Publications

1. Harry-Paul Yeshoda Y, Lachapelle Josianne, Ness Rob W. 2024. The evolution of gene expression plasticity during adaptation to salt in Chlamydomonas reinhardtii. Genome biology and evolution. Oct 8:evae214. doi:10.1093/gbe/evae214/59640200/evae214

2. Ford Scott A, Ness Rob W, Kwon Moonhyuk, Ro Dae-Kyun, Phillips Michael A. 2024. A chromosome level reference genome of Diviner’s sage (Salvia divinorum) provides insight into salvinorin A biosynthesis. BMC plant biology. 24(1):914. doi:10.1186/s12870-024-05633-0

3. Johnson Marc TJ, Arif Irtaqa, Marchetti Francesco, Munshi-South Jason, Ness Rob W, Szulkin Marta, Verrelli Brian C, Yauk Carole L, Anstett Daniel N, Booth Warren, … Winchell Kristin M. 2024. Effects of urban-induced mutations on ecology, evolution and health. Nature ecology & evolution. Apr 19. doi:10.1038/s41559-024-02401-z

4. Caizergues Aude E, Santangelo James S, Ness Rob W, Angeoletto Fabio, Anstett Daniel N, Anstett Julia, Baena-Diaz Fernanda, Carlen Elizabeth J, Chaves Jaime A, Comerford Mattheau S, … Johnson Marc TJ. 2024. Does urbanisation lead to parallel demographic shifts across the world in a cosmopolitan plant? Molecular ecology. 33(7):e17311. doi:10.1111/mec.17311

5. Balogun Eniolaye J, Ness Rob W. 2024. The Effects of De Novo Mutation on Gene Expression and the Consequences for Fitness in Chlamydomonas reinhardtii. Molecular biology and evolution. 41(3). doi:10.1093/molbev/msae035

6. Santangelo James S, Battlay Paul, Hendrickson Brandon T, Kuo Wen-Hsi, Olsen Kenneth M, Kooyers Nicholas J, Johnson Marc TJ, Hodgins Kathryn A, Ness Rob W. 2023. Haplotype-Resolved, Chromosome-Level Assembly of White Clover (Trifolium repens L., Fabaceae). Genome biology and evolution. 15(8). doi:10.1093/gbe/evad146

7. Ford Scott A, Craig Rory J, Ness Rob W. 2022. A novel method for identifying Chlamydomonas reinhardtii (Chlorophyta) and closely related species from nature. Journal of phycology. Dec 1. doi:10.1111/jpy.13306

8. Hasan Ahmed R, Lachapelle Josianne, El-Shawa Sara A, Potjewyd Roman, Ford Scott A, Ness Rob W. 2022. Salt stress alters the spectrum of de novo mutation available to selection during experimental adaptation of Chlamydomonas reinhardtii. Evolution; international journal of organic evolution. 76(10):2450–2463. doi:10.1111/evo.14604

9. Böndel Katharina B, Samuels Toby, Craig Rory J, Ness Rob W, Colegrave Nick, Keightley Peter D. 2022. The distribution of fitness effects of spontaneous mutations in Chlamydomonas reinhardtii inferred using frequency changes under experimental evolution. PLoS genetics. 18(6):e1009840. doi:10.1371/journal.pgen.1009840

10. Garrett Phen, Becher Hannes, Gussarova Galina, dePamphilis Claude W, Ness Rob W, Gopalakrishnan Shyam, Twyford Alex D. 2022. Pervasive Phylogenomic Incongruence Underlies Evolutionary Relationships in Eyebrights (Euphrasia, Orobanchaceae). Frontiers in plant science. 13:869583. doi:10.3389/fpls.2022.869583

11. Santangelo James S, Ness Rob W, Cohan Beata, Fitzpatrick Connor R, Innes Simon G, Koch Sophie, Miles Lindsay S, Munim Samreen, Peres-Neto Pedro R, Prashad Cindy, … Johnson Marc TJ. 2022. Global urban environmental change drives adaptation in white clover. Science. 375(6586):1275–1281. doi:10.1126/science.abk0989

12. Oman Madeleine, Alam Aqsa, Ness Rob W. 2022. How Sequence Context-Dependent Mutability Drives Mutation Rate Variation in the Genome. Genome biology and evolution. 14(3). doi:10.1093/gbe/evac032

13. López-Cortegano Eugenio, Craig Rory J, Chebib Jobran, Samuels Toby, Morgan Andrew D, Kraemer Susanne A, Böndel Katharina B, Ness Rob W, Colegrave Nick, Keightley Peter D. 2021. De novo mutation rate variation and its determinants in Chlamydomonas. Molecular biology and evolution. 38(9):3709–3723. doi:10.1093/molbev/msab140

14. Craig Rory J, Hasan Ahmed R, Ness Rob W, Keightley Peter D. 2021. Comparative genomics of Chlamydomonas. The Plant cell. 33(4):1016–1041. doi:10.1093/plcell/koab026

15. Murray Rosalind L, Herridge Elizabeth J, Ness Rob W, Wiberg R Axel W, Bussière Luc F. 2020. Competition for access to mates predicts female-specific ornamentation and male investment in relative testis size. Evolution. 74(8):1741–1754. doi:10.1111/evo.13986

16. Santangelo James S, Thompson Ken A, Cohan Beata, Syed Jibran, Ness Rob W, Johnson Marc TJ. 2020. Predicting the strength of urban-rural clines in a Mendelian polymorphism along a latitudinal gradient. Evolution letters. 4(3):212–225. doi:10.1002/evl3.163

17. Hasan Ahmed R, Ness Rob W. 2020. Recombination rate variation and infrequent sex influence genetic diversity in Chlamydomonas reinhardtii. Genome biology and evolution. 12(4):370–380. doi:10.1093/gbe/evaa057

18. James S Santangelo, Lindsay S Miles, Sophie T Breitbart, David Murray-Stoker, L Ruth Rivkin, Marc T J Johnson, and Rob W Ness. 2020. Urban environments as a framework to study parallel evolution. In: Marta Szulkin, Jason Munshi-South, and Anne Charmantier, editor. Urban Evolutionary Biology. Oxford Scholarship Online.

19. Hasan Ahmed R, Duggal Jaspreet K, Ness Rob W. 2019. Consequences of recombination for the evolution of the mating type locus in Chlamydomonas reinhardtii. The New phytologist. 224(3):1339–1348. doi:10.1111/nph.16003

20. Craig Rory J, Böndel Katharina B, Arakawa Kazuharu, Nakada Takashi, Ito Takuro, Bell Graham, Colegrave Nick, Keightley Peter D, Ness Rob W. 2019. Patterns of population structure and complex haplotype sharing among field isolates of the green alga Chlamydomonas reinhardtii. Molecular ecology. 28(17):3977–3993. doi:10.1111/mec.15193

21. Carmona Diego, Hollister Jesse D, Greiner Stephan, Wright Stephen I, Ness Rob W, Johnson Marc TJ. 2019. The effects of losing sex on the molecular evolution of plant defense. bioRxiv.:683219. doi:10.1101/683219

22. Böndel Katharina B, Kraemer Susanne A, Samuels Toby, McClean Deirdre, Lachapelle Josianne, Ness Rob W, Colegrave Nick, Keightley Peter D. 2019. Inferring the distribution of fitness effects of spontaneous mutations in Chlamydomonas reinhardtii. PLoS biology. 17(6):e3000192. doi:10.1371/journal.pbio.3000192

23. Cheng Arthur H, Bouchard-Cannon Pascale, Ness Rob W, Cheng Hai-Ying Mary. 2019. RNA-sequencing data highlighting the time-of-day-dependent transcriptome of the central circadian pacemaker in SOX2-deficient mice. Data in brief. 24:103909. doi:10.1016/j.dib.2019.103909

24. Cheng Arthur H, Bouchard-Cannon Pascale, Hegazi Sara, Lowden Christopher, Fung Samuel W, Chiang Cheng-Kang, Ness Rob W, Cheng Hai-Ying Mary. 2019. SOX2-dependent transcription in clock neurons promotes the robustness of the central circadian pacemaker. Cell reports. 26(12):3191-3202.e8. doi:10.1016/j.celrep.2019.02.068

25. Rivkin L Ruth, Santangelo James S, Alberti Marina, Aronson Myla FJ, de Keyzer Charlotte W, Diamond Sarah E, Fortin Marie-Josée, Frazee Lauren J, Gorton Amanda J, Hendry Andrew P, … Johnson Marc TJ. 2019. A roadmap for urban evolutionary ecology. Evolutionary applications. 12(3):384–398. doi:10.1111/eva.12734

26. Santangelo James S, Johnson Marc TJ, Ness Rob W. 2018. Modern spandrels: the roles of genetic drift, gene flow and natural selection in the evolution of parallel clines. Proceedings. Biological sciences / The Royal Society. 285(1878). doi:10.1098/rspb.2018.0230

27. Exposito-Alonso Moises, Becker Claude, Schuenemann Verena J, Reiter Ella, Setzer Claudia, Slovak Radka, Brachi Benjamin, Hagmann Jörg, Grimm Dominik G, Chen Jiahui, Busch Wolfgang, Bergelson Joy, Ness Rob W, Krause Johannes, Burbano Hernán A, Weigel Detlef. 2018. The rate and potential relevance of new mutations in a colonizing plant lineage. PLoS genetics. 14(2):e1007155. doi:10.1371/journal.pgen.1007155

28. Kraemer Susanne A, Böndel Katharina B, Ness Robert W, Keightley Peter D, Colegrave Nick. 2017. Fitness change in relation to mutation number in spontaneous mutation accumulation lines of Chlamydomonas reinhardtii. Evolution. 71(12):2918–2929. doi:10.1111/evo.13360

29. Booker Tom R, Ness Rob W, Keightley Peter D. 2017. The recombination landscape in wild house mice inferred using population genomic data. Genetics. 207(1):297–309. doi:10.1534/genetics.117.300063

30. Twyford Alex D, Ness Rob W. 2017. Strategies for complete plastid genome sequencing. Molecular ecology resources. 17(5):858–868. doi:10.1111/1755-0998.12626

31. Trivedi Jigar, Lachapelle Josianne, Vanderwolf Karen J, Misra Vikram, Willis Craig KR, Ratcliffe John M, Ness Rob W, Anderson James B, Kohn Linda M. 2017. Fungus causing white-nose syndrome in bats accumulates genetic variability in North America with no sign of recombination. mSphere. 2(4). doi:10.1128/mSphereDirect.00271-17

32. Murray Rosalind L, Herridge Elizabeth J, Ness Rob W, Bussière Luc F. 2017. Are sex ratio distorting endosymbionts responsible for mating system variation among dance flies (Diptera: Empidinae)? PloS one. 12(6):e0178364. doi:10.1371/journal.pone.0178364

33. Kraemer SA, Morgan AD, Ness RW, Keightley PD, Colegrave N. 2016. Fitness effects of new mutations in Chlamydomonas reinhardtii across two stress gradients. Journal of evolutionary biology. 29(3):583–593. doi:10.1111/jeb.12807

34. Ness Rob W, Kraemer Susanne A, Colegrave Nick, Keightley Peter D. 2016. Direct estimate of the spontaneous mutation rate uncovers the effects of drift and recombination in the Chlamydomonas reinhardtii plastid genome. Molecular biology and evolution. 33(3):800–808. doi:10.1093/molbev/msv272

35. Ness Rob W, Morgan Andrew D, Vasanthakrishnan Radhakrishnan B, Colegrave Nick, Keightley Peter D. 2015. Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii. Genome research. 25(11):1739–1749. doi:10.1101/gr.191494.115

36. Deinum Eva E, Halligan Daniel L, Ness Rob W, Zhang Yao-Hua, Cong Lin, Zhang Jian-Xu, Keightley Peter D. 2015. Recent evolution in Rattus norvegicus is shaped by declining effective population size. Molecular biology and evolution. 32(10):2547–2558. doi:10.1093/molbev/msv126

37. Wiberg R Axel W, Halligan Daniel L, Ness Rob W, Necsulea Anamaria, Kaessmann Henrik, Keightley Peter D. 2015. Assessing recent selection and functionality at long noncoding RNA loci in the mouse genome. Genome biology and evolution. 7(8):2432–2444. doi:10.1093/gbe/evv155

38. Booker Tom, Ness Rob W, Charlesworth Deborah. 2015. Molecular evolution: breakthroughs and mysteries in Batesian mimicry. Current biology: CB. 25(12):R506-8. doi:10.1016/j.cub.2015.04.024

39. Arunkumar Ramesh, Ness Rob W, Wright Stephen I, Barrett Spencer CH. 2015. The evolution of selfing is accompanied by reduced efficacy of selection and purging of deleterious mutations. Genetics. 199(3):817–829. doi:10.1534/genetics.114.172809

40. Keightley Peter D, Pinharanda Ana, Ness Rob W, Simpson Fraser, Dasmahapatra Kanchon K, Mallet James, Davey John W, Jiggins Chris D. 2015. Estimation of the spontaneous mutation rate in Heliconius melpomene. Molecular biology and evolution. 32(1):239–243. doi:10.1093/molbev/msu302

41. Morgan Andrew D, Ness Rob W, Keightley Peter D, Colegrave Nick. 2014. Spontaneous mutation accumulation in multiple strains of the green alga, Chlamydomonas reinhardtii. Evolution. 68(9):2589–2602. doi:10.1111/evo.12448

42. Keightley Peter D, Ness Rob W, Halligan Daniel L, Haddrill Penelope R. 2014. Estimation of the spontaneous mutation rate per nucleotide site in a Drosophila melanogaster full-sib family. Genetics. 196(1):313–320. doi:10.1534/genetics.113.158758

43. Kelleher Jerome, Ness Rob W, Halligan Daniel L. 2013. Processing genome scale tabular data with wormtable. BMC bioinformatics. 14:356. doi:10.1186/1471-2105-14-356

44. Halligan Daniel L, Kousathanas Athanasios, Ness Rob W, Harr Bettina, Eöry Lél, Keane Thomas M, Adams David J, Keightley Peter D. 2013. Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents. PLoS genetics. 9(12):e1003995. doi:10.1371/journal.pgen.1003995

45. Hazzouri Khaled M, Escobar Juan S, Ness Rob W, Killian Newman L, Randle April M, Kalisz Susan, Wright Stephen I. 2013. Comparative population genomics in Collinsia sister species reveals evidence for reduced effective population size, relaxed selection, and evolution of biased gene conversion with an ongoing mating system shift. Evolution. 67(5):1263–1278. doi:10.1111/evo.12027

46. Ness Rob W, Morgan Andrew D, Colegrave Nick, Keightley Peter D. 2012. Estimate of the spontaneous mutation rate in Chlamydomonas reinhardtii. Genetics. 192(4):1447–1454. doi:10.1534/genetics.112.145078

47. Ness Rob W, Zhang Yao-Hua, Cong Lin, Wang Yu, Zhang Jian-Xu, Keightley Peter D. 2012. Nuclear gene variation in wild brown rats. G3 . 2(12):1661–1664. doi:10.1534/g3.112.004713

48. Ness Rob W, Siol Mathieu, Barrett Spencer CH. 2012. Genomic consequences of transitions from cross- to self-fertilization on the efficacy of selection in three independently derived selfing plants. BMC genomics. 13:611. doi:10.1186/1471-2164-13-611

49. Ness Rob W, Graham Sean W, Barrett Spencer CH. 2011. Reconciling gene and genome duplication events: using multiple nuclear gene families to infer the phylogeny of the aquatic plant family Pontederiaceae. Molecular biology and evolution. 28(11):3009–3018. doi:10.1093/molbev/msr119

50. Ness Rob W, Siol Mathieu, Barrett Spencer CH. 2011. De novo sequence assembly and characterization of the floral transcriptome in cross- and self-fertilizing plants. BMC genomics. 12:298. doi:10.1186/1471-2164-12-298

51. Ness Rob W, Wright Stephen I, Barrett Spencer CH. 2010. Mating-system variation, demographic history and patterns of nucleotide diversity in the Tristylous plant Eichhornia paniculata. Genetics. 184(2):381–392. doi:10.1534/genetics.109.110130

52. Barrett Spencer CH, Ness Rob W, Vallejo-Marín Mario. 2009. Evolutionary pathways to self-fertilization in a tristylous plant species. The New phytologist. 183(3):546–556. doi:10.1111/j.1469-8137.2009.02937.x

53. Wright Stephen I, Ness Rob W, Foxe John Paul, Barrett Spencer CH. 2008. Genomic consequences of outcrossing and selfing in plants. International journal of plant sciences. 169(1):105–118. doi:10.1086/523366