Hartl Lab publications

2011

  • Costanzo, M. S., K. M. Brown and D. L Hartl, 2011 Fitness trade-offs in the evolution of drug resistance in dihydrofolate reductase in Plasmodium falcipaurm. PLoS One 6: e19636. PDF
  • Costanzo, M. S. and D. L Hartl, 2011 The evolutionary landscape of antifolate resistance in Plasmodium falciparum. J. Genet. 90: 187-190. PDF
  • Geiler-Samerotte, K. A., M. F. Dion, B. A. Budnik, S. M. Wang, D. L. Hartl and D. A. Drummond 2011 Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast. Proc. Natl. Acad. Sci. USA 108: 680-685. PDF
  • Paredes, S., A. T. Branco, D. L. Hartl, K. A. Maggert and B. Lemos 2011 Ribosomal DNA deletions modulate genome-wide gene expression: "rDNA-sensitive" genes and natural variation. PLoS Genetics 7: e1001376. PDF
  • Sackton, T. B., H. Montenegro, D. L. Hartl, and B. Lemos, 2011 Interspecific Y chromosome introgressions disrupt testis-specific gene expression and male reproductive phenotypes in Drosophila. Proc. Natl. Acad. Sci. USA 108: 17046-17051. PDF
  • Van Tyne, D., D. J. Park, S. F. Schaffner, D. E. Neafsey, E. Angelino, J. F. Cortese, K. G. Barnes, D. M. Rosen, A. K. Lukens, R. F. Daniels, D. A. Milner, Jr., C. A. Johnson, I. Shlyakhter, S. R. Grossman, J. S. Becker, D. Yamins, E. K. Karlsson, D. Ndiaye, O. Sarr, S. Mboup, C. Happi, N. A. Furlotte, E. Eskin, H. M. Kang, D. L. Hartl, B. W. Birren, R. C. Wiegand, E. S. Lander, D. F. Wirth, S. K. Volkman, P. C. Sabeti, 2011. Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum. PLoS Genetics 4: e1001383. PDF
  • Zhou, J., B. Lemos, E. B. Dopman, and D. L. Hartl 2011 Copy number variation: The balance between gene dosage and expression in Drosophila melanogaster. Genome Biol. Evol. 3: 1014-1024. PDF

2010

  • Araripe, L. O., H. Montenegro, B. Lemos and D. L. Hartl, 2010 Fine-scale genetic mapping of a hybrid sterility factor between Drosophila simulans and D. mauritiana: The varied and elusive functions of "speciation genes." BMC Evol. Biol. 10: 385. PDF
  • Brown K. M., M. Costanzo, W. Xu, S. Roy, E. R. Lozovsky and D. L Hartl, 2010 Compensatory mutations restore fitness during the evolution of dihydrofolate reductase. Mol. Biol. Evol. 27: 2682-2690. PDF
  • Fontanillas, P., C. R. Landry, P. J. Wittkopp, C. Russ, J. D. Gruber, and D. L. Hartl, 2010 Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing. Mol. Ecol. 19 (Suppl. 1): 212-227. PDF
  • Gunawardena, S., N. D. Karunaweera, M. U. Ferreira, M. Phone-Kyaw, R. J. Pollack, M. Alifrangis, R. S. Rajakaruna, F. Konradsen, P. H. Amerasinghe, M. L. Schousboe, G. N. L. Galappaththy, R. R. Abeyasinghe, D. L. Hartl, and D. F. Wirth, 2010 Geographic structure of Plasmodium vivax: Microsatellite analysis of parasite populations from Sri Lanka, Myanmar and Ethiopia. Am. J. Trop. Med. Hyg. 82: 235-242. PDF
  • Jiang, P.-P., D. L. Hartl, and B. Lemos, 2010 Y not a dead end: Epistatic interactions between Y-linked regulatory polymorphisms and genetic background affect global gene expression. Genetics 186: 109-118. PDF
  • Kingan, S. B., D. Garrigan and D. L. Hartl, 2010 Recurrent selection on the Winters sex-ratio genes in Drosophila simulans. Genetics 184: 253–265. PDF
  • Lemos, B., A. Branco and D. L. Hartl, 2010 Epigenetic effects of polymorphic Y chromosomes modulate chromatin components, immune response, and sexual conflict. Proc. Natl. Acad. Sci. USA. 107: 15826-15831. PDF
  • Rogers, R. L., T. Bedford, A. M. Lyons and D. L. Hartl, 2010 Adaptive impact of the chimeric gene Quetzalcoatl in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 107: 10943-10948. PDF
  • Zilversmit, M. M., S K. Volkman, M. A. DePristo, D. F. Wirth, P. Awadalla and D. L. Hartl, 2010 Low-complexity regions in Plasmodium falciparum: Missing Links in the evolution of an extreme genome. Mol. Biol. Evol. 27: 2198-2209. PDF

2009

  • Bedford, T. and D. L. Hartl, 2009 Optimization of gene expression by natural selection. Proc. Natl. Acad. Sci. USA 106: 1133-1138. PDF
  • Brown, K. M., M. A. DePristo, D. M. Weinreich and D. L. Hartl, 2009 Temporal constraints on the incorporation of regulatory mutants in evolutionary pathways. Mol. Biol. Evol. 26: 2455–2462. PDF
  • Carneiro, M. and D. L. Hartl, 2010 Adaptive landscapes and protein evolution. Proc. Natl. Acad. Sci. USA 107 Suppl 1: 1747-1751. PDF
  • Lozovsky, E. R., T. Chookajorn, K. M. Brown, M. Imwong, P. J. Shaw, S. Kamchonwongpaisan, D. E. Neafsey, D. M. Weinreich, D. L. Hartl, 2009 Stepwise acquisition of pyrimethamine resistance in the malaria parasite. Proc. Natl. Acad. Sci. USA 106: 12025-12030. PDF
  • Mayer, D. C. G., J. Cofie, L. Jiang, D. L. Hartl, E. Tracy, J. Kabat, L. H. Mendoza , and L. H. Miller, 2009 Glycophorin B is the erythrocyte receptor of Plasmodium falciparum erythrocyte-binding ligand, EBL-1. Proc. Natl. Acad. Sci. USA 106: 5348-5352. PDF
  • Rogers, R. L., T. Bedford and D. L. Hartl, 2009 Formation and longevity of chimeric and duplicate genes in Drosophila melanogaster. Genetics 181: 313–322. PDF
  • Sackton, T. B., R. J. Kulathinal, C. M. Bergman, A. R. Quinlan, E. Dopman, G. T. Marth, M. Carneiro, E. Mardis, , D. L. Hartl and A. G. Clark, 2009 Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster. Genome Biol. Evol. 18: 449-465. PDF

2008

  • Amodu, O. K., D. L. Hartl, and S. W. Roy. 2008. Patterns of polymorphism in
    genomic regions flanking three highly polymorphic surface antigens in Plasmodium falciparum.
    Mol. Biochem. Parasitol. 159: 1-6. PDF
  • Baines, J. F., S. A. Sawyer, D. L. Hartl, and J. Parsch. 2008. Effects of X-linkage and sex-biased gene expression on the rate of adaptive protein evolution in Drosophila. Mol. Biol. Evol. In press.
  • Bedford, T., I. Wapinski, and D. L. Hartl. 2008. Overdispersion of the
    molecular clock varies between yeast, Drosophila and mammals. Genetics 179: 977-984. PDF
  • Bedford, T., and D. L. Hartl. 2008. Overdispersion of the molecular clock: temporal variation of gene-specific substitution rates in Drosophila. Mol. Biol. Evol. Advance access.
  • Brown, K. M., C. R. Landry, D. L. Hartl, and D. Cavalieri. 2008. Cascading transcriptional effects of a naturally occurring frameshift mutation in Saccharomyces cerevisiae. Mol. Ecol. 17: 2985-2997. PDF
  • Karunaweera, N. D., M. U. Ferreira, A. Munasinghe, J. W. Barnwell, W. E. Collins, C. L. King, F. Kawamoto, D. L. Hartl, and D. F. Wirth. 2008. Extensive microsatellite diversity in the human malaria parasite Plasmodium vivax. Gene 410: 105-112.
  • Lynch, M., W. Sung, K. Morris, N. Coffey, C. R. Landry, E. B. Dopman, W. J. Dickinson, K. Okamoto, S. Kulkarni, D. L. Hartl and W. K. Thomas. 2008 A genome-wide view of the spectrum of spontaneous mutations in yeast. Proc. Natl. Acad. Sci. USA 105: 9272-9277. PDF
  • Roy, S. W., M. U. Ferreira, and D. L. Hartl. 2008. Evolution of allelic dimorphism in malarial surface antigens. Heredity 100: 103-110. PDF

2007

  • Chookajorn, T., M. S. Costanzo, D. L. Hartl, and K. W. Deitsch. 2007. Malaria: a peek at the var variorum. Trends Parasitol. 23:563-565. PDF
  • Chookajorn, T., R. Dzikowski, M. Frank, F. Li, A. Z. Jiwani, D. L. Hartl, K. W. Deitsch. 2007. Epigenetic memory at malaria virulence genes. Proc. Natl. Acad. Sci. USA 104:899-902. PDF
  • DePristo, M. A., D. L. Hartl, and D. M. Weinreich. 2007. Mutational reversions during adaptive protein evolution. Mol. Biol. Evol. 24:1608-1610. PDF
  • Dopman, E. B., and D. L. Hartl. 2007. A portrait of copy-number polymorphism in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 104:19920-19925.PDF
  • Ferreira, M. U., and D. L. Hartl. 2007. Plasmodium falciparum: worldwide sequence diversity and evolution of the malaria vaccine candidate merozoite surface protein-2 (MSP-2). Exp. Parasitol. 115:32-40. PDF
  • Fontanillas, P., D. L. Hartl, and M. Reuter. 2007. Genome organization and gene expression shape the transposable element distribution in the Drosophila melanogaster euchromatin. PLoS Genet. 3:e210. PDF
  • Hartl, D. L., and D. J. Fairbanks. 2007. Mud sticks: on the alleged falsification of Mendel's data. Genetics 175:975-979. PDF
  • Landry, C. R., D. L. Hartl, and J. M. Ranz. 2007. Genome clashes in hybrids: insights from gene expression. Heredity. 99:483-493. PDF
  • Landry, C. R., B. Lemos, S. A. Rifkin, W. J. Dickinson, and D. L. Hartl. 2007. Genetic properties influencing the evolvability of gene expression. Science 317:118-121. PDF
  • Landry, C. R., C. I. Castillo-Davis, A. Ogura, J. S. Liu, and D. L. Hartl. 2007. Systems-level analysis and evolution of the phototransduction network in Drosophila. Proc. Natl. Acad. Sci. USA 104:3283-3288. PDF
  • Sawyer, S. A., J. Parsch, Z. Zhang, and D. L. Hartl. 2007. Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila. Proc. Natl. Acad. Sci. USA 104:6504-6510. PDF
  • Tao, Y., J. P. Masly, L. Araripe, Y. Ke, and D. L. Hartl. 2007. A sex-ratio meiotic drive system in Drosophila simulans. I: an autosomal suppressor. PLoS Biol. 5:e292. PDF
  • Tao, Y., L. Araripe, S. B. Kingan, Y. Ke, H. Xiao, and D. L. Hartl. 2007. A sex-ratio meiotic drive system in Drosophila simulans. II: an X-linked distorter. PLoS Biol. 5:e293. PDF
  • Volkman, S. K., E. Lozovsky, A. E. Barry, T. Bedford, L. Bethke, A. Myrick, K. P. Day, D. L. Hartl, D. F. Wirth, and S. A. Sawyer. 2007. Genomic heterogeneity in the density of noncoding single-nucleotide and microsatellite polymorphisms in Plasmodium falciparum. Gene 387:1-6. PDF

2006

  • Barry, A. E., A. Leliwa-Sytek, K. Man, J. M. Kasper, D. L. Hartl, and K. P. Day. 2006. Variable SNP density in aspartyl-protease genes of the malaria parasite Plasmodium falciparum. Gene 376:163-173.
  • Bethke, L. L., M. Zilversmit, K. Nielsen, J. Daily, S. K. Volkman, D. Ndiaye, E. R. Lozovsky, D. L. Hartl, and D. F. Wirth. 2006. Duplication, gene conversion, and genetic diversity in the species-specific acyl-CoA synthetase gene family of Plasmodium falciparum. Mol. Biochem. Parasitol. 150:10-24. PDF
  • Chookajorn, T., and D. L. Hartl. 2006. Position-specific polymorphism of Plasmodium falciparum Stuttering motif in a PHISTc PFI1780w. Exp. Parasitol. 114:126-128. PDF
  • DePristo, M. A., M. M. Zilversmit, and D. L. Hartl. 2006. On the abundance, amino acid composition, and evolutionary dynamics of low-complexity regions in proteins. Gene 378:19-30. PDF
  • Landry, C. R., J. P. Townsend, D. L. Hartl, and D. Cavalieri. 2006. Ecological and evolutionary genomics of Saccharomyces cerevisiae. Mol. Ecol. 15:575-591. PDF
  • Landry, C. R., J. Oh, D. L. Hartl, and D. Cavalieri. 2006. Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes. Gene 366:343-351. PDF
  • Ponce, R., and D. L. Hartl. 2006. The evolution of the novel Sdic gene cluster in Drosophila melanogaster. Gene 376:174-183. PDF
  • Roy, S. W., and D. L. Hartl. 2006. Very little intron loss/gain in Plasmodium: intron loss/gain mutation rates and intron number. Genome Res. 16:750-756. PDF
  • Weinreich, D. M., N. F. Delaney, M. A. Depristo, and D. L. Hartl. 2006. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312:111-114. PDF

2005 and prior years

  • Armstrong, P. A., S. M. Rich, R. D. Smith, D. L. Hartl, A. Spielman and S. R. Telford, III, 1996 A new Borrelia infecting Lone Star ticks. Lancet 347: 67-68.
  • Ayala, F. J., J. K. Wetterer, J. T. Longino, and D. L. Hartl, 1996 Molecular phylogeny of Azteca ants (Hymenoptera: Formicidae), and the colonization of Cecropia trees. Mol. Phylogen. Evol. 5: 423-428.
  • Bensasson, D., D-X. Zhang, D. L. Hartl, and G. M. Hewitt, 2001 Mitochondrial pseudogenes: evolution's misplaced witnesses. Trends Ecol. Evol. 16: 314-321. PDF
  • Bensasson, D., D. A. Petrov, D-X. Zhang, D. L. Hartl, and G. M. Hewitt, 2001 Genomic gigantism: DNA loss is slow in mountain grasshoppers. Mol. Biol. Evol. 18: 246-253. PDF
  • Blumenstiel, J. P., and D. L. Hartl. 2005. Evidence for maternally transmitted small interfering RNA in the repression of transposition in Drosophila virilis. Proc. Natl. Acad. Sci. USA 102:15965-15970. PDF
  • Blumenstiel, J. P., D. L. Hartl, and E. R. Lozovsky, 2002 Patterns of insertion and deletion in contrasting chromatin domains. Mol. Biol. Evol. 19(12): 2211-2225.
  • Boyd, E. F. and D. L. Hartl, 1999 Analysis of the type I pilin gene cluster fim in Salmonella: Its distinct evolutionary histories in the 5' and 3' regions. J. Bacteriol. 181: 1301-1308.
  • Boyd, E. F. and D. L. Hartl, 1998 Diversifying selection governs sequence polymorphism in the major adhesin proteins FimA, PapA, and SfaA of Escherichia coli. J. Mol. Evol. 47: 258-267.
  • Boyd, E. F. and D. L. Hartl, 1998 Chromosomal regions specific to pathogenic isolates of Escherichia coli have a phylogenetically clustered distribution. J. Bacteriol. 180: 1159-1165.
  • Boyd, E. F. and D. L. Hartl, 1998 Salmonella virulence plasmid: Modular acquisition of the spv virulence region by an F plasmid in S. enterica subspecies I and insertion into the chromosome of subspecies II, IIIa, IV and VII isolates. Genetics 149: 1183-1190.
  • Boyd, E. F. and D. L. Hartl, 1997 Recent horizontal transmission of plasmids between natural populations of Escherichia coli and Salmonella enterica. J. Bacteriol. 179: 1622-1627. PDF
  • Boyd, E. F. and D. L. Hartl, 1997 Nonrandom location of IS1 elements in the genomes of natural isolates of Escherichia coli. Mol. Biol. Evol. 14: 725-732.
  • Boyd, E. F., C. W. Hill, S. Rich, and D. L. Hartl, 1996 Mosaic structure of plasmids from natural populations of Escherichia coli. Genetics 143: 1091-1100.
  • Bustamante, C., R. Nielsen, and D. L. Hartl, 2003 Maximum likelihood and Bayesian methods for estimating the distribution of selective effects among classes of mutations using DNA polymorphism data. Theor. Pop. Biol. 63(2): 91-103. PDF
  • Bustamante, C., R. Nielsen, S. A. Sawyer, K. M. Olsen, M. D. Purugganan, and D. L. Hartl, 2002 The cost of inbreeding in Arabidopsis. Nature 416: 531-534. PDF
  • Bustamante, C. D., R. Nielsen, and D. L. Hartl, 2002 A maximum likelihood method for analyzing pseudogene evolution: Implications for silent site evolution in humans and rodents. Mol. Biol. Evol. 19: 110-117. PDF
  • Bustamante, C. D., J. R. Wakeley, S. Sawyer, and D. L. Hartl, 2001 Directional selection and the site-frequency spectrum. Genetics 159: 1779-1788. PDF
  • Bustamante, C., J. P. Townsend and D. L. Hartl, 2000 Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica. Mol. Biol. Evol. 17: 301-308. PDF
  • Castillo-Davis, C. I., D. L. Hartl, and G. Achaz. 2004. cis-regulatory and protein evolution in orthologous and duplicate genes. Genome Res. 14: 1530-1536. PDF
  • Castillo-Davis, C. I., T. B. Bedford, and D. L. Hartl. 2004. Accelerated rates of intron gain/loss and protein evolution in duplicate genes in human and mouse malaria parasites. Mol. Biol. Evol. 1422-1427. PDF
  • Castillo-Davis, C. I., F. A. Kondrashov, D. L. Hartl, and R. J. Kulathinal. 2004. The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint. Genome Res. 14: 802-811. PDF
  • Castillo-Davis, C. I., and D. L. Hartl, 2003 GeneMerge--post-genomic analysis, data mining, and hypothesis testing. Bioinformatics 19(7): 891-892. PDF
  • Castillo-Davis, C. I., S. L. Mekhedov, D. L. Hartl, E. V. Koonin, and F. A. Kondrashov, 2002 Selection for shorter introns in highly expressed genes. Nature Genet. 31: 415-418. PDF
  • Castillo-Davis, C. I., and D. L. Hartl, 2002 Genome evolution and developmental constraint in Caenorhabditis elegans. Mol. Biol. Evol. 19: 728-735. PDF
  • Cavalieri, D., P. E. McGovern, D. L. Hartl, R. Mortimer, and M. Polsinelli. 2003. Evidence for S. cerevisiae fermentation in ancient wine. J. Mol. Evol. 57: S226-S232. PDF
  • Cavalieri, D., J. P. Townsend and D. L. Hartl, 2000 Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis. Proc. Natl. Acad. Sci. USA 97: 12369-12374. PDF
  • Chang, B. S. W., K. A. Crandall, J. P. Carulli, and D. L. Hartl, 1995 Opsin phylogeny and evolution: A model for blue shifts in wavelength regulation. Mol. Phylogenet. Evol. 4: 31-43.
  • Coelho, P. A., J. Queiroz-Machado, D. L. Hartl and C. E. Sunkel, 1998 Pattern of chromosomal localization of the Hoppel transposable element family in the Drosophila melanogaster subgroup. Chromosome Research 6: 385-395.
  • Coelho, P. A., D. I. Nurminsky, D. L. Hartl and C. E. Sunkel, 1996 Identification of Porto-1, a new repeated sequence that localizes close to the centromere of chromosome 2 of Drosophila melanogaster. Chromosoma 105: 211-222.
  • De Aguiar, D. and D. L. Hartl, 1999 Regulatory potential of nonautonomous mariner elements and subfamily crosstalk. Genetica 107: 79-85.
  • DePristo, M. A., D. M. Weinreich, and D. L. Hartl. 2005. Missense meanderings in sequence space: a biophysical view of protein evolution. Nature Rev. Genet. 6: 678-687. PDF
  • Fadool, J. M., D. L. Hartl and J. E. Dowling, 1998 Transposition of the mariner element from Drosophila mauritiana in zebrafish. Proc. Natl. Acad. Sci. USA 95: 5182-5186.
  • Goldfeld, A. E., J. Y. Leung, S. A. Sawyer and D. L. Hartl, 2000 Post-genomics and the neutral theory: Variation and conservation in the TNF-a promoter. Gene 30: 19-25.
  • Grosu, P., J. P. Townsend, D. L. Hartl and D. Cavalieri, 2002 Pathway Processor: A tool for integrating whole-genome expression results into metabolic networks. Genome Research 12: 1121-1126. PDF
  • Hartl, D. L. 2004. The origin of malaria: mixed messages from genetic diversity. Nat. Rev. Micobiol. 2: 15-22. PDF
  • Hartl, D. L., C. D. Meiklejohn, C. I. Castillo-Davis, D. Cavalieri, J. M. Ranz, and J. P. Townsend, 2003 Gene expression profiling in evolutionary genetics. In The Evolution of Population Biology: Modern Synthesis, Eds. R. Singh, S. Jain, and M. Uyenoyama. Cambridge University Press, Cambridge. PDF
  • Hartl, D. L., S. K. Volkman, K. M. Nielsen, A. E. Barry, K. P. Day, D. F. Wirth, and E. A. Winzeler, 2002 The paradoxical population genetics of Plasmodium falciparum. Trends Parasit. 18: 266-272. PDF
  • Hartl, D. L., 2001 Genetic management of Gold Standard outbred laboratory populations. Charles River Laboratories, Wilmington, MA, technical documents.
  • Hartl, D. L., 2001 Discovery of the transposable element mariner. Genetics 157: 471-476. PDF
  • Hartl, D. L., 2000 Molecular melodies in high and low C. Nature Rev. Genet. 1: 145-149. PDF
  • Hartl, D. L., E. F. Boyd, C. D. Bustamante and S. A. Sawyer, 2000 The glean machine: What can we learn from DNA sequence polymorphisms? pp. 37-49 in Sandor Suhai (editor) Genomics and Proteomics, Plenum Press, New York.
  • Hartl, D. L. 2000 Fly meets shotgun: Shotgun wins. Nature Genetics 24: 327-328. PDF
  • Hartl, D. L. and C. H. Taubes, 1998 Towards a theory of evolutionary adaptation. Genetica 102/103: 525-533. PDF
  • Hartl, D. L., A. R. Lohe, and E. R. Lozovskaya, 1997 Regulation of the transposable element mariner. Genetica 100: 177-184.
  • Hartl, D. L., A. R. Lohe, and E. R. Lozovskaya, 1997 Modern thoughts on an ancyent marinere: Function, evolution, regulation. Ann. Rev. Genet. 31: 337-358. PDF
  • Hartl, D. L., 1997 Mariner sails into Leishmania. Science 276: 1659-1660.
  • Hartl, D. L., 1997 Mendel and Galton: contrasting approaches to the study of heredity. The Mendel Newsletter, New Series, No. 6 (February 1997) pp. 1-8.
  • Hartl, D. L., E. R. Lozovskaya, D. I. Nurminsky, and A. R. Lohe, 1997 What restricts the activity of mariner-like transposable elements? Trends Genet. 13: 197-201.
  • Hartl, D. L., 1996 EST! EST!! EST!!! BioEssays 12: 1021-1023.
  • Hartl, D. L., and C. H. Taubes, 1996 Compensatory nearly neutral mutations: selection without adaptation. J. Theor. Biol. 182: 303-309.
  • Hartl, D. L., 1996 The most unkindest cut of all. Nature Genetics 12: 227-229.
  • Hartl, D. L. and H. Ochman, 1996 Inverse polymerase chain reaction, pp. 293-301 in A. J. Harwood (editor), Methods in Molecular Biology, Volume 58: Basic DNA and RNA Protocols, Humana Press, Totowa, New Jersey. (Reprint of Hartl, D. L. and H. Ochman, 1994 Inverse polymerase chain reaction, pp. 187-196 in A. J. Harwood (editor), Methods in Molecular Biology, Volume 31: Protocols for Gene Analysis, Humana Press, Totowa, New Jersey.)
  • Hartl, D. L., F. C. Kafatos and S. J. O'Brien, 1995 Editorial overview: Genome evolution comes of age. Current Opinion in Genetics and Development 5: 705-708.
  • Hartl, D. L., D. I. Nurminsky, R. W. Jones, and E. R. Lozovskaya, 1995 Genome structure and evolution in Drosophila: Applications of the framework P1 map, pp. 299-314 in W. M. Fitch and F. J. Ayala (editors) Tempo and Mode in Evolution, National Academy of Sciences, Washington, DC. (Reprint of Hartl, D. L., D. I. Nurminsky, R. W. Jones, and E. R. Lozovskaya, 1994 Proc. Natl. Acad. Sci. USA 91: 6824-6829.)
  • Kulathinal, R. J., and D. L. Hartl. 2005. The latest buzz in comparative genomics. Genome Biol. 6: 201. PDF
  • Kulathinal, R. J., B. R. Bettencourt, and D. L. Hartl. 2004. Compensated deleterious mutations in insect genomes. Science 306: 1553-1554. PDF
  • Landry, C. R., P. J. Wittkopp, C. H. Taubes, J. M. Ranz, A. G. Clark, and D. L. Hartl. 2005. Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila. Genetics 171:1813-1822.
  • Lemos, B., B. R. Bettencourt, C. D. Meiklejohn, and D. L. Hartl. 2005. 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. Mol. Biol. Evol. 22: 1345-1354. PDF
  • Lemos, B., C. D. Meiklejohn, M. Caceres, and D. L. Hartl. 2005. Rates of divergence in gene expression profiles of primates, mice, and flies: stabilizing selection and variability among functional categories. Evolution 59: 126-137. PDF
  • Lemos, B., C. D. Meiklejohn, and D. L. Hartl. 2004. Regulatory evolution across the protein interaction network. Nat. Genet. 36: 1059-1060. PDF
  • Leung, J. Y., F. E. McKenzie, A. M. Uglialoro, P. O. Flores-Villaneuva, B. C. Sorkin, E. J. Yunis, D. L. Hartl and A. E. Goldfeld, 2000 Identification of phylogenetic footprints in primate tumor necrosis factor-a promoters. Proc. Natl Acad. Sci. USA 97: 6614-6618.
  • Lohe, A. R. and D. L. Hartl, 2002 Efficient mobilization of mariner in vivo requires multiple internal sequences. Genetics 160: 519-526. PDF
  • Lohe, A. R., C. Timmons, I. Beerman, E. R. Lozovskaya, D. L. Hartl, 2000 Self-inflicted wounds, template-directed gap repair, and a recombination hotspot: Effects of the mariner transposase. Genetics 154: 647-656. PDF
  • Lohe, A. R., D. De Aguiar and D. L. Hartl, 1997 Mutations in the mariner transposase: The "D,D(35)E" consensus sequence is nonfunctional. Proc. Natl. Acad. Sci. USA 94: 1293-1297.
  • Lohe, A. R., D. T. Sullivan and D. L. Hartl, 1996 Subunit interactions in the transposase of the transposable element mariner. Genetics 144: 1087-1095.
  • Lohe, A. R. and D. L. Hartl, 1996 Reduced germline mobility of a mariner vector containing exogenous DNA: Effect of size or site? Genetics 143: 1299-1306.
  • Lohe, A. R. and D. L. Hartl, 1996 Germline transformation of Drosophila virilis with the transposable element mariner. Genetics 143: 365-374.
  • Lohe, A. R. and D. L. Hartl, 1996 Autoregulation of mariner transposase activity by overproduction inhibition and dominant-negative complementation. Mol. Biol. Evol. 13: 549-555.
  • Lohe, A. R., D.-A. Lidholm and D. L. Hartl, 1995 Genotypic effects, maternal effects, and grand-maternal effects of immobilized derivatives of the transposable element mariner. Genetics 140: 183-192.
  • Lohe, A. R., E. N. Moriyama, D.-A. Lidholm, and D. L. Hartl, 1995 Horizontal transmission, vertical inactivation, and stochastic loss of mariner-like transposable elements. Mol. Biol. Evol. 12: 62-72.
  • Lozovsky, E. R., D. Nurminsky, E. A. Wimmer and D. L. Hartl, 2002 Unexpected stability of mariner transgenes in Drosophila. Genetics 160: 527-535. PDF
  • Lozovskaya, E. R., D. I. Nurminsky, D. A. Petrov and D. L. Hartl 1999 Genome size as a mutation-selection-drift process. Genes Genet. Syst. 74: 201-207. PDF
  • Lozovskaya, E. R., D. I. Nurminsky, D. L. Hartl and D. T. Sullivan, 1996 Germline tranformation of Drosophila virilis mediated by the transposable element hobo. Genetics 142: 173-177.
  • Lozovskaya, E. R., D. L. Hartl and D. A. Petrov, 1995 Genomic regulation of transposable elements in Drosophila. Current Opinion in Genetics and Development 5: 768-773.
  • Meiklejohn, C. D., Y. Kim, D. L. Hartl, and J. Parsch. 2004. Identification of a locus under complex positive selection in Drosophila simulans by haplotype mapping and composite-likelihood estimation. Genetics 168: 265-279. PDF
  • Meiklejohn, C. D., and D. L. Hartl, 2002 A single mode of canalization. Trends Ecol. Evol. 17: 468-473.PDF
  • Moriyama, E. N., D. A. Petrov and D. L. Hartl, 1997 Genome size and intron size in Drosophila. Mol. Biol. Evol. 15: 770-773.
  • Neafsey, D. E., D. L. Hartl, and M. Berriman. 2005. Evolution of noncoding and silent coding sites in the Plasmodium falciparum and Plasmodium reichenowi genomes. Mol. Biol. Evol. 22: 1621-1626. PDF
  • Neafsey, D. E., and D. L. Hartl. 2005. Convergent loss of an anciently duplicated, functionally divergent RH2 opsin gene in the fugu and Tetraodon lineages. Gene 350: 161-171. PDF
  • Neafsey, D. E., J. P. Blumenstiel, and D. L. Hartl. 2004. Different regulatory mechanisms underlie similar transposable element profiles in pufferfish and fruitflies. Mol. Biol. Evol. 21: 2310-2318. PDF
  • Nielsen, K. M., J. Kasper, M. Choi, T. Bedford, K. Kristiansen, D. F. Wirth, S. K. Volkman, E. R. Lozovsky, and D. L. Hartl, 2003 Gene conversion as a source of nucleotide diversity in Plasmodium falciparum. Mol. Biol. Evol. 20: 726-734. PDF
  • Nurminsky, D., D. De Aguiar, C. D. Bustamante and D. L. Hartl, 2001 Chromosomal effects of rapid gene evolution in Drosophila melanogaster. Science 291: 128-130. PDF
  • Nurminsky, D. I., M. V. Nurminskaya, D. De Aguiar, and D. L. Hartl, 1998 Selective sweep of a newly evolved sperm-specific gene in Drosophila. Nature 396: 572-575. PDF
  • Nurminsky, D. I., E. V. Benevolenskaya, M. V. Nurminskaya, Y. Y. Shevelyov, D. L. Hartl, and V. A. Gvozdev, 1998 Cytoplasmic dynein intermediate chain isoforms with different targeting properties created by tissue-specific alternative splicing. Mol. Cell. Biol. 18: 6816-6825.
  • Nurminsky, D. I. and D. L. Hartl, 1996 Sequence scanning: A method for rapid sequence acquisition from large-fragment DNA clones. Proc. Natl. Acad. Sci. USA 93: 1694-1698.
  • Nurminsky, D. I., E. N. Moriyama, E. R. Lozovskaya, and D. L. Hartl, 1996 Molecular phylogeny and genome evolution in the Drosophila virilis species group: Duplications of the alcohol dehydrogenase gene. Mol. Biol. Evol. 13: 132-149.
  • Parsch, J. C. Meiklejohn, and D. L. Hartl, 2001 Patterns of DNA sequence variation suggest the recent action of positive selection in the janus-ocnus region of D. simulans. Genetics 159: 647-657. PDF
  • Parsch, J. C. Meiklejohn, E. Hauschteck-Jungen, and D. L. Hartl, 2001 Molecular evolution of the ocnus and janus genes in the Drosophila melanogaster species subgroup. Mol. Biol. Evol. 18: 801-811. PDF
  • Parsch, J., J. Russell, I. Beerman, D. L. Hartl, and W. Stephan, 2000 Deletion of a conserved regulatory element in the Drosophila Adh gene leads to increased ADH activity but also delays development. Genetics 156: 219-227.
  • Petrov, D. A. and D. L. Hartl, 2000 Pseudogene evolution and natural selection for a compact genome. Heredity 91: 221-227.
  • Petrov, D. A., T. Sangster, J. S. Johnston, D. L. Hartl and K. L. Shaw, 2000 Evidence for DNA loss as a determinant of genome size. Science 287: 1060-1062.
  • Petrov, D. A. and D. L. Hartl, 1999 Patterns of nucleotide substitution in Drosophila and mammalian genomes. Proc. Natl. Acad. Sci. USA 96: 1475-1479.
  • Petrov, D. A., Y.-C. Chao, E. C. Stephenson, and D. L. Hartl, 1998. Pseudogene evolution in Drosophila suggests a high rate of DNA loss. Mol. Biol. Evol. 15: 1562-1567.
  • Petrov, D. A. and D. L. Hartl, 1998 High rate of DNA loss in the D. melanogaster and D. virilis species groups. Mol. Biol. Evol. 15: 293-302.
  • Petrov, D. A. and D. L. Hartl, 1997 Trash DNA is what gets thrown away: High rate of DNA loss in Drosophila. Gene 205: 279-289.
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  • Ranz, J. M., K. Namgyal, G. Gibson, and D. L. Hartl. 2004. Anomalies in the expression profile of interspecific hybrids of Drosophila melanogaster and Drosophila simulans. Genome Res. 14: 373-379. PDF
  • Ranz, J. M., A. R. Ponce, D. L. Hartl, and D. Nurminsky, 2003 Origin and evolution of a new gene expressed in the Drosophila sperm axoneme. Genetica 118: 233-244. PDF
  • Ranz, J. M., C. I. Castillo-Davis, C. D. Meiklejohn, and D. L. Hartl, 2003 Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science 300: 1742-1745. PDF
  • Rich, S. M., B. M. Rosenthal, S. R. Telford III, A. Spielman, D. L. Hartl, and F. J. Ayala, 1997 Heterogeneity of the internal transcribed spacer (ITS-2) region among individual deer ticks. Insect Mol. Biol. 6: 123-129.
  • Rich, S. M., D. Caporale, S. R. Telford III, T. D. Kocher, D. L. Hartl and A. Spielman, 1995 Distribution of Ixodes ricinus-like ticks of eastern North America. Proc. Natl. Acad. Sci. USA 92: 6284-6288.
  • Robertson. H. M., K. L. Zumpano, A. R. Lohe and D. L. Hartl, 1996 Reconstructing the ancient mariners of humans. Nature Genetics 12: 360-361.
  • Sawyer, S. A., D. Krane, A. Podleski, and D. L. Hartl, 1996 DNA fingerprinting loci do show population differences. Am. J. Hum. Genet. 59: 272-274.
  • Segarra, C., E. R.Lozovskaya, G. Rib—, M. Aguade, and D. L. Hartl, 1995 P1 clones from Drosophila melanogaster as markers to study chromosomal evolution of Muller's A element in two species of the obscura group of Drosophila. Chromosoma 104: 129-136.
  • Siegal, M. L. and D. L. Hartl, 2000 Application of Cre/loxP in Drosophila: Site-specific recombination and transgene coplacement, pp. 487-495 in R. S. Tuan and C. W. Lo (editors), Methods in Molecular Biology, Vol. 136: Developmental Biology Protocols, Volume 2, Humana Press, Totowa, New Jersey.
  • Siegal, M. L. and D. L. Hartl, 1999 Oviposition-site preference in Drosophila following interspecific gene transfer of the alcohol dehydrogenase locus. Behavior Genet. 29: 199-204.
  • Siegal, M. L. and D. L. Hartl, 1998 An experimental test for lineage-specific position effects on alcohol dehydrogenase genes in Drosophila. Proc. Natl. Acad. Sci. 95: 15513-15518.
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  • Silander, O., D. M. Weinreich, K. Wright, K. O'Keefe, C. Rang, P. Turner, and L. Chao 2005. Widespread genetic exchange among terrestrial bacteriophages. PNAS 102:19009-19014. PDF
  • Tao, Y., D. L. Hartl, and C. C. Laurie, 2001 Sex-ratio segregation distortion associated with reproductive isolation in Drosophila. Proc. Natl. Acad. Sci. USA 98: 13183-13188. PDF
  • Townsend, J. P., D. Cavalieri, and Daniel L. Hartl, 2003 Population genetic variation in genome-wide gene expression. Mol. Biol. Evol. 20(6): 955-963. PDF
  • Townsend, J. P., K. M. Nielsen, D. S. Fisher, and D. L. Hartl, 2003 Horizontal acquisition of divergent chromosomal DNA in bacteria: effects of mutator phenotypes. Genetics 164: 13-21. PDF
  • Townsend, J. P., and D. L. Hartl, 2002 Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments. Genome Biol. 3: research0071.1 - 0071.16. PDF
  • Townsend, J. P., D. Cavalieri, and D. L. Hartl, 2001 Population genomics: Gene expression in a vineyard yeast from Tuscany. Biology International, Special Issue Number 41 (Biological Sciences, Challenges for the 21st Century), pp. 91-98.
  • Townsend, J. P. and D. L. Hartl, 2000 The kinetics of transposable element autoregulation. Genetica 108: 229-237.
  • Uglialoro, A. M., D. Turbay, P. A. Pesavento, J. C. Delgado, F. E. McKenzie, J. G. Gribben, D. Hartl, E. J. Yunis, A. E. Goldfeld, 1998 Identification of three new single nucleotide polymorphisms in the human tumor necrosis factor-a gene promoter. Tissue Antigens 52: 359-367.
  • Vieira, J., C. P. Vieira, D. L. Hartl, and E. R. Lozovskaya. 1998 Factors contributing to the hybrid dysgenesis syndrome in Drosophila virilis. Genet. Res. 71: 109-117.
  • Vieira, C. P., J. Vieira and D. L. Hartl, 1997 The evolution of small gene clusters: Evidence for an independent origin of the maltase gene cluster in D. virilis and D. melanogaster. Mol. Biol. Evol. 14: 985-993.
  • Vieira, J., C. P. Vieira, D. L. Hartl and E. R. Lozovskaya, 1997 Discordant rates of chromosome evolution in the Drosophila virilis species group. Genetics 147: 223-230.
  • Vieira, J., C. P. Vieira, D. L. Hartl and E. R. Lozovskaya, 1997 A framework physical map of Drosophila virilis based on P1 clones: Applications in genome evolution. Chromosoma 106: 99-107. PDF
  • Volkman, S., and D. L. Hartl, 2003 A game of cat and mouth. Science 299: 353-354. PDF
  • Volkman, S., D. L. Hartl, D. F. Wirth, K. Nielsen, M. Choi, S. Batalov, Y. Zhou, D. Plouffe, K. Le Roch, R. Abagyan, and E. Winzeler, 2002 Excess polymorphisms in genes for membrane proteins in Plasmodium falciparum. Science 298: 216-218. PDF
  • Volkman, S. K., A. E. Barry, E. J. Lyons, K. M. Nielsen, S. M. Thomas, M. Choi, S. S. Thakore, K. P. Day, D. F. Wirth and D. L. Hartl, 2001 Recent origin of Plasmodium falciparum from a single progenitor. Science 293: 482-484. PDF
  • Weinreich, D. M. 2005. The rank ordering of genotypic fitness values predicts genetic constraint on natural selection on landscapes lacking sign epistasis. Genetics 171:1397-1405. PDF
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  • Weinreich, D. M., and L. Chao 2005. Rapid evolutionary escape in large populations from local peaks on the Wrightian fitness landscape. Evolution 59:1175-1182. PDF
  • Winzeler, E. A., C. I. Castillo-Davis, G. Oshiro, D. Liang, D. R. Richards, Y. Zhou, and D. L. Hartl, 2003 Genetic diversity in yeast assessed with whole-genome oligonucleotide arrays. Genetics 163: 79-89. PDF
  • Zilversmit, M., and D. L. Hartl. 2005. Evolutionary history and population genetics of human malaria parasites. Pp. 95-109 in Molecular Approaches to Malaria, Eds. I. W. Sherman. American Society for Microbiology Press, Washington, D.C.