Browsing by Author "Hartl, Daniel"
Now showing items 1-20 of 55
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Accessible Mutational Trajectories for the Evolution of Pyrimethamine Resistance in the Malaria Parasite Plasmodium Vivax
Jiang, Pan-Pan Xueke; Corbett-Detig, Russell B.; Hartl, Daniel L.; Lozovsky, Elena (Springer Science + Business Media, 2013)Antifolate antimalarials, such as pyrimethamine, have experienced a dramatic reduction in therapeutic efficacy as resistance has evolved in multiple malaria species. We present evidence from one such species, Plasmodium ... -
Adaptive Landscape by Environment Interactions Dictate Evolutionary Dynamics in Models of Drug Resistance
Ogbunugafor, C. Brandon; Wylie, C. Scott; Diakite, Ibrahim; Weinreich, Daniel M.; Hartl, Daniel L. (Public Library of Science, 2016)The adaptive landscape analogy has found practical use in recent years, as many have explored how their understanding can inform therapeutic strategies that subvert the evolution of drug resistance. A major barrier to ... -
Adaptive Landscapes and Protein Evolution
Carneiro, Mauricio; Hartl, Daniel L. (National Academy of Sciences, 2010)The principles governing protein evolution under strong selection are important because of the recent history of evolved resistance to insecticides, antibiotics, and vaccines. One experimental approach focuses on studies ... -
Bayesian Analysis of Gene Expression Levels: Statistical Quantification of Relative mRNA Level across Multiple Strains or Treatments
Townsend, Jeffrey P; Hartl, Daniel L. (BioMed Central, 2002)Background: Methods of microarray analysis that suit experimentalists using the technology are vital. Many methodologies discard the quantitative results inherent in cDNA microarray comparisons or cannot be flexibly applied ... -
Biophysical principles predict fitness landscapes of drug resistance
Rodrigues, Joao Vierira; Bershtein, Shimon; Li, Annabel; Lozovsky, Elena; Hartl, Daniel L.; Shakhnovich, Eugene Isaacovitch (Proceedings of the National Academy of Sciences, 2016)Fitness landscapes of drug resistance constitute powerful tools to elucidate mutational pathways of antibiotic escape. Here, we de- veloped a predictive biophysics-based fitness landscape of trimeth- oprim (TMP) resistance ... -
Chimeric Genes as a Source of Rapid Evolution in Drosophila melanogaster
Rogers, Rebekah; Hartl, Daniel L. (Oxford University Press (OUP), 2011)Chimeric genes form through the combination of portions of existing coding sequences to create a new open reading frame. These new genes can create novel protein structures that are likely to serve as a strong source of ... -
Chromatin-Associated Proteins HP1 and Mod(mdg4) Modify Y-Linked Regulatory Variation in the Drosophila Testis
Branco, Alan; Hartl, Daniel L.; Silva, Bernardo Lemos (Genetics Society of America, 2013)Chromatin remodeling is crucial for gene regulation. Remodeling is often mediated through chemical modifications of the DNA template, DNA-associated proteins, and RNA-mediated processes. Y-linked regulatory variation (YRV) ... -
Compensatory Mutations Restore Fitness During the Evolution of Dihydrofolate Reductase
Brown, Kyle M.; Costanzo, Marna; Xu, Wenxin; Roy, Scott; Hartl, Daniel L. (Oxford University Press, 2010)Whether a trade-off exists between robustness and evolvability is an important issue for protein evolution. While traditional viewpoints have assumed that existing functions must be compromised by the evolution of novel ... -
Direct Gamete Sequencing Reveals No Evidence for Segregation Distortion in House Mouse Hybrids
Corbett-Detig, Russell; Jacobs-Palmer, Emily; Hartl, Daniel; Hoekstra, Hopi (Public Library of Science, 2015)Understanding the molecular basis of species formation is an important goal in evolutionary genetics, and Dobzhansky-Muller incompatibilities are thought to be a common source of postzygotic reproductive isolation between ... -
DNA-Binding Specificity Changes in the Evolution of Forkhead Transcription Factors
Nakagawa, So; Gisselbrecht, Stephen; Rogers, Julia Maria; Hartl, Daniel L.; Bulyk, Martha Leonia (Proceedings of the National Academy of Sciences, 2013)The evolution of transcriptional regulatory networks entails the expansion and diversification of transcription factor (TF) families. The forkhead family of TFs, defined by a highly conserved winged helix DNA-binding domain ... -
Effects of X-Linkage and Sex-Biased Gene Expression on the Rate of Adaptive Protein Evolution in Drosophila
Baines, John F.; Sawyer, Stanley A.; Hartl, Daniel L.; Parsch, John (Oxford University Press, 2008)Patterns of polymorphism and divergence in Drosophila protein-coding genes suggest that a considerable fraction of amino acid differences between species can be attributed to positive selection and that genes with sex-biased ... -
Epigenetic Effects of Polymorphic Y Chromosomes Modulate Chromatin Components, Immune Response, and Sexual Conflict
Silva, Bernardo Lemos; Hartl, Daniel L.; Branco, Alan T. (National Academy of Sciences, 2010)Genetic conflicts between sexes and generations provide a foundation for understanding the functional evolution of sex chromosomes and sexually dimorphic phenotypes. Y chromosomes of Drosophila contain multi-megabase ... -
Fine-scale genetic mapping of a hybrid sterility factor between Drosophila simulans and D. mauritiana: the varied and elusive functions of "speciation genes"
Araripe, Luciana Ordunha; Montenegro, Horácio; Lemos, Bernardo; Hartl, Daniel L. (BioMed Central, 2010)Background: Hybrid male sterility (HMS) is a usual outcome of hybridization between closely related animal species. It arises because interactions between alleles that are functional within one species may be disrupted in ... -
Fitness Trade-Offs in the Evolution of Dihydrofolate Reductase and Drug Resistance in Plasmodium falciparum
Costanzo, Marna S.; Brown, Kyle M.; Hartl, Daniel L. (Public Library of Science, 2011)Background: Patterns of emerging drug resistance reflect the underlying adaptive landscapes for specific drugs. In Plasmodium falciparum, the parasite that causes the most serious form of malaria, antifolate drugs inhibit ... -
Formation and Longevity of Chimeric and Duplicate Genes in Drosophila Melanogaster
Rogers, Rebekah Lee; Bedford, Trevor; Hartl, Daniel L. (Genetics Society of America, 2009)Historically, duplicate genes have been regarded as a major source of novel genetic material. However,recent work suggests that chimeric genes formed through the fusion of pieces of different genes may also contribute to ... -
Genetic incompatibilities are widespread within species
Corbett-Detig, Russell B.; Zhou, Jun; Clark, Andrew G.; Hartl, Daniel L.; Ayroles, Julien (Nature Publishing Group, 2013)The importance of epistasis—non-additive interactions between alleles—in shaping population fitness has long been a controversial topic, hampered in part by lack of empirical evidence1, 2, 3, 4. Traditionally, epistasis ... -
Genetic relatedness analysis reveals the cotransmission of genetically related Plasmodium falciparum parasites in Thiès, Senegal
Wong, Wesley; Griggs, Allison D.; Daniels, Rachel F.; Schaffner, Stephen F.; Ndiaye, Daouda; Bei, Amy K.; Deme, Awa B.; MacInnis, Bronwyn; Volkman, Sarah K.; Hartl, Daniel L.; Neafsey, Daniel E.; Wirth, Dyann F. (BioMed Central, 2017)Background: As public health interventions drive parasite populations to elimination, genetic epidemiology models that incorporate population genomics can be powerful tools for evaluating the effectiveness of continued ... -
Genetic Surveillance Detects Both Clonal and Epidemic Transmission of Malaria following Enhanced Intervention in Senegal
Daniels, Rachel Fath; Chang, Hsiao-Han; Séne, Papa Diogoye; Park, Danny C.; Neafsey, Daniel Edward; Schaffner, Stephen; Hamilton, Elizabeth Julia; Lukens, Amanda Kathleen; Van Tyne, Daria Natalie; Mboup, Souleymane; Sabeti, Pardis Christine; Ndiaye, Daouda; Wirth, Dyann Fergus; Hartl, Daniel L.; Cooke, Sarah Volkman (Public Library of Science, 2013)Using parasite genotyping tools, we screened patients with mild uncomplicated malaria seeking treatment at a clinic in Thiès, Senegal, from 2006 to 2011. We identified a growing frequency of infections caused by genetically ... -
Genome Organization and Gene Expression Shape the Transposable Element Distribution in the Drosophila Melanogaster Euchromatin
Fontanillas, Pierre; Hartl, Daniel L.; Reuter, Max; Malik, Harmit S (Public Library of Science, 2007)The distribution of transposable elements (TEs) in a genome reflects a balance between insertion rate and selection against new insertions. Understanding the distribution of TEs therefore provides insights into the forces ... -
Genome-Wide SNP Genotyping Highlights the Role of Natural Selection in Plasmodium Falciparum Population Divergence
Wirth, Dyann F.; Sabeti, Pardis C.; Lander, Eric S.; Birren, Bruce W.; Hartl, Daniel; Wiegand, Roger; Chitnis, Chetan E.; Dash, Aditya P.; do Lago Moraes, Sandra; Ferreira, Marcelo U.; Mboup, Soulyemane; Ndir, Omar; Ndiaye, Daouda; Ousmane, Sarr; Stange-Thomann, Nicole; Gates, Casey; Tyndall, Erin; Cortese, Joseph F.; Houde, Nathan; Daniels, Rachel; Rosen, David; Lukens, Amanda; Milner, Danny; Montgomery, Philip; Park, Daniel; Volkman, Sarah K.; Schaffner, Stephen F.; Neafsey, Daniel (BioMed Central, 2008)Background: The malaria parasite Plasmodium falciparum exhibits abundant genetic diversity, and this diversity is key to its success as a pathogen. Previous efforts to study genetic diversity in P. falciparum have begun ...