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Kitano J, Yoshida K. Do sex-linked male meiotic drivers contribute to intrinsic hybrid incompatibilities? Recent empirical studies from flies and rodents. Curr Opin Genet Dev 2023; 81:102068. [PMID: 37354886 DOI: 10.1016/j.gde.2023.102068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/29/2023] [Accepted: 05/29/2023] [Indexed: 06/26/2023]
Abstract
Intrinsic hybrid incompatibility is one of the important isolating barriers between species. In organisms with sex chromosomes, intrinsic hybrid incompatibility often follows two rules: Haldane's rule and large-X effects. One explanation for these two rules is that sex chromosomes are hotspots for meiotic drivers that can cause intrinsic hybrid incompatibility between geographically isolated populations. Although this hypothesis seems plausible and several empirical data are consistent with it, we are still unsure whether such mechanisms occur in nature, particularly with respect to speciation with gene flow. Here, we review empirical studies that have investigated the roles of meiotic drive in sex-chromosome evolution and speciation and propose future studies necessary for testing this hypothesis.
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Affiliation(s)
- Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima 1111, Shizuoka 411-8540, Japan.
| | - Kohta Yoshida
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima 1111, Shizuoka 411-8540, Japan; Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany. https://twitter.com/PristionXY
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2
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Reinhardt JA, Baker RH, Zimin AV, Ladias C, Paczolt KA, Werren JH, Hayashi CY, Wilkinson GS. Impacts of Sex Ratio Meiotic Drive on Genome Structure and Function in a Stalk-Eyed Fly. Genome Biol Evol 2023; 15:evad118. [PMID: 37364298 PMCID: PMC10319772 DOI: 10.1093/gbe/evad118] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 06/02/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023] Open
Abstract
Stalk-eyed flies in the genus Teleopsis carry selfish genetic elements that induce sex ratio (SR) meiotic drive and impact the fitness of male and female carriers. Here, we assemble and describe a chromosome-level genome assembly of the stalk-eyed fly, Teleopsis dalmanni, to elucidate patterns of divergence associated with SR. The genome contains tens of thousands of transposable element (TE) insertions and hundreds of transcriptionally and insertionally active TE families. By resequencing pools of SR and ST males using short and long reads, we find widespread differentiation and divergence between XSR and XST associated with multiple nested inversions involving most of the SR haplotype. Examination of genomic coverage and gene expression data revealed seven X-linked genes with elevated expression and coverage in SR males. The most extreme and likely drive candidate involves an XSR-specific expansion of an array of partial copies of JASPer, a gene necessary for maintenance of euchromatin and associated with regulation of TE expression. In addition, we find evidence for rapid protein evolution between XSR and XST for testis expressed and novel genes, that is, either recent duplicates or lacking a Dipteran ortholog, including an X-linked duplicate of maelstrom, which is also involved in TE silencing. Overall, the evidence suggests that this ancient XSR polymorphism has had a variety of impacts on repetitive DNA and its regulation in this species.
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Affiliation(s)
| | - Richard H Baker
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Aleksey V Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Chloe Ladias
- Biology Department, State University of New York at Geneseo, Geneseo, New York, USA
| | - Kimberly A Paczolt
- Department of Biology, University of Maryland, College Park, Maryland, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, New York, USA
| | - Cheryl Y Hayashi
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Gerald S Wilkinson
- Department of Biology, University of Maryland, College Park, Maryland, USA
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Kopania EEK, Watson EM, Rathje CC, Skinner BM, Ellis PJI, Larson EL, Good JM. The contribution of sex chromosome conflict to disrupted spermatogenesis in hybrid house mice. Genetics 2022; 222:iyac151. [PMID: 36194004 PMCID: PMC9713461 DOI: 10.1093/genetics/iyac151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/27/2022] [Indexed: 12/13/2022] Open
Abstract
Incompatibilities on the sex chromosomes are important in the evolution of hybrid male sterility, but the evolutionary forces underlying this phenomenon are unclear. House mice (Mus musculus) lineages have provided powerful models for understanding the genetic basis of hybrid male sterility. X chromosome-autosome interactions cause strong incompatibilities in M. musculus F1 hybrids, but variation in sterility phenotypes suggests a more complex genetic basis. In addition, XY chromosome conflict has resulted in rapid expansions of ampliconic genes with dosage-dependent expression that is essential to spermatogenesis. Here, we evaluated the contribution of XY lineage mismatch to male fertility and stage-specific gene expression in hybrid mice. We performed backcrosses between two house mouse subspecies to generate reciprocal Y-introgression strains and used these strains to test the effects of XY mismatch in hybrids. Our transcriptome analyses of sorted spermatid cells revealed widespread overexpression of the X chromosome in sterile F1 hybrids independent of Y chromosome subspecies origin. Thus, postmeiotic overexpression of the X chromosome in sterile F1 mouse hybrids is likely a downstream consequence of disrupted meiotic X-inactivation rather than XY gene copy number imbalance. Y chromosome introgression did result in subfertility phenotypes and disrupted expression of several autosomal genes in mice with an otherwise nonhybrid genomic background, suggesting that Y-linked incompatibilities contribute to reproductive barriers, but likely not as a direct consequence of XY conflict. Collectively, these findings suggest that rapid sex chromosome gene family evolution driven by genomic conflict has not resulted in strong male reproductive barriers between these subspecies of house mice.
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Affiliation(s)
- Emily E K Kopania
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Eleanor M Watson
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Claudia C Rathje
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | | | - Peter J I Ellis
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Erica L Larson
- Department of Biological Sciences, University of Denver, Denver, CO 80208, USA
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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Patten MM. Selfish X chromosomes and speciation. Mol Ecol 2018; 27:3772-3782. [PMID: 29281152 DOI: 10.1111/mec.14471] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 11/29/2017] [Accepted: 12/11/2017] [Indexed: 12/24/2022]
Abstract
In two papers published at about the same time almost thirty years ago, Frank (Evolution, 45, 1991a, 262) and Hurst and Pomiankowski (Genetics, 128, 1991, 841) independently suggested that divergence of meiotic drive systems-comprising genes that cheat meiosis and genes that suppress this cheating-might provide a general explanation for Haldane's rule and the large X-effect in interspecific hybrids. Although at the time, the idea was met with skepticism and a conspicuous absence of empirical support, the tide has since turned. Some of the clearest mechanistic explanations we have for hybrid male sterility involve meiotic drive systems, and several other cases of hybrid sterility are suggestive of a role for meiotic drive. In this article, I review these ideas and their descendants and catalog the current evidence for the meiotic drive model of speciation. In addition, I suggest that meiotic drive is not the only intragenomic conflict to involve the X chromosome and contribute to hybrid incompatibility. Sexually and parentally antagonistic selection pressures can also pit the X chromosome and autosomes against each other. The resulting intragenomic conflicts should lead to co-evolution within populations and divergence between them, thus increasing the likelihood of incompatibilities in hybrids. I provide a sketch of these ideas and interpret some empirical patterns in the light of these additional X-autosome conflicts.
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Affiliation(s)
- Manus M Patten
- Department of Biology, Georgetown University, Washington, DC, USA
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Paczolt KA, Reinhardt JA, Wilkinson GS. Contrasting patterns of X-chromosome divergence underlie multiple sex-ratio polymorphisms in stalk-eyed flies. J Evol Biol 2017; 30:1772-1784. [PMID: 28688201 DOI: 10.1111/jeb.13140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 06/27/2017] [Accepted: 07/04/2017] [Indexed: 11/28/2022]
Abstract
Sex-linked segregation distorters cause offspring sex ratios to differ from equality. Theory predicts that such selfish alleles may either go to fixation and cause extinction, reach a stable polymorphism or initiate an evolutionary arms race with genetic modifiers. The extent to which a sex ratio distorter follows any of these trajectories in nature is poorly known. Here, we used X-linked sequence and simple tandem repeat data for three sympatric species of stalk-eyed flies (Teleopsis whitei and two cryptic species of T. dalmanni) to infer the evolution of distorting X chromosomes. By screening large numbers of field and recently laboratory-bred flies, we found no evidence of males with strongly female-biased sex ratio phenotypes (SR) in one species but high frequencies of SR males in the other two species. In the two species with SR males, we find contrasting patterns of X-chromosome evolution. T. dalmanni-1 shows chromosome-wide differences between sex-ratio (XSR ) and standard (XST ) X chromosomes consistent with a relatively old sex-ratio haplotype based on evidence including genetic divergence, an inversion polymorphism and reduced recombination among XSR chromosomes relative to XST chromosomes. In contrast, we found no evidence of genetic divergence on the X between males with female-biased and nonbiased sex ratios in T. whitei. Taken with previous studies that found evidence of genetic suppression of sex ratio distortion in this clade, our results illustrate that sex ratio modification in these flies is undergoing recurrent evolution with diverse genomic consequences.
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Affiliation(s)
- K A Paczolt
- Department of Biology, University of Maryland College Park, College Park, MD, USA
| | - J A Reinhardt
- Department of Biology, SUNY Geneseo, Geneseo, NY, USA
| | - G S Wilkinson
- Department of Biology, University of Maryland College Park, College Park, MD, USA
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Delph LF, Demuth JP. Haldane’s Rule: Genetic Bases and Their Empirical Support. J Hered 2016; 107:383-91. [DOI: 10.1093/jhered/esw026] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/27/2016] [Indexed: 11/14/2022] Open
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Lindholm AK, Dyer KA, Firman RC, Fishman L, Forstmeier W, Holman L, Johannesson H, Knief U, Kokko H, Larracuente AM, Manser A, Montchamp-Moreau C, Petrosyan VG, Pomiankowski A, Presgraves DC, Safronova LD, Sutter A, Unckless RL, Verspoor RL, Wedell N, Wilkinson GS, Price TA. The Ecology and Evolutionary Dynamics of Meiotic Drive. Trends Ecol Evol 2016; 31:315-326. [DOI: 10.1016/j.tree.2016.02.001] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/29/2016] [Accepted: 02/01/2016] [Indexed: 12/24/2022]
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Baker RH, Narechania A, DeSalle R, Johns PM, Reinhardt JA, Wilkinson GS. Spermatogenesis Drives Rapid Gene Creation and Masculinization of the X Chromosome in Stalk-Eyed Flies (Diopsidae). Genome Biol Evol 2016; 8:896-914. [PMID: 26951781 PMCID: PMC4824122 DOI: 10.1093/gbe/evw043] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Throughout their evolutionary history, genomes acquire new genetic material that facilitates phenotypic innovation and diversification. Developmental processes associated with reproduction are particularly likely to involve novel genes. Abundant gene creation impacts the evolution of chromosomal gene content and general regulatory mechanisms such as dosage compensation. Numerous studies in model organisms have found complex and, at times contradictory, relationships among these genomic attributes highlighting the need to examine these patterns in other systems characterized by abundant sexual selection. Therefore, we examined the association among novel gene creation, tissue-specific gene expression, and chromosomal gene content within stalk-eyed flies. Flies in this family are characterized by strong sexual selection and the presence of a newly evolved X chromosome. We generated RNA-seq transcriptome data from the testes for three species within the family and from seven additional tissues in the highly dimorphic species, Teleopsis dalmanni. Analysis of dipteran gene orthology reveals dramatic testes-specific gene creation in stalk-eyed flies, involving numerous gene families that are highly conserved in other insect groups. Identification of X-linked genes for the three species indicates that the X chromosome arose prior to the diversification of the family. The most striking feature of this X chromosome is that it is highly masculinized, containing nearly twice as many testes-specific genes as expected based on its size. All the major processes that may drive differential sex chromosome gene content—creation of genes with male-specific expression, development of male-specific expression from pre-existing genes, and movement of genes with male-specific expression—are elevated on the X chromosome of T. dalmanni. This masculinization occurs despite evidence that testes expressed genes do not achieve the same levels of gene expression on the X chromosome as they do on the autosomes.
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Affiliation(s)
- Richard H Baker
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY
| | - Apurva Narechania
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY
| | - Philip M Johns
- Life Sciences Department, Yale-NUS College, Singapore, Singapore
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