Jackson BC, Campos JL, Haddrill PR, Charlesworth B, Zeng K. Variation in the intensity of selection on codon bias over time causes contrasting patterns of base composition evolution in Drosophila. Genome Biol Evol. In press. (Click here to access the D. simulans dataset, including VCF files, various scripts used in the analysis, and final sequence alignments in FASTA format).

Nagylaki T, Zeng K. 2016. Clines with partial panmixia across a geographical barrier in an environmental pocket. Theor Popul Biol 110:1-11.

Laine VN*, Gossmann TI*, Schachtschneider KM*, Garroway CJ, Madsen O, Verhoeven KJF, de Jager V, Megens H-J, Warren WC, Minx P, Crooijmans RPMA, Corcoran P, The Great Tit Hapmap Consortium, Sheldon BC, Slate J, Zeng K, van Oers K, Visser ME, Groenen MAM. Evolutionary signals of selection on cognition from the great tit genome and methylome. 2016. Nat Commun 7:10474 (* co-first authors).

Küpper C, Stocks M, Risse JE, dos Remedios N, Farrell LL, McRae SB, Morgan TC, Karlionova N, Pinchuk P, Verkuil YI, Kitaysky AS, Wingfield JC, Piersma T, Zeng K, Slate J, Blaxter M, Lank DB, Burke T. 2016. A supergene determines highly divergent male reproductive morphs in the ruff. Nat Genet 48:79-83.


Zeng K, Corcoran P. The effects of background and interference selection on patterns of genetic variation in subdivided populations. Genetics 201:1539-54.

Jackson BC, Campos JL, Zeng K. 2015. The effects of purifying selection on patterns of genetic differentiation between Drosophila melanogaster populations. Heredity (Edinb) 114:163-174.


Gossmann TI, Santure AW, Sheldon BC, Slate J, Zeng K. 2014. Highly variable recombinational landscape modulates efficacy of natural selection in birds. Genome Biol Evol 6: 2061-2075.

Gossmann TI, Ziegler M. 2014. Sequence divergence and diversity suggests ongoing functional diversification of vertebrate NAD metabolism, DNA Repair 23: 39–48.

Evans B, Zeng K, Esselstyn JA, Charlesworth B, Melnick DJ. 2014. Reduced representation genome sequencing suggests low diversity on the sex chromosomes of tonkean macaque monkeys. Mol Biol Evol 31: 2425-2440.

Nagylaki T, Zeng K. 2014. Clines with complete dominance and partial panmixia in an unbounded unidimensional habitat. Theor Popul Biol 93:63-74.


T. I. Gossmann, M. W. Schmid, U. Grossniklaus, and K. J. Schmid. Selection-Driven Evolution of Sex-Biased Genes Is Consistent with Sexual Selection in Arabidopsis thaliana. Mol Biol Evol, Dec 2013

Campos JL, Zeng K, Parker DJ, Charlesworth B, Haddrill PR 2013. Codon Usage Bias and Effective Population Sizes on the X Chromosome versus the Autosomes in Drosophila melanogaster. Mol Biol Evol 30: 811-823.

Zeng K 2013. A coalescent model of background selection with recombination, demography and variation in selection coefficients. Heredity 110: 363-371.


Fang S, Yukilevich R, Chen Y, Turissini DA, Zeng K, Boussy IA, Wu CI 2012. Incompatibility and competitive exclusion of genomic segments between sibling Drosophila species. PLoS Genet 8: e1002795.

Zeng K. The application of population genetics in the study of codon usage bias. In: Cannarozzi GM, Schneider A, editors. Codon evolution: mechanisms and models. Oxford University Press.

de Proce SM, Zeng K, Betancourt AJ, Charlesworth B 2012. Selection on codon usage and base composition in Drosophila americana. Biol Lett 8: 82-85.


Qiu S*, Zeng K*, Slotte T*, Wright S, Charlesworth D. 2011. Reduced efficacy of natural selection on codon usage bias in selfing Arabidopsis and Capsella species. Genome Biol. Evol. 3: 868-880. (* co-first author).

Zeng K, Charlesworth B. 2011. The joint effects of background selection and genetic recombination on local gene genealogies. Genetics 189: 251-266.

Haddrill PR, Zeng K, Charlesworth B. 2011. Determinants of synonymous and nonsynonymous variability in three species of Drosophila. Mol. Biol. Evol. 28:1731-1743.


Zeng K, Charlesworth B. 2010. The effects of demography and linkage on the estimation of selection and mutation parameters. Genetics 186:1411–1424.

Qiu S, Bergero R, Zeng K, Charlesworth D. 2010. Patterns of codon usage bias in Silene latifolia. Mol. Biol. Evol. 28:771-780.

Zeng K. 2010. A simple multi-allele model and its application to identifying preferred/unpreferred codons using polymorphism data. Mol. Biol. Evol. 27:1327-1337.

Zeng K, Charlesworth B. 2010. Studying patterns of recent evolution at synonymous sites and intronic sites in Drosophila melanogaster. J. Mol. Evol. 70:116-128.

Sharp P, Emery L, Zeng K. 2010. Forces that influence the evolution of codon bias. Phil. Trans. R. Soc. B 365:1203-1212.


Zeng K, Charlesworth B. 2009. Estimating selection intensity on synonymous codon usage in a non-equilibrium population. Genetics 183: 651-662.

2005 – 2008

Lu J, Fu Y, Kumar S, Shen Y, Zeng K, Xu A, Carthew R, Wu C.-I. 2008. Adaptive evolution of newly emerged micro-RNA genes in Drosophila. Mol. Biol. Evol. 25: 929-938.

Zhou R*, Zeng K*, Wu W, Chen X, Yang Z, Shi S, Wu C.-I. 2007. Population genetics of speciation in non-model organisms: I. Ancestral polymorphism in mangroves. Mol. Biol. Evol. 24: 2746-2754. (* co-first authors).

Zeng K, Shi S, Wu C.-I. 2007. Compound tests for the detection of hitchhiking under positive selection. Mol. Biol. Evol. 24: 1898-1908.

Zeng K, Mano S, Shi S, Wu C.-I. 2007. Comparisons of site- and haplotype-frequency methods for detecting positive selection. Mol. Biol. Evol. 24: 1562-1574.

Zeng K, Fu Y.-X, Shi S, Wu C.-I. 2006. Statistical tests for detecting positive selection by utilizing high-frequency variants. Genetics 174: 1431-1439.

Tang T, Lu J, Huang J, He J, McCouch SR, Shen Y, Zeng K, Purugganan MD, Shi S, Wu C.-I. 2006. Genomic variation in rice: genesis of highly polymorphic linkage blocks during domestication. PLoS Genet. 2: e199.

Liu X, Fu Y, Liu Z, Lin B, Xie Y, Liu Y, Xu Y, Lin J, Fan X, Dong M, Zeng K, Wu C.-I, Xu A. 2006. An ancient balanced polymorphism in a regulatory region of human major histocompatibility complex is retained in Chinese minorities but lost worldwide. Am. J. Hum. Genet. 78: 393-400.

Shi S, Huang Y, Zeng K, Tan F, He H, Huang J, Fu Y.-X. 2005. Molecular phylogenetic analysis of mangroves: independent evolutionary origins of vivipary and salt secretion. Mol. Phylogenet. Evol. 34: 159-166.