Master of Science

thesisThe chromosomal inversions of D. persimilis and D. pseudoobscura have deeply influenced our understanding of the evolutionary forces that shape natural variation, speciation, and selfish chromosome dynamics. Here, we perform a comprehensive reconstruction of the evolutionary histories of the chromosomal inversions in these species and provide a solution to the puzzling origins of the selfish Sex-Ratio chromosome in D. persimilis. We show that this Sex-Ratio chromosome directly descends from an ancestrally-arranged chromosome, suggesting that unsuppressed selfish chromosomes may remain polymorphic within populations for long periods of time. We further show that all fixed inversions between D. persimilis and D. pseudoobscura were segregating in the ancestral population long before speciation, and that the genes contributing to reproductive barriers must have evolved within them afterwards. We propose a new model for the role of chromosomal inversions in speciation and suggest that higher levels of divergence and an over-abundance of hybrid incompatibilities are emergent properties of ancestrally segregating inversions. Our findings force a reconsideration of the role of chromosomal inversions in speciation, not as a protector of existing hybrid incompatibility alleles, but as fertile ground for their formation

Large-Scale Selective Sweep among Segregation Distorter Chromosomes in African Populations of Drosophila melanogaster

Segregation Distorter (SD) is a selfish, coadapted gene complex on chromosome 2 of Drosophila melanogaster that strongly distorts Mendelian transmission; heterozygous SD/SD+ males sire almost exclusively SD-bearing progeny. Fifty years of genetic, molecular, and theory work have made SD one of the best-characterized meiotic drive systems, but surprisingly the details of its evolutionary origins and population dynamics remain unclear. Earlier analyses suggested that the SD system arose recently in the Mediterranean basin and then spread to a low, stable equilibrium frequency (1–5%) in most natural populations worldwide. In this report, we show, first, that SD chromosomes occur in populations in sub-Saharan Africa, the ancestral range of D. melanogaster, at a similarly low frequency (∼2%), providing evidence for the robustness of its equilibrium frequency but raising doubts about the Mediterranean-origins hypothesis. Second, our genetic analyses reveal two kinds of SD chromosomes in Africa: inversion-free SD chromosomes with little or no transmission advantage; and an African-endemic inversion-bearing SD chromosome, SD-Mal, with a perfect transmission advantage. Third, our population genetic analyses show that SD-Mal chromosomes swept across the African continent very recently, causing linkage disequilibrium and an absence of variability over 39% of the length of the second chromosome. Thus, despite a seemingly stable equilibrium frequency, SD chromosomes continue to evolve, to compete with one another, or evade suppressors in the genome

Transposable element control disrupted by meiotic drive in a stalk-eyed fly genome

Some 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 produce a chromosome-level genome assembly of the stalk-eyed fly, T. dalmanni, to elucidate the pattern of genomic divergence associated with the presence of drive elements. We find evidence for multiple nested inversions along the sex ratio haplotype and widespread differentiation and divergence between the inversion types along the entire X chromosome. In addition, the genome contains tens of thousands of transposable element (TE) insertions and hundreds of transcriptionally active TE families that have produced new insertions. Moreover, we find that many TE families are expressed at a significantly higher level in SR male testis, suggesting a molecular connection between these two types of selfish genetic elements in this species. We identify T. dalmanni orthologs of genes involved in genome defense via the piRNA pathway, including core members maelstrom, piwi and Argonaute3, that are diverging in sequence, expression or copy number between the SR and standard (ST) chromosomes, and likely influence TE regulation in flies carrying a sex ratio X chromosome

Evolutionary Conservation of a Modified Spermatogenesis Program in Rhabditis Nematodes with Skewed Sex Ratios

The cellular divisions in Rhabditis sp. SB347 male spermatogenesis have been modified to re-purpose an asymmetric division. This results in the dramatically skewed sex ratios observed in the progeny of males of this species. Here we confirm this asymmetry in the division of tubulin and major sperm protein (MSP). MSP, a necessary sperm component, is segregated exclusively into spermatids bearing the X chromosome while tubulin is segregated into the nullo-X sperm. Timing of the partitioning events reveals that MSP migration is not directly dependent on tubulin spindle asymmetry. Additionally, the endoplasmic reticulum is also segregated asymmetrically to the nullo-X spermatid during the partitioning phase of spermatogenesis. This results in only the X-bearing spermatids being functional, and thus the exclusive production of feminine offspring. This pattern of asymmetry appears to not be isolated to SB347. We investigated several other species in the Rhabditis clade including SB372, JU1809, and JU1782. Using MSP and tubulin as markers, each species was noted to display asymmetric divisions very similar to those in SB347. This corresponds with data suggesting that these species demonstrate similar skews in the sex ratios of offspring (Pires daSilva, unpublished). Not only do these species display unusual cellular divisions, but the size of the spermatids is greatly diminished compared to other closely related nematodes that have been studied. These two features make the species in the Rhabditis clade interesting subjects of study. They may serve as models to bolster our current understanding of cellular polarization in spermatogenesis and the mechanisms of distinction between residual body and spermatid. They may also yield important insights into the evolution of sex and gamete size. Lastly, evidence suggests that the non-functional sperm, lacking the X chromosome, produced by Rhabditis sp. SB347 form large clusters in the male gonad. The fate of these aggregates is unknown, but they appear to be removed from the spermatid population. This draws some parallels to the apoptotic fate of the residual body in C. elegans. Study of the Rhabditis nematodes is just beginning, but it promises some interesting findings and novel insights into nematode biology

Integrative genomic analysis of sporadic colorectal cancer

Inherited genetic mutations cause a small percentage of all cancers in the United States. The combination of risk factors and accumulated low penetrance susceptibility alleles are the determinants of an individual's predisposition. Identifying these risk alleles, particularly in colorectal cancer (CRC), a leading cause of cancer deaths, is of great importance. We report using the laboratory mouse and the powerful classical genetics mapping approach to identify novel susceptibility to colon cancer loci (Scc) and their associated networks. Our study mimics sporadic CRC by exposing a genetically diverse mouse population to a colon specific carcinogen, azoxymethane. In addition, we extend our understanding of CRC susceptibility by applying systems genetics to clarify the genetic interactions and cancer specific networks. The combination of genomics with classical genetics produced the field of genetical genomics, which is now expanding to systems genetics by integrating multiple, systems-level biomolecular data in the context of segregating genetic populations. This new integrative field has the power to elucidate molecular networks associated with biological phenotypes by anchoring variability in networks to natural genetic variants. As initial applications of this technology was transcriptional profiling, which is providing new insights into the genetic networks underlying normal and disease states. Classical and systems genetics have enabled us to elucidate CRC susceptibility networks and the cellular re-wiring that occurs during cancer development. These approaches offer the possibility to identify and pharmaceutically-target networks that are cancer-specific, resulting in more effective, and safer anti-cancer drugs

Development of gene drive system for genetic engineering of natural populations of the African malaria vector

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Meiosis and beyond – understanding the mechanistic and evolutionary processes shaping the germline genome

The separation of germ cell populations from the soma is part of the evolutionary transition to multicellularity. Only genetic information present in the germ cells will be inherited by future generations, and any molecular processes affecting the germline genome are therefore likely to be passed on. Despite its prevalence across taxonomic kingdoms, we are only starting to understand details of the underlying micro‐evolutionary processes occurring at the germline genome level. These include segregation, recombination, mutation and selection and can occur at any stage during germline differentiation and mitotic germline proliferation to meiosis and post‐meiotic gamete maturation. Selection acting on germ cells at any stage from the diploid germ cell to the haploid gametes may cause significant deviations from Mendelian inheritance and may be more widespread than previously assumed. The mechanisms that affect and potentially alter the genomic sequence and allele frequencies in the germline are pivotal to our understanding of heritability. With the rise of new sequencing technologies, we are now able to address some of these unanswered questions. In this review, we comment on the most recent developments in this field and identify current gaps in our knowledge

The Evolution of Recombination Landscapes and Mechanisms in Drosophila in Light of Intragenomic Conflict

Sex and recombination are ubiquitous across the vast majority of life on earth. In eukaryotes, recombination during meiosis yields new variation that selection acts upon and, thus, facilitates evolution. However, meiosis provides an arena for manipulation and exploitation by selfish genetic elements. Selfish elements can increase in abundance independently of their host organism and frequently at a cost to host fitness. Several types of selfish elements act during meiosis and therefore it is possible for recombination rates and mechanisms to evolve to counteract and ameliorate their negative effects. However, few studies have investigated the interaction between recombination and selfish genetic elements. I conducted three studies on the evolution of recombination mechanisms in light of the impact of selfish elements. I begin my thesis with an introduction on selfish elements, recombination, and their possible interactions in Chapter 1. In Chapter 2, I found evidence that the synaptonemal complex (SC), a protein complex necessary for proper meiotic recombination, is evolving rapidly in Drosophila due to positive selection. I proposed several hypotheses to explain the rapid evolution of the SC including the interaction between the SC and centromere-mediated meiotic drive. In the next two experiments, I utilized advances in DNA sequencing to genotype hundreds of Drosophila progeny to quantify recombination events. In Chapter 3, I demonstrate that recombination frequency and distribution is robust to transposable element activity in D. virilis. The only effect of increased transposable element activity that I discovered was found in rare cases of aberrant recombination events that occur prior to meiosis. In Chapter 4, I constructed the first complete genetic map for D. yakuba, a close relative of D. melanogaster. The genetic map and previous studies of recombination in species within the melanogaster subgroup suggest rapid evolution of recombination, especially in regards to the suppression of recombination near the centromere. My findings support theoretical work that suggests that centromere-mediated meiotic drive can result in the rapid evolution of recombination rates near centromeres. Further studies are needed to definitively prove the link between selfish genetic element behavior and meiotic recombination and how their interaction impacts the evolution of genes, genomes, and species