Browsing by Author "Noor, Mohamed"

Recombination is the process in which genetic material is exchanged between one's homologous chromosome pairs during egg or sperm development (meiosis). Recombination is necessary for proper segregation of chromosomes during meiosis, and also plays a role in purging deleterious mutations, accelerating adaptation, and influencing the distribution of genomic features over evolutionary time. While recombination is clearly an important process, recombination rate is known to vary within and between individuals, populations, and species. Furthermore, what causes this variation remains relatively unknown. Using empirical and sequenced based estimates of recombination rate for the closely related species Drosophila pseudoobscura and Drosophila miranda, I seek to understand where recombination happens across the genome, to what extent recombination changes between species, and what genomic features are responsible for these changes. These data will deepen our understanding of mechanisms determining the recombination landscape, and shed light on generalized patterns and exceptions of recombination rate variation across the tree of life.

Recombination occurs during meiosis to produce new allelic combinations in natural populations, and thus strongly affects evolutionary processes. The model system Drosophila has been crucial for understanding the mechanics underlying recombination and assessing the association between recombination rate and several evolutionary parameters. Drosophila was the first system in which genetic maps were developed using recombination frequencies between genes. Further, Drosophila has been used to determine genetic and environmental conditions that cause variation in recombination rate. Finally, Drosophila has been instrumental in elucidating associations between local recombination rate and nucleotide diversity, divergence and codon bias, as well as helping determine the causes of these associations.

Here I present a fine-scale map of recombination rates across two major chromosomes in Drosophila persimilis using 181 SNP markers spanning two of five major chromosome arms. Using this map, I report significant fine-scale heterogeneity of local recombination rates. However, I also observed "recombinational neighborhoods", where adjacent intervals had similar recombination rates after excluding regions near the centromere and telomere. I further found significant positive associations of fine-scale recombination rate with repetitive element abundance and a 13-bp sequence motif known to associate with human recombination rates. I noted strong crossover interference extending 5-7 Mb from the initial crossover event. Further, I observed that fine-scale recombination rates in D. persimilis are strongly correlated with those obtained from a comparable study of its sister species, D. pseudoobscura. I documented a significant relationship between recombination rates and intron nucleotide sequence diversity within species, but no relationship between recombination rate and intron divergence between species. These results are consistent with selection models (hitchhiking and background selection) rather than mutagenic recombination models for explaining the relationship of recombination with nucleotide diversity within species. Finally, I found significant correlations between recombination rate and GC content, supporting both GC-biased gene conversion (BGC) models and selection-driven codon bias models.

Next, I looked at the role of chromosomal inversions in species maintenance by examining the impact of inversions distinguishing species to disrupt recombination rates within inverted regions, at inversion boundaries and throughout the remainder of the genome. By screening nearly 10,000 offspring from females heterozygous for 3 major inversions, I observed recombination rates within an inverted region in hybrids between Drosophila pseudoobscura and D. persimilis to be ~10-4 (similar to rates of exchange for inversion heterozygotes within species). However, despite the apparent potential for exchange, I do not find empirical evidence of ongoing gene exchange within the largest of 3 major inversions in DNA sequence analyses of strains isolated from natural populations. Finally, I observe a strong 'interchromosomal effect' with up to 9-fold higher (>800% different) recombination rates along collinear segments of chromosome 2 in hybrids, revealing a significantly negative association between interchromosomal effect and recombination rate in homokaryotypes, and I show that interspecies nucleotide divergence is lower in regions with larger changes in recombination rates in hybrids, potentially resulting from greater interspecies exchange. This last result suggests an effect of chromosomal inversions on interspecies gene exchange not considered previously.

Finally, I experimentally tested for a novel male-mediated effect on female recombination rates by crossing males that differed by either induced treatment variation or standing genetic variation to genetically identical females. After assaying recombination frequency in the offspring of these genetic crosses, I fitted these data to a statistical model where I showed no effect of male temperature treatment or male genetic background on offspring recombination rate. However, I did observe a difference of recombination rates of offspring laid 5-8 days post-mating between males treated with Juvenile Hormone relative to control males. Environmental variation in male ability to affect recombination rate in their mates suggests the potential for sexual conflict on optimal proportion of recombinant offspring, perhaps leading to changes in population-level recombination rates with varying levels of sexual selection.

Overall, my map of fine-scale recombination rates allowed me to confirm findings of broader-scale studies and identify multiple novel features that merit further investigation. Furthermore, I have identified several similarities and differences between inversions segregating within vs. between species in their effects on recombination and divergence, and I have identified possible effects of inversions on interspecies gene exchange that had not been considered previously. Finally, I have provided some evidence that males may impact female recombination rates, although future work should attempt to explore the range of male differences that impact this trait and the mechanism through which males impact the outcome of female meiosis.

Although much research has focused on cognitive ability and the genetic and environmental factors that might influence it, this aspect of human nature is still far from being well understood. It has been well-established that certain factors such as age and education have significant impacts on performance on most cognitive tests, but the effects of variables such as cognitive pastimes and strategies used during testing have generally not been assessed. Additionally, no genetic variant has yet been unequivocally shown to influence the normal variation in cognitive ability of healthy individuals. Candidate gene studies of cognition have produced conflicting results that have not been replicable, and genome-wide association studies have not found common variants with large influences on this trait.

Here, we have recruited a large cohort of healthy volunteers (n=1,887) and administered a brief cognitive battery utilizing diverse, common, and well-known tests. In addition to providing standard demographic information, the subjects also filled out a questionnaire that was designed to assess novel factors such as whether they had seen the test before, in what cognitive pastimes they participated, and what strategies they had used during testing. Linear regression models were built to assess the effects of these variables on the test scores. I found that the addition of novel covariates to standard ones increased the percent of the variation in test score that was explained for all tests; for some tests, the increase was as high as 70%.

Next, I examined the effects of genetic variants on test scores. I first performed a genome-wide association study using the Illumina HumanHap 550 and 610 chips. These chips are designed to directly genotype or tag the vast majority of the common variants in the genome. Despite having 80% power to detect a common variant explaining at least 3-6% (depending on the test) of the variation in the trait, I did not find any genetic variants that were significantly associated after correction for multiple testing. This is in line with the general findings from GWA studies that single common variants have a limited impact on complex traits.

Because of the recent technological advances in next-generation sequencing and the apparently limited role of very common variants, many human geneticists are making a transition from genome-wide association study to whole-genome and whole-exome sequencing, which allow for the identification of rarer variants. Because these methods are currently costly, it is important to utilize study designs that have the best chance of finding causal variants in a small sample size. One such method is the extreme-trait design, where individuals from one or both ends of a trait distribution are sequenced and variants that are enriched in the group(s) are identified. Here, I have sequenced the exomes of 20 young individuals of European ethnicity: 10 that performed at the top of the distribution for the cognitive battery and 10 that performed at the bottom. I identified rare genetic variants that were enriched in one extreme group as compared to the other and performed follow-up genotyping of the best candidate variant that emerged from this analysis. Unfortunately, this variant was not found to be associated in a larger sample of individuals. This pilot study indicates that a larger sample size will be needed to identify variants enriched in cognition extremes.

Finally, I assessed the effect of topiramate, an antiepileptic drug that causes marked side effects in certain cognitive areas in certain individuals, on some of the healthy volunteers (n=158) by giving them a 100 mg dose and then administering the cognitive test two hours later. I compared their scores at this testing session to those at the previous session and calculated the overall level to which they were affected by topiramate. I found that the topiramate blood levels, which were highly dependent on weight and the time from dosing to testing, varied widely between individuals after this acute dose, and that this variation explained 35% of the variability in topiramate response. A genome-wide association study of the remaining variability in topiramate response did not identify a genome-wide significant association.

In sum, I studied the contributions of both environmental and genetic variables to cognitive ability and cognitive response to topiramate. I found that I could identify environmental variables explaining large proportions of the variation in these traits, but that I could not identify genetic variants that influenced the traits. My analysis of genetic variants was for the most part restricted to the very common ones found on genotyping chips, and this and other studies have generally found that single common genetic variants do not have large affects on complex traits. As we move forward into studies that involve the sequencing of whole exomes and genomes, genetic variants with large effects on these complex traits may finally be found.

Meiotic recombination creates genetic diversity by shuffling combinations of alleles across loci, yet alleles at neighboring loci often remain non-randomly associated. This non-random association is known as linkage-disequilibrium (LD), and it has evolutionarily important effects both within and between species. Nucleotide diversity at a given locus may be reduced by directional selection on the locus, or by selection on neighboring linked loci. Recombination rates and nucleotide diversity are positively correlated across loci within many species, which can be explained by linked selection reducing nucleotide variation disproportionately in regions of low recombination. However, the independent contributions of different types of linked selection are difficult to disentangle. Between species, chromosomal inversions have been proposed to suppress recombination in hybrid inversion heterozygotes and thereby maintain LD and species distinction, but many models of how this happens are overly simplistic—they often ignore non-crossover gene conversion, which reduces LD. Little direct empirical data exist on gene conversion with respect to inversions in hybrids, so despite existing models, inversions may be quite ineffective at keeping hybridizing species distinct. Here, I examine the evolutionary consequences of LD at two levels: nucleotide diversity within species, and recombination-suppression in hybrids between species. I present three investigations driven by this overarching goal of understanding how LD plays into fundamental evolutionary mechanisms. First, I examine nucleotide variation in Drosophila pseudoobscura, and I present a novel test for evidence that particular kinds of selection at linked sites (background selection and/or soft sweeps) may reduce nucleotide variation even in the absence of hard selective sweeps. Second, I show that inversions are permeable to non-crossover gene conversion, which occurs throughout inverted regions in intra- and inter-specific hybrids. I provide a genome-wide empirical analysis of gene conversion rates both within species and in species hybrids, and I estimate that gene conversion occurs at a rate of 1 x 10-5 to 2.5 x 10-5 converted sites per bp per generation in experimental crosses within D. pseudoobscura and between D. pseudoobscura and its naturally-hybridizing sister species D. persimilis. Finally, I use extensive whole-genome sequence data to re-examine patterns of introgression and divergence in the D. pseudoobscura / D. persimilis system. I show how failing to consider variation in evolutionary rate can lead and has led to misinterpretations regarding effects of introgression. Through these genomic examinations, I refine our understanding of how recombination and linkage disequilibrium have shaped the divergence and speciation of Drosophila pseudoobscura and D. persimilis.

Speciation has occurred countless times throughout history, and yet the genetic mechanisms that lead to speciation are still missing pieces. Here, we describe the genetics of two processes that can act alone or together to cause speciation: hybrid sterility and meiotic drive. We use the Drosophila pseudoobscura/D, persimilis species as a model system to study these processes. We expanded on a prior study and saw little variation in strength of previously known hybrid sterility alleles between distinct strains of D. persimilis and the Bogota subspecies of D. pseudoobscura. Introgression of an autosomal, noninverted hybrid sterility allele from the USA subspecies of D. pseudoobscura into D. persimilis demonstrated that the D. pseudoobscura copy of a D. persimilis hybrid sterility factor also causes hybrid male sterility in a D. pseudoobscura bogotana background. This allelism suggests that the introgressed allele is ancestral, but was lost in the Bogota lineage, or that gene flow between D. pseudoobscura USA and D. persimilis moved the sterility-conferring allele from D. persimilis into D. pseudoobscura. To further understand the genetic basis of speciation, we asked if meiotic drive in D. persimilis is associated with hybrid sterility seen in D. persimilis/D. pseudoobscura hybrids. QTL mapping of both traits along the right arm of the X chromosome, where both drive and hybrid sterility loci are found, suggest that some of the causal loci overlap and may be allelic.

Measures of genetic divergence have long been used to identify evolutionary processes operating within and between species. However, recent reviews have described a bias in the use of relative divergence measures towards incorrectly identifying genomic regions that are seemingly immune to introgression. Here, we present a novel and opposite bias of relative divergence measures: misidentifying regions of introgression between sister species. We examine two distinct haplotypes of intermediate frequency within Drosophila pseudoobscura at the DPSX009 locus. One of these haplotypes had lower relative divergence than another to sister species D. persimilis. Although we and others initially presumed one haplotype have spread via introgression between D. pseudoobscura and D. persimilis, absolute divergence measures and individual sequence analysis suggest that haplotype structuring occurred as the result of within-species processes. The potential for this type of misinference may occur with any haplotype that recently spread within a species. We conclude that absolute measures of genetic divergence are necessary for confirming putative regions of introgression.

Many molecular ecological and evolutionary studies sample wild populations at a single point in time, failing to consider that data they collect represents genetic variation from a potentially unrepresentative snapshot in time. Variation across time in genetic parameters may occur quickly in species that produce multiple generations of offspring per year. However, many studies of rapid contemporary microevolution examine phenotypic trait divergence as opposed to molecular evolutionary divergence. Here, we compare genetic diversity in wild caught populations of Drosophila persimilis and D. pseudoobscura collected 16 years apart at the same time of year and same site at four X-linked and two mitochondrial loci to assess genetic stability. We found no major changes in nucleotide diversity in either species, but we observed a drastic shift in Tajima’s D between D. pseudoobscura timepoints at one locus associated with the increased abundance of a set of related haplotypes. Our data also suggests that D. persimilis may have recently accelerated its demographic expansion. While the changes we observed were modest, this study reinforces the importance of considering potential temporal variation in genetic parameters within single populations over short evolutionary timescales.

Biodiversity is generated by the process of speciation. Because biological species are defined as populations that are unable to exchange genes with one another, the study of the evolution of reproductive isolation occupies the center of speciation research. A key to deciphering how reproductive isolation evolves is to understand the genetic changes that underlie these barriers to gene flow. Intrinsic postzygotic barriers, such as hybrid sterility or inviability, are known to impede gene flow and especially lend themselves to genetic analysis because of their ease of study in a laboratory setting. Because hybrid sterility likely evolves before hybrid inviability, it potentially plays an important role in the cessation of gene flow. Yet, while their X-linked counterparts have been precisely localized, we remain ignorant of the numbers of and interactions among dominant autosomal loci that are predicted to contribute to F1 hybrid male sterility.

To address this conceptual void, I examine the genetic architecture of hybrid male sterility between the allopatric sister species Drosophila persimilis and D. pseudoobscura bogotana. First, using a large-scale backcross analysis, I fine-map autosomal QTL from D. persimilis that confer sterility in male hybrids. This fine-mapping shows that loci contributing to hybrid male sterility reside outside chromosomal rearrangements (i.e., regions of reduced recombination) in this allopatric species pairs. In contrast, these QTL do not contribute to hybrid male sterility in the comparable sympatric hybridizing species D. persimilis and D. pseudoobscura, as predicted by models that suggest that hybridizing species persist because of broad regions of reduced recombination. Next, I use a serial backcross design to introgress these sterility-conferring QTL from D. persimilis into a D. p. bogatana genetic background devoid of other alleles from D. persimilis. This introgression study tested a prediction of the dominance theory proposed to explain Haldane's rule: dominant-acting autosomal loci should interact with recessive-acting X-linked loci to produce sterile hybrid males. Surprisingly, the results demonstrated that the "composite" dominance of the autosomal QTL is more important than the dominance of individual QTL for producing Haldane's rule: epistasis among loci elevated their dominant effects on sterility such that individually-recessive-acting autosomal QTL can contribute to F1 male infertility. Finally, using recombination to generate independent lines bearing only small segments of the identified QTL regions, I examine whether single or multiple loci within these regions contribute to the overall effect of hybrid sterility. While the effect of one QTL depends on epistasis between several loci within that small region, the effect of the other QTL appears to derive from a single genetic factor. These results suggest that estimates of the number of genes that contribute to reproductive isolation are at best, likely too low and, at worst, unattainable with the mapping resolution attainable by standard backcross and introgression approaches.

This dissertation addresses both evolutionary and genetic hypotheses of intrinsic postzygotic isolation. Hybrid male sterility between D. persimilis and D. p. bogotana clearly involves highly specific and complex interactions between homoospecific loci. The mapping results presented here also lay the foundation for the identification and cloning of multiple autosomal sterility-conferring "speciation genes."