Gene flow mediates the role of sex chromosome meiotic drive during complex speciation

During speciation, sex chromosomes often accumulate interspecific genetic incompatibilities faster than the rest of the genome. The drive theory posits that sex chromosomes are susceptible to recurrent bouts of meiotic drive and suppression, causing the evolutionary build- up of divergent cryptic sex-linked drive systems and, incidentally, genetic incompatibilities. To assess the role of drive during speciation, we combine high-resolution genetic mapping of X-linked hybrid male sterility with population genomics analyses of divergence and recent gene flow between the fruitfly species, Drosophila mauritiana and D. simulans. Our findings reveal a high density of genetic incompatibilities and a corresponding dearth of gene flow on the X chromosome. Surprisingly, we find that a known drive element recently migrated between species and, rather than contributing to interspecific divergence, caused a strong reduction in local sequence divergence, undermining the evolution of hybrid sterility. Gene flow can therefore mediate the effects of selfish genetic elements during speciation

Evolutionary genomics of piRNA mediated transposon silencing in Drosophila

Thesis (Ph. D.)--University of Rochester. Department of Biology, 2016.Transposable elements (TEs) are abundant throughout the genomes of most living organisms. A recently identified piwi-interacting RNA (piRNA) pathway has been shown to defend against TEs in the Drosophila germline. This dissertation research is an evolutionary genomic analysis of the piRNA pathway in closely related Drosophila species. In Chapter 1, we characterize the rate of evolution for proteins affecting 26 RNAi knockdown phenotypes, which include three phenotypes related to regulation of transposon integration. When RNAi phenotypes are grouped into categories according to cellular function, we find that genes involved in the greatest number of phenotypic categories are also significantly more likely to have a history of rapid protein evolution. Defining pleiotropy using phenotypic categories yields different results than studies that define pleiotropy based on physical interactions. In Chapter 2, we characterize the expression diversity of several families of TEs using piRNAs. Comparative genomic analysis of piRNA expression finds dynamic changes in expression levels of several families of TEs in D. melanogaster and the D. simulans clade. Measuring ping-pong activity— a signature of piRNA amplification finds higher mean piRNA amplification in D. simulans and D. mauritiana, suggesting increased activity of several TEs in these species compared to D. melanogaster. Furthermore, McDonald-Kreitman tests identify three genes in the piRNA pathway as having experienced recent positive selection in D. simulans, and one gene each in D. melanogaster and D. mauritiana. All four genes are components of nuage, which is a macromolecular complex that mediate protein-protein and protein-RNA interactions. Our results are consistent with a model of antagonistic co-evolution between TEs and the piRNA pathway. In Chapter 3, we use single-molecule sequencing to perform a detailed comparative analysis of the flamenco piRNA cluster in both D. melanogaster and D. mauritiana. Our analysis reveals that there is very little sequence homology of flamenco between the two species, indicating rapid turnover of TE sequence. Furthermore, spatial heterogeneity in piRNA abundance in the flamenco region identifies two putative piRNA clusters adjacent to flamenco that may be functionally distinct. This study is the first practical demonstration of re-constructing the genome sequence of highly repetitive piRNA clusters in closely related Drosophila species

Gene flow mediates the role of sex chromosome meiotic drive during complex speciation

During speciation, sex chromosomes often accumulate interspecific genetic incompatibilities faster than the rest of the genome. The drive theory posits that sex chromosomes are susceptible to recurrent bouts of meiotic drive and suppression, causing the evolutionary build- up of divergent cryptic sex-linked drive systems and, incidentally, genetic incompatibilities. To assess the role of drive during speciation, we combine high-resolution genetic mapping of X-linked hybrid male sterility with population genomics analyses of divergence and recent gene flow between the fruitfly species, Drosophila mauritiana and D. simulans. Our findings reveal a high density of genetic incompatibilities and a corresponding dearth of gene flow on the X chromosome. Surprisingly, we find that a known drive element recently migrated between species and, rather than contributing to interspecific divergence, caused a strong reduction in local sequence divergence, undermining the evolution of hybrid sterility. Gene flow can therefore mediate the effects of selfish genetic elements during speciation

Data from: Gene flow mediates the role of sex chromosome meiotic drive during complex speciation

During speciation, sex chromosomes often accumulate interspecific genetic incompatibilities faster than the rest of the genome. The drive theory posits that sex chromosomes are susceptible to recurrent bouts of meiotic drive and suppression, causing the evolutionary build-up of divergent cryptic sex-linked drive systems and, incidentally, genetic incompatibilities. To assess the role of drive during speciation, we combine high-resolution genetic mapping of X-linked hybrid male sterility with population genomics analyses of divergence and recent gene flow between the fruitfly species, Drosophila mauritiana and D. simulans. Our findings reveal a high density of genetic incompatibilities and a corresponding dearth of gene flow on the X chromosome. Surprisingly, we find that a known drive element recently migrated between species and, rather than contributing to interspecific divergence, caused a strong reduction in local sequence divergence, undermini ng the evolution of hybrid sterility. Gene flow can therefore mediate the effects of selfish genetic elements during speciation

The m⁶A Pathway Facilitates Sex Determination in Drosophila

The conserved modification N⁶-methyladenosine (m⁶A) modulates mRNA processing and activity. Here, we establish the Drosophila system to study the m⁶A pathway. We first apply miCLIP to map m 6 A across embryogenesis, characterize its m⁶A 'writer' complex, validate its YTH 'readers' CG6422 and YT521-B, and generate mutants in five m⁶A factors. While m⁶A factors with additional roles in splicing are lethal, m⁶A-specific mutants are viable but present certain developmental and behavioural defects. Notably, m⁶A facilitates the master female determinant Sxl, since multiple m⁶A components enhance female lethality in Sxl sensitized backgrounds. The m⁶A pathway regulates Sxl processing directly, since miCLIP data reveal Sxl as a major intronic m⁶A target, and female-specific Sxl splicing is compromised in multiple m⁶A pathway mutants. YT521-B is a dominant m⁶A effector for Sxl regulation, and YT521-B overexpression can induce female-specific Sxl splicing. Overall, our transcriptomic and genetic toolkit reveals in vivo biologic function for the Drosophila m⁶A pathway