Dr Kai Zeng

School of Biosciences

Senior Lecturer

k.zeng@sheffield.ac.uk
+44 114 222 4708

Room B88, Alfred Denny Building

Full contact details

Dr Kai Zeng
School of Biosciences
Room B88
Alfred Denny Building
Western Bank
Sheffield
S10 2TN

Profile

BSc, double major in Statistics and Computer Science, Sun Yat-Sen University, Guangzhou, China (1999)
PhD, Sun Yat-Sen University, Guangzhou, China (2007)
Visiting PhD student, University of Chicago, USA (2004–2007)
Royal Society International Incoming Postdoctoral Research Fellow, University of Edinburgh, UK (2008-2009)
Royal Society of Edinburgh/Caledonian Research Foundation Biomedical Personal Research Fellow, University of Edinburgh, UK (2009-201)
Lecturer then Senior Lecturer, School of Biosciences, University of Sheffield, UK (2011-present)

Research interests

My research is focused on population genetics. I am particularly interested in developing realistic and computationally tractable models for analyzing DNA sequence data.

The aim is to understand how fundamental evolutionary processes such as mutation, genetic drift, genetic recombination, and natural selection interact with one another, and the impact of these interactions on evolution.

Publications

Show: Featured publications All publications

Featured publications

Journal articles

Kim K-W, Jackson BC, Zhang H, Toews DPL, Taylor SA, Greig EI, Lovette IJ, Liu MM, Davison A, Griffith SC , Zeng K et al (2019) Genetics and evidence for balancing selection of a sex-linked colour polymorphism in a songbird. Nature Communications, 10. View this article in WRRO
Zeng K, Jackson BC & Barton HJ (2019) Methods for Estimating Demography and Detecting Between-Locus Differences in the Effective Population Size and Mutation Rate. Molecular Biology and Evolution, 36(2), 423-433. View this article in WRRO
Barton HJ & Zeng K (2018) New Methods for Inferring the Distribution of Fitness Effects for INDELs and SNPs.. Molecular Biology and Evolution, 35(6), 1536-1546. View this article in WRRO
Laine VN, Gossmann TI, Schachtschneider KM, Garroway CJ, Madsen O, Verhoeven KJF, de Jager V, Megens H-J, Warren WC, Minx P , Crooijmans RPMA et al (2016) Evolutionary signals of selection on cognition from the great tit genome and methylome. Nature Communications, 7. View this article in WRRO
Zeng K & Charlesworth B (2011) The joint effects of background selection and genetic recombination on local gene genealogies.. Genetics, 189(1), 251-266.
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 Biology and Evolution, 3, 868-880.
Qiu S, Bergero R, Zeng K & Charlesworth D (2011) Patterns of Codon Usage Bias in Silene latifolia. MOL BIOL EVOL, 28(1), 771-780.
Zeng K & Charlesworth B (2010) The effects of demography and linkage on the estimation of selection and mutation parameters.. Genetics, 186(4), 1411-1424.
Zeng K (2010) A simple multiallele model and its application to identifying preferred-unpreferred codons using polymorphism data.. Mol Biol Evol, 27(6), 1327-1337.
Sharp PM, Emery LR & Zeng K (2010) Forces that influence the evolution of codon bias.. Philos Trans R Soc Lond B Biol Sci, 365(1544), 1203-1212.
Zeng K & Charlesworth B (2010) Studying patterns of recent evolution at synonymous sites and intronic sites in Drosophila melanogaster.. J Mol Evol, 70(1), 116-128.
Zeng K & Charlesworth B (2009) Estimating selection intensity on synonymous codon usage in a nonequilibrium population.. Genetics, 183(2), 651-23SI.

All publications

Journal articles

Zeng K, Charlesworth B & Hobolth A (2021) Studying models of balancing selection using phase-type theory. Genetics.
Hayes K, Barton HJ & Zeng K (2020) A study of faster-Z evolution in the great tit (Parus major). Genome Biology and Evolution. View this article in WRRO
Olofsson JK, Dunning LT, Lundgren MR, Barton HJ, Thompson J, Cuff N, Ariyarathne M, Yakandawala D, Sotelo G, Zeng K , Osborne CP et al (2019) Population-specific selection on standing variation generated by lateral gene transfers in a grass. Current Biology, 29. View this article in WRRO
Barton HJ & Zeng K (2019) The Impact of Natural Selection on Short Insertion and Deletion Variation in the Great Tit Genome. Genome Biology and Evolution, 11(6), 1514-1524. View this article in WRRO
Kim K-W, Jackson BC, Zhang H, Toews DPL, Taylor SA, Greig EI, Lovette IJ, Liu MM, Davison A, Griffith SC , Zeng K et al (2019) Genetics and evidence for balancing selection of a sex-linked colour polymorphism in a songbird. Nature Communications, 10. View this article in WRRO
Zeng K, Jackson BC & Barton HJ (2019) Methods for Estimating Demography and Detecting Between-Locus Differences in the Effective Population Size and Mutation Rate. Molecular Biology and Evolution, 36(2), 423-433. View this article in WRRO
Barton HJ & Zeng K (2018) New Methods for Inferring the Distribution of Fitness Effects for INDELs and SNPs.. Molecular Biology and Evolution, 35(6), 1536-1546. View this article in WRRO
Corcoran P, Gossmann TI, Barton HJ, The Great Tit HapMap Consortium , Slate J & Zeng K (2017) Determinants of the Efficacy of Natural Selection on Coding and Noncoding Variability in Two Passerine Species. Genome Biology and Evolution, 9(11), 2987-3007. View this article in WRRO
Evans BJ, Tosi AJ, Zeng K, Dushoff J, Corvelo A & Melnick DJ (2017) Speciation over the edge: gene flow among non-human primate species across a formidable biogeographic barrier. Royal Society Open Science, 4. View this article in WRRO
Jackson BC, Campos JL, Haddrill PR, Charlesworth B & Zeng K (2017) Variation in the Intensity of Selection on Codon Bias over Time Causes Contrasting Patterns of Base Composition Evolution in Drosophila. Genome Biology and Evolution, 9(1), 102-123. View this article in WRRO
Nagylaki T & Zeng K (2016) Clines with partial panmixia across a geographical barrier in an environmental pocket. Theoretical Population Biology, 110, 1-11. View this article in WRRO
Laine VN, Gossmann TI, Schachtschneider KM, Garroway CJ, Madsen O, Verhoeven KJF, de Jager V, Megens H-J, Warren WC, Minx P , Crooijmans RPMA et al (2016) Evolutionary signals of selection on cognition from the great tit genome and methylome. Nature Communications, 7. View this article in WRRO
Zeng K & Corcoran P (2015) The Effects of Background and Interference Selection on Patterns of Genetic Variation in Subdivided Populations. Genetics, 201(4), 1539-1554. View this article in WRRO
Küpper C, Stocks M, Risse JE, dos Remedios N, Farrell LL, McRae SB, Morgan TC, Karlionova N, Pinchuk P, Verkuil YI , Kitaysky AS et al (2015) A supergene determines highly divergent male reproductive morphs in the ruff. Nature Genetics, 48(1), 79-83. View this article in WRRO
Jackson BC, Campos JL & Zeng K (2015) The effects of purifying selection on patterns of genetic differentiation between Drosophila melanogaster populations. Heredity, 114(2), 163-174. View this article in WRRO
Gossmann TI, Santure AW, Sheldon BC, Slate J & Zeng K (2014) Highly Variable Recombinational Landscape Modulates Efficacy of Natural Selection in Birds. Genome Biology and Evolution, 6(8), 2061-2075. View this article in WRRO
Evans BJ, 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(9), 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.
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(4), 811-823. View this article in WRRO
Zeng K (2013) A coalescent model of background selection with recombination, demography and variation in selection coefficients.. Heredity (Edinb), 110(4), 363-371.
Fang S, Yukilevich R, Chen Y, Turissini DA, Zeng K, Boussy IA & Wu C-I (2012) Incompatibility and Competitive Exclusion of Genomic Segments between Sibling Drosophila Species. PLOS GENETICS, 8(6). View this article in WRRO
de Procé SM, Zeng K, Betancourt AJ & Charlesworth B (2012) Selection on codon usage and base composition in Drosophila americana.. Biol Lett, 8(1), 82-85.
Zeng K & Charlesworth B (2011) The joint effects of background selection and genetic recombination on local gene genealogies.. Genetics, 189(1), 251-266.
Haddrill PR, Zeng K & Charlesworth B (2011) Determinants of synonymous and nonsynonymous variability in three species of Drosophila.. Mol Biol Evol, 28(5), 1731-1743.
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 Biology and Evolution, 3, 868-880.
Qiu S, Bergero R, Zeng K & Charlesworth D (2011) Patterns of Codon Usage Bias in Silene latifolia. MOL BIOL EVOL, 28(1), 771-780.
Zeng K & Charlesworth B (2010) The effects of demography and linkage on the estimation of selection and mutation parameters.. Genetics, 186(4), 1411-1424.
Zeng K (2010) A simple multiallele model and its application to identifying preferred-unpreferred codons using polymorphism data.. Mol Biol Evol, 27(6), 1327-1337.
Sharp PM, Emery LR & Zeng K (2010) Forces that influence the evolution of codon bias.. Philos Trans R Soc Lond B Biol Sci, 365(1544), 1203-1212.
Zeng K & Charlesworth B (2010) Studying patterns of recent evolution at synonymous sites and intronic sites in Drosophila melanogaster.. J Mol Evol, 70(1), 116-128.
Zeng K & Charlesworth B (2009) Estimating selection intensity on synonymous codon usage in a nonequilibrium population.. Genetics, 183(2), 651-23SI.
Mano S, Zeng K & Wu CI (2008) Detecting positive selection based on haplotype frequency distribution. GENES GENET SYST, 83(6), 525-525.
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(5), 929-938.
Zhou RC, Zeng K, Wu W, Chen XS, Yang ZH, Shi SH & Wu CI (2007) Population genetics of speciation in nonmodel organisms: I. Ancestral polymorphism in mangroves. MOL BIOL EVOL, 24(12), 2746-2754.
Zeng K, Shi S & Wut CI (2007) Compound tests for the detection of hitchhiking under positive selection. MOL BIOL EVOL, 24(8), 1898-1908.
Zeng K, Mano SH, Shi SH & Wu CI (2007) Comparisons of site- and haplotype-frequency methods for detecting positive selection. MOL BIOL EVOL, 24(7), 1562-1574.
Zeng K, Mano S & Wu CI (2006) Detecting positive selection by the most common haplotype. GENES GENET SYST, 81(6), 428-428.
Zeng K, Fu YX, Shi SH & Wu CI (2006) Statistical tests for detecting positive selection by utilizing high-frequency variants. GENETICS, 174(3), 1431-1439.
Liu XY, Fu YG, Liu ZH, Lin B, Xie B, Xie Y, Liu Y, Xu YP, Lin JH, Fan XL , Dong ML et al (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(3), 393-400.
Tang T, Lu J, Huang J, He J, McCouch SR, Shen Y, Kai Z, Purugganan MD, Shi S & Wu CI (2006) Genomic variation in rice: Genesis of highly polymorphic linkage blocks during domestication. PLoS Genetics, 2(11), 1824-1833.
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. Molecular Phylogenetics and Evolution, 34, 159-166.

Chapters

Zeng K (2012) The application of population genetics in the study of codon usage bias In Cannarozzi GM & Schneider A (Ed.), Codon Evolution: Mechanisms and Models (pp. 245-257). Oxford University Press

Teaching activities

I currently teach on the following modules:

APS135 - Skills for Biologists 1
APS222 - Level 2 Tutorials
APS274 - The Molecular Revolution in Biology
APS330 - Level 3 Projects
APS331 - Level 3 Dissertations
APS344 - Topics in Evolutionary Genetics
APS351 - Human Evolutionary Genetics
APS407 - Research and Study Skills in Biology

Professional activities

Fellow of The Higher Education Academy