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Cridland JM, Contino CE, Begun DJ. Selection and geography shape male reproductive tract transcriptomes in Drosophila melanogaster. Genetics 2023; 224:iyad034. [PMID: 36869688 PMCID: PMC10474930 DOI: 10.1093/genetics/iyad034] [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: 01/25/2023] [Revised: 01/25/2023] [Accepted: 02/20/2023] [Indexed: 03/05/2023] Open
Abstract
Transcriptome analysis of several animal clades suggests that male reproductive tract gene expression evolves quickly. However, the factors influencing the abundance and distribution of within-species variation, the ultimate source of interspecific divergence, are poorly known. Drosophila melanogaster, an ancestrally African species that has recently spread throughout the world and colonized the Americas in the last roughly 100 years, exhibits phenotypic and genetic latitudinal clines on multiple continents, consistent with a role for spatially varying selection in shaping its biology. Nevertheless, geographic expression variation in the Americas is poorly described, as is its relationship to African expression variation. Here, we investigate these issues through the analysis of two male reproductive tissue transcriptomes [testis and accessory gland (AG)] in samples from Maine (USA), Panama, and Zambia. We find dramatic differences between these tissues in differential expression between Maine and Panama, with the accessory glands exhibiting abundant expression differentiation and the testis exhibiting very little. Latitudinal expression differentiation appears to be influenced by the selection of Panama expression phenotypes. While the testis shows little latitudinal expression differentiation, it exhibits much greater differentiation than the accessory gland in Zambia vs American population comparisons. Expression differentiation for both tissues is non-randomly distributed across the genome on a chromosome arm scale. Interspecific expression divergence between D. melanogaster and D. simulans is discordant with rates of differentiation between D. melanogaster populations. Strongly heterogeneous expression differentiation across tissues and timescales suggests a complex evolutionary process involving major temporal changes in the way selection influences expression evolution in these organs.
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Affiliation(s)
- Julie M Cridland
- Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
| | - Colin E Contino
- Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
| | - David J Begun
- Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, 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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Normal segregation of a foreign-species chromosome during Drosophila female meiosis despite extensive heterochromatin divergence. Genetics 2014; 199:73-83. [PMID: 25406466 DOI: 10.1534/genetics.114.172072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The abundance and composition of heterochromatin changes rapidly between species and contributes to hybrid incompatibility and reproductive isolation. Heterochromatin differences may also destabilize chromosome segregation and cause meiotic drive, the non-Mendelian segregation of homologous chromosomes. Here we use a range of genetic and cytological assays to examine the meiotic properties of a Drosophila simulans chromosome 4 (sim-IV) introgressed into D. melanogaster. These two species differ by ∼12-13% at synonymous sites and several genes essential for chromosome segregation have experienced recurrent adaptive evolution since their divergence. Furthermore, their chromosome 4s are visibly different due to heterochromatin divergence, including in the AATAT pericentromeric satellite DNA. We find a visible imbalance in the positioning of the two chromosome 4s in sim-IV/mel-IV heterozygote and also replicate this finding with a D. melanogaster 4 containing a heterochromatic deletion. These results demonstrate that heterochromatin abundance can have a visible effect on chromosome positioning during meiosis. Despite this effect, however, we find that sim-IV segregates normally in both diplo and triplo 4 D. melanogaster females and does not experience elevated nondisjunction. We conclude that segregation abnormalities and a high level of meiotic drive are not inevitable byproducts of extensive heterochromatin divergence. Animal chromosomes typically contain large amounts of noncoding repetitive DNA that nevertheless varies widely between species. This variation may potentially induce non-Mendelian transmission of chromosomes. We have examined the meiotic properties and transmission of a highly diverged chromosome 4 from a foreign species within the fruitfly Drosophila melanogaster. This chromosome has substantially less of a simple sequence repeat than does D. melanogaster 4, and we find that this difference results in altered positioning when chromosomes align during meiosis. Yet this foreign chromosome segregates at normal frequencies, demonstrating that chromosome segregation can be robust to major differences in repetitive DNA abundance.
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Reinhardt JA, Brand CL, Paczolt KA, Johns PM, Baker RH, Wilkinson GS. Meiotic drive impacts expression and evolution of x-linked genes in stalk-eyed flies. PLoS Genet 2014; 10:e1004362. [PMID: 24832132 PMCID: PMC4022487 DOI: 10.1371/journal.pgen.1004362] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 03/25/2014] [Indexed: 12/22/2022] Open
Abstract
Although sex chromosome meiotic drive has been observed in a variety of species for over 50 years, the genes causing drive are only known in a few cases, and none of these cases cause distorted sex-ratios in nature. In stalk-eyed flies (Teleopsis dalmanni), driving X chromosomes are commonly found at frequencies approaching 30% in the wild, but the genetic basis of drive has remained elusive due to reduced recombination between driving and non-driving X chromosomes. Here, we used RNAseq to identify transcripts that are differentially expressed between males carrying either a driving X (XSR) or a standard X chromosome (XST), and found hundreds of these, the majority of which are X-linked. Drive-associated transcripts show increased levels of sequence divergence (dN/dS) compared to a control set, and are predominantly expressed either in testes or in the gonads of both sexes. Finally, we confirmed that XSR and XST are highly divergent by estimating sequence differentiation between the RNAseq pools. We found that X-linked transcripts were often strongly differentiated (whereas most autosomal transcripts were not), supporting the presence of a relatively large region of recombination suppression on XSR presumably caused by one or more inversions. We have identified a group of genes that are good candidates for further study into the causes and consequences of sex-chromosome drive, and demonstrated that meiotic drive has had a profound effect on sequence evolution and gene expression of X-linked genes in this species. Sex chromosome meiotic drive causes changes in the sex-ratios of natural populations, and may even lead to extinction if the driving element reaches high frequency. However, very little is known about the genes that cause sex-ratio drive, and no causal gene has been identified in a species that consistently exhibits distorted sex ratios in natural populations. Several species of stalk-eyed flies in southeast Asia – genus Teleopsis – express X chromosome drive, but the genes underlying drive have been difficult to locate due to reduced recombination between drive and standard X chromosomes presumably caused by the presence of a large inversion. Here, we use high throughput RNA sequencing to identify over 500 transcripts that are differentially expressed in the testes due to the effects of a driving X chromosome (XSR) in T. dalmanni. Most of these are X-linked, evolve more rapidly than control genes, and exhibit elevated expression in the gonads. Finally, XSR has become genetically differentiated from standard X chromosomes – using the RNA sequence data, we found nearly 1000 sites in X-linked transcripts and only a handful in autosomal transcripts where there was a fixed nucleotide difference. We conclude that XSR has led to widespread sequence and expression divergence on the X chromosome in T. dalmanni.
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Affiliation(s)
- Josephine A. Reinhardt
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
| | - Cara L. Brand
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Kimberly A. Paczolt
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
| | - Philip M. Johns
- Bard College, Annadale-on-Hudson, New York, United States of America
| | - Richard H. Baker
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - Gerald S. Wilkinson
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
- * E-mail:
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Corbett-Detig RB, Hartl DL. Population genomics of inversion polymorphisms in Drosophila melanogaster. PLoS Genet 2012; 8:e1003056. [PMID: 23284285 PMCID: PMC3527211 DOI: 10.1371/journal.pgen.1003056] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 09/06/2012] [Indexed: 12/22/2022] Open
Abstract
Chromosomal inversions have been an enduring interest of population geneticists since their discovery in Drosophila melanogaster. Numerous lines of evidence suggest powerful selective pressures govern the distributions of polymorphic inversions, and these observations have spurred the development of many explanatory models. However, due to a paucity of nucleotide data, little progress has been made towards investigating selective hypotheses or towards inferring the genealogical histories of inversions, which can inform models of inversion evolution and suggest selective mechanisms. Here, we utilize population genomic data to address persisting gaps in our knowledge of D. melanogaster's inversions. We develop a method, termed Reference-Assisted Reassembly, to assemble unbiased, highly accurate sequences near inversion breakpoints, which we use to estimate the age and the geographic origins of polymorphic inversions. We find that inversions are young, and most are African in origin, which is consistent with the demography of the species. The data suggest that inversions interact with polymorphism not only in breakpoint regions but also chromosome-wide. Inversions remain differentiated at low levels from standard haplotypes even in regions that are distant from breakpoints. Although genetic exchange appears fairly extensive, we identify numerous regions that are qualitatively consistent with selective hypotheses. Finally, we show that In(1)Be, which we estimate to be ∼60 years old (95% CI 5.9 to 372.8 years), has likely achieved high frequency via sex-ratio segregation distortion in males. With deeper sampling, it will be possible to build on our inferences of inversion histories to rigorously test selective models-particularly those that postulate that inversions achieve a selective advantage through the maintenance of co-adapted allele complexes.
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Affiliation(s)
- Russell B Corbett-Detig
- Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.
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Surprising differences in the variability of Y chromosomes in African and cosmopolitan populations of Drosophila melanogaster. Genetics 2012; 193:201-14. [PMID: 23086221 DOI: 10.1534/genetics.112.146167] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The nonrecombining Drosophila melanogaster Y chromosome is heterochromatic and has few genes. Despite these limitations, there remains ample opportunity for natural selection to act on the genes that are vital for male fertility and on Y factors that modulate gene expression elsewhere in the genome. Y chromosomes of many organisms have low levels of nucleotide variability, but a formal survey of D. melanogaster Y chromosome variation had yet to be performed. Here we surveyed Y-linked variation in six populations of D. melanogaster spread across the globe. We find surprisingly low levels of variability in African relative to Cosmopolitan (i.e., non-African) populations. While the low levels of Cosmopolitan Y chromosome polymorphism can be explained by the demographic histories of these populations, the staggeringly low polymorphism of African Y chromosomes cannot be explained by demographic history. An explanation that is entirely consistent with the data is that the Y chromosomes of Zimbabwe and Uganda populations have experienced recent selective sweeps. Interestingly, the Zimbabwe and Uganda Y chromosomes differ: in Zimbabwe, a European Y chromosome appears to have swept through the population.
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Abstract
Theories to explain the prevalence of sex and recombination have long been a central theme of evolutionary biology. Yet despite decades of attention dedicated to the evolution of sex and recombination, the widespread pattern of sex differences in the recombination rate is not well understood and has received relatively little theoretical attention. Here, we argue that female meiotic drivers--alleles that increase in frequency by exploiting the asymmetric cell division of oogenesis--present a potent selective pressure favoring the modification of the female recombination rate. Because recombination plays a central role in shaping patterns of variation within and among dyads, modifiers of the female recombination rate can function as potent suppressors or enhancers of female meiotic drive. We show that when female recombination modifiers are unlinked to female drivers, recombination modifiers that suppress harmful female drive can spread. By contrast, a recombination modifier tightly linked to a driver can increase in frequency by enhancing female drive. Our results predict that rapidly evolving female recombination rates, particularly around centromeres, should be a common outcome of meiotic drive. We discuss how selection to modify the efficacy of meiotic drive may contribute to commonly observed patterns of sex differences in recombination.
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Seidel HS, Rockman MV, Kruglyak L. Widespread genetic incompatibility in C. elegans maintained by balancing selection. Science 2008; 319:589-94. [PMID: 18187622 PMCID: PMC2421010 DOI: 10.1126/science.1151107] [Citation(s) in RCA: 203] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Natural selection is expected to eliminate genetic incompatibilities from interbreeding populations. We have discovered a globally distributed incompatibility in the primarily selfing species Caenorhabditis elegans that has been maintained despite its negative consequences for fitness. Embryos homozygous for a naturally occurring deletion of the zygotically acting gene zeel-1 arrest if their sperm parent carries an incompatible allele of a second, paternal-effect locus, peel-1. The two interacting loci are tightly linked, with incompatible alleles occurring in linkage disequilibrium in two common haplotypes. These haplotypes exhibit elevated sequence divergence, and population genetic analyses of this region indicate that natural selection is preserving both haplotypes in the population. Our data suggest that long-term maintenance of a balanced polymorphism has permitted the incompatibility to persist despite gene flow across the rest of the genome.
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Affiliation(s)
- Hannah S Seidel
- Lewis-Sigler Institute for Integrative Genomics and Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
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Tishkoff SA, Reed FA, Ranciaro A, Voight BF, Babbitt CC, Silverman JS, Powell K, Mortensen HM, Hirbo JB, Osman M, Ibrahim M, Omar SA, Lema G, Nyambo TB, Ghori J, Bumpstead S, Pritchard JK, Wray GA, Deloukas P. Convergent adaptation of human lactase persistence in Africa and Europe. Nat Genet 2006; 39:31-40. [PMID: 17159977 PMCID: PMC2672153 DOI: 10.1038/ng1946] [Citation(s) in RCA: 831] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2006] [Accepted: 11/20/2006] [Indexed: 12/29/2022]
Abstract
A SNP in the gene encoding lactase (LCT) (C/T-13910) is associated with the ability to digest milk as adults (lactase persistence) in Europeans, but the genetic basis of lactase persistence in Africans was previously unknown. We conducted a genotype-phenotype association study in 470 Tanzanians, Kenyans and Sudanese and identified three SNPs (G/C-14010, T/G-13915 and C/G-13907) that are associated with lactase persistence and that have derived alleles that significantly enhance transcription from the LCT promoter in vitro. These SNPs originated on different haplotype backgrounds from the European C/T-13910 SNP and from each other. Genotyping across a 3-Mb region demonstrated haplotype homozygosity extending >2.0 Mb on chromosomes carrying C-14010, consistent with a selective sweep over the past approximately 7,000 years. These data provide a marked example of convergent evolution due to strong selective pressure resulting from shared cultural traits-animal domestication and adult milk consumption.
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Affiliation(s)
- Sarah A Tishkoff
- Department of Biology, University of Maryland, College Park, Maryland 20742, USA.
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Reed FA, Tishkoff SA. Positive selection can create false hotspots of recombination. Genetics 2006; 172:2011-4. [PMID: 16387873 PMCID: PMC1456281 DOI: 10.1534/genetics.105.052183] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2005] [Accepted: 12/23/2005] [Indexed: 11/18/2022] Open
Abstract
Simulations of positive directional selection, under parameter values appropriate for approximating human genetic diversity and rates of recombination, reveal that the effects of strong selective sweeps on patterns of linkage disequilibrium (LD) mimic the pattern expected with recombinant hotspots.
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Affiliation(s)
- Floyd A Reed
- Department of Biology, University of Maryland, College Park, Maryland 20742, USA.
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