@article{schwarzkopf_brandt_heil_2024, title={The recombination landscape of introgression in yeast}, url={https://doi.org/10.1101/2024.01.04.574263}, DOI={10.1101/2024.01.04.574263}, abstractNote={Meiotic recombination is an important evolutionary force that acts by breaking up genomic linkage, thereby increasing the efficacy of selection. Meiotic recombination is initiated with a double-strand break which is resolved via a crossover, which involves the reciprocal exchange of genetic material between homologous chromosomes, or a non-crossover, which results in small tracts of non-reciprocal exchange of genetic material. While the meiotic process is largely conserved, crossover and non-crossover rates vary between species, populations, individuals, and across the genome. In recent years, recombination is observed to be positively associated with the distribution of ancestry derived from past interspecific hybridization (introgression) in a variety of species. This trend has been interpreted to signify that introgression carries genetic incompatibilities that are selected against, such that introgression is enriched in regions of high recombination. However, recombination is well known to be suppressed in divergent sequence to prevent non-homologous recombination. Since introgressed DNA is often divergent, we sought to explore this interaction of recombination and introgression by sequencing spores and detecting crossover and non-crossover events from two crosses of the budding yeast Saccharomyces uvarum. One cross is between strains isolated from natural environments, and the other cross is between strains from fermentation environments, in which each strain contains introgression from their sister species, S. eubayanus. We find that the recombination landscape is significantly different between S. uvarum crosses, and that most of these differences can be explained by the presence of heterozygous introgression in the fermentation cross. Crossovers are significantly reduced and non-crossovers are increased in heterozygous introgression compared to syntenic regions in the natural cross without introgression. This translates to reduced allele shuffling within introgressed regions, and an overall reduction of shuffling on most chromosomes with introgression compared to the syntenic regions and chromosomes without introgression. Our results indicate that recent hybridization can significantly influence the recombination landscape, and suggest that the reduction in allele shuffling contributes to the initial purging of introgressed ancestry in the generations following a hybridization event.}, author={Schwarzkopf, Enrique J. and Brandt, Nathan and Heil, Caiti Smukowski}, year={2024}, month={Jan} }
 @article{schwarzkopf_brandt_heil_2024, title={The recombination landscape of introgression in yeast}, url={https://doi.org/10.7554/eLife.96184.1}, DOI={10.7554/eLife.96184.1}, abstractNote={Meiotic recombination is an important evolutionary force that acts by breaking up genomic linkage, thereby increasing the efficacy of selection. Meiotic recombination is initiated with a double-strand break which is resolved via a crossover, which involves the reciprocal exchange of genetic material between homologous chromosomes, or a non-crossover, which results in small tracts of non-reciprocal exchange of genetic material. While the meiotic process is largely conserved, crossover and non-crossover rates vary between species, populations, individuals, and across the genome. In recent years, recombination is observed to be positively associated with the distribution of ancestry derived from past interspecific hybridization (introgression) in a variety of species. This trend has been interpreted to signify that introgression carries genetic incompatibilities that are selected against, such that introgression is enriched in regions of high recombination. However, recombination is well known to be suppressed in divergent sequence to prevent non-homologous recombination. Since introgressed DNA is often divergent, we sought to explore this interaction of recombination and introgression by sequencing spores and detecting crossover and non-crossover events from two crosses of the budding yeast Saccharomyces uvarum . One cross is between strains isolated from natural environments, and the other cross is between strains from fermentation environments, in which each strain contains introgression from their sister species, S. eubayanus . We find that the recombination landscape is significantly different between S. uvarum crosses, and that most of these differences can be explained by the presence of heterozygous introgression in the fermentation cross. Crossovers are significantly reduced and non-crossovers are increased in heterozygous introgression compared to syntenic regions in the natural cross without introgression. This translates to reduced allele shuffling within introgressed regions, and an overall reduction of shuffling on most chromosomes with introgression compared to the syntenic regions and chromosomes without introgression. Our results indicate that recent hybridization can significantly influence the recombination landscape, and suggest that the reduction in allele shuffling contributes to the initial purging of introgressed ancestry in the generations following a hybridization event.}, author={Schwarzkopf, Enrique J. and Brandt, Nathan and Heil, Caiti Smukowski}, year={2024}, month={Mar} }
 @article{schwarzkopf_brandt_heil_2024, title={The recombination landscape of introgression in yeast}, url={https://doi.org/10.7554/eLife.96184}, DOI={10.7554/eLife.96184}, abstractNote={Meiotic recombination is an important evolutionary force that acts by breaking up genomic linkage, thereby increasing the efficacy of selection. Meiotic recombination is initiated with a double-strand break which is resolved via a crossover, which involves the reciprocal exchange of genetic material between homologous chromosomes, or a non-crossover, which results in small tracts of non-reciprocal exchange of genetic material. While the meiotic process is largely conserved, crossover and non-crossover rates vary between species, populations, individuals, and across the genome. In recent years, recombination is observed to be positively associated with the distribution of ancestry derived from past interspecific hybridization (introgression) in a variety of species. This trend has been interpreted to signify that introgression carries genetic incompatibilities that are selected against, such that introgression is enriched in regions of high recombination. However, recombination is well known to be suppressed in divergent sequence to prevent non-homologous recombination. Since introgressed DNA is often divergent, we sought to explore this interaction of recombination and introgression by sequencing spores and detecting crossover and non-crossover events from two crosses of the budding yeast Saccharomyces uvarum . One cross is between strains isolated from natural environments, and the other cross is between strains from fermentation environments, in which each strain contains introgression from their sister species, S. eubayanus . We find that the recombination landscape is significantly different between S. uvarum crosses, and that most of these differences can be explained by the presence of heterozygous introgression in the fermentation cross. Crossovers are significantly reduced and non-crossovers are increased in heterozygous introgression compared to syntenic regions in the natural cross without introgression. This translates to reduced allele shuffling within introgressed regions, and an overall reduction of shuffling on most chromosomes with introgression compared to the syntenic regions and chromosomes without introgression. Our results indicate that recent hybridization can significantly influence the recombination landscape, and suggest that the reduction in allele shuffling contributes to the initial purging of introgressed ancestry in the generations following a hybridization event.}, author={Schwarzkopf, Enrique J. and Brandt, Nathan and Heil, Caiti Smukowski}, year={2024}, month={Mar} }
 @article{heil_2023, title={Loss of Heterozygosity and Its Importance in Evolution}, volume={2}, ISSN={["1432-1432"]}, url={https://doi.org/10.1007/s00239-022-10088-8}, DOI={10.1007/s00239-022-10088-8}, abstractNote={Abstract Loss of heterozygosity (LOH) is a mitotic recombination event that converts heterozygous loci to homozygous loci. This mutation event is widespread in organisms that have asexual reproduction like budding yeasts, and is also an important and frequent mutation event in tumorigenesis. Mutation accumulation studies have demonstrated that LOH occurs at a rate higher than the point mutation rate, and can impact large portions of the genome. Laboratory evolution experiments of heterozygous yeasts have revealed that LOH often unmasks beneficial recessive alleles that can confer large fitness advantages. Here, I highlight advances in understanding dominance, fitness, and phenotypes in laboratory evolved heterozygous yeast strains. I discuss best practices for detecting LOH in intraspecific and interspecific evolved clones and populations. Utilizing heterozygous strain backgrounds in laboratory evolution experiments offers an opportunity to advance our understanding of this important mutation type in shaping adaptation and genome evolution in wild, domesticated, and clinical populations.}, journal={JOURNAL OF MOLECULAR EVOLUTION}, author={Heil, Caiti Smukowski}, year={2023}, month={Feb} }
 @article{madden_lahue_gordy_little_nichols_calvert_dunn_smukowski heil_2021, title={Sugar‐seeking insects as a source of diverse bread‐making yeasts with enhanced attributes}, volume={39}, ISSN={0749-503X 1097-0061}, url={http://dx.doi.org/10.1002/yea.3676}, DOI={10.1002/yea.3676}, abstractNote={Insects represent a particularly interesting habitat in which to search for novel yeasts of value to industry. Insect‐associated yeasts have the potential to have traits relevant to modern food and beverage production due to insect–yeast interactions, with such traits including diverse carbohydrate metabolisms, high sugar tolerance, and general stress tolerance. Here, we consider the potential value of insect‐associated yeasts in the specific context of baking. We isolated 63 yeast strains from 13 species of hymenoptera from the United States, representing 37 yeast species from 14 genera. Screening for the ability to ferment maltose, a sugar important for bread production, resulted in the identification of 13 strains of Candida, Lachancea, and Pichia species. We assessed their ability to leaven dough. All strains produced baked loaves comparable to a commercial baking strain of Saccharomyces cerevisiae. The same 13 strains were also grown under various sugar and salt conditions relevant to osmotic challenges experienced in the manufacturing processes and the production of sweet dough. We show that many of these yeast strains, most notably strains of Lachancea species, grow at a similar or higher rate and population size as commercial baker's yeast. We additionally assessed the comparative phenotypes and genetics of insect‐associated S. cerevisiae strains unable to ferment maltose and identified baking‐relevant traits, including variations in the HOG1 signaling pathway and diverse carbohydrate metabolisms. Our results suggest that non‐conventional yeasts have high potential for baking and, more generally, showcase the success of bioprospecting in insects for identifying yeasts relevant for industrial uses.}, number={1-2}, journal={Yeast}, publisher={Wiley}, author={Madden, Anne A. and Lahue, Caitlin and Gordy, Claire L. and Little, Joy L. and Nichols, Lauren M. and Calvert, Martha D. and Dunn, Robert R. and Smukowski Heil, Caiti}, year={2021}, month={Nov}, pages={108–127} }
 @inbook{heil_lahue_2021, title={The Evolutionary History of Bread and Beer Yeast}, url={http://dx.doi.org/10.52750/526619}, DOI={10.52750/526619}, booktitle={Fermentology}, publisher={North Carolina State University Libraries}, author={Heil, Caiti and Lahue, Caiti}, editor={Dufresne, KelseyEditor}, year={2021}, month={May} }
 @article{heil_patterson_hickey_alcantara_dunham_2020, title={Transposable element mobilization in interspecific yeast hybrids}, volume={6}, url={https://doi.org/10.1101/2020.06.16.155218}, DOI={10.1101/2020.06.16.155218}, abstractNote={Abstract Barbara McClintock first hypothesized that interspecific hybridization could provide a “genomic shock” that leads to the mobilization of transposable elements. This hypothesis is based on the idea that regulation of transposable element movement is potentially disrupted in hybrids. However, the handful of studies testing this hypothesis have yielded mixed results. Here, we set out to identify if hybridization can increase transposition rate and facilitate colonization of transposable elements in Saccharomyces cerevisiae x Saccharomyces uvarum interspecific yeast hybrids. S. cerevisiae have a small number of active long terminal repeat (LTR) retrotransposons (Ty elements), while their distant relative S. uvarum have lost the Ty elements active in S. cerevisiae . While the regulation system of Ty elements is known in S. cerevisiae , it is unclear how Ty elements are regulated in other Saccharomyces species, and what mechanisms contributed to the loss of most classes of Ty elements in S. uvarum . Therefore, we first assessed whether transposable elements could insert in the S. uvarum sub-genome of a S. cerevisiae x S. uvarum hybrid. We induced transposition to occur in these hybrids and developed a sequencing technique to show that Ty elements insert readily and non-randomly in the S. uvarum genome. We then used an in vivo reporter construct to directly measure transposition rate in hybrids, demonstrating that hybridization itself does not alter rate of mobilization. However, we surprisingly show that species-specific mitochondrial inheritance can change transposition rate by an order of magnitude. Overall, our results provide evidence that hybridization can facilitate the introduction of transposable elements across species boundaries and alter transposition via mitochondrial transmission, but that this does not lead to unrestrained proliferation of transposable elements suggested by the genomic shock theory.}, publisher={Cold Spring Harbor Laboratory}, author={Heil, Caiti Smukowski and Patterson, Kira and Hickey, Angela Shang-Mei and Alcantara, Erica and Dunham, Maitreya J.}, year={2020}, month={Jun} }
 @article{lancaster_payen_heil_dunham_2019, title={Fitness benefits of loss of heterozygosity in Saccharomyces hybrids}, volume={29}, url={https://doi.org/10.1101/gr.245605.118}, DOI={10.1101/gr.245605.118}, abstractNote={With two genomes in the same organism, interspecific hybrids have unique opportunities and costs. In both plants and yeasts, wild, pathogenic, and domesticated hybrids may eliminate portions of one parental genome, a phenomenon known as loss of heterozygosity (LOH). Laboratory evolution of hybrid yeast recapitulates these results, with LOH occurring in just a few hundred generations of propagation. In this study, we systematically looked for alleles that are beneficial when lost in order to determine how prevalent this mode of adaptation may be, and to determine candidate loci that might underlie the benefits of larger-scale chromosome rearrangements. These aims were accomplished by mating Saccharomyces uvarum with the S. cerevisiae deletion collection to create hybrids, such that each nonessential S. cerevisiae allele is deleted. Competitive fitness assays of these pooled, barcoded, hemizygous strains, and accompanying controls, revealed a large number of loci for which LOH is beneficial. We found that the fitness effects of hemizygosity are dependent on the species context, the selective environment, and the species origin of the deleted allele. Further, we found that hybrids have a larger distribution of fitness consequences vs. matched S. cerevisiae hemizygous diploids. Our results suggest that LOH can be a successful strategy for adaptation of hybrids to new environments, and we identify candidate loci that drive the chromosomal rearrangements observed in evolution of yeast hybrids.}, number={10}, journal={Genome Research}, publisher={Cold Spring Harbor Laboratory}, author={Lancaster, Samuel M. and Payen, Celia and Heil, Caiti Smukowski and Dunham, Maitreya J.}, year={2019}, month={Oct}, pages={1685–1692} }
 @article{heil_large_patterson_hickey_yeh_dunham_2019, title={Temperature preference can bias parental genome retention during hybrid evolution}, volume={15}, url={https://doi.org/10.1371/journal.pgen.1008383}, DOI={10.1371/journal.pgen.1008383}, abstractNote={Interspecific hybridization can introduce genetic variation that aids in adaptation to new or changing environments. Here, we investigate how hybrid adaptation to temperature and nutrient limitation may alter parental genome representation over time. We evolved Saccharomyces cerevisiae x Saccharomyces uvarum hybrids in nutrient-limited continuous culture at 15°C for 200 generations. In comparison to previous evolution experiments at 30°C, we identified a number of responses only observed in the colder temperature regime, including the loss of the S. cerevisiae allele in favor of the cryotolerant S. uvarum allele for several portions of the hybrid genome. In particular, we discovered a genotype by environment interaction in the form of a loss of heterozygosity event on chromosome XIII; which species’ haplotype is lost or maintained is dependent on the parental species’ temperature preference and the temperature at which the hybrid was evolved. We show that a large contribution to this directionality is due to a temperature dependent fitness benefit at a single locus, the high affinity phosphate transporter gene PHO84. This work helps shape our understanding of what forces impact genome evolution after hybridization, and how environmental conditions may promote or disfavor the persistence of hybrids over time.}, number={9}, journal={PLOS Genetics}, publisher={Public Library of Science (PLoS)}, author={Heil, Caiti S. Smukowski and Large, Christopher R. L. and Patterson, Kira and Hickey, Angela Shang-Mei and Yeh, Chiann-Ling C. and Dunham, Maitreya J.}, editor={HITTINGER, CHRIS TODDEditor}, year={2019}, month={Sep}, pages={e1008383} }
 @article{lancaster_payen_heil_dunham_2018, title={Fitness Benefits of Loss of Heterozygosity in Saccharomyces Hybrids}, volume={10}, url={https://doi.org/10.1101/452748}, DOI={10.1101/452748}, abstractNote={ABSTRACT With two genomes in the same organism, interspecific hybrids have unique opportunities and costs. In both plants and yeasts, wild, pathogenic, and domesticated hybrids may eliminate portions of one parental genome, a phenomenon known as loss of heterozygosity (LOH). Laboratory evolution of hybrid yeast recapitulates these results, with LOH occurring in just a few hundred generations of propagation. In this study, we systematically looked for alleles that are beneficial when lost in order to determine how prevalent this mode of adaptation may be, and to determine candidate loci that might underlie the benefits of larger-scale chromosome rearrangements. These aims were accomplished by mating Saccharomyces uvarum with the S. cerevisiae deletion collection to create hybrids, such that each nonessential S. cerevisiae allele is deleted. Competitive fitness assays of these pooled, barcoded, hemizygous strains, and accompanying controls, revealed a large number of loci for which LOH is beneficial. We found that the fitness effects of hemizygosity are dependent on the species context, the selective environment, and the species origin of the deleted allele. Further, we found that hybrids have a larger distribution of fitness consequences vs. matched S. cerevisiae hemizygous diploids. Our results suggest that LOH can be a successful strategy for adaptation of hybrids to new environments, and we identify candidate loci that drive the chromosomal rearrangements observed in evolution of yeast hybrids.}, publisher={Cold Spring Harbor Laboratory}, author={Lancaster, Samuel M. and Payen, Celia and Heil, Caiti Smukowski and Dunham, Maitreya J.}, year={2018}, month={Oct} }
 @article{heil_large_patterson_dunham_2018, title={Temperature preference biases parental genome retention during hybrid evolution}, volume={9}, url={https://doi.org/10.1101/429803}, DOI={10.1101/429803}, abstractNote={Interspecific hybridization can introduce genetic variation that aids in adaptation to new or changing environments. Here we investigate how the environment, and more specifically temperature, interacts with hybrid genomes to alter parental genome representation over time. We evolved Saccharomyces cerevisiae x Saccharomyces uvarum hybrids in nutrient-limited continuous culture at 15°C for 200 generations. In comparison to previous evolution experiments at 30°C, we identified a number of temperature specific responses, including the loss of the S. cerevisiae allele in favor of the cryotolerant S. uvarum allele for several portions of the hybrid genome. In particular, we discovered a genotype by environment interaction in the form of a reciprocal loss of heterozygosity event on chromosome XIII. Which species haplotype is lost or maintained is dependent on the parental species temperature preference and the temperature at which the hybrid was evolved. We show that a large contribution to this directionality is due to temperature sensitivity at a single locus, the high affinity phosphate transporter PHO84. This work helps shape our understanding of what forces impact genome evolution after hybridization, and how environmental conditions may favor or disfavor hybrids over time.}, publisher={Cold Spring Harbor Laboratory}, author={Heil, Caiti Smukowski and Large, Christopher R. L. and Patterson, Kira and Dunham, Maitreya J.}, year={2018}, month={Sep} }
 @article{hope_amorosi_miller_dang_heil_dunham_2017, title={Experimental Evolution Reveals Favored Adaptive Routes to Cell Aggregation in Yeast}, volume={206}, DOI={10.1534/genetics.116.198895}, abstractNote={Yeast flocculation is a community-building cell aggregation trait that is an important mechanism of stress resistance and a useful phenotype for brewers; however, it is also a nuisance in many industrial processes, in clinical settings, and in the laboratory. Chemostat-based evolution experiments are impaired by inadvertent selection for aggregation, which we observe in 35% of populations. These populations provide a testing ground for understanding the breadth of genetic mechanisms Saccharomyces cerevisiae uses to flocculate, and which of those mechanisms provide the biggest adaptive advantages. In this study, we employed experimental evolution as a tool to ask whether one or many routes to flocculation are favored, and to engineer a strain with reduced flocculation potential. Using a combination of whole genome sequencing and bulk segregant analysis, we identified causal mutations in 23 independent clones that had evolved cell aggregation during hundreds of generations of chemostat growth. In 12 of those clones, we identified a transposable element insertion in the promoter region of known flocculation gene FLO1, and, in an additional five clones, we recovered loss-of-function mutations in transcriptional repressor TUP1, which regulates FLO1 and other related genes. Other causal mutations were found in genes that have not been previously connected to flocculation. Evolving a flo1 deletion strain revealed that this single deletion reduces flocculation occurrences to 3%, and demonstrated the efficacy of using experimental evolution as a tool to identify and eliminate the primary adaptive routes for undesirable traits.}, number={2}, journal={Genetics}, publisher={Genetics Society of America}, author={Hope, Elyse A. and Amorosi, Clara J. and Miller, Aaron W. and Dang, Kolena and Heil, Caiti Smukowski and Dunham, Maitreya J.}, year={2017}, month={Apr}, pages={1153–1167} }
 @article{heil_burton_liachko_friedrich_hanson_morris_schacherer_shendure_thomas_dunham_2017, title={Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi-C}, volume={6}, DOI={10.1101/150722}, abstractNote={Abstract Interspecific hybridization is a common mechanism enabling genetic diversification and adaptation; however, the detection of hybrid species has been quite difficult. The identification of microbial hybrids is made even more complicated, as most environmental microbes are resistant to culturing and must be studied in their native mixed communities. We have previously adapted the chromosome conformation capture method Hi-C to the assembly of genomes from mixed populations. Here, we show the method’s application in assembling genomes directly from an uncultured, mixed population from a spontaneously inoculated beer sample. Our assembly method has enabled us to de-convolute 4 bacterial and 4 yeast genomes from this sample, including a putative yeast hybrid. Downstream isolation and analysis of this hybrid confirmed its genome to consist of Pichia membranifaciens and that of another related, but undescribed yeast. Our work shows that Hi-C-based metagenomic methods can overcome the limitation of traditional sequencing methods in studying complex mixtures of genomes.}, publisher={Cold Spring Harbor Laboratory}, author={Heil, Caiti Smukowski and Burton, Joshua N. and Liachko, Ivan and Friedrich, Anne and Hanson, Noah A. and Morris, Cody L. and Schacherer, Joseph and Shendure, Jay and Thomas, James H. and Dunham, Maitreya J.}, year={2017}, month={Jun} }
 @article{heil_desevo_pai_tucker_hoang_dunham_2017, title={Loss of Heterozygosity Drives Adaptation in Hybrid Yeast}, volume={34}, DOI={10.1093/molbev/msx098}, abstractNote={Abstract Hybridization is often considered maladaptive, but sometimes hybrids can invade new ecological niches and adapt to novel or stressful environments better than their parents. The genomic changes that occur following hybridization that facilitate genome resolution and/or adaptation are not well understood. Here, we examine hybrid genome evolution using experimental evolution of de novo interspecific hybrid yeast Saccharomyces cerevisiae × Saccharomyces uvarum and their parentals. We evolved these strains in nutrient-limited conditions for hundreds of generations and sequenced the resulting cultures identifying numerous point mutations, copy number changes, and loss of heterozygosity (LOH) events, including species-biased amplification of nutrient transporters. We focused on a particularly interesting example, in which we saw repeated LOH at the high-affinity phosphate transporter gene PHO84 in both intra- and interspecific hybrids. Using allele replacement methods, we tested the fitness of different alleles in hybrid and S. cerevisiae strain backgrounds and found that the LOH is indeed the result of selection on one allele over the other in both S. cerevisiae and the hybrids. This is an example where hybrid genome resolution is driven by positive selection on existing heterozygosity and demonstrates that even infrequent outcrossing may have lasting impacts on adaptation.}, number={7}, journal={Molecular Biology and Evolution}, publisher={Oxford University Press (OUP)}, author={Heil, Caiti S. Smukowski and DeSevo, Christopher G. and Pai, Dave A. and Tucker, Cheryl M. and Hoang, Margaret L. and Dunham, Maitreya J.}, year={2017}, month={Mar}, pages={1596–1612} }
 @article{hope_amorosi_miller_dang_heil_dunham_2016, title={Experimental evolution reveals favored adaptive routes to cell aggregation in yeast}, volume={12}, DOI={10.1101/091876}, abstractNote={Abstract Yeast flocculation is a community-building cell aggregation trait that is an important mechanism of stress resistance and a useful phenotype for brewers; however, it is also a nuisance in many industrial processes, in clinical settings, and in the laboratory. Chemostat-based evolution experiments are impaired by inadvertent selection for aggregation, which we observe in 35% of populations. These populations provide a testing ground for understanding the breadth of genetic mechanisms Saccharomyces cerevisiae uses to flocculate, and which of those mechanisms provide the biggest adaptive advantages. In this study, we employed experimental evolution as a tool to ask whether one or many routes to flocculation are favored, and to engineer a strain with reduced flocculation potential. Using a combination of whole genome sequencing and bulk segregant analysis, we identified causal mutations in 23 independent clones that had evolved cell aggregation during hundreds of generations of chemostat growth. In 12 of those clones we identified a transposable element insertion in the promoter region of known flocculation gene FLO1 , and in an additional five clones we recovered loss-of-function mutations in transcriptional repressor TUP1 , which regulates FLO1 and other related genes. Other causal mutations were found in genes that have not been previously connected to flocculation. Evolving a flo 1 deletion strain revealed that this single deletion reduces flocculation occurrences to 3%, and demonstrated the efficacy of using experimental evolution as a tool to identify and eliminate the primary adaptive routes for undesirable traits.}, publisher={Cold Spring Harbor Laboratory}, author={Hope, Elyse A. and Amorosi, Clara J. and Miller, Aaron W. and Dang, Kolena and Heil, Caiti Smukowski and Dunham, Maitreya J.}, year={2016} }
 @article{heil_ellison_dubin_noor_2015, title={Recombining without Hotspots: A Comprehensive Evolutionary Portrait of Recombination in Two Closely Related Species ofDrosophila}, volume={7}, DOI={10.1093/gbe/evv182}, abstractNote={Meiotic recombination rate varies across the genome within and between individuals, populations, and species in virtually all taxa studied. In almost every species, this variation takes the form of discrete recombination hotspots, determined in Metazoans by a protein called PRDM9. Hotspots and their determinants have a profound effect on the genomic landscape, and share certain features that extend across the tree of life. Drosophila, in contrast, are anomalous in their absence of hotspots, PRDM9, and other species-specific differences in the determination of recombination. To better understand the evolution of meiosis and general patterns of recombination across diverse taxa, we present what may be the most comprehensive portrait of recombination to date, combining contemporary recombination estimates from each of two sister species along with historic estimates of recombination using linkage-disequilibrium-based approaches derived from sequence data from both species. Using Drosophila pseudoobscura and Drosophila miranda as a model system, we compare recombination rate between species at multiple scales, and we replicate the pattern seen in human-chimpanzee that recombination rate is conserved at broad scales and more divergent at finer scales. We also find evidence of a species-wide recombination modifier, resulting in both a present and historic genome wide elevation of recombination rates in D. miranda, and identify broad scale effects on recombination from the presence of an inter-species inversion. Finally, we reveal an unprecedented view of the distribution of recombination in D. pseudoobscura, illustrating patterns of linked selection and where recombination is taking place. Overall, by combining these estimation approaches, we highlight key similarities and differences in recombination between Drosophila and other organisms. Author Summary Recombination, or crossing over, describes an essential exchange of genetic material that occurs during egg and sperm development and has consequences for the proper segregation of chromosomes, and for the evolution of genomes and genomic features. In our study, we compare genome wide recombination rate in two closely related species of the fruit fly Drosophila to understand if and how recombination changes over time. We find that recombination does indeed change, we observe globally increased recombination in one species, and differences in regional recombination likely reflecting the result of a chromosomal rearrangement in both species. Moreover, we show that the extent that recombination changes is dependent on the physical scale at which recombination is measured, likely reflecting selection pressures on recombination distribution and replicating a pattern seen in human-chimpanzee recombination. Apart from between-species differences, we note several ways in which the Drosophila recombination landscape has changed since Drosophila diverged from other organisms. In contrast to species of fungi, plants, and animals, Drosophila recombination is not concentrated in discrete regions known as hotspots, nor is it increased near the start of genes, suggesting that despite the importance of the recombination process, the determinants of recombination have been shifting over evolutionary time.}, number={10}, journal={Genome Biology and Evolution}, publisher={Oxford University Press (OUP)}, author={Heil, Caiti S. Smukowski and Ellison, Chris and Dubin, Matthew and Noor, Mohamed A.F.}, year={2015}, month={Oct}, pages={2829–2842} }
 @article{heil_ellison_dubin_noor_2015, title={Recombining without hotspots: A comprehensive evolutionary portrait of recombination in two closely related species of Drosophila}, volume={3}, DOI={10.1101/016972}, abstractNote={Meiotic recombination rate varies across the genome within and between individuals, populations, and species in virtually all taxa studied. In almost every species, this variation takes the form of discrete recombination hotspots, determined in Metazoans by a protein called PRDM9. Hotspots and their determinants have a profound effect on the genomic landscape, and share certain features that extend across the tree of life. Drosophila, in contrast, are anomalous in their absence of hotspots, PRDM9, and other species-specific differences in the determination of recombination. To better understand the evolution of meiosis and general patterns of recombination across diverse taxa, we present what may be the most comprehensive portrait of recombination to date, combining contemporary recombination estimates from each of two sister species along with historic estimates of recombination using linkage-disequilibrium-based approaches derived from sequence data from both species. Using Drosophila pseudoobscura and Drosophila miranda as a model system, we compare recombination rate between species at multiple scales, and we replicate the pattern seen in human-chimpanzee that recombination rate is conserved at broad scales and more divergent at finer scales. We also find evidence of a species-wide recombination modifier, resulting in both a present and historic genome wide elevation of recombination rates in D. miranda, and identify broad scale effects on recombination from the presence of an inter-species inversion. Finally, we reveal an unprecedented view of the distribution of recombination in D. pseudoobscura, illustrating patterns of linked selection and where recombination is taking place. Overall, by combining these estimation approaches, we highlight key similarities and differences in recombination between Drosophila and other organisms.}, publisher={Cold Spring Harbor Laboratory}, author={Heil, Caiti Smukowski and Ellison, Chris and Dubin, Matthew and Noor, Mohamed}, year={2015}, month={Mar} }
 @article{heil_2014, title={            No Detectable Effect of the DNA Methyltransferase DNMT2 on            Drosophila            Meiotic Recombination          }, volume={4}, DOI={10.1534/g3.114.012393}, abstractNote={Epigenetics is known to be involved in recombination initiation, but the effects of specific epigenetic marks like DNA methylation on recombination are relatively unknown. Studies in Arabidopsis and the fungus Ascobolus immersus suggest that DNA methylation may suppress recombination rates and/or alter its distribution across the genome; however, these patterns appear complex, and more direct inquiries are needed. Unlike other organisms, Drosophila only have one known DNA methyltransferase, DNMT2, which is expressed in the ovaries and historically has been thought to be responsible for limited genomic DNA methylation. To test for a role of DNMT2 on the frequency and distribution of recombination, I compared recombination rates between Dnmt2 −/− and Dnmt2 +/− Drosophila melanogaster individuals in two euchromatic regions and one heterochromatic region across the genome. I failed to detect an altered pattern of recombination rate in the absence of DNMT2 in all regions surveyed, and conclude that other epigenetic effects are regulating recombination initiation in Drosophila.}, number={11}, journal={G3: Genes|Genomes|Genetics}, publisher={Genetics Society of America}, author={Heil, Caiti S. Smukowski}, year={2014}, month={Aug}, pages={2095–2100} }
 @article{heil_noor_2012, title={Mentor vs. Monolith}, volume={100}, DOI={10.1511/2012.99.450}, number={6}, journal={American Scientist}, publisher={Sigma Xi}, author={Heil, Caiti and Noor, Mohamed}, year={2012}, pages={450} }
 @article{mcgaugh_heil_manzano-winkler_loewe_goldstein_himmel_noor_2012, title={Recombination Modulates How Selection Affects Linked Sites in Drosophila}, volume={10}, DOI={10.1371/journal.pbio.1001422}, abstractNote={Recombination rate in Drosophila species shapes the impact of selection in the genome and is positively correlated with nucleotide diversity.}, number={11}, journal={PLoS Biology}, publisher={Public Library of Science (PLoS)}, author={McGaugh, Suzanne E. and Heil, Caiti S. S. and Manzano-Winkler, Brenda and Loewe, Laurence and Goldstein, Steve and Himmel, Tiffany L. and Noor, Mohamed A. F.}, editor={Barton, Nick H.Editor}, year={2012}, month={Nov}, pages={e1001422} }
 @article{heil_hunter_noor_miglia_manzano-winkler_mcdermott_noor_2012, title={Witnessing Phenotypic and Molecular Evolution in the Fruit Fly}, volume={5}, DOI={10.1007/s12052-012-0447-5}, abstractNote={This multi-day exercise is designed for a college Genetics and Evolution laboratory to demonstrate concepts of inheritance and phenotypic and molecular evolution using a live model organism, Drosophila simulans. Students set up an experimental fruit fly population consisting of ten white eyed flies and one red eyed fly. Having red eyes is advantageous compared to having white eyes, allowing students to track the spread of this advantageous trait over several generations. Ultimately, the students perform PCR and gel electrophoresis at two neutral markers, one located in close proximity to the eye-color locus, and one located at the other end of the chromosome. Students observe that most flies have red eyes, and these red-eyed flies have lost variation at the near marker, but maintained variation at the far marker, hence observing a "selective sweep" and the "hitchhiking" of a nearby neutral variant. Students literally observe phenotypic and molecular evolution in their classroom!}, number={4}, journal={Evolution: Education and Outreach}, publisher={Springer Nature}, author={Heil, Caiti S. S. and Hunter, Mika J. and Noor, Juliet K. F. and Miglia, Kathleen and Manzano-Winkler, Brenda and McDermott, Shannon R. and Noor, Mohamed A. F.}, year={2012}, month={Sep}, pages={629–634} }
 @article{heil_noor_2012, title={Zinc Finger Binding Motifs Do Not Explain Recombination Rate Variation within or between Species of Drosophila}, volume={7}, DOI={10.1371/journal.pone.0045055}, abstractNote={In humans and mice, the Cys2His2 zinc finger protein PRDM9 binds to a DNA sequence motif enriched in hotspots of recombination, possibly modifying nucleosomes, and recruiting recombination machinery to initiate Double Strand Breaks (DSBs). However, since its discovery, some researchers have suggested that the recombinational effect of PRDM9 is lineage or species specific. To test for a conserved role of PRDM9-like proteins across taxa, we use the Drosophila pseudoobscura species group in an attempt to identify recombination associated zinc finger proteins and motifs. We leveraged the conserved amino acid motifs in Cys2His2 zinc fingers to predict nucleotide binding motifs for all Cys2His2 zinc finger proteins in Drosophila pseudoobscura and identified associations with empirical measures of recombination rate. Additionally, we utilized recombination maps from D. pseudoobscura and D. miranda to explore whether changes in the binding motifs between species can account for changes in the recombination landscape, analogous to the effect observed in PRDM9 among human populations. We identified a handful of potential recombination-associated sequence motifs, but the associations are generally tenuous and their biological relevance remains uncertain. Furthermore, we found no evidence that changes in zinc finger DNA binding explains variation in recombination rate between species. We therefore conclude that there is no protein with a DNA sequence specific human-PRDM9-like function in Drosophila. We suggest these findings could be explained by the existence of a different recombination initiation system in Drosophila.}, number={9}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Heil, Caiti S. S. and Noor, Mohamed A. F.}, editor={Singh, NadiaEditor}, year={2012}, month={Sep}, pages={e45055} }
 @article{smukowski_noor_2011, title={Recombination rate variation in closely related species}, volume={107}, DOI={10.1038/hdy.2011.44}, abstractNote={Despite their importance to successful meiosis and various evolutionary processes, meiotic recombination rates sometimes vary within species or between closely related species. For example, humans and chimpanzees share virtually no recombination hotspot locations in the surveyed portion of the genomes. However, conservation of recombination rates between closely related species has also been documented, raising an apparent contradiction. Here, we evaluate how and why conflicting patterns of recombination rate conservation and divergence may be observed, with particular emphasis on features that affect recombination, and the scale and method with which recombination is surveyed. Additionally, we review recent studies identifying features influencing fine-scale and broad-scale recombination patterns and informing how quickly recombination rates evolve, how changes in recombination impact selection and evolution in natural populations, and more broadly, which forces influence genome evolution.}, number={6}, journal={Heredity}, publisher={Springer Nature}, author={Smukowski, C S and Noor, M A F}, year={2011}, month={Jun}, pages={496–508} }