Daniel Hartl

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc Model transcriptional networks with continuously varying expression levels
    Mauricio O Carneiro
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    BMC Evol Biol 11:363. 2011
  2. pmc Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence
    Daniel E Neafsey
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Genome Biol 9:R171. 2008
  3. pmc The latest buzz in comparative genomics
    Rob J Kulathinal
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Genome Biol 6:201. 2005
  4. pmc Fine-scale genetic mapping of a hybrid sterility factor between Drosophila simulans and D. mauritiana: the varied and elusive functions of "speciation genes"
    Luciana O Araripe
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    BMC Evol Biol 10:385. 2010
  5. ncbi request reprint The origin of malaria: mixed messages from genetic diversity
    Daniel L Hartl
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Nat Rev Microbiol 2:15-22. 2004
  6. ncbi request reprint Gene conversion as a source of nucleotide diversity in Plasmodium falciparum
    Kaare M Nielsen
    Department of Organismic and Evolutionary Biology, Harvard University, USA
    Mol Biol Evol 20:726-34. 2003
  7. pmc Mud sticks: on the alleged falsification of Mendel's data
    Daniel L Hartl
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 175:975-9. 2007
  8. pmc James F. Crow and the art of teaching and mentoring
    Daniel L Hartl
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 189:1129-33. 2011
  9. ncbi request reprint EST! EST!! EST!!!
    D L Hartl
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Bioessays 18:1021-3. 1996
  10. ncbi request reprint What restricts the activity of mariner-like transposable elements
    D L Hartl
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Trends Genet 13:197-201. 1997

Research Grants

  1. Evolutionary Genomics of Drosophila
    Daniel Hartl; Fiscal Year: 2005
  2. GENETICS OF A NEWLY EVOLVED TESTES SPECIFIC GENE SDIC
    Daniel Hartl; Fiscal Year: 2000
  3. GENOME EVOLUTION AND THE INSERTION/DELETION SPECTRUM
    Daniel Hartl; Fiscal Year: 2001
  4. Evolutionary Genomics of Drosophila
    Daniel Hartl; Fiscal Year: 2007
  5. Complex Genetics of D-M Incompatibilities
    Daniel Hartl; Fiscal Year: 2006
  6. Evolutionary Genomics of Drosophila
    Daniel Hartl; Fiscal Year: 2006
  7. The Evolution of Malerial Antifiolate Resistance
    Daniel Hartl; Fiscal Year: 2007
  8. The Evolution of Malerial Antifiolate Resistance
    Daniel Hartl; Fiscal Year: 2009
  9. Novel genomic effects of Y-linked polymorphisms
    Daniel Hartl; Fiscal Year: 2009
  10. Evolution of Genome Incompatibilities
    Daniel Hartl; Fiscal Year: 2009

Detail Information

Publications83

  1. pmc Model transcriptional networks with continuously varying expression levels
    Mauricio O Carneiro
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    BMC Evol Biol 11:363. 2011
    ..In our model, each network is described by a matrix representing the interactions between transcription factors, and a vector of continuous values representing the transcription factor expression in an individual...
  2. pmc Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence
    Daniel E Neafsey
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Genome Biol 9:R171. 2008
    ..To that end, we have developed a high throughput single nucleotide polymorphism (SNP) genotyping platform for P. falciparum...
  3. pmc The latest buzz in comparative genomics
    Rob J Kulathinal
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Genome Biol 6:201. 2005
    ..The publication of the Drosophila pseudoobscura sequence provides a snapshot of how genomes have changed over tens of millions of years and sets the stage for the analysis of more fly genomes...
  4. pmc Fine-scale genetic mapping of a hybrid sterility factor between Drosophila simulans and D. mauritiana: the varied and elusive functions of "speciation genes"
    Luciana O Araripe
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    BMC Evol Biol 10:385. 2010
    ..In the current work we used marked P-element insertions as dominant markers to efficiently locate one genetic factor causing a severe reduction in fertility in hybrid males of Drosophila simulans and D. mauritiana...
  5. ncbi request reprint The origin of malaria: mixed messages from genetic diversity
    Daniel L Hartl
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Nat Rev Microbiol 2:15-22. 2004
    ..Patterns of genetic variation in mitochondrial DNA support this model, but variation in nuclear genes gives an ambiguous message. Resolving these discrepancies has implications for the evolution of drug resistance and vaccine evasion...
  6. ncbi request reprint Gene conversion as a source of nucleotide diversity in Plasmodium falciparum
    Kaare M Nielsen
    Department of Organismic and Evolutionary Biology, Harvard University, USA
    Mol Biol Evol 20:726-34. 2003
    ..The 5' and 3' flanking regions differ in 47.7% and 39.8% of the nucleotide sites, respectively. Hence synonymous sites and flanking regions are not conserved in sequence in spite of their high AT content and T skew...
  7. pmc Mud sticks: on the alleged falsification of Mendel's data
    Daniel L Hartl
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 175:975-9. 2007
  8. pmc James F. Crow and the art of teaching and mentoring
    Daniel L Hartl
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 189:1129-33. 2011
    ..This Perspective examines Professor Crow as teacher and mentor through the eyes and experiences of one student who was enrolled in his genetics course as an undergraduate and who later studied with him as a graduate student...
  9. ncbi request reprint EST! EST!! EST!!!
    D L Hartl
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Bioessays 18:1021-3. 1996
    ..In each region, the phenotypes of all known human diseases were compared with the phenotypes of known Drosophila mutations in order to identify candidate genes for the human diseases. Are the correspondences real or coincidental?..
  10. ncbi request reprint What restricts the activity of mariner-like transposable elements
    D L Hartl
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Trends Genet 13:197-201. 1997
    ....
  11. ncbi request reprint Modern thoughts on an ancyent marinere: function, evolution, regulation
    D L Hartl
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Annu Rev Genet 31:337-58. 1997
    ....
  12. ncbi request reprint Molecular melodies in high and low C
    D L Hartl
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Nat Rev Genet 1:145-9. 2000
    ..The difference in genome size of a factor of 100 is difficult to explain in view of the apparently similar levels of evolutionary, developmental and behavioural complexity of these organisms...
  13. ncbi request reprint The paradoxical population genetics of Plasmodium falciparum
    Daniel L Hartl
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave, Cambridge, MA 02138, USA
    Trends Parasitol 18:266-72. 2002
    ..Resolution of this issue is important for the evaluation of the long-term efficacy of drug and immunological control strategies...
  14. ncbi request reprint Sex-dependent gene expression and evolution of the Drosophila transcriptome
    Jose M Ranz
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Science 300:1742-5. 2003
    ..Our results suggest that sex-dependent selection may drive changes in expression of many of the most rapidly evolving genes in the Drosophila transcriptome...
  15. ncbi request reprint Compensated deleterious mutations in insect genomes
    Rob J Kulathinal
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Science 306:1553-4. 2004
    ..Surprisingly, the fraction 10% is not affected by phylogenetic distance. These results support a selection-driven process that allows compensated amino acid substitutions to become rapidly fixed in taxa with large populations...
  16. ncbi request reprint Convergent loss of an anciently duplicated, functionally divergent RH2 opsin gene in the fugu and Tetraodon pufferfish lineages
    Daniel E Neafsey
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Gene 350:161-71. 2005
    ..Interspecific comparison of the remaining fugu RH2-2 coding sequence paradoxically indicates that the gene was under strong purifying selection until the truncation occurred...
  17. ncbi request reprint The evolution of the novel Sdic gene cluster in Drosophila melanogaster
    Rita Ponce
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Gene 376:174-83. 2006
    ..There is also a retrotransposon located at the 3' end of each Sdic gene copy. We argue that this gene cluster was formed in the last two million years by at least three tandem duplications and one retrotransposition event...
  18. pmc Systems-level analysis and evolution of the phototransduction network in Drosophila
    Christian R Landry
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 104:3283-8. 2007
    ..These results provide a preliminary quantification of variation and divergence of gene expression between species in a known gene network and provide a foundation for a system-level understanding of functional and evolutionary change...
  19. pmc Anomalies in the expression profile of interspecific hybrids of Drosophila melanogaster and Drosophila simulans
    Jose M Ranz
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genome Res 14:373-9. 2004
    ..The net result of the multiple incompatibilities is that the gene-expression profiles of the parental females are more similar to each other than either is to that of the hybrid...
  20. pmc Overdispersion of the molecular clock: temporal variation of gene-specific substitution rates in Drosophila
    Trevor Bedford
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
    Mol Biol Evol 25:1631-8. 2008
    ..Also, the presence of substantial variation in gene-specific substitution rates has broad implications for work in phylogeny reconstruction and evolutionary rate estimation...
  21. pmc A sex-ratio meiotic drive system in Drosophila simulans. II: an X-linked distorter
    Yun Tao
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
    PLoS Biol 5:e293. 2007
    ..We postulate that recurrent bouts of sex-ratio meiotic drive and its subsequent suppression might underlie several common features observed in the heterogametic sex, including meiotic sex chromosome inactivation and achiasmy...
  22. ncbi request reprint Population genetic variation in genome-wide gene expression
    Jeffrey P Townsend
    Department of Organismic and Evolutionary Biology, Harvard University, USA
    Mol Biol Evol 20:955-63. 2003
    ..Genetic variation in gene expression among isolates from a natural population is present on a genomic scale. It remains to be determined what role differential gene expression may play in adaptation to new or changing environments...
  23. pmc Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments
    Jeffrey P Townsend
    Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
    Genome Biol 3:RESEARCH0071. 2002
    ..This framework can be used to analyze normalized microarray data acquired by any replicated experimental design in which any number of treatments, genotypes, or developmental states are studied using a continuous chain of comparisons...
  24. pmc Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks
    Paul Grosu
    Bauer Center for Genomics Research, Harvard University, Cambridge, Massachusetts 02138, USA
    Genome Res 12:1121-6. 2002
    ..This program features a graphical output displaying differences in expression on metabolic charts of the biochemical pathways to which the open reading frames are assigned...
  25. pmc Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila
    Christian R Landry
    Department of Organismic and Evolutionary Biology, The Biological Laboratories, 16 Divinity Avenue, Harvard University, Cambridge, MA 02138, USA
    Genetics 171:1813-22. 2005
    ..Using a mathematical model for the regulation of gene expression, we explored the conditions under which cis-trans compensatory evolution can lead to misexpression in interspecific hybrids...
  26. ncbi request reprint Genome evolution and developmental constraint in Caenorhabditis elegans
    Cristian I Castillo-Davis
    Department of Organismic and Evolutionary Biology, Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Mol Biol Evol 19:728-35. 2002
    ..Developmental constraint at the level of gene duplication may have important implications for macroevolutionary change...
  27. doi request reprint Patterns of polymorphism in genomic regions flanking three highly polymorphic surface antigens in Plasmodium falciparum
    Olukemi K Amodu
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Mol Biochem Parasitol 159:1-6. 2008
    ..A higher ratio of SNPs to indels than previously reported for P. falciparum was observed. An 11 bp repeat upstream of msp2 showed an intriguing pattern of polymorphism possibly suggestive of purifying selection on total allele length...
  28. ncbi request reprint Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes
    Christian R Landry
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA, USA
    Gene 366:343-51. 2006
    ..We also found that genes with genetic variation for plasticity were less likely to be essential and were significantly biased towards genes that have paralogs...
  29. ncbi request reprint Origin and evolution of a new gene expressed in the Drosophila sperm axoneme
    José María Ranz
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 33143, USA
    Genetica 118:233-44. 2003
    ..The implications of these findings are discussed relative to the origin of new gene functions and the process of speciation...
  30. ncbi request reprint Evolution of noncoding and silent coding sites in the Plasmodium falciparum and Plasmodium reichenowi genomes
    Daniel E Neafsey
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
    Mol Biol Evol 22:1621-6. 2005
    ..Divergence rates of different classes of silent sites in these Plasmodium genomes are determined by a combination of mutational and selective pressures...
  31. pmc Formation and longevity of chimeric and duplicate genes in Drosophila melanogaster
    Rebekah L Rogers
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 181:313-22. 2009
    ..Our results paint a dynamic picture of both chimeras and duplicate genes within the genome and suggest that chimeric genes contribute substantially to genomic novelty...
  32. pmc Epigenetic memory at malaria virulence genes
    Thanat Chookajorn
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 104:899-902. 2007
    ..We also discuss how gene transcription memory may affect the mechanism of pathogenesis and immune evasion...
  33. ncbi request reprint On the abundance, amino acid composition, and evolutionary dynamics of low-complexity regions in proteins
    Mark A DePristo
    Department of Organismic and Evolutionary Biology, Hartl Lab, 16 Divinity Street, Harvard University, Cambridge, MA 02138, USA
    Gene 378:19-30. 2006
    ..We conclude with a mechanistic model for LCR evolution that links the pattern of LCRs within P. falciparum to its high genomic A+T content and recombination rate...
  34. ncbi request reprint Genetic properties influencing the evolvability of gene expression
    Christian R Landry
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Science 317:118-21. 2007
    ..These results provide a mechanistic basis for gene expression evolvability that can serve as a foundation for realistic models of regulatory evolution...
  35. pmc Epigenetic effects of polymorphic Y chromosomes modulate chromatin components, immune response, and sexual conflict
    Bernardo Lemos
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 107:15826-31. 2010
    ....
  36. pmc Optimization of gene expression by natural selection
    Trevor Bedford
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 106:1133-8. 2009
    ..These findings highlight the power of natural selection to shape phenotype, even when the fitness effects of mutations are in the nearly neutral range...
  37. pmc Genetic dissection of hybrid incompatibilities between Drosophila simulans and D. mauritiana. I. Differential accumulation of hybrid male sterility effects on the X and autosomes
    Yun Tao
    DCMB and Department of Zoology, Duke University, Durham, NC 27708, USA
    Genetics 164:1383-97. 2003
    ..Possible mechanisms of a "large X" effect include selective fixation of new mutations that are recessive or partially recessive and the evolution of sex-ratio distortion systems...
  38. pmc Stepwise acquisition of pyrimethamine resistance in the malaria parasite
    Elena R Lozovsky
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 106:12025-30. 2009
    ..Our results also suggest an explanation for why I164L is detected in Southeast Asia and South America, but not at significant frequencies in Africa...
  39. pmc Overdispersion of the molecular clock varies between yeast, Drosophila and mammals
    Trevor Bedford
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 179:977-84. 2008
    ..Our research suggests that mutational robustness is more pervasive in organisms with large population sizes and that robustness acts to stabilize the molecular evolutionary clock of sequence change...
  40. pmc Adaptive impact of the chimeric gene Quetzalcoatl in Drosophila melanogaster
    Rebekah L Rogers
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 107:10943-8. 2010
    ..Together, these results show that chimeric genes can produce structural and regulatory changes in a single mutational step and may be a major factor in adaptive evolution...
  41. pmc Y not a dead end: epistatic interactions between Y-linked regulatory polymorphisms and genetic background affect global gene expression in Drosophila melanogaster
    Pan Pan Jiang
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 186:109-18. 2010
    ....
  42. ncbi request reprint Cascading transcriptional effects of a naturally occurring frameshift mutation in Saccharomyces cerevisiae
    Kyle M Brown
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Mol Ecol 17:2985-97. 2008
    ....
  43. pmc Dominance and the evolutionary accumulation of cis- and trans-effects on gene expression
    Bernardo Lemos
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 105:14471-6. 2008
    ..We suggest that widespread regulatory effects of recessive low-frequency homozygous variation may provide a general mechanism mediating disease phenotypes and the genetic load of natural populations...
  44. doi request reprint Polymorphic Y chromosomes harbor cryptic variation with manifold functional consequences
    Bernardo Lemos
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Science 319:91-3. 2008
    ..Functionally, they affect microtubule stability, lipid and mitochondrial metabolism, and the thermal sensitivity of spermatogenesis. Our findings provide a mechanism for adaptive phenotypic variation associated with the Y chromosome...
  45. pmc A portrait of copy-number polymorphism in Drosophila melanogaster
    Erik B Dopman
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 104:19920-5. 2007
    ..Most patterns of CNP in D. melanogaster suggest that negative selection and mutational biases are the primary agents responsible for shaping structural variation...
  46. pmc Very little intron loss/gain in Plasmodium: intron loss/gain mutation rates and intron number
    Scott William Roy
    Department of Organismic and Evolutionary Biology, Harvard, Cambridge, Massachusetts 02138, USA
    Genome Res 16:750-6. 2006
    ..The observed pattern suggests that the availability of stochastic intron loss and gain mutations can be a major determinant of changes in intron number...
  47. ncbi request reprint Position-specific polymorphism of Plasmodium falciparum Stuttering motif in a PHISTc PFI1780w
    Thanat Chookajorn
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Exp Parasitol 114:126-8. 2006
    ..The repeat variation was analyzed in different strains of P. falciparum. The PFI1780w Stuttering motif can be a model to study gene diversification and used as a tool for strain typing...
  48. ncbi request reprint Darwinian evolution can follow only very few mutational paths to fitter proteins
    Daniel M Weinreich
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Science 312:111-4. 2006
    ..This implies that the protein tape of life may be largely reproducible and even predictable...
  49. pmc Identification of a locus under complex positive selection in Drosophila simulans by haplotype mapping and composite-likelihood estimation
    Colin D Meiklejohn
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 168:265-79. 2004
    ....
  50. ncbi request reprint Regulatory evolution across the protein interaction network
    Bernardo Lemos
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Nat Genet 36:1059-60. 2004
    ..Our results suggest that interacting proteins undergo similar evolutionary dynamics, and that their expression levels are evolutionarily coupled. These patterns hold for organisms as diverse as budding yeast and fruit flies...
  51. ncbi request reprint The cost of inbreeding in Arabidopsis
    Carlos D Bustamante
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA
    Nature 416:531-4. 2002
    ....
  52. ncbi request reprint Accelerated rates of intron gain/loss and protein evolution in duplicate genes in human and mouse malaria parasites
    Cristian I Castillo-Davis
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Masschusetts, USA
    Mol Biol Evol 21:1422-7. 2004
    ....
  53. ncbi request reprint Evidence for S. cerevisiae fermentation in ancient wine
    Duccio Cavalieri
    Bauer Center for Genomics Research, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
    J Mol Evol 57:S226-32. 2003
    ..This inference has major implications for the evolution of bread and beer yeasts, since it suggests that S. cerevisiae yeast, which occurs naturally on the surface bloom of grapes, was also used as an inoculum to ferment cereal products...
  54. ncbi request reprint Genetic dissection of hybrid incompatibilities between Drosophila simulans and D. mauritiana. III. Heterogeneous accumulation of hybrid incompatibilities, degree of dominance, and implications for Haldane's rule
    Yun Tao
    Developmental, Cell and Molecular Biology Group, Department of Zoology, Duke University, Durham, North Carolina 27708, USA
    Evolution 57:2580-98. 2003
    ..This hypothesis not only explains Haldane's rule in a simple way, but also suggests that genomic conflicts play a major role in evolution and speciation...
  55. pmc Genetic dissection of hybrid incompatibilities between Drosophila simulans and D. mauritiana. II. Mapping hybrid male sterility loci on the third chromosome
    Yun Tao
    DCMB and Department of Zoology, Duke University, Durham, NC 27708, USA
    Genetics 164:1399-418. 2003
    ..These results are consistent with the gradual evolution of hybrid incompatibilities as a by-product of genetic divergence in allopatric populations...
  56. pmc Rapid evolution of male-biased gene expression in Drosophila
    Colin D Meiklejohn
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 100:9894-9. 2003
    ..This finding has implications for our understanding of the importance of sexual dimorphism for speciation and rates of phenotypic evolution...
  57. ncbi request reprint GeneMerge--post-genomic analysis, data mining, and hypothesis testing
    Cristian I Castillo-Davis
    Department of Organismic and Evolutionary Biology, Harvard University, Biological Laboratories, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Bioinformatics 19:891-2. 2003
    ..GeneMerge can perform analyses on a wide variety of genomic data quickly and easily and facilitates both data mining and hypothesis testing...
  58. ncbi request reprint Patterns of insertion and deletion in contrasting chromatin domains
    Justin P Blumenstiel
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Mol Biol Evol 19:2211-25. 2002
    ....
  59. ncbi request reprint Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions
    Bernardo Lemos
    Department of Organismic and Evolutionary Biology, Harvard University, USA
    Mol Biol Evol 22:1345-54. 2005
    ....
  60. ncbi request reprint Rates of divergence in gene expression profiles of primates, mice, and flies: stabilizing selection and variability among functional categories
    Bernardo Lemos
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Evolution 59:126-37. 2005
    ..Finally, we argue that differences in mRNA levels of the magnitudes observed herein could be explained by a remarkably small number of generations of directional selection...
  61. ncbi request reprint Ecological and evolutionary genomics of Saccharomyces cerevisiae
    Christian R Landry
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Mol Ecol 15:575-91. 2006
    ....
  62. ncbi request reprint Missense meanderings in sequence space: a biophysical view of protein evolution
    Mark A DePristo
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Nat Rev Genet 6:678-87. 2005
    ..We then advance a biophysical model of protein evolution that helps us to understand phenomena that range from the dynamics of molecular adaptation to the clock-like rate of protein evolution...
  63. pmc Evidence for maternally transmitted small interfering RNA in the repression of transposition in Drosophila virilis
    Justin P Blumenstiel
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 102:15965-70. 2005
    ..virilis. We also present evidence that the maternal inheritance of these endogenous siRNAs may contribute to maternal repression of Penelope...
  64. ncbi request reprint Different regulatory mechanisms underlie similar transposable element profiles in pufferfish and fruitflies
    Daniel E Neafsey
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
    Mol Biol Evol 21:2310-8. 2004
    ..Inference of regulatory processes governing TE profiles should take into account factors such as effective population size, incidence of inbreeding/outcrossing, and other species-specific traits...
  65. ncbi request reprint Genetic diversity and selection at the Plasmodium vivax apical membrane antigen-1 (PvAMA-1) locus in a Sri Lankan population
    Anusha M Gunasekera
    Department of Immunology and Infectious Diseases, Harvard School of Public Health, Harvard University, USA
    Mol Biol Evol 24:939-47. 2007
    ..Regions of this surface that show constrained variability may prove to be promising vaccine targets...
  66. pmc The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint
    Cristian I Castillo-Davis
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genome Res 14:802-11. 2004
    ..Thus, strong purifying selection appears to act on the same core cellular processes in both mammalian and nematode lineages, whereas positive and/or relaxed selection acts on different biological processes in each lineage...
  67. ncbi request reprint Conservation, relocation and duplication in genome evolution
    Cristian I Castillo-Davis
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Trends Genet 19:593-7. 2003
  68. ncbi request reprint Mutational reversions during adaptive protein evolution
    Mark A DePristo
    Department of Organismic and Evolutionary Biology, Harvard University, MA, USA
    Mol Biol Evol 24:1608-10. 2007
    ..Altogether, this discovery highlights the unusual and potentially circuitous routes natural selection can follow during adaptation...
  69. pmc Genome organization and gene expression shape the transposable element distribution in the Drosophila melanogaster euchromatin
    Pierre Fontanillas
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
    PLoS Genet 3:e210. 2007
    ....
  70. pmc Horizontal acquisition of divergent chromosomal DNA in bacteria: effects of mutator phenotypes
    Jeffrey P Townsend
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genetics 164:13-21. 2003
    ..We conclude that mutators can accelerate bacterial adaptation when desired genetic variability is present within DNA fragments of up to approximately 30% divergence...
  71. pmc The evolutionary landscape of antifolate resistance in Plasmodium falciparum
    Marna S Costanzo
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    J Genet 90:187-90. 2011
    ....
  72. pmc Genomic heterogeneity in the density of noncoding single-nucleotide and microsatellite polymorphisms in Plasmodium falciparum
    Sarah K Volkman
    Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, MA, USA
    Gene 387:1-6. 2007
    ....
  73. ncbi request reprint Excess polymorphisms in genes for membrane proteins in Plasmodium falciparum
    Sarah K Volkman
    Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
    Science 298:216-8. 2002
    ..Genetic variation is also enriched in subtelomeric regions, which account for 22% of the chromosome but 76% of the polymorphisms...
  74. pmc Genetic diversity in yeast assessed with whole-genome oligonucleotide arrays
    Elizabeth A Winzeler
    Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA
    Genetics 163:79-89. 2003
    ..This subtelomeric bias may arise through recombination between nonhomologous sequences because full-gene deletions are more common in these regions than in more central regions of the chromosome...
  75. ncbi request reprint Variable SNP density in aspartyl-protease genes of the malaria parasite Plasmodium falciparum
    Alyssa E Barry
    Peter Medawar Building for Pathogen Research and Zoology Department, University of Oxford, South Parks Road, Oxford, OX1 3SY, UK
    Gene 376:163-73. 2006
    ..We discuss the importance of diversity and local selection effects when choosing drug targets for intervention strategies...
  76. ncbi request reprint Plasmodium falciparum: worldwide sequence diversity and evolution of the malaria vaccine candidate merozoite surface protein-2 (MSP-2)
    Marcelo U Ferreira
    Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Av Prof Lineu Prestes 1374, 05508 900 São Paulo SP, Brazil
    Exp Parasitol 115:32-40. 2007
    ..1%) isolates, mostly from Africa. We found no evidence for an extremely ancient origin of allelic dimorphism at the msp-2 locus, predating P. falciparum speciation, in contrast with recent findings for other surface malarial antigens...
  77. ncbi request reprint Parasitology. A game of cat and mouth
    Sarah K Volkman
    Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
    Science 299:353-4. 2003
  78. ncbi request reprint DNA sequence artifacts and the estimation of time to the most recent common ancestor (TMRCA) of Plasmodium falciparum
    Alyssa E Barry
    The Peter Medawar Building for Pathogen Research and Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
    Mol Biochem Parasitol 130:143-7. 2003
  79. ncbi request reprint A genome-wide map of diversity in Plasmodium falciparum
    Sarah K Volkman
    Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, USA
    Nat Genet 39:113-9. 2007
    ..We provide an initial map of genetic diversity in P. falciparum and demonstrate its potential utility in identifying genes subject to recent natural selection and in understanding the population genetics of this parasite...
  80. ncbi request reprint Duplication, gene conversion, and genetic diversity in the species-specific acyl-CoA synthetase gene family of Plasmodium falciparum
    Lara L Bethke
    Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
    Mol Biochem Parasitol 150:10-24. 2006
    ..We also found that the gene encoding acyl-CoA binding protein has expanded and diversified in P. falciparum. We have described a new class of subtelomeric gene family with a unique capacity for diversity in P. falciparum...
  81. ncbi request reprint Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection
    Stanley A Sawyer
    Department of Mathematics, Washington University, St Louis, MO 63130, USA
    J Mol Evol 57:S154-64. 2003
    ..These results are model dependent and we discuss possible modifications of the model that might allow more neutral and nearly neutral amino acid replacements to be fixed...
  82. pmc Effects of X-linkage and sex-biased gene expression on the rate of adaptive protein evolution in Drosophila
    John F Baines
    Section of Evolutionary Biology, Department of Biology, University of Munich, 82152 Munich, Germany
    Mol Biol Evol 25:1639-50. 2008
    ....
  83. pmc Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila
    Stanley A Sawyer
    Department of Mathematics, Washington University, St Louis, MO 63130, USA
    Proc Natl Acad Sci U S A 104:6504-10. 2007
    ....

Research Grants25

  1. Evolutionary Genomics of Drosophila
    Daniel Hartl; Fiscal Year: 2005
    ..abstract_text> ..
  2. GENETICS OF A NEWLY EVOLVED TESTES SPECIFIC GENE SDIC
    Daniel Hartl; Fiscal Year: 2000
    ..Aim 5 recognizes Sdic as a candidate gene with a possible role in postmating reproductive isolation between D. melanogaster and D. simulans, which will be tested by interspecific germline transformation. ..
  3. GENOME EVOLUTION AND THE INSERTION/DELETION SPECTRUM
    Daniel Hartl; Fiscal Year: 2001
    ..Analysis of the limited data presently available for these pseudogenes yields inconclusive, and possibly inconsistent, results. ..
  4. Evolutionary Genomics of Drosophila
    Daniel Hartl; Fiscal Year: 2007
    ..abstract_text> ..
  5. Complex Genetics of D-M Incompatibilities
    Daniel Hartl; Fiscal Year: 2006
    ..melanogaster, D. simulans and D. mauritiana, and intrapopulation analysis of polymorphisms and haplotypes to look for evidence of recent selective sweeps. ..
  6. Evolutionary Genomics of Drosophila
    Daniel Hartl; Fiscal Year: 2006
    ..abstract_text> ..
  7. The Evolution of Malerial Antifiolate Resistance
    Daniel Hartl; Fiscal Year: 2007
    ..The research may prolong the effectiveness of present antifolates, and help in the development of new ones. ..
  8. The Evolution of Malerial Antifiolate Resistance
    Daniel Hartl; Fiscal Year: 2009
    ..The research may prolong the effectiveness of present antifolates, and help in the development of new ones. ..
  9. Novel genomic effects of Y-linked polymorphisms
    Daniel Hartl; Fiscal Year: 2009
    ..We predict that important phenotypic variation affecting human health and disease will ultimately be traced to variation in sequence repeats of noncoding DNA in the human Y chromosome. ..
  10. Evolution of Genome Incompatibilities
    Daniel Hartl; Fiscal Year: 2009
    ..Uncovering genome incompatibilities is likely to reveal novel molecular and cellular mechanisms that underlie reproductive isolation between species. ..
  11. Novel genomic effects of Y-linked polymorphisms
    Daniel L Hartl; Fiscal Year: 2010
    ..We predict that important phenotypic variation affecting human health and disease will ultimately be traced to variation in sequence repeats of noncoding DNA in the human Y chromosome. ..
  12. GENOME EVOLUTION AND THE INSERTION/DELETION SPECTRUM
    Daniel Hartl; Fiscal Year: 1999
    ..Analysis of the limited data presently available for these pseudogenes yields inconclusive, and possibly inconsistent, results. ..
  13. GENETICS OF A NEWLY EVOLVED TESTES SPECIFIC GENE SDIC
    Daniel Hartl; Fiscal Year: 1999
    ..Aim 5 recognizes Sdic as a candidate gene with a possible role in postmating reproductive isolation between D. melanogaster and D. simulans, which will be tested by interspecific germline transformation. ..
  14. GENOME EVOLUTION AND THE INSERTION/DELETION SPECTRUM
    Daniel Hartl; Fiscal Year: 2000
    ..Analysis of the limited data presently available for these pseudogenes yields inconclusive, and possibly inconsistent, results. ..
  15. GENETICS OF A NEWLY EVOLVED TESTES SPECIFIC GENE SDIC
    Daniel Hartl; Fiscal Year: 2001
    ..Aim 5 recognizes Sdic as a candidate gene with a possible role in postmating reproductive isolation between D. melanogaster and D. simulans, which will be tested by interspecific germline transformation. ..
  16. GENETICS OF A NEWLY EVOLVED TESTES SPECIFIC GENE SDIC
    Daniel Hartl; Fiscal Year: 2001
    ..Aim 5 recognizes Sdic as a candidate gene with a possible role in postmating reproductive isolation between D. melanogaster and D. simulans, which will be tested by interspecific germline transformation. ..
  17. GENOME EVOLUTION AND THE INSERTION/DELETION SPECTRUM
    Daniel Hartl; Fiscal Year: 2002
    ..Analysis of the limited data presently available for these pseudogenes yields inconclusive, and possibly inconsistent, results. ..
  18. GENETICS OF A NEWLY EVOLVED TESTES SPECIFIC GENE SDIC
    Daniel Hartl; Fiscal Year: 2003
    ..Aim 5 recognizes Sdic as a candidate gene with a possible role in postmating reproductive isolation between D. melanogaster and D. simulans, which will be tested by interspecific germline transformation. ..
  19. Complex Genetics of D-M Incompatibilities
    Daniel Hartl; Fiscal Year: 2003
    ..melanogaster, D. simulans and D. mauritiana, and intrapopulation analysis of polymorphisms and haplotypes to look for evidence of recent selective sweeps. ..
  20. Evolutionary Genomics of Drosophila
    Daniel Hartl; Fiscal Year: 2004
    ..abstract_text> ..
  21. Evolution of Genome Incompatibilities
    Daniel L Hartl; Fiscal Year: 2010
    ..Uncovering genome incompatibilities is likely to reveal novel molecular and cellular mechanisms that underlie reproductive isolation between species. ..