Nguyen AH, Bachtrog D (submitted) Toxic Y chromosome: increased repeat expression and age-associated heterochromatin loss in male Drosophila with a young Y chromosome.

Nalley MJ, Bachtrog D (submitted) Rapid evolution of male courtship songs in the Drosophila nasuta species cluster.

Wei KH, Chan C, Bachtrog D (submitted) Sparse nucleation and piRNA-mediated establishment of heterochromatin during Drosophila embryo development.


Wei KH, Gibilisco L, Bachtrog D (2020) Epigenetic conflict creates toxic Y chromosome and increased mutational burden in Drosophila males. Nature Communication 11(1):5537.

Wei KH, Mantha A, Bachtrog D (2020) The theory and practice of measuring broad-range recombination rate from marker selected pools. Molecular Biology and Evolution. 37(12):3654-3671.

Bachtrog D (2020) The Y chromosome as a battleground for intragenomic conflict. Trends in Genetics. 36(7):510-522.

Brown E, Nguyen AH, Bachtrog D (2020)  The Drosophila Y chromosome affects heterochromatin integrity genome-wide. Molecular Biology and Evolution. 37(10):2808-2824.

Brown E, Nguyen AH, Bachtrog D (2020) The Y chromosome may contribute to sex-specific aging in Drosophila. Nature Ecology & Evolution. 4(6):853-862..

Bracewell R, Bachtrog D (2020) Complex evolutionary history of the Y chromosome in flies of the Drosophila obscura species group. Genome Biology and Evolution. 12(5):494-505. 

Bracewell R, Tran A, Chatla K, Bachtrog D (2020) Chromosome-level assembly of Drosophila bifasciata reveals important karyotypic transition of the X chromosome. G3, Jan 22. pii: g3.400922.2019.

Mai D, Nalley MJ & Bachtrog D (2020). Patterns of genomic differentiation in the Drosophila nasuta species complex. Molecular Biology and Evolution. Jan 1;37(1):208-220.


Wei KH & Bachtrog D (2019) Ancestral male recombination in Drosophila albomicans produced geographically restricted neo-Y chromosome haplotypes varying in age and onset of decay. PLoS Genetics, 18;15(11):e1008502. 

Bachtrog D, Mahajan S & Bracewell R (2019). Massive gene amplification on a recently formed Drosophila Y chromosome. Nature Ecology & Evolution. Nov;3(11):1587-1597.

Bracewell R, Chatla K, Nalley MJ & Bachtrog D (2019). Dynamic turnover of centromeres drives karyotype evolution in Drosophila. Elife. 2019 Sep 16;8. pii: e49002.

Ellison CE & D Bachtrog (2019) Recurrent gene co-amplification on Drosophila X and Y chromosomes. PLoS Genetics, Jul 22;15(7):e1008251.

Ellison CE & D Bachtrog (2019). Contingency in the convergent evolution of a regulatory network: Dosage compensation in Drosophila. PLoS Biology, 17(2):e3000094.


Mahajan S, Wei KH, Nalley MJ, Gibilisco L, Bachtrog D (2018). De novo assembly of a young Drosophila Y chromosome using single-molecule sequencing and chromatin conformation capture. PLoS Biology. 16(7):e2006348.


Mahajan S & D Bachtrog (2017). Convergent evolution of Y chromosome gene content in flies. Nature Communications. Oct 4;8(1):785.

Wong Miller KM, B Bracewell, MB Eisen & D Bachtrog (2017). Patterns of genome-wide diversity and population structure in the Drosophila athabasca species complex. Molecular Biology and Evolution. 34(8):1912-1923.

Blackmon H, Ross L & D Bachtrog (2017). Sex determination, sex chromosomes and karyotype evolution in insects. J Hered, Jan;108(1):78-93.


Giblisco L, Zhou Q, Mahajan S & D Bachtrog (2016). Alternative Splicing Within and Between Drosophila Species, Sexes, Tissues, and Developmental Stages. PLoS Genetics, Dec 9; 12:e1006464.


Zhou Q & D Bachtrog (2015). Ancestral chromatin configuration constrains chromatin evolution on differentiating sex chromosomes in Drosophila. PLoS Genetics, 11(6): e1005331. doi:10.1371/journal.pgen.1005331.

Assis R & Bachtrog D (2015). Rapid divergence and diversification of mammalian duplicate gene functions. BMC Evolutionary Biology, Jul 15;15:138.

Ellison CE & D Bachtrog (2015). Non-allelic gene conversion enables rapid evolutionary change at multiple regulatory sites encoded by transposable elements. eLife Feb 17;4. doi: 10.7554/eLife.05899.

Mahajan S & Bachtrog D (2015). Partial dosage compensation in Strepsiptera, a sister group of beetles. Genome Biology and Evolution, 2015 Jan 18;7(2):591-600. doi: 10.1093/gbe/evv008.

Vicoso B & D Bachtrog (2015). Numerous transitions of sex chromosomes in Diptera. PLoS Biology, Apr 16;13(4):e1002078. doi: 10.1371/journal.pbio.1002078. eCollection 2015 Apr.


Zhou*, Q., Zhang*, J., Bachtrog*, D., An, N., Huang, Q., Nanda, I., Gilbert, T., Jarvis, E.D., and Zhang, G. (2014). “Sex Chromosomes Demonstrate Complex Evolutionary Trajectories Across Bird Taxa. Science, Dec 12;346(6215):1246338. doi: 10.1126/science.1246338. *co-first authors

Bachtrog D (2014). Signs of Genomic Battles in Mouse Sex Chromosomes (Preview). Cell, 159 (Nov 6).

The Tree of Sex Consortium (2014). Tree of Sex: A database of sexual systems. Scientific Data, 1:140015

Bastien B, Walton Z, Delgado JA, Collantes F, Beani L, Stewart IJ, Cameron SA, Whitfield JB, Johnston S, Holland PWH, Bachtrog D, Kathirithamby J, Huelsenbeck JP (2014). Strepsiptera, phylogenomics and the long branch attraction problem. PLoS ONE, 9(10): e107709.

Kaiser VB, Bachtrog D. (2014). De novo transcriptome assembly reveals sex-specific selection acting on evolving neo-sex chromosomes in Drosophila miranda. BMC Genomics. 15(1):241.

Brown, E., and Bachtrog, D. (2014). The chromatin landscape of Drosophila miranda: comparison between species, sexes and chromosomes. Genome Research, 24(7): 1125-37.

Lott, S.E., Villalta, J.E., Zhou, Q., Bachtrog, D., and Eisen, M.B. (2014). Sex-specific embryonic gene expression in species with newly evolved sex chromosomes. PLoS Genetics, 10(2):e1004159.

Bachtrog D, Mank J, Peichel C, Otto S, Kirkpatrick M, Ashman TL, Hahn M, Kitano J, Mayrose I, Ming R, Perrin N, Ross L, Valenzuela N, Vamosi J (2014). Sex determination: Why so many ways of doing it? PLoS Biology, 12(7):e1001899.


Zhou* Q, Ellison* CE, Kaiser VB, Alekseyenko AA, Gorchakov AA, Bachtrog D (2013). The epigenome of evolving Drosophila neo-sex chromosomes: dosage compensation and heterochromatin formation, PLoS Biology, 11: e1001711 *co-first authors

Assis R, D Bachtrog (2013). Neofunctionalization of young duplicates in Drosophila. Proceedings of the National Academy of Sciences, 110: 17409-17414.

Ellison C, D Bachtrog (2013). Dosage compensation via transposable element mediated rewiring of a regulatory network. Science, 342: 846-850.

Bachtrog D (2013). Evolution of sex chromosomes. To appear in forth-coming book “Princeton Guide to Evolution”. Princeton University Press.

Husnik F, N Nikoh, R Koga, L Ross, M Fujie, M Tanaka, N Satoh, D Bachtrog, CD von Dohlen, T Fukatsu, JP McCutcheon (2013). Horizontal gene transfer from diverse bacteria to an insect genome enables a tripartite nested mealybug symbiosis. Cell, 153:1567-78.

Vicoso B, Emerson JJ, Zekster Y, Mahajan S & D Bachtrog (2013). Comparative sex chromosome genomics in snakes: differentiation, evolutionary strata, and lack of global dosage compensation. PLoS Biology, 11:e1001643.

Vicoso B & D Bachtrog (2013). Reversal of an ancient sex chromosome to an autosome in Drosophila. Nature, 499:332-5.

Alekseyenko* AA, Ellison* CE, Gorchakov* AA, Zhou Q, Kaiser VB, Toda N, Walton Z, Peng S, Park PJ, D Bachtrog#, M Kuroda# (2013). Conservation and de novo acquisition of dosage compensation on newly evolved sex chromosomes in Drosophila, Genes & Development, 27:853-8. *co-first authors, #co-corresponding authors

Vicoso B, Kaiser VB & D Bachtrog (2013) Sex-biased gene expression at homomorphic sex chromosomes in emus, and its implication for sex chromosome evolution. Proceedings of the National Academy of Sciences, 110:6453-8.

Bachtrog D (2013). Y chromosome evolution: emerging insights into processes of Y degeneration. Nature Review Genetics, 14:113-124.


Assis R, Zhou Q & D Bachtrog (2012). Sex-biased transcriptome evolution in Drosophila. Genome Biology and Evolution, 4:1189-1200.

Zhou Q & D Bachtrog (2012). Sex-specific adaptation drives early sex chromosome evolution in Drosophila. Science, 337(6092):341-5.

Zhou Q & D Bachtrog (2012). Chromosome-wide gene silencing initiates Y degeneration. Current Biology, 22(6):522-5.

Zhou Q, Zhu HM, Huang QF, Zhao L, Zhang GJ, Roy SW, Vicoso B, Xuan ZL, Ruan J, Zhang Y, Zhao RP, Ye C, Zhang XQ, J Wang, W Wang, D Bachtrog (2012). Deciphering neo-sex and B chromosome evolution by ultrashort-reads assembly of the whole genome of Drosophila albomicans. BMC Genomics, 13:109.


Bachtrog D (2011). Plant sex chromosomes: a non-degenerated Y? Current Biology, 21: R685-688.

Kaiser V, Q Zhou & D Bachtrog (2011). Non-random gene loss from the Drosophila miranda neo-Y chromosome. Genome Biology and Evolution, 3:1329-37.

Jensen J & D Bachtrog (2011). Characterizing the influence of effective population size on the rate of adaptation: Gillespie’s Darwin Domain. Genome Biology and Evolution, 3: 687-701.

Bachtrog D, M Kirkpatrick, J Mank, JC Pires, W Rice & N Valenzuela (2011). Are all sex chromosomes created equal? Trends in Genetics, 27: 350-357.

Vicoso B & D Bachtrog (2011). Lack of dosage compensation in Schistosoma mansoni, a female-heterogametic parasite. Genome Biology and Evolution, 3:230-5

Andolfatto P, K Wong & D Bachtrog (2011). Effective population size and the efficacy of selection on the X in two closely related Drosophila species. Genome Biology and Evolution, doi:10.1093/gbe/evq086.

Callahan B, RA Neher, D Bachtrog, P Andolfatto, BI Shraiman (2011). Correlated evolution of nearby residues in Drosophila genomes. PLoS Genetics, 7(2)e1001315.


Kaiser V & D Bachtrog (2010). Evolution of sex chromosomes in Insects. Annual Review of Genetics, 44: 91-112.

Bachtrog D, N Toda & S Lockton (2010). Dosage compensation and Demasculinization of X chromosomes in Drosophila. Current Biology, 20(16): 1476-1481.

Jensen J & D Bachtrog (2010). Characterizing recurrent positive selection at fast-evolving genes in Drosophila miranda and pseudoobcurca. Genome Biology and Evolution, 2: 371-378.

Vicoso B & D Bachtrog (2009) Progress and prospects toward our understanding of the evolution of dosage compensation. Chromosome Research, 17 (5): 585-602.

Bachtrog D, J Jensen & Z Zhang (2009) Accelerated adaptive evolution on a newly formed X chromosome. PLoS Biology, 7(4):e82.

Bachtrog D (2008) Similar rates of protein adaptation in Drosophila miranda and melanogaster, two species with different current effective population sizes. BMC Evolutionary Biology, Dec 18;8:334.

Gurbich T & D Bachtrog (2008) Gene content evolution on the X chromosome. Current Opinion in Genetics and Development, Dec;18 (6):493-8.

Bachtrog D (2008) Positive selection at the binding sites of the male-specific lethal complex involved in dosage compensation in Drosophila. Genetics, 180 (2): 1123-1129.

Haddrill P, D Bachtrog, P Andolfatto (2008) Positive and negative selection on noncoding DNA in Drosophila simulans. Molecular Biology and Evolution, 25 (9): 1825-1834.

Bachtrog D (2008) The temporal dynamics of processes underlying Y chromosome degeneration. Genetics, 179 (3): 1513-1525.

Bachtrog D (2008) Male-driven evolution in Drosophila. Molecular Biology and Evolution, 25 (4): 617-619.

Bachtrog D, E Hom, KM Wong, X Maside & P de Jong (2008) Genomic degradation of a young Y chromosome in Drosophila miranda. Genome Biology, 9 (2): R30.

Bachtrog D (2007) Reduced selection for codon usage bias in Drosophila miranda. Journal of Molecular Evolution, 64 (5): 586-590.

Bachtrog D & Andolfatto P (2006) Selection, recombination and the demographic history of Drosophila miranda. Genetics, 174 (4): 2045-2059.

Bachtrog D (2006) A dynamic view of sex chromosome evolution. Current Opinion in Genetics and Development, 16 (6): 578-585.

Bachtrog D (2006) Expression profile of a degenerating neo-Y chromosome in Drosophila. Current Biology, 16 (17): 1694-1699.

Bachtrog D (2006) The speciation history of the Drosophila nasuta Genetical Research, 88 (1): 13-26.

Bachtrog D, K Thornton, A Clark & P Andolfatto (2006) Extensive introgression of mitochondrial DNA relative to nuclear gene flow in the Drosophila yakuba species group. Evolution, 60 (2): 292-302.

Thornton K, D Bachtrog & P Andolfatto (2006) X-chromosomes and autosomes evolve at similar rates in Drosophila – no evidence for faster-X protein evolution. Genome Research, 16 (4): 498-504.

Bachtrog D (2005) Sex chromosome evolution: Molecular aspects of Y chromosome degeneration in Drosophila. Genome Research, 15 (10): 1393-1401.

Bachtrog D & I Gordo (2004) Adaptive evolution of asexual populations under Muller’s ratchet. Evolution, 58 (7): 1403-1413.

Bachtrog D (2004) Evidence that positive selection drives Y chromosome degeneration in Drosophila miranda. Nature Genetics, 36 (5): 518-522.

Bachtrog D (2003) Protein evolution and codon usage bias on the neo-sex chromosomes of Drosophila miranda. Genetics, 165: 1221-1232.

Bachtrog D (2003) Adaptation shapes patterns of genome evolution on sexual and asexual chromosomes in Drosophila. Nature Genetics, 34 (2): 215-219.

Bachtrog D (2003) Accumulation of spock and worf, two novel retrotransposons, on the neo-Y chromosome of Drosophila miranda. Molecular Biology and Evolution, 20 (2): 173-181.

Bachtrog D & B Charlesworth (2003) On the genomic location of the exuperantia1 gene in Drosophila miranda – the limits of in situ hybridization experiments. Genetics, 164 (3): 1237-1240.

Yi S, D Bachtrog & B Charlesworth (2003) A survey of chromosomal and nucleotide sequence variation in Drosophila miranda. Genetics, 164 (4): 1369-1381.

Bachtrog D & B Charlesworth (2002) Reduced adaptation on a non-recombining neo-Y chromosome. Nature, 416 (6878): 323-326.

Bachtrog D & B Charlesworth (2001) Towards a complete sequence of the human Y chromosome. Genome Biology, 2 (5):1016.1-1016.5.

Bachtrog D & B Charlesworth (2000) Reduced levels of microsatellite variability on the neo-Y chromosome of Drosophila miranda. Current Biology, 10 (17): 1025-1031.

Bachtrog D, M Imhof, M Agis & C Schlötterer (2000) Microsatellite variability differs between dinucleotide repeat motifs – evidence from Drosophila melanogaster. Molecular Biology and Evolution, 17 (9): 1277-1285.

Bachtrog D, S Weiss, B Zangerl, G Brem & C Schlötterer (1999) Distribution of microsatellites in the Drosophila melanogaster Molecular Biology and Evolution,16 (5): 602-610.

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