic. Overall, patterns of genetic variation resemble that of other fishes that use the same estuarine habitats as nurseries, regardless of the presence/absence of a larval phase, supporting the idea that adult/juvenile behavior and habitat are important predictors of contemporary patterns of genetic structure.
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Affiliation(s)
- David S. Portnoy
- Marine Genomics Laboratory, Department of Life SciencesTexas A&M University – Corpus ChristiCorpus ChristiTexasUSA
| | - Shannon J. O'Leary
- Department of Biological SciencesSaint Anselm CollegeManchesterNew HampshireUSA
| | - Andrew T. Fields
- Marine Genomics Laboratory, Department of Life SciencesTexas A&M University – Corpus ChristiCorpus ChristiTexasUSA
| | - Christopher M. Hollenbeck
- Marine Genomics Laboratory, Department of Life SciencesTexas A&M University – Corpus ChristiCorpus ChristiTexasUSA
| | - R. Dean Grubbs
- Florida State University Coastal and Marine LaboratorySt. TeresaFloridaUSA
| | | | | | - Douglas H. Adams
- Florida Fish and Wildlife Conservation CommissionFish and Wildlife Research Institute, Indian River Field LabMelbourneFloridaUSA
| | | | - J. Marcus Drymon
- Mississippi State University Coastal Research and Extension CenterBiloxiMississippiUSA
- Mississippi‐Alabama Sea Grant ConsortiumOcean SpringsMississippiUSA
| | - Jeremy M. Higgs
- Center for Fisheries Research and DevelopmentThe University of Southern MississippiOcean SpringsMississippiUSA
| | - Erin L. Pulster
- U.S. Geological Survey, Columbia Environmental Research CenterColumbiaMissouriUSA
- College of Marine ScienceUniversity of South FloridaSt. PetersburgFloridaUSA
| | | | - Steven A. Murawski
- College of Marine ScienceUniversity of South FloridaSt. PetersburgFloridaUSA
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Vangestel C, Swaegers J, De Corte Z, Dekoninck W, Gharbi K, Gillespie R, Vandekerckhove M, Van Belleghem SM, Hendrickx F. Chromosomal inversions from an initial ecotypic divergence drive a gradual repeated radiation of Galápagos beetles. SCIENCE ADVANCES 2024; 10:eadk7906. [PMID: 38820159 PMCID: PMC11141621 DOI: 10.1126/sciadv.adk7906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/30/2024] [Indexed: 06/02/2024]
Abstract
Island faunas exhibit some of the most iconic examples where similar forms repeatedly evolve within different islands. Yet, whether these deterministic evolutionary trajectories within islands are driven by an initial, singular divergence and the subsequent exchange of individuals and adaptive genetic variation between islands remains unclear. Here, we study a gradual, repeated evolution of low-dispersive highland ecotypes from a dispersive lowland ecotype of Calosoma beetles along the island progression of the Galápagos. We show that repeated highland adaptation involved selection on multiple shared alleles within extensive chromosomal inversions that originated from an initial adaptation event on the oldest island. These highland inversions first spread through dispersal of highland individuals. Subsequent admixture with the lowland ecotype resulted in polymorphic dispersive populations from which the highland populations evolved on the youngest islands. Our findings emphasize the significance of an ancient divergence in driving repeated evolution and highlight how a mixed contribution of inter-island colonization and within-island evolution can shape parallel species communities.
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Affiliation(s)
- Carl Vangestel
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Terrestrial Ecology Unit, Biology Department, Ghent University, Gent, Belgium
| | - Janne Swaegers
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Ecology, Evolution and Conservation Biology, Biology Department, University of Leuven, Leuven, Belgium
| | - Zoë De Corte
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Terrestrial Ecology Unit, Biology Department, Ghent University, Gent, Belgium
| | | | - Karim Gharbi
- Earlham Institute, Norwich Research Park, Norfolk, United Kingdom
| | - Rosemary Gillespie
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Matthias Vandekerckhove
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Terrestrial Ecology Unit, Biology Department, Ghent University, Gent, Belgium
| | - Steven M. Van Belleghem
- Ecology, Evolution and Conservation Biology, Biology Department, University of Leuven, Leuven, Belgium
| | - Frederik Hendrickx
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Terrestrial Ecology Unit, Biology Department, Ghent University, Gent, Belgium
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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.
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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.
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Di Pietro V, Menezes C, de Britto Frediani MG, Pereira DJ, Fajgenblat M, Ferreira HM, Wenseleers T, Oliveira RC. The inheritance of alternative nest architectural traditions in stingless bees. Curr Biol 2024; 34:1996-2001.e3. [PMID: 38508185 DOI: 10.1016/j.cub.2024.02.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/14/2024] [Accepted: 02/29/2024] [Indexed: 03/22/2024]
Abstract
The transmission of complex behavior and culture in humans has long been attributed to advanced forms of social learning,1,2 which play a crucial role in our technological advancement.3 While similar phenomena of behavioral traditions and cultural inheritance have been observed in animals,1,2,4,5,6 including in primates,7 whales,8 birds,9 and even insects,10 the underlying mechanisms enabling the persistence of such animal traditions, particularly in insects, are less well understood. This study introduces pioneering evidence of enduring architectural traditions in the stingless bee Scaptotrigona depilis, which are maintained without any evidence for social learning. We demonstrate that S. depilis exhibits two distinct nest architectures, comprising either helicoidal or flat, stacked horizontal combs, which are transmitted across generations through stigmergy11,12,13,14,15,16,17-an environmental feedback mechanism whereby the presence of the existing comb structures guides subsequent construction behaviors-thereby leading to a form of environmental inheritance.18,19,20 Cross-fostering experiments further show that genetic factors or prior experience does not drive the observed variation in nest architecture. Moreover, the experimental introduction of corkscrew dislocations within the combs prompted helicoidal building, confirming the use of stigmergic building rules. At a theoretical level, we establish that the long-term equilibrium of building in the helicoidal pattern fits with the expectations of a two-state Markov chain model. Overall, our findings provide compelling evidence for the persistence of behavioral traditions in an insect, based on a simple mechanism of environmental inheritance and stigmergic interactions, without requiring any sophisticated learning mechanism, thereby expanding our understanding of how traditions can be maintained in non-human species.
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Affiliation(s)
- Viviana Di Pietro
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Cristiano Menezes
- Embrapa Environment, Laboratory of Entomology and Phytopathology, SP-340 Road, 13918-110 Jaguariúna, Brazil
| | | | - David José Pereira
- Embrapa Environment, Laboratory of Entomology and Phytopathology, SP-340 Road, 13918-110 Jaguariúna, Brazil
| | - Maxime Fajgenblat
- Laboratory of Freshwater Ecology, Evolution and Conservation, Department of Biology, KU Leuven, Charles Deberiotstraat 32, Leuven 3000, Belgium; I-BioStat, Data Science Institute, Hasselt University, Agoralaan 1, Diepenbeek 3590, Belgium
| | - Helena Mendes Ferreira
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium
| | - Tom Wenseleers
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Ricardo Caliari Oliveira
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium; Universitat Autònoma de Barcelona, Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Av. de l'Eix Central, edifici C, 08193 Bellaterra (Barcelona), Spain.
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7
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Lin RC, Ferreira BT, Yuan YW. The molecular basis of phenotypic evolution: beyond the usual suspects. Trends Genet 2024:S0168-9525(24)00097-0. [PMID: 38704304 DOI: 10.1016/j.tig.2024.04.010] [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: 02/09/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024]
Abstract
It has been well documented that mutations in coding DNA or cis-regulatory elements underlie natural phenotypic variation in many organisms. However, the development of sophisticated functional tools in recent years in a wide range of traditionally non-model systems have revealed many 'unusual suspects' in the molecular bases of phenotypic evolution, including upstream open reading frames (uORFs), cryptic splice sites, and small RNAs. Furthermore, large-scale genome sequencing, especially long-read sequencing, has identified a cornucopia of structural variation underlying phenotypic divergence and elucidated the composition of supergenes that control complex multi-trait polymorphisms. In this review article we highlight recent studies that demonstrate this great diversity of molecular mechanisms producing adaptive genetic variation and the panoply of evolutionary paths leading to the 'grandeur of life'.
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Affiliation(s)
- Rong-Chien Lin
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Bianca T Ferreira
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Yao-Wu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.
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8
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Peng F, Sun X, van Vloten C, Correll J, Langdon M, Ngochanthra W, Johnson K, Amador Kane S. Hybrid Mimulus flowers attract a new pollinator. THE NEW PHYTOLOGIST 2024; 242:1324-1332. [PMID: 38482697 DOI: 10.1111/nph.19668] [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: 10/03/2023] [Accepted: 02/23/2024] [Indexed: 04/12/2024]
Abstract
Hybridization is common in flowering plants and is believed to be an important force driving adaptation and speciation. The flowers of hybrids often exhibit new trait combinations, which, theoretically, could attract new species of pollinators. In this study, we found that the hybrids between a hummingbird-pollinated species Mimulus cardinalis and a self-pollinated species Mimulus parishii attract bumblebees (Bombus impatiens), a pollinator not attracted to either of the progenitor species. This novel attraction is explained by new combinations of floral traits in hybrids, including, most importantly, petal color, in addition to nectar concentration and corolla size. To understand how petal color variation is perceived by bumblebees, we performed reflectance spectroscopy and multispectral imaging to model the flower appearance in bee vision. This analysis showed that color variation would impact the ease of detection. We also found that YUP, the genetic locus responsible for a large portion of floral color variation and previously shown to be important in bee interactions with other Mimulus species, also played an important role in this novel attraction. These results together suggest that the attraction of new pollinators to hybrid plants could be an underexplored avenue for pollinator shift and speciation.
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Affiliation(s)
- Foen Peng
- Department of Biology, Haverford College, Haverford, PA, 19041, USA
| | - Xiaohe Sun
- Department of Biology, Haverford College, Haverford, PA, 19041, USA
| | | | - Jude Correll
- Department of Biology, Haverford College, Haverford, PA, 19041, USA
| | - Marlena Langdon
- Department of Biology, Haverford College, Haverford, PA, 19041, USA
| | | | - Karl Johnson
- Department of Biology, Haverford College, Haverford, PA, 19041, USA
| | - Suzanne Amador Kane
- Department of Physics and Astronomy, Haverford College, Haverford, PA, 19041, USA
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Tetrault E, Aaronson B, Gilbert MC, Albertson RC. Foraging-induced craniofacial plasticity is associated with an early, robust and dynamic transcriptional response. Proc Biol Sci 2024; 291:20240215. [PMID: 38654651 PMCID: PMC11040245 DOI: 10.1098/rspb.2024.0215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/19/2024] [Indexed: 04/26/2024] Open
Abstract
Phenotypic plasticity is the ability of a single genotype to vary its phenotype in response to the environment. Plasticity of the skeletal system in response to mechanical input is widely studied, but the timing of its transcriptional regulation is not well understood. Here, we used the cichlid feeding apparatus to examine the transcriptional dynamics of skeletal plasticity over time. Using three closely related species that vary in their ability to remodel bone and a panel of 11 genes, including well-studied skeletal differentiation markers and newly characterized environmentally sensitive genes, we examined plasticity at one, two, four and eight weeks following the onset of alternate foraging challenges. We found that the plastic species exhibited environment-specific bursts in gene expression beginning at one week, followed by a sharp decline in levels, while the species with more limited plasticity exhibited consistently low levels of gene expression. This trend held across nearly all genes, suggesting that it is a hallmark of the larger plasticity regulatory network. We conclude that plasticity of the cichlid feeding apparatus is not the result of slowly accumulating gene expression difference over time, but rather is stimulated by early bursts of environment-specific gene expression followed by a return to homeostatic levels.
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Affiliation(s)
- Emily Tetrault
- Molecular and Cell Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Ben Aaronson
- Department of Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Michelle C. Gilbert
- Department of Biology, Pennsylvania State University, State College, PA 16802, USA
| | - R. Craig Albertson
- Department of Biology, University of Massachusetts, Amherst, MA 01003, USA
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10
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Soboleva ES, Kirilenko KM, Fedorova VS, Kokhanenko AA, Artemov GN, Sharakhov IV. Two Nested Inversions in the X Chromosome Differentiate the Dominant Malaria Vectors in Europe, Anopheles atroparvus and Anopheles messeae. INSECTS 2024; 15:312. [PMID: 38786868 PMCID: PMC11122324 DOI: 10.3390/insects15050312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024]
Abstract
The Maculipennis subgroup of malaria mosquitoes includes both dominant malaria vectors and non-vectors in Eurasia. Understanding the genetic factors, particularly chromosomal inversions, that differentiate Anopheles species can provide valuable insights for vector control strategies. Although autosomal inversions between the species in this subgroup have been characterized based on the chromosomal banding patterns, the number and positions of rearrangements in the X chromosome remain unclear due to the divergent banding patterns. Here, we identified two large X chromosomal inversions, approximately 13 Mb and 10 Mb in size, using fluorescence in situ hybridization. The inversion breakpoint regions were mapped by hybridizing 53 gene markers with polytene chromosomes of An. messeae. The DNA probes were designed based on gene sequences from the annotated An. atroparvus genome. The two nested inversions resulted in five syntenic blocks. Only two small syntenic blocks, which encompass 181 annotated genes in the An. atroparvus genome, changed their position and orientation in the X chromosome. The analysis of the An. atroparvus genome revealed an enrichment of gene ontology terms associated with immune system and mating behavior in the rearranged syntenic blocks. Additionally, the enrichment of DNA transposons was found in sequences homologous to three of the four breakpoint regions. This study demonstrates the successful application of the physical genome mapping approach to identify rearrangements that differentiate species in insects with polytene chromosomes.
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Affiliation(s)
- Evgenia S. Soboleva
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 36 Lenin Avenue, Tomsk 634050, Russia
| | - Kirill M. Kirilenko
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 36 Lenin Avenue, Tomsk 634050, Russia
| | - Valentina S. Fedorova
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 36 Lenin Avenue, Tomsk 634050, Russia
| | - Alina A. Kokhanenko
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 36 Lenin Avenue, Tomsk 634050, Russia
| | - Gleb N. Artemov
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 36 Lenin Avenue, Tomsk 634050, Russia
| | - Igor V. Sharakhov
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 36 Lenin Avenue, Tomsk 634050, Russia
- Department of Entomology, the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, 360 West Campus Drive, Blacksburg, VA 24061, USA
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11
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Dowling CA, Shi J, Toth JA, Quade MA, Smart LB, McCabe PF, Schilling S, Melzer R. A FLOWERING LOCUS T ortholog is associated with photoperiod-insensitive flowering in hemp (Cannabis sativa L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38625758 DOI: 10.1111/tpj.16769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/15/2024] [Accepted: 04/02/2024] [Indexed: 04/18/2024]
Abstract
Hemp (Cannabis sativa L.) is an extraordinarily versatile crop, with applications ranging from medicinal compounds to seed oil and fibre products. Cannabis sativa is a short-day plant, and its flowering is highly controlled by photoperiod. However, substantial genetic variation exists for photoperiod sensitivity in C. sativa, and photoperiod-insensitive ("autoflower") cultivars are available. Using a bi-parental mapping population and bulked segregant analysis, we identified Autoflower2, a 0.5 Mbp locus significantly associated with photoperiod-insensitive flowering in hemp. Autoflower2 contains an ortholog of the central flowering time regulator FLOWERING LOCUS T (FT) from Arabidopsis thaliana which we termed CsFT1. We identified extensive sequence divergence between alleles of CsFT1 from photoperiod-sensitive and insensitive cultivars of C. sativa, including a duplication of CsFT1 and sequence differences, especially in introns. Furthermore, we observed higher expression of one of the CsFT1 copies found in the photoperiod-insensitive cultivar. Genotyping of several mapping populations and a diversity panel confirmed a correlation between CsFT1 alleles and photoperiod response, affirming that at least two independent loci involved in the photoperiodic control of flowering, Autoflower1 and Autoflower2, exist in the C. sativa gene pool. This study reveals the multiple independent origins of photoperiod insensitivity in C. sativa, supporting the likelihood of a complex domestication history in this species. By integrating the genetic relaxation of photoperiod sensitivity into novel C. sativa cultivars, expansion to higher latitudes will be permitted, thus allowing the full potential of this versatile crop to be reached.
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Affiliation(s)
- Caroline A Dowling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- UCD Earth Institute, University College Dublin, Dublin, Ireland
| | - Jiaqi Shi
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- UCD Earth Institute, University College Dublin, Dublin, Ireland
| | - Jacob A Toth
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, New York, USA
| | - Michael A Quade
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, New York, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, New York, USA
| | - Paul F McCabe
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- UCD Earth Institute, University College Dublin, Dublin, Ireland
| | - Susanne Schilling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- UCD Earth Institute, University College Dublin, Dublin, Ireland
| | - Rainer Melzer
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- UCD Earth Institute, University College Dublin, Dublin, Ireland
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12
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Jay P, Aubier TG, Joron M. The interplay of local adaptation and gene flow may lead to the formation of supergenes. Mol Ecol 2024:e17297. [PMID: 38415327 DOI: 10.1111/mec.17297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 12/28/2023] [Accepted: 01/10/2024] [Indexed: 02/29/2024]
Abstract
Supergenes are genetic architectures resulting in the segregation of alternative combinations of alleles underlying complex phenotypes. The co-segregation of alleles at linked loci is often facilitated by polymorphic chromosomal rearrangements suppressing recombination locally. Supergenes are involved in many complex polymorphisms, including sexual, colour or behavioural polymorphisms in numerous plants, fungi, mammals, fish, and insects. Despite a long history of empirical and theoretical research, the formation of supergenes remains poorly understood. Here, using a two-island population genetic model, we explore how gene flow and the evolution of overdominant chromosomal inversions may jointly lead to the formation of supergenes. We show that the evolution of inversions in differentiated populations, both under disruptive selection, leads to an increase in frequency of poorly adapted, immigrant haplotypes. Indeed, rare allelic combinations, such as immigrant haplotypes, are more frequently reshuffled by recombination than common allelic combinations, and therefore benefit from the recombination suppression generated by inversions. When an inversion capturing a locally adapted haplotype spreads but is associated with a fitness cost hampering its fixation (e.g. a recessive mutation load), the maintenance of a non-inverted haplotype in the population is enhanced; under certain conditions, the immigrant haplotype persists alongside the inverted local haplotype, while the standard local haplotype disappears. This establishes a stable, local polymorphism with two non-recombining haplotypes encoding alternative adaptive strategies, that is, a supergene. These results bring new light to the importance of local adaptation, overdominance, and gene flow in the formation of supergenes and inversion polymorphisms in general.
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Affiliation(s)
- Paul Jay
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | - Thomas G Aubier
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UT3), Toulouse, France
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
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13
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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.
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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
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14
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Thomson L, Espinosa DP, Brandvain Y, Van Cleve J. Linked selection and the evolution of altruism in family-structured populations. Ecol Evol 2024; 14:e10980. [PMID: 38371869 PMCID: PMC10870336 DOI: 10.1002/ece3.10980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/12/2024] [Accepted: 01/29/2024] [Indexed: 02/20/2024] Open
Abstract
Much research on the evolution of altruism via kin selection, group selection, and reciprocity focuses on the role of a single locus or quantitative trait. Very few studies have explored how linked selection, or selection at loci neighboring an altruism locus, impacts the evolution of altruism. While linked selection can decrease the efficacy of selection at neighboring loci, it might have other effects including promoting selection for altruism by increasing relatedness in regions of low recombination. Here, we used population genetic simulations to study how negative selection at linked loci, or background selection, affects the evolution of altruism. When altruism occurs between full siblings, we found that background selection interfered with selection on the altruistic allele, increasing its fixation probability when the altruistic allele was disfavored and reducing its fixation when the allele was favored. In other words, background selection has the same effect on altruistic genes in family-structured populations as it does on other, nonsocial, genes. This contrasts with prior research showing that linked selective sweeps can favor the evolution of cooperation, and we discuss possibilities for resolving these contrasting results.
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Affiliation(s)
- Lia Thomson
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesotaUSA
| | | | - Yaniv Brandvain
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesotaUSA
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15
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Meyer L, Barry P, Riquet F, Foote A, Der Sarkissian C, Cunha RL, Arbiol C, Cerqueira F, Desmarais E, Bordes A, Bierne N, Guinand B, Gagnaire PA. Divergence and gene flow history at two large chromosomal inversions underlying ecotype differentiation in the long-snouted seahorse. Mol Ecol 2024:e17277. [PMID: 38279695 DOI: 10.1111/mec.17277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 12/18/2023] [Accepted: 01/04/2024] [Indexed: 01/28/2024]
Abstract
Chromosomal inversions can play an important role in divergence and reproductive isolation by building and maintaining distinct allelic combinations between evolutionary lineages. Alternatively, they can take the form of balanced polymorphisms that segregate within populations until one arrangement becomes fixed. Many questions remain about how inversion polymorphisms arise, how they are maintained over the long term, and ultimately, whether and how they contribute to speciation. The long-snouted seahorse (Hippocampus guttulatus) is genetically subdivided into geographic lineages and marine-lagoon ecotypes, with shared structural variation underlying lineage and ecotype divergence. Here, we aim to characterize structural variants and to reconstruct their history and suspected role in ecotype formation. We generated a near chromosome-level genome assembly and described genome-wide patterns of diversity and divergence through the analysis of 112 whole-genome sequences from Atlantic, Mediterranean, and Black Sea populations. By also analysing linked-read sequencing data, we found evidence for two chromosomal inversions that were several megabases in length and showed contrasting allele frequency patterns between lineages and ecotypes across the species range. We reveal that these inversions represent ancient intraspecific polymorphisms, one likely being maintained by divergent selection and the other by pseudo-overdominance. A possible selective coupling between the two inversions was further supported by the absence of specific haplotype combinations and a putative functional interaction between the two inversions in reproduction. Lastly, we detected gene flux eroding divergence between inverted alleles at varying levels for the two inversions, with a likely impact on their dynamics and contribution to divergence and speciation.
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Affiliation(s)
- Laura Meyer
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Pierre Barry
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto, Vairão, Portugal
| | | | - Andrew Foote
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Clio Der Sarkissian
- Centre for Anthropobiology and Genomics of Toulouse, CNRS, University of Toulouse Paul Sabatier, Toulouse, France
| | - Regina L Cunha
- Centre of Marine Sciences-CCMAR, University of Algarve, Faro, Portugal
| | | | | | - Erick Desmarais
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Anaïs Bordes
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Nicolas Bierne
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Bruno Guinand
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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16
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Stubbs RL, Theodoridis S, Mora-Carrera E, Keller B, Potente G, Yousefi N, Jay P, Léveillé-Bourret É, Choudhury RR, Celep F, Kochjarová J, Conti E. The genomes of Darwin's primroses reveal chromosome-scale adaptive introgression and differential permeability of species boundaries. THE NEW PHYTOLOGIST 2024; 241:911-925. [PMID: 37921572 DOI: 10.1111/nph.19361] [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: 06/13/2023] [Accepted: 10/05/2023] [Indexed: 11/04/2023]
Abstract
Introgression is an important source of genetic variation that can determine species adaptation to environmental conditions. Yet, definitive evidence of the genomic and adaptive implications of introgression in nature remains scarce. The widespread hybrid zones of Darwin's primroses (Primula elatior, Primula veris, and Primula vulgaris) provide a unique natural laboratory for studying introgression in flowering plants and the varying permeability of species boundaries. Through analysis of 650 genomes, we provide evidence of an introgressed genomic region likely to confer adaptive advantage in conditions of soil toxicity. We also document unequivocal evidence of chloroplast introgression, an important precursor to species-wide chloroplast capture. Finally, we provide the first evidence that the S-locus supergene, which controls heterostyly in primroses, does not introgress in this clade. Our results contribute novel insights into the adaptive role of introgression and demonstrate the importance of extensive genomic and geographical sampling for illuminating the complex nature of species boundaries.
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Affiliation(s)
- Rebecca L Stubbs
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
| | - Spyros Theodoridis
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, 60325, Germany
| | - Emiliano Mora-Carrera
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
| | - Barbara Keller
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
| | - Giacomo Potente
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
| | - Narjes Yousefi
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
| | - Paul Jay
- Center for GeoGenetics, University of Copenhagen, Copenhagen, 1350, Denmark
| | - Étienne Léveillé-Bourret
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, Montreal, QC, H1X 2B2, Canada
| | | | - Ferhat Celep
- Department of Biology, Faculty of Arts and Sciences, Kırıkkale University, Kırıkkale, 71450, Turkey
| | - Judita Kochjarová
- Department of Phytology, Faculty of Forestry, Technical University in Zvolen, Zvolen, 96001, Slovak Republic
| | - Elena Conti
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, 8008, Switzerland
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17
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Hill J, Enbody ED, Bi H, Lamichhaney S, Lei W, Chen J, Wei C, Liu Y, Schwochow D, Younis S, Widemo F, Andersson L. Low Mutation Load in a Supergene Underpinning Alternative Male Mating Strategies in Ruff (Calidris pugnax). Mol Biol Evol 2023; 40:msad224. [PMID: 37804117 DOI: 10.1093/molbev/msad224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/23/2023] [Accepted: 09/28/2023] [Indexed: 10/08/2023] Open
Abstract
A paradox in evolutionary biology is how supergenes can maintain high fitness despite reduced effective population size, the suppression of recombination, and the expected accumulation of mutational load. The ruff supergene involves 2 rare inversion haplotypes (satellite and faeder). These are recessive lethals but with dominant effects on male mating strategies, plumage, and body size. Sequence divergence to the wild-type (independent) haplotype indicates that the inversion could be as old as 4 million years. Here, we have constructed a highly contiguous genome assembly of the inversion region for both the independent and satellite haplotypes. Based on the new data, we estimate that the recombination event(s) creating the satellite haplotype occurred only about 70,000 yr ago. Contrary to expectations for supergenes, we find no substantial expansion of repeats and only a modest mutation load on the satellite and faeder haplotypes despite high sequence divergence to the non-inverted haplotype (1.46%). The essential centromere protein N (CENPN) gene is disrupted by the inversion and is as well conserved on the inversion haplotypes as on the noninversion haplotype. These results suggest that the inversion may be much younger than previously thought. The low mutation load, despite recessive lethality, may be explained by the introgression of the inversion from a now extinct lineage.
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Affiliation(s)
- Jason Hill
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Erik D Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Huijuan Bi
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Sangeet Lamichhaney
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
- Department of Biological Sciences, Kent State University, Kent, OH 44241, USA
| | - Weipan Lei
- Key Laboratory for Biodiversity Science and Ecological Engineering, National Demonstration Center for Experimental Life Sciences and Biotechnology Education, College of Life Sciences, Beijing Normal University, 100875 Beijing, China
| | - Juexin Chen
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, 510275 Guangzhou, China
| | - Chentao Wei
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, 510275 Guangzhou, China
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, 510275 Guangzhou, China
| | - Doreen Schwochow
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Shady Younis
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
- Division of Immunology and Rheumatology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Fredrik Widemo
- Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
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18
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Saul F, Scharmann M, Wakatake T, Rajaraman S, Marques A, Freund M, Bringmann G, Channon L, Becker D, Carroll E, Low YW, Lindqvist C, Gilbert KJ, Renner T, Masuda S, Richter M, Vogg G, Shirasu K, Michael TP, Hedrich R, Albert VA, Fukushima K. Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis. NATURE PLANTS 2023; 9:2000-2015. [PMID: 37996654 DOI: 10.1038/s41477-023-01562-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/09/2023] [Indexed: 11/25/2023]
Abstract
Subgenome dominance after whole-genome duplication generates distinction in gene number and expression at the level of chromosome sets, but it remains unclear how this process may be involved in evolutionary novelty. Here we generated a chromosome-scale genome assembly of the Asian pitcher plant Nepenthes gracilis to analyse how its novel traits (dioecy and carnivorous pitcher leaves) are linked to genomic evolution. We found a decaploid karyotype and a clear indication of subgenome dominance. A male-linked and pericentromerically located region on the putative sex chromosome was identified in a recessive subgenome and was found to harbour three transcription factors involved in flower and pollen development, including a likely neofunctionalized LEAFY duplicate. Transcriptomic and syntenic analyses of carnivory-related genes suggested that the paleopolyploidization events seeded genes that subsequently formed tandem clusters in recessive subgenomes with specific expression in the digestive zone of the pitcher, where specialized cells digest prey and absorb derived nutrients. A genome-scale analysis suggested that subgenome dominance likely contributed to evolutionary innovation by permitting recessive subgenomes to diversify functions of novel tissue-specific duplicates. Our results provide insight into how polyploidy can give rise to novel traits in divergent and successful high-ploidy lineages.
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Affiliation(s)
- Franziska Saul
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Mathias Scharmann
- Institute for Biochemistry and Biology (IBB), University of Potsdam, Potsdam, Germany
| | - Takanori Wakatake
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Sitaram Rajaraman
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Matthias Freund
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Gerhard Bringmann
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Louisa Channon
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Dirk Becker
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Emily Carroll
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Yee Wen Low
- Singapore Botanic Gardens, National Parks Board, Singapore, Singapore
| | | | - Kadeem J Gilbert
- Department of Plant Biology & W.K. Kellogg Biological Station & Program in Ecology, Evolution, and Behavior, Michigan State University, Hickory Corners, MI, USA
| | - Tanya Renner
- Department of Entomology, The Pennsylvania State University, University Park, PA, USA
| | - Sachiko Masuda
- Riken Center for Sustainable Resource Science, Yokohama, Japan
| | - Michaela Richter
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Gerd Vogg
- Botanical Garden, University of Würzburg, Würzburg, Germany
| | - Ken Shirasu
- Riken Center for Sustainable Resource Science, Yokohama, Japan
| | - Todd P Michael
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA.
| | - Kenji Fukushima
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Würzburg, Germany.
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19
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Márquez-Corro JI, Martín-Bravo S, Blanco-Pastor JL, Luceño M, Escudero M. The holocentric chromosome microevolution: From phylogeographic patterns to genomic associations with environmental gradients. Mol Ecol 2023. [PMID: 37795678 DOI: 10.1111/mec.17156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/06/2023]
Abstract
Geographic isolation and chromosome evolution are two of the major drivers of diversification in eukaryotes in general, and specifically, in plants. On one hand, range shifts induced by Pleistocene glacial oscillations deeply shaped the evolutionary trajectories of species in the Northern Hemisphere. On the other hand, karyotype variability within species or species complexes may have adaptive potential as different karyotypes may represent different recombination rates and linkage groups that may be associated with locally adapted genes or supergenes. Organisms with holocentric chromosomes are ideal to study the link between local adaptation and chromosome evolution, due to their high cytogenetic variability, especially when it seems to be related to environmental variation. Here, we integrate the study of the phylogeography, chromosomal evolution and ecological requirements of a plant species complex distributed in the Western Euro-Mediterranean region (Carex gr. laevigata, Cyperaceae). We aim to clarify the relative influence of these factors on population differentiation and ultimately on speciation. We obtained a well-resolved RADseq phylogeny that sheds light on the phylogeographic patterns of molecular and chromosome number variation, which are compatible with south-to-north postglacial migration. In addition, landscape genomics analyses identified candidate loci for local adaptation, and also strong significant associations between the karyotype and the environment. We conclude that karyotype distribution in C. gr. laevigata has been constrained by both range shift dynamics and local adaptation. Our study demonstrates that chromosome evolution may be responsible, at least partially, for microevolutionary patterns of population differentiation and adaptation in Carex.
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Affiliation(s)
- José Ignacio Márquez-Corro
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Seville, Spain
- Jodrell Laboratory, Department of Trait Diversity and Function, Royal Botanic Gardens, Kew, Richmond, UK
| | - Santiago Martín-Bravo
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Seville, Spain
| | - José Luis Blanco-Pastor
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Seville, Spain
- Departamento de Biología, IVAGRO, Universidad de Cádiz, Campus de Excelencia Internacional Agroalimentario (CeiA3), Cádiz, Spain
| | - Modesto Luceño
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Seville, Spain
| | - Marcial Escudero
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Seville, Spain
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20
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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.
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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
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21
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Arnqvist G, Rowe L. Ecology, the pace-of-life, epistatic selection and the maintenance of genetic variation in life-history genes. Mol Ecol 2023; 32:4713-4724. [PMID: 37386734 DOI: 10.1111/mec.17062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 06/09/2023] [Accepted: 06/19/2023] [Indexed: 07/01/2023]
Abstract
Evolutionary genetics has long struggled with understanding how functional genes under selection remain polymorphic in natural populations. Taking as a starting point that natural selection is ultimately a manifestation of ecological processes, we spotlight an underemphasized and potentially ubiquitous ecological effect that may have fundamental effects on the maintenance of genetic variation. Negative frequency dependency is a well-established emergent property of density dependence in ecology, because the relative profitability of different modes of exploiting or utilizing limiting resources tends to be inversely proportional to their frequency in a population. We suggest that this may often generate negative frequency-dependent selection (NFDS) on major effect loci that affect rate-dependent physiological processes, such as metabolic rate, that are phenotypically manifested as polymorphism in pace-of-life syndromes. When such a locus under NFDS shows stable intermediate frequency polymorphism, this should generate epistatic selection potentially involving large numbers of loci with more minor effects on life-history (LH) traits. When alternative alleles at such loci show sign epistasis with a major effect locus, this associative NFDS will promote the maintenance of polygenic variation in LH genes. We provide examples of the kind of major effect loci that could be involved and suggest empirical avenues that may better inform us on the importance and reach of this process.
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Affiliation(s)
- Göran Arnqvist
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Locke Rowe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Swedish Collegium of Advanced Study, Uppsala, Sweden
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22
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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.
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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
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23
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Blanchet S, Fargeot L, Raffard A. Phylogenetically-conserved candidate genes unify biodiversity-ecosystem function relationships and eco-evolutionary dynamics across biological scales. Mol Ecol 2023; 32:4467-4481. [PMID: 37296539 DOI: 10.1111/mec.17043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/24/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023]
Abstract
The intra- and interspecific facets of biodiversity have traditionally been analysed separately, limiting our understanding of how evolution has shaped biodiversity, how biodiversity (as a whole) alters ecological dynamics and hence eco-evolutionary feedbacks at the community scale. Here, we propose using candidate genes phylogenetically-conserved across species and sustaining functional traits as an inclusive biodiversity unit transcending the intra- and interspecific boundaries. This framework merges knowledge from functional genomics and functional ecology, and we first provide guidelines and a concrete example for identifying phylogenetically-conserved candidate genes (PCCGs) within communities and for measuring biodiversity from PCCGs. We then explain how biodiversity measured at PCCGs can be linked to ecosystem functions, which unifies recent observations that both intra- and interspecific biodiversity are important for ecosystem functions. We then highlight the eco-evolutionary processes shaping PCCG diversity patterns and argue that their respective role can be inferred from concepts derived from population genetics. Finally, we explain how PCCGs may shift the field of eco-evolutionary dynamics from a focal-species approach to a more realistic focal-community approach. This framework provides a novel perspective to investigate the global ecosystem consequences of diversity loss across biological scales, and how these ecological changes further alter biodiversity evolution.
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Affiliation(s)
- Simon Blanchet
- Centre National de la Recherche Scientifique (CNRS), Station d'Écologie Théorique et Expérimentale du CNRS à Moulis, UAR2029, Moulis, France
| | - Laura Fargeot
- Centre National de la Recherche Scientifique (CNRS), Station d'Écologie Théorique et Expérimentale du CNRS à Moulis, UAR2029, Moulis, France
| | - Allan Raffard
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, Thonon-les-Bains, France
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24
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Baird RB, Mongue AJ, Ross L. Why put all your eggs in one basket? Evolutionary perspectives on the origins of monogenic reproduction. Heredity (Edinb) 2023:10.1038/s41437-023-00632-7. [PMID: 37328587 PMCID: PMC10382564 DOI: 10.1038/s41437-023-00632-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/18/2023] Open
Abstract
Sexual reproduction is ubiquitous in eukaryotes, but the mechanisms by which sex is determined are diverse and undergo rapid turnovers in short evolutionary timescales. Usually, an embryo's sex is fated at the moment of fertilisation, but in rare instances it is the maternal genotype that determines the offspring's sex. These systems are often characterised by mothers producing single-sex broods, a phenomenon known as monogeny. Monogenic reproduction is well documented in Hymenoptera (ants, bees and wasps), where it is associated with a eusocial lifestyle. However, it is also known to occur in three families in Diptera (true flies): Sciaridae, Cecidomyiidae and Calliphoridae. Here we review current knowledge of monogenic reproduction in these dipteran clades. We discuss how this strange reproductive strategy might evolve, and we consider the potential contributions of inbreeding, sex ratio distorters, and polygenic control of the sex ratio. Finally, we provide suggestions on future work to elucidate the origins of this unusual reproductive strategy. We propose that studying these systems will contribute to our understanding of the evolution and turnover of sex determination systems.
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Affiliation(s)
- Robert B Baird
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, EH9 3JT, UK.
| | - Andrew J Mongue
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, 32611, USA
| | - Laura Ross
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, EH9 3JT, UK
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25
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Meyer M, Slot J. The evolution and ecology of psilocybin in nature. Fungal Genet Biol 2023; 167:103812. [PMID: 37210028 DOI: 10.1016/j.fgb.2023.103812] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/19/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023]
Abstract
Fungi produce diverse metabolites that can have antimicrobial, antifungal, antifeedant, or psychoactive properties. Among these metabolites are the tryptamine-derived compounds psilocybin, its precursors, and natural derivatives (collectively referred to as psiloids), which have played significant roles in human society and culture. The high allocation of nitrogen to psiloids in mushrooms, along with evidence of convergent evolution and horizontal transfer of psilocybin genes, suggest they provide a selective benefit to some fungi. However, no precise ecological roles of psilocybin have been experimentally determined. The structural and functional similarities of psiloids to serotonin, an essential neurotransmitter in animals, suggest that they may enhance the fitness of fungi through interference with serotonergic processes. However, other ecological mechanisms of psiloids have been proposed. Here, we review the literature pertinent to psilocybin ecology and propose potential adaptive advantages psiloids may confer to fungi.
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Affiliation(s)
- Matthew Meyer
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA; Environmental Science Graduate Program, The Ohio State University, Columbus, OH 43210, USA; Center for Psychedelic Drug Research and Education, The Ohio State University, Columbus, OH 43210, USA.
| | - Jason Slot
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA; Center for Psychedelic Drug Research and Education, The Ohio State University, Columbus, OH 43210, USA.
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26
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Haberkorn C, David J, Henri H, Delpuech J, Lasseur R, Vavre F, Varaldi J. A major 6 Mb superlocus is involved in pyrethroid resistance in the common bed bug Cimex lectularius. Evol Appl 2023; 16:1012-1028. [PMID: 37216030 PMCID: PMC10197226 DOI: 10.1111/eva.13550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/23/2023] [Accepted: 04/04/2023] [Indexed: 05/24/2023] Open
Abstract
In the last few years, the bed bug Cimex lectularius has been an increasing problem worldwide, mainly due to the development of insecticide resistance to pyrethroids. The characterization of resistance alleles is a prerequisite to improve surveillance and resistance management. To identify genomic variants associated with pyrethroid resistance in Cimex lectularius, we compared the genetic composition of two recent and resistant populations with that of two ancient-susceptible strains using a genome-wide pool-seq design. We identified a large 6 Mb "superlocus" showing particularly high genetic differentiation and association with the resistance phenotype. This superlocus contained several clustered resistance genes and was also characterized by a high density of structural variants (inversions, duplications). The possibility that this superlocus constitutes a resistance "supergene" that evolved after the clustering of alleles adapted to insecticide and after reduction in recombination is discussed.
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Affiliation(s)
- Chloé Haberkorn
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
- IZInovationLyonFrance
| | - Jean‐Philippe David
- Laboratoire d'Écologie AlpineUMR UGA‐USMB‐CNRS 5553 Université Grenoble Alpes CS 40700Grenoble cedex 9France
| | - Hélène Henri
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
| | - Jean‐Marie Delpuech
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
| | | | - Fabrice Vavre
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
| | - Julien Varaldi
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
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27
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Bikchurina T, Pavlenko M, Kizilova E, Rubtsova D, Sheremetyeva I, Kartavtseva I, Torgasheva A, Borodin P. Chromosome Asynapsis Is the Main Cause of Male Sterility in the Interspecies Hybrids of East Asian Voles ( Alexandromys, Rodentia, Arvicolinae). Genes (Basel) 2023; 14:genes14051022. [PMID: 37239382 DOI: 10.3390/genes14051022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Closely related mammalian species often have differences in chromosome number and morphology, but there is still a debate about how these differences relate to reproductive isolation. To study the role of chromosome rearrangements in speciation, we used the gray voles in the Alexandromys genus as a model. These voles have a high level of chromosome polymorphism and substantial karyotypic divergence. We investigated testis histology and meiotic chromosome behavior in the captive-bred colonies of Alexandromys maximowiczii, Alexandromys mujanensis, two chromosome races of Alexandromys evoronensis, and their interracial and interspecies hybrids, to explore the relationship between karyotypic differences and male hybrid sterility. We found that the seminiferous tubules of the males of the parental species and the interracial hybrids, which were simple heterozygotes for one or more chromosome rearrangements, contained germ cells at all stages of spermatogenesis, indicating their potential fertility. Their meiotic cells displayed orderly chromosome synapsis and recombination. In contrast, all interspecies male hybrids, which were complex heterozygotes for a series of chromosome rearrangements, showed signs of complete sterility. Their spermatogenesis was mainly arrested at the zygotene- or pachytene-like stages due to the formation of complex multivalent chains, which caused extended chromosome asynapsis. The asynapsis led to the silencing of unsynapsed chromatin. We suggest that chromosome asynapsis is the main cause of meiotic arrest and male sterility in the interspecies hybrids of East Asian voles.
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Affiliation(s)
- Tatiana Bikchurina
- Department of Cytology and Genetics, Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Marina Pavlenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far East Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
| | - Elena Kizilova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Daria Rubtsova
- Department of Cytology and Genetics, Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Irina Sheremetyeva
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far East Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
| | - Irina Kartavtseva
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far East Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
| | - Anna Torgasheva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Pavel Borodin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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28
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Sumner S, Favreau E, Geist K, Toth AL, Rehan SM. Molecular patterns and processes in evolving sociality: lessons from insects. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220076. [PMID: 36802779 PMCID: PMC9939270 DOI: 10.1098/rstb.2022.0076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/16/2022] [Indexed: 02/21/2023] Open
Abstract
Social insects have provided some of the clearest insights into the origins and evolution of collective behaviour. Over 20 years ago, Maynard Smith and Szathmáry defined the most complex form of insect social behaviour-superorganismality-among the eight major transitions in evolution that explain the emergence of biological complexity. However, the mechanistic processes underlying the transition from solitary life to superorganismal living in insects remain rather elusive. An overlooked question is whether this major transition arose via incremental or step-wise modes of evolution. We suggest that examination of the molecular processes underpinning different levels of social complexity represented across the major transition from solitary to complex sociality can help address this question. We present a framework for using molecular data to assess to what extent the mechanistic processes that take place in the major transition to complex sociality and superorganismality involve nonlinear (implying step-wise evolution) or linear (implying incremental evolution) changes in the underlying molecular mechanisms. We assess the evidence for these two modes using data from social insects and discuss how this framework can be used to test the generality of molecular patterns and processes across other major transitions. This article is part of a discussion meeting issue 'Collective behaviour through time'.
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Affiliation(s)
- Seirian Sumner
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Emeline Favreau
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Katherine Geist
- Department of Ecology, Evolution and Organismal Biology, and Department of Entomology, Iowa State University, Ames, IA 50011, USA
| | - Amy L. Toth
- Department of Ecology, Evolution and Organismal Biology, and Department of Entomology, Iowa State University, Ames, IA 50011, USA
| | - Sandra M. Rehan
- Department of Biology, York University, Toronto, Canada M3J 1P3
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29
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Taylor KL, Wade EJ, Wells MM, Henry CS. Genomic regions underlying the species-specific mating songs of green lacewings. INSECT MOLECULAR BIOLOGY 2023; 32:79-85. [PMID: 36281633 DOI: 10.1111/imb.12815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Rapid species radiations provide insight into the process of speciation and diversification. The radiation of Chrysoperla carnea-group lacewings seems to be driven, at least in part, by their species-specific pre-mating vibrational duets. We associated genetic markers from across the genome with courtship song period in the offspring of a laboratory cross between Chrysoperla plorabunda and Chrysoperla adamsi, two species primarily differentiated by their mating songs. Two genomic regions were strongly associated with the song period phenotype. Large regions of chromosomes one and two were associated with song phenotype, as fewer recombination events occurred on these chromosomes relative to the other autosomes. Candidate genes were identified by functional annotation of proteins from the C. carnea reference genome. The majority of genes that are associated with vibrational courtship signals in other insects were found within QTL for lacewing song phenotype. Together these findings suggest that decreased recombination may be acting to keep together loci important to reproductive isolation between these species. Using wild-caught individuals from both species, we identified signals of genomic divergence across the genome. We identified several candidate genes both in song-associated regions and near divergence outliers including nonA, fruitless, paralytic, period, and doublesex. Together these findings bring us one step closer to identifying the genomic basis of a mating song trait critical to the maintenance of species boundaries in green lacewings.
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Affiliation(s)
- Katherine L Taylor
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
- Department of Entomology, University of Maryland, College Park, Maryland, USA
| | - Elizabeth J Wade
- Department of Natural Sciences and Mathematics, Curry College, Milton, Massachusetts, USA
| | - Marta M Wells
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Charles S Henry
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
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30
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Villoutreix R, de Carvalho CF, Feder JL, Gompert Z, Nosil P. Disruptive selection and the evolution of discrete color morphs in Timema stick insects. SCIENCE ADVANCES 2023; 9:eabm8157. [PMID: 37000882 PMCID: PMC10065444 DOI: 10.1126/sciadv.abm8157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
A major unresolved issue in biology is why phenotypic and genetic variation is sometimes continuous, yet other times packaged into discrete units of diversity, such as morphs, ecotypes, and species. In theory, ecological discontinuities can impose strong disruptive selection that promotes the evolution of discrete forms, but direct tests of this hypothesis are lacking. Here, we show that Timema stick insects exhibit genetically determined color morphs that range from weakly to strongly discontinuous. Color data from nature and a manipulative field experiment demonstrate that greater morph differentiation is associated with shifts from host plants exhibiting more continuous color variation to those exhibiting greater coloration distance between green leaves and brown stems, the latter of which generates strong disruptive selection. Our results show how ecological factors can promote discrete variation, and we further present results on how this can have variable effects on the genetic differentiation that promotes speciation.
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Affiliation(s)
| | - Clarissa F. de Carvalho
- CEFE, Université Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Departamento de Ecologia e Biologia Evolutiva, UNIFESP, Diadema 09972-270, Brazil
| | - Jeffrey L. Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | | | - Patrik Nosil
- CEFE, Université Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Department of Biology, Utah State University, Logan, UT 84322, USA
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31
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Arsenault SV, Riba-Grognuz O, Shoemaker D, Hunt BG, Keller L. Direct and indirect genetic effects of a social supergene. Mol Ecol 2023; 32:1087-1097. [PMID: 36541826 DOI: 10.1111/mec.16830] [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: 05/31/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Indirect genetic effects describe phenotypic variation that results from differences in the genotypic composition of social partners. Such effects represent heritable sources of environmental variation in eusocial organisms because individuals are typically reared by their siblings. In the fire ant Solenopsis invicta, a social supergene exhibits striking indirect genetic effects on worker regulation of colony queen number, such that the genotypic composition of workers at the supergene determines whether colonies contain a single or multiple queens. We assessed the direct and indirect genetic effects of this supergene on gene expression in brains and abdominal tissues from laboratory-reared workers and compared these with previously published data from field-collected prereproductive queens. We found that direct genetic effects caused larger gene expression changes and were more consistent across tissue types and castes than indirect genetic effects. Indirect genetic effects influenced the expression of many loci but were generally restricted to the abdominal tissues. Further, indirect genetic effects were only detected when the genotypic composition of social partners differed throughout the development and adult life of focal workers, and were often only significant with relatively lenient statistical cutoffs. Our study provides insight into direct and indirect genetic effects of a social supergene on gene regulatory dynamics across tissues and castes in a complex society.
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Affiliation(s)
| | - Oksana Riba-Grognuz
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - DeWayne Shoemaker
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, USA
| | - Brendan G Hunt
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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32
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Chapuisat M. Evolution: A social parasite was born from a virgin. Curr Biol 2023; 33:R225-R228. [PMID: 36977384 DOI: 10.1016/j.cub.2023.02.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
The sudden appearance of small winged queens within a lineage of asexually reproducing ant workers reveals that such social parasites can appear abruptly. The parasitic queens differ in a large genomic region, suggesting that a supergene instantly equipped the social parasite with a suite of co-adapted traits.
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Affiliation(s)
- Michel Chapuisat
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
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33
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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.
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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
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Trible W, Chandra V, Lacy KD, Limón G, McKenzie SK, Olivos-Cisneros L, Arsenault SV, Kronauer DJC. A caste differentiation mutant elucidates the evolution of socially parasitic ants. Curr Biol 2023; 33:1047-1058.e4. [PMID: 36858043 PMCID: PMC10050096 DOI: 10.1016/j.cub.2023.01.067] [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: 05/31/2022] [Revised: 08/31/2022] [Accepted: 01/31/2023] [Indexed: 03/03/2023]
Abstract
Most ant species have two distinct female castes-queens and workers-yet the developmental and genetic mechanisms that produce these alternative phenotypes remain poorly understood. Working with a clonal ant, we discovered a variant strain that expresses queen-like traits in individuals that would normally become workers. The variants show changes in morphology, behavior, and fitness that cause them to rely on workers in wild-type (WT) colonies for survival. Overall, they resemble the queens of many obligately parasitic ants that have evolutionarily lost the worker caste and live inside colonies of closely related hosts. The prevailing theory for the evolution of these workerless social parasites is that they evolve from reproductively isolated populations of facultative intermediates that acquire parasitic phenotypes in a stepwise fashion. However, empirical evidence for such facultative ancestors remains weak, and it is unclear how reproductive isolation could gradually arise in sympatry. In contrast, we isolated these variants just a few generations after they arose within their WT parent colony, implying that the complex phenotype reported here was induced in a single genetic step. This suggests that a single genetic module can decouple the coordinated mechanisms of caste development, allowing an obligately parasitic variant to arise directly from a free-living ancestor. Consistent with this hypothesis, the variants have lost one of the two alleles of a putative supergene that is heterozygous in WTs. These findings provide a plausible explanation for the evolution of ant social parasites and implicate new candidate molecular mechanisms for ant caste differentiation.
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Affiliation(s)
- Waring Trible
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; John Harvard Distinguished Science Fellowship Program, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
| | - Vikram Chandra
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Department of Organismic and Evolutionary Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Kip D Lacy
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Gina Limón
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Department of Microbiology, New York University School of Medicine, 430 E. 29th Street, New York, NY 10016, USA
| | - Sean K McKenzie
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Oxford Nanopore Technologies, Oxford OX4 4DQ, UK
| | - Leonora Olivos-Cisneros
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Samuel V Arsenault
- John Harvard Distinguished Science Fellowship Program, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA; Department of Organismic and Evolutionary Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Daniel J C Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, New York, NY 10065, USA.
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Marion SB, Noor MAF. Interrogating the Roles of Mutation-Selection Balance, Heterozygote Advantage, and Linked Selection in Maintaining Recessive Lethal Variation in Natural Populations. Annu Rev Anim Biosci 2023; 11:77-91. [PMID: 36315650 DOI: 10.1146/annurev-animal-050422-092520] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
For nearly a century, evolutionary biologists have observed chromosomes that cause lethality when made homozygous persisting at surprisingly high frequencies (>25%) in natural populations of many species. The evolutionary forces responsible for the maintenance of such detrimental mutations have been heavily debated-are some lethal mutations under balancing selection? We suggest that mutation-selection balance alone cannot explain lethal variation in nature and the possibility that other forces play a role. We review the potential that linked selection in particular may drive maintenance of lethal alleles through associative overdominance or linkage to beneficial mutations or by reducing effective population size. Over the past five decades, investigation into this mystery has tapered. During this time, key scientific advances have provided the ability to collect more accurate data and analyze them in new ways, making the underlying genetic bases and evolutionary forces of lethal alleles timely for study once more.
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Affiliation(s)
- Sarah B Marion
- Department of Biology, Duke University, Durham, North Carolina, USA; ,
| | - Mohamed A F Noor
- Department of Biology, Duke University, Durham, North Carolina, USA; ,
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36
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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.
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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:
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Rodriguero MS, Confalonieri VA, Mackay Smith A, Dornon MK, Zagoren E, Palmer A, Sequeira AS. Genetically Depauperate and Still Successful: Few Multilocus Genotypes of the Introduced Parthenogenetic Weevil Naupactus cervinus (Coleoptera: Curculionidae) Prevail in the Continental United States. INSECTS 2023; 14:113. [PMID: 36835682 PMCID: PMC9958569 DOI: 10.3390/insects14020113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Naupactus cervinus is a parthenogenetic weevil native to South America that is currently distributed worldwide. This flightless species is polyphagous and capable of modifying gene expression regimes for responding to stressful situations. Naupactus cervinus was first reported in the continental United States in 1879 and has rapidly colonized most of the world since. Previous studies suggested that an invader genotype successfully established even in areas of unsuitable environmental conditions. In the present work, we analyze mitochondrial and nuclear sequences from 71 individuals collected in 13 localities across three states in the southern US, in order to describe the genetic diversity in this area of introduction that has not yet been previously studied. Our results suggest that 97% of the samples carry the most prevalent invader genotype already reported, while the rest shows a close mitochondrial derivative. This would support the hypothesis of a general purpose genotype, with parthenogenesis and its associated lack of recombination maintaining the linkage of genetic variants capable of coping with adverse conditions and enlarging its geographical range. However, demographic advantages related to parthenogenetic reproduction as the main driver of geographic expansion (such as the foundation of a population with a single virgin female) cannot be ruled out. Given the historical introduction records and the prevalence of the invader genotype, it is possible that the continental US may act as a secondary source of introductions to other areas. We propose that both the parthenogenesis and scarce genetic variation in places of introduction may, in fact, be an asset that allows N. cervinus to thrive across a range of environmental conditions.
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Affiliation(s)
- Marcela S. Rodriguero
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires 1428, Argentina
- Instituto de Ecología, Genética y Evolución (IEGEBA), CONICET–Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires 1428, Argentina
| | - Viviana A. Confalonieri
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires 1428, Argentina
- Instituto de Ecología, Genética y Evolución (IEGEBA), CONICET–Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires 1428, Argentina
| | - Ava Mackay Smith
- Department of Biological Sciences, Wellesley College, Wellesley, MA 02481, USA
| | - Mary Kate Dornon
- Department of Biological Sciences, Wellesley College, Wellesley, MA 02481, USA
| | - Eleanor Zagoren
- Department of Biological Sciences, Wellesley College, Wellesley, MA 02481, USA
| | - Alice Palmer
- Department of Biological Sciences, Wellesley College, Wellesley, MA 02481, USA
| | - Andrea S. Sequeira
- Department of Biological Sciences, Wellesley College, Wellesley, MA 02481, USA
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38
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Zhao Z, Zhang Y, Shi M, Liu Z, Xu Y, Luo Z, Yuan S, Tu T, Sun Z, Zhang D, Barrett SCH. Genomic evidence supports the genetic convergence of a supergene controlling the distylous floral syndrome. THE NEW PHYTOLOGIST 2023; 237:601-614. [PMID: 36239093 DOI: 10.1111/nph.18540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Heterostyly, a plant sexual polymorphism controlled by the S-locus supergene, has evolved numerous times among angiosperm lineages and represents a classic example of convergent evolution in form and function. Determining whether underlying molecular convergence occurs could provide insights on constraints to floral evolution. Here, we investigated S-locus genes in distylous Gelsemium (Gelsemiaceae) to determine whether there is evidence of molecular convergence with unrelated distylous species. We used several approaches, including anatomical measurements of sex-organ development and transcriptome and whole-genome sequencing, to identify components of the S-locus supergene. We also performed evolutionary analysis with candidate S-locus genes and compared them with those reported in Primula and Turnera. The candidate S-locus supergene of Gelsemium contained four genes, of which three appear to have originated from gene duplication events within Gelsemiaceae. The style-length genes GeCYP in Gelsemium and CYP734A50 in Primula likely arose from duplication of the same gene, CYP734A1. Three out of four S-locus genes in Gelsemium elegans were hemizygous, as previously reported in Primula and Turnera. We provide genomic evidence on the genetic convergence of the supergene underlying distyly among distantly related angiosperm lineages and help to illuminate the genetic architecture involved in the evolution of heterostyly.
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Affiliation(s)
- Zhongtao Zhao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- College of Life Sciences, Gannan Normal University, Ganzhou, 34100, China
| | - Yu Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Miaomiao Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zhaoying Liu
- Hunan Engineering Technology Research Center of Veterinary Drugs, Hunan Agricultural University, Changsha, 410128, China
| | - Yuanqing Xu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zhonglai Luo
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Shuai Yuan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Tieyao Tu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zhiliang Sun
- Hunan Engineering Technology Research Center of Veterinary Drugs, Hunan Agricultural University, Changsha, 410128, China
| | - Dianxiang Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- College of Life Sciences, Gannan Normal University, Ganzhou, 34100, China
| | - Spencer C H Barrett
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
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39
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Singh P, Taborsky M, Peichel CL, Sturmbauer C. Genomic basis of Y-linked dwarfism in cichlids pursuing alternative reproductive tactics. Mol Ecol 2023; 32:1592-1607. [PMID: 36588349 DOI: 10.1111/mec.16839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 12/08/2022] [Accepted: 12/19/2022] [Indexed: 01/03/2023]
Abstract
Sexually antagonistic selection, which favours different optima in males and females, is predicted to play an important role in the evolution of sex chromosomes. Body size is a sexually antagonistic trait in the shell-brooding cichlid fish Lamprologous callipterus, as "bourgeois" males must be large enough to carry empty snail shells to build nests whereas females must be small enough to fit into shells for breeding. In this species, there is also a second male morph: smaller "dwarf" males employ an alternative reproductive strategy by wriggling past spawning females into shells to fertilize eggs. L. callipterus male morphology is passed strictly from father to son, suggesting Y-linkage. However, sex chromosomes had not been previously identified in this species, and the genomic basis of size dimorphism was unknown. Here we used whole-genome sequencing to identify a 2.4-Mb sex-linked region on scaffold_23 with reduced coverage and single nucleotide polymorphism density in both male morphs compared to females. Within this sex region, distinct Y-haplotypes delineate the two male morphs, and candidate genes for body size (GHRHR, a known dwarfism gene) and sex determination (ADCYAP1R1) are in high linkage disequilibrium. Because differences in body size between females and males are under strong selection in L. callipterus, we hypothesize that sexual antagonism over body size initiated early events in sex chromosome evolution, followed by Y divergence to give rise to bourgeois and dwarf male reproductive strategies. Our results are consistent with the hypothesis that sexually antagonistic traits should be linked to young sex chromosomes.
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Affiliation(s)
- Pooja Singh
- Institute of Biology, University of Graz, Graz, Austria.,Aquatic Ecology Division, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
| | - Michael Taborsky
- Behavioural Ecology Division, Institute of Ecology and Evolution, University of Bern, Switzerland.,Max Planck Institute of Animal Behavior, Constance, Germany.,Institute for Advanced Study (Wissenschaftskolleg) Berlin, Berlin, Germany
| | - Catherine L Peichel
- Evolutionary Ecology Division, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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40
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Sex-specific morphs: the genetics and evolution of intra-sexual variation. Nat Rev Genet 2023; 24:44-52. [PMID: 35971002 DOI: 10.1038/s41576-022-00524-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2022] [Indexed: 11/08/2022]
Abstract
Sex-specific morphs exhibit discrete phenotypes, often including many disparate traits, that are observed in only one sex. These morphs have evolved independently in many different animals and are often associated with alternative mating strategies. The remarkable diversity of sex-specific morphs offers unique opportunities to understand the genetic basis of complex phenotypes, as the distinct nature of many morphs makes it easier to both categorize and compare genomes than for continuous traits. Sex-specific morphs also expand the study of sexual dimorphism beyond traditional bimodal comparisons of male and female averages, as they allow for a more expansive range of sexualization. Although ecological and endocrinological studies of sex-specific morphs have been advancing for some time, genomic and transcriptomic studies of morphs are far more recent. These studies reveal not only many different paths to the evolution of sex-specific morphs but also many commonalities, such as the role of sex-determining genes and hormone signalling in morph development, and the mixing of male and female traits within some morphs.
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41
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Shipilina D, Näsvall K, Höök L, Vila R, Talavera G, Backström N. Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly. Genomics 2022; 114:110481. [PMID: 36115505 DOI: 10.1016/j.ygeno.2022.110481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 09/01/2022] [Accepted: 09/10/2022] [Indexed: 01/14/2023]
Abstract
Characterization of gene family expansions and crossing over is crucial for understanding how organisms adapt to the environment. Here, we develop a high-density linkage map and detailed genome annotation of the painted lady butterfly (Vanessa cardui) - a non-diapausing, highly polyphagous species famous for its long-distance migratory behavior and almost cosmopolitan distribution. Our results reveal a complex interplay between regional recombination rate variation, gene duplications and transposable element activity shaping the genome structure of the painted lady. We identify several lineage specific gene family expansions. Their functions are mainly associated with protein and fat metabolism, detoxification, and defense against infection - critical processes for the painted lady's unique life-history. Furthermore, the detailed recombination maps allow us to characterize the regional recombination landscape, data that reveal a strong effect of chromosome size on the recombination rate, a limited impact of GC-biased gene conversion and a positive association between recombination and short interspersed elements.
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Affiliation(s)
- Daria Shipilina
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden; Swedish Collegium for Advanced Study, Thunbergsvägen 2, 75236 Uppsala, Sweden.
| | - Karin Näsvall
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Lars Höök
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Roger Vila
- The Butterfly Diversity and Evolution Lab, Institut de Biologia Evolutiva, Passeig Martim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB), CSIC-Ajuntament de Barcelona, Passeig del Migdia s/n, 08038 Barcelona, Spain
| | - Niclas Backström
- Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
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Hollenbeck CM, Portnoy DS, Garcia de la Serrana D, Magnesen T, Matejusova I, Johnston IA. Temperature-associated selection linked to putative chromosomal inversions in king scallop ( Pecten maximus). Proc Biol Sci 2022; 289:20221573. [PMID: 36196545 PMCID: PMC9532988 DOI: 10.1098/rspb.2022.1573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The genomic landscape of divergence—the distribution of differences among populations or species across the genome—is increasingly characterized to understand the role that microevolutionary forces such as natural selection and recombination play in causing and maintaining genetic divergence. This line of inquiry has also revealed chromosome structure variation to be an important factor shaping the landscape of adaptive genetic variation. Owing to a high prevalence of chromosome structure variation and the strong pressure for local adaptation necessitated by their sessile nature, bivalve molluscs are an ideal taxon for exploring the relationship between chromosome structure variation and local adaptation. Here, we report a population genomic survey of king scallop (Pecten maximus) across its natural range in the northeastern Atlantic Ocean, using a recent chromosome-level genome assembly. We report the presence of at least three large (12–22 Mb), putative chromosomal inversions associated with sea surface temperature and whose frequencies are in contrast to neutral population structure. These results highlight a potentially large role for recombination-suppressing chromosomal inversions in local adaptation and suggest a hypothesis to explain the maintenance of differences in reproductive timing found at relatively small spatial scales across king scallop populations.
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Affiliation(s)
- Christopher M Hollenbeck
- Department of Life Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA.,Texas A&M AgriLife Research, College Station, TX, USA
| | - David S Portnoy
- Department of Life Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
| | - Daniel Garcia de la Serrana
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Thorolf Magnesen
- Department of Biological Sciences, University of Bergen, Thormøhlensgt 53B, Bergen, Norway
| | - Iveta Matejusova
- Marine Science Scotland, Marine Laboratory, 375 Victoria Road, Aberdeen AB11 9DB, UK
| | - Ian A Johnston
- Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, Fife KY16 8LB, UK.,Xelect Ltd, Horizon House, Abbey Walk, St Andrews KY16 9LB, UK
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Henning PM, Shore JS, McCubbin AG. The S-Gene YUC6 Pleiotropically Determines Male Mating Type and Pollen Size in Heterostylous Turnera (Passifloraceae): A Novel Neofunctionalization of the YUCCA Gene Family. PLANTS (BASEL, SWITZERLAND) 2022; 11:2640. [PMID: 36235506 PMCID: PMC9572539 DOI: 10.3390/plants11192640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/27/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
In heterostylous, self-incompatible Turnera species, a member of the YUCCA gene family, YUC6, resides at the S-locus and has been hypothesized to determine the male mating type. YUCCA gene family members synthesize the auxin, indole-3-acetic acid, via a two-step process involving the TAA gene family. Consequently, it has been speculated that differences in auxin concentration in developing anthers are the biochemical basis underlying the male mating type. Here, we provide empirical evidence that supports this hypothesis. Using a transgenic knockdown approach, we show that YUC6 acts pleiotropically to control both the male physiological mating type and pollen size, but not the filament length dimorphism associated with heterostyly in Turnera. Using qPCR to assess YUC6 expression in different transgenic lines, we demonstrate that the level of YUC6 knockdown correlates with the degree of change observed in the male mating type. Further assessment of YUC6 expression through anther development, in the knockdown lines, suggests that the male mating type is irreversibly determined during a specific developmental window prior to microsporogenesis, which is consistent with the genetically sporophytic nature of this self-incompatibility system. These results represent the first gene controlling male mating type to be characterized in any species with heterostyly.
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Affiliation(s)
- Paige M. Henning
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Joel S. Shore
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada
| | - Andrew G. McCubbin
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
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44
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Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level. Curr Biol 2022; 32:4360-4371.e6. [PMID: 36087578 DOI: 10.1016/j.cub.2022.08.042] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/23/2022]
Abstract
Supergenes govern multi-trait-balanced polymorphisms in a wide range of systems; however, our understanding of their origins and evolution remains incomplete. The reciprocal placement of stigmas and anthers in pin and thrum floral morphs of distylous species constitutes an iconic example of a balanced polymorphism governed by a supergene, the distyly S-locus. Recent studies have shown that the Primula and Turnera distyly supergenes are both hemizygous in thrums, but it remains unknown whether hemizygosity is pervasive among distyly S-loci. As hemizygosity has major consequences for supergene evolution and loss, clarifying whether this genetic architecture is shared among distylous species is critical. Here, we have characterized the genetic architecture and evolution of the distyly supergene in Linum by generating a chromosome-level genome assembly of Linum tenue, followed by the identification of the S-locus using population genomic data. We show that hemizygosity and thrum-specific expression of S-linked genes, including a pistil-expressed candidate gene for style length, are major features of the Linum S-locus. Structural variation is likely instrumental for recombination suppression, and although the non-recombining dominant haplotype has accumulated transposable elements, S-linked genes are not under relaxed purifying selection. Our findings reveal remarkable convergence in the genetic architecture and evolution of independently derived distyly supergenes, provide a counterexample to classic inversion-based supergenes, and shed new light on the origin and maintenance of an iconic floral polymorphism.
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45
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Arora UP, Dumont BL. Meiotic drive in house mice: mechanisms, consequences, and insights for human biology. Chromosome Res 2022; 30:165-186. [PMID: 35829972 PMCID: PMC9509409 DOI: 10.1007/s10577-022-09697-2] [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: 01/16/2022] [Revised: 04/20/2022] [Accepted: 04/27/2022] [Indexed: 11/27/2022]
Abstract
Meiotic drive occurs when one allele at a heterozygous site cheats its way into a disproportionate share of functional gametes, violating Mendel's law of equal segregation. This genetic conflict typically imposes a fitness cost to individuals, often by disrupting the process of gametogenesis. The evolutionary impact of meiotic drive is substantial, and the phenomenon has been associated with infertility and reproductive isolation in a wide range of organisms. However, cases of meiotic drive in humans remain elusive, a finding that likely reflects the inherent challenges of detecting drive in our species rather than unique features of human genome biology. Here, we make the case that house mice (Mus musculus) present a powerful model system to investigate the mechanisms and consequences of meiotic drive and facilitate translational inferences about the scope and potential mechanisms of drive in humans. We first detail how different house mouse resources have been harnessed to identify cases of meiotic drive and the underlying mechanisms utilized to override Mendel's rules of inheritance. We then summarize the current state of knowledge of meiotic drive in the mouse genome. We profile known mechanisms leading to transmission bias at several established drive elements. We discuss how a detailed understanding of meiotic drive in mice can steer the search for drive elements in our own species. Lastly, we conclude with a prospective look into how new technologies and molecular tools can help resolve lingering mysteries about the prevalence and mechanisms of selfish DNA transmission in mammals.
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Affiliation(s)
- Uma P Arora
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, 136 Harrison Ave, Boston, MA, 02111, USA
| | - Beth L Dumont
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA.
- Graduate School of Biomedical Sciences, Tufts University, 136 Harrison Ave, Boston, MA, 02111, USA.
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46
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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.
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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
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Abstract
Some of the most striking polymorphisms in nature are regulated by “supergenes,” which are clusters of tightly linked genes that coordinately control complex phenotypes. Here, we study the evolutionary history of a supergene regulating colony social organization in fire ants. We show that the three inversions constituting the social supergene emerged sequentially during the separation of the ancestral lineages of Solenopsis invicta and Solenopsis richteri. Once completely assembled in S. richteri, the supergene introgressed into multiple closely related species despite recent hybridization being uncommon between several of the species. These findings provide a rare and striking example of how introgression can lead to the rapid spread of a novel variant controlling complex traits. Supergenes are clusters of tightly linked genes that jointly produce complex phenotypes. Although widespread in nature, how such genomic elements are formed and how they spread are in most cases unclear. In the fire ant Solenopsis invicta and closely related species, a “social supergene controls whether a colony maintains one or multiple queens. Here, we show that the three inversions constituting the Social b (Sb) supergene emerged sequentially during the separation of the ancestral lineages of S. invicta and Solenopsis richteri. The two first inversions arose in the ancestral population of both species, while the third one arose in the S. richteri lineage. Once completely assembled in the S. richteri lineage, the supergene first introgressed into S. invicta, and from there into the other species of the socially polymorphic group of South American fire ant species. Surprisingly, the introgression of this large and important genomic element occurred despite recent hybridization being uncommon between several of the species. These results highlight how supergenes can readily move across species boundaries, possibly because of fitness benefits they provide and/or expression of selfish properties favoring their transmission.
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48
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Komata S, Kajitani R, Itoh T, Fujiwara H. Genomic architecture and functional unit of mimicry supergene in female limited Batesian mimic Papilio butterflies. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210198. [PMID: 35694751 PMCID: PMC9189499 DOI: 10.1098/rstb.2021.0198] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
It has long been suggested that dimorphic female-limited Batesian mimicry of two closely related Papilio butterflies, Papilio memnon and Papilio polytes, is controlled by supergenes. Whole-genome sequencing, genome-wide association studies and functional analyses have recently identified mimicry supergenes, including the doublesex (dsx) gene. Although supergenes of both the species are composed of highly divergent regions between mimetic and non-mimetic alleles and are located at the same chromosomal locus, they show critical differences in genomic architecture, particularly with or without an inversion: P. polytes has an inversion, but P. memnon does not. This review introduces and compares the detailed genomic structure of mimicry supergenes in two Papilio species, including gene composition, repetitive sequence composition, breakpoint/boundary site structure, chromosomal inversion and linkage disequilibrium. Expression patterns and functional analyses of the respective genes within or flanking the supergene suggest that dsx and other genes are involved in mimetic traits. In addition, structural comparison of the corresponding region for the mimicry supergene among further Papilio species suggests three scenarios for the evolution of the mimicry supergene between the two Papilio species. The structural features revealed in the Papilio mimicry supergene provide insight into the formation, maintenance and evolution of supergenes. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.
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Affiliation(s)
- Shinya Komata
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Rei Kajitani
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Haruhiko Fujiwara
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
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49
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Berdan EL, Flatt T, Kozak GM, Lotterhos KE, Wielstra B. Genomic architecture of supergenes: connecting form and function. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210192. [PMID: 35694757 PMCID: PMC9189501 DOI: 10.1098/rstb.2021.0192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Supergenes are tightly linked sets of loci that are inherited together and control complex phenotypes. While classical supergenes-governing traits such as wing patterns in Heliconius butterflies or heterostyly in Primula-have been studied since the Modern Synthesis, we still understand very little about how they evolve and persist in nature. The genetic architecture of supergenes is a critical factor affecting their evolutionary fate, as it can change key parameters such as recombination rate and effective population size, potentially redirecting molecular evolution of the supergene in addition to the surrounding genomic region. To understand supergene evolution, we must link genomic architecture with evolutionary patterns and processes. This is now becoming possible with recent advances in sequencing technology and powerful forward computer simulations. The present theme issue brings together theoretical and empirical papers, as well as opinion and synthesis papers, which showcase the architectural diversity of supergenes and connect this to critical processes in supergene evolution, such as polymorphism maintenance and mutation accumulation. Here, we summarize those insights to highlight new ideas and methods that illuminate the path forward for the study of supergenes in nature. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.
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Affiliation(s)
- Emma L Berdan
- Institute of Biology Leiden, Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands.,Naturalis Biodiversity Center, PO Box 9517, 2300 RA Leiden, The Netherlands.,Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, 45296 Strömstad, Sweden
| | - Thomas Flatt
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Genevieve M Kozak
- Department of Biology, University of Massachusetts Dartmouth, 285 Old Westport Road, MA 02747, USA
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University, 430 Nahant Road, Nahant, MA 01908, USA
| | - Ben Wielstra
- Institute of Biology Leiden, Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands.,Naturalis Biodiversity Center, PO Box 9517, 2300 RA Leiden, The Netherlands
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50
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Tafreshi AG, Otto SP, Chapuisat M. Unbalanced selection: the challenge of maintaining a social polymorphism when a supergene is selfish. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210197. [PMID: 35694754 PMCID: PMC9189496 DOI: 10.1098/rstb.2021.0197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Supergenes often have multiple phenotypic effects, including unexpected detrimental ones, because recombination suppression maintains associations among co-adapted alleles but also allows the accumulation of recessive deleterious mutations and selfish genetic elements. Yet, supergenes often persist over long evolutionary periods. How are such polymorphisms maintained in the face of selection, drive and drift? We present a population genetic model that investigates the conditions necessary for a stable polymorphic equilibrium when one of the supergene haplotypes is a selfish genetic element. The model fits the characteristics of the Alpine silver ant, Formica selysi, in which a large supergene underlies colony social organization, and one haplotype distorts Mendelian transmission by killing progeny that did not inherit it. The model shows that such maternal-effect killing strongly limits the maintenance of social polymorphism. Under random mating, transmission ratio distortion prevents rare single-queen colonies from invading populations of multiple-queen colonies, regardless of the fitness of each genotype. A stable polymorphic equilibrium can, however, be reached when high rates of assortative mating are combined with large fitness differences among supergene genotypes. The model reveals that the persistence of the social polymorphism is non-trivial and expected to occur only under restrictive conditions that deserve further empirical investigation. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.
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Affiliation(s)
- Alireza G Tafreshi
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Sarah P Otto
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Michel Chapuisat
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
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