73. Cardoso LL, Durão P, Amicone M, Gordo I (2020) Dysbiosis individualizes the fitness effect of antibiotic resistance in the mammalian gut. Nat Ecol Evol.

72. HC Barreto, N Frazão, A Sousa, A Konrad, I Gordo (2020) Mutation Accumulation and Horizontal Gene Transfer in Escherichia coli Colonizing the Gut of Old Mice. Communicative & Integrative Biology.

71. P Durão, RS Ramiro, C Pereira, J Jurič, D Pereira, I Gordo (2020) Radial expansion facilitates the maintenance of double antibiotic resistances. Antimicrobial Agents and Chemotherapy. DOI: 10.1128/AAC.00668-20

70. RS Ramiro, P Durão, C Bank, I Gordo (2020) Low mutational load and high mutation rate variation in gut commensal bacteria. PLoS biology 18 (3), e3000617,

           Data and code for doi:10.1101/568709

69. HC Barreto, Sousa A and Gordo I (2020) The landscape of adaptive evolution of a gut commensal bacteria in aging mice. Current Biology.

68. João Barroso-Batista, Miguel F Pedro, Joana Sales-Dias, Catarina JG Pinto, Jessica A Thompson, Helena Pereira, Jocelyne Demengeot, Isabel Gordo, Karina B Xavier (2020). Specific eco-evolutionary contexts in the mouse gut reveal Escherichia coli metabolic versatility.Current Biology

67. R Balbontín, N Frazão, I Gordo (2020) DNA breaks-mediated cost reveals RNase HI as a new target for selectively eliminating antibiotic resistance. bioRxiv, 756767. doi:

66. Barreto HC, Cordeiro TN, Henriques AO, Gordo I (2019) Rampant loss of social traits during domestication of a wild Bacillus subtilis. bioRxiv. 751438. doi: 10.1101/751438

65. Gordo I (2019). Evolutionary change in the human gut microbiome: From a static to a dynamic view. PloS Biology. doi: 10.1371/journal.pbio.3000126

64. Pedro M, Batista-Barroso J, Pinto C, Dias J, Gordo I, Xavier K (2019) Understanding metabolic processes shaping adaptation of E. coli in the gut. Access Microbiology. doi: 10.1099/acmi.ac2019.po0215

63. Frazão N, Sousa A, Lässig M, Gordo I (2019) Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut. Proc Natl Acad Sci USA. doi: 10.1073/pnas.1906958116

62. Özkaya Ö, Balbontín R, Gordo I and Xavier KB (2018) Cheating on Cheaters Stabilizes Cooperation in Pseudomonas aeruginosa. Current Biology 28(13):2070-2080.e6. doi:10.1016/j.cub.2018.04.093. Press coverage: and EurekAlert

61. Durão P, Balbontín R and Gordo I (2018) Evolutionary mechanisms shaping the maintenance of antibiotic resistance. Trends in Microbiology. doi: 10.1016/j.tim.2018.01.005 Recommended by F1000Prime

60. Sousa A, Ramiro RS, Barroso-Batista J, Güleresi D, Lourenço M, Gordo I (2017) Recurrent Reverse Evolution Maintains Polymorphism After Strong Bottlenecks in Commensal Gut Bacteria. Molecular Biology and Evolution 34(11):2879-2892. doi: 10.1093/molbev/msx221

59. Sousa A, Frazão N, Ramiro RS, Gordo I (2017) Evolution of commensal bacteria in the intestinal tract of mice. Current Opinion in Microbiology 38:114-121.

58. Proença JT, Barral D, Gordo I (2017) Commensal-to-pathogen transition: One-single transposon insertion results in two pathoadaptive traits in Escherichia coli-macrophage interaction. Scientific Reports 7:4504

57. Moura de Sousa J, Balbontín R, Durão P, Gordo I (2017) Multidrug-resistant bacteria compensate for the epistasis between resistances. PLOS Biology 15(4): e2001741. Press coverage: EurekAlert and

Find supporting data here:
- Code for the two marker ABC method (CPP and shell file)
- Sequencing data (fastq files)

 56. Lourenço M, Ramiro RS, Güleresi D, Barroso-Batista J, Xavier KB, Gordo I, et al. (2016) A Mutational Hotspot and Strong Selection Contribute to the Order of Mutations Selected for during Escherichia coli Adaptation to the Gut. PLoS Genet 12(11): e1006420. doi:10.1371/journal.pgen.1006420

55. Moura de Sousa JA, Alpedrinha J, Campos PRA, Gordo I (2016) Competition and fixation of cohorts of adaptive mutations under Fisher geometrical model. PeerJ 4:e2256

54. Ramiro RS, Costa H and Gordo I (2016), Macrophage adaptation leads to parallel evolution of genetically diverse Escherichia coli small-colony variants with increased fitness in vivo and antibiotic collateral sensitivity. Evol Appl, 9: 994–1004. doi:10.1111/eva.12397 Press coverage

53. Durão P, Gülereşi D, Proença J, Gordo I (2016) Enhanced Survival of Rifampin- and Streptomycin-Resistant Escherichia coli Inside Macrophages. Antimicrobial Agents and Chemotherapy. 60(7):4324-4332. doi:10.1128/AAC.00624-16. Press coverage

52. Azevedo M, Sousa A, Moura de Sousa J, Thompson JA, Proença JT, Gordo I (2016) Trade-Offs of Escherichia coli Adaptation to an Intracellular Lifestyle in Macrophages. PLoS ONE. 11(1):e0146123. doi:10.1371/journal.pone.0146123.

51. Barroso-Batista J, Demengeot J & Gordo I (2015) Adaptive immunity increases
the pace and predictability of evolutionary change in commensal gut
bacteria. Nat Commun. 6: 8945. DOI: 10.1038/ncomms9945 Winner of the Gilbert S. Omenn Prize 2015

50. Moura de Sousa JA, Sousa A, Bourgard C, Gordo I (2015) Potential for Adaptation Overrides Cost of Resistance. Future Microbiol. 10:1415-31. doi: 10.2217/fmb.15.61

49. Durão P, Trindade S, Sousa A & Gordo I (2015) Multiple Resistance at no cost: Rifampicin and Streptomycin a dangerous liaison in the spread of antibiotic resistance. Mol Biol Evol. 32(10):2675-80. doi: 10.1093/molbev/msv143

48. Gordo I, Demengeot J, Xavier K (2014) Escherichia coli adaption to the gut environment: a constant fight for survival. Future Microbiol. 9 (11), 1235-1238. doi:10.2217/fmb.14.86

47. Barroso-Batista J, Sousa A, Lourenço M, Bergman ML, Demengeot J, Xavier KB, Gordo I (2014) The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps. PLoS Genet 10(3): e1004182. doi:10.1371/journal.pgen.1004182 Winner of the PLOS Genetics Research Prize 2015

46. Gordo I, M Miskinyte (2014) Fitness Measurements of Evolved Esherichia coli. Bio-protocol 4 (17), e1228. DOI: 10.21769/BioProtoc.1228

45. Gordo I, M Miskinyte (2014) Evolution of Escherichia coli to macrophage cell line. Bio-protocol 4 (17), e1227. DOI: 10.21769/BioProtoc.1227

44. Miskinyte, M., Sousa, A., Ramiro, R.S., de Sousa, J.A.M., Kotlinowski, J., Caramalho, I, Magalhães, S., Soares, M.P. & Gordo, I. 2013 The Genetic Basis of Escherichia coli Pathoadaptation to Macrophages. PLoS Pathog. 9(12): e1003802. doi:10.1371/journal.ppat.1003802 Press coverage

43. Sousa, A., Bourgard, C., Wahl, L.M. & Gordo, I. 2013 Rates of transposition in Escherichia coli. Biol. Lett. 9: 20130838. doi:10.1098/rsbl.2013.0838

42. Chelo, I. M., Nédli, J., Gordo, I. & Teotónio, H. 2013 An experimental test on the probability of extinction of new genetic variants. Nat. Commun. 4:2417 (doi:10.1038/ncomms3417)

41. Perfeito, L., Sousa, A., Bataillon, T. & Gordo, I. 2013 Rates of fitness decline and rebound suggest pervasive epistasis. Evolution. (doi: 10.1111/evo.12234)

40. Avelar, A.T., Perfeito, L., Gordo, I., Ferreira, M.G. 2013 Genome architecture is a selectable trait that can be maintained by antagonistic pleiotropy. Nat. Commun. 4:2235 (doi: 10.1038/ncomms3235)

39. de Sousa, J. A. M., P. R. A. Campos, and I. Gordo. 2013. An ABC method for estimating the rate and distribution of effects of beneficial mutations. Genome Biology and Evolution. Genome Biol. Evol. 5(5):794–806. (doi:10.1093/gbe/evt045)

38. Miskinyte, M. & Gordo, I. 2013 Increased Survival of Antibiotic-Resistant Escherichia coli inside Macrophages. Antimicrob. Agents Chemother. 57, 189–195. (doi:10.1128/AAC.01632-12)

37. Brito, P. H., Rocha, E. P. C., Xavier, K. B. & Gordo, I. 2013 Natural Genome Diversity of AI-2 Quorum Sensing in Escherichia coli: Conserved Signal Production but Labile Signal Reception. Genome Biol. Evol. 5, 16–30. (doi:10.1093/gbe/evs122)

36. Gordo, I. & Campos, P. R.A. 2012 Evolution of clonal populations approaching a fitness peak. Biol. Lett. 9: 20120239. (doi:10.1098/rsbl.2012.0239)

35. Trindade, S., Sousa, A. & Gordo, I. 2012 Antibiotic Resistance and Stress in the Light of Fisher’s Model. Evolution 66, 3815–3824. (doi:10.1111/j.1558-5646.2012.01722.x)

34. Sousa, A., Magalhaes, S. & Gordo, I. 2012 Cost of Antibiotic Resistance and the Geometry of Adaptation. Mol. Biol. Evol. 29, 1417–1428. (doi:10.1093/molbev/msr302)

33. Silva, R. F., Mendonca, S. C. M., Carvalho, L. M., Reis, A. M., Gordo, I., Trindade, S. & Dionisio, F. 2011 Pervasive Sign Epistasis between Conjugative Plasmids and Drug-Resistance Chromosomal Mutations. Plos Genet. 7. (doi:10.1371/journal.pgen.1002181)

32. Gordo, I., Perfeito, L. & Sousa, A. 2011 Fitness Effects of Mutations in Bacteria. J. Mol. Microbiol. Biotechnol. 21, 20–35. (doi:10.1159/000332747)

31. Brito, P. H., Guilherme, E., Soares, H. & Gordo, I. 2010 Mutation accumulation in Tetrahymena. Bmc Evol. Biol. 10. (doi:10.1186/1471-2148-10-354)

30. Gordo, I. & Sousa, A. 2010 Mutation, selection and genetic interactions in bacteria. Enciclopedia of Life Sciences (doi:10.1002/9780470015902.a0022175)

29. Trindade, S., Perfeito, L. & Gordo, I. 2010 Rate and effects of spontaneous mutations that affect fitness in mutator Escherichia coli. Philos. Trans. R. Soc. B-Biol. Sci. 365, 1177–1186. (doi:10.1098/rstb.2009.0287)

28. Viana, D. S., Gordo, I., Sucena, E. & Moita, M. A. P. 2010 Cognitive and Motivational Requirements for the Emergence of Cooperation in a Rat Social Game. PLoS One 5. (doi:10.1371/journal.pone.0008483)

27. Marais, G. A. B., Campos, P. R. A. & Gordo, I. 2010 Can Intra-Y Gene Conversion Oppose the Degeneration of the Human Y Chromosome? A Simulation Study. Genome Biol. Evol. 2, 347–357. (doi:10.1093/gbe/evq026)

26. Charlesworth, B., Betancourt, A.J., Kaiser, V.B. & Gordo, I. 2009 Genetic Recombination and molecular evolution. Cold Spring Harbor Symposia on Quantitative Biology 74, 177-186 (doi: 10.1101/sqb.2009.74.015)

25. Trindade, S., Sousa, A., Xavier, K. B., Dionisio, F., Ferreira, M. G. & Gordo, I. 2009 Positive Epistasis Drives the Acquisition of Multidrug Resistance. Plos Genet. 5. (doi:10.1371/journal.pgen.1000578)

24. Gordo, I., Gomes, M. G. M., Reis, D. G. & Campos, P. R. A. 2009 Genetic Diversity in the SIR Model of Pathogen Evolution. PLoS One 4. (doi:10.1371/journal.pone.0004876)

23. Campos, P. R. A., Neto, P. S. C. A., de Oliveira, V. M. & Gordo, I. 2008 Environmental heterogeneity enhances clonal interference. Evolution 62, 1390–1399. (doi:10.1111/j.1558-5646.2008.00380.x)

22. Gordo, I. & Campos, P. R. A. 2008 Sex and deleterious mutations. Genetics 179, 621–626. (doi:10.1534/genetics.108.086637)

21. Perfeito, L., Pereira, M. I., Campos, P. R. A. & Gordo, I. 2008 The effect of spatial structure on adaptation in Escherichia coli. Biol. Lett. 4, 57–59. (doi:10.1098/rsbl.2007.0481)

20. Perfeito, L., Fernandes, L., Mota, C. & Gordo, I. 2007 Adaptive mutations in bacteria: High rate and small effects. Science 317, 813–815. (doi:10.1126/science.1142284)

19. Gordo, I. & Campos, P. R. A. 2007 Patterns of genetic variation in populations of infectious agents. BMC Evol. Biol. 7. (doi:10.1186/1471-2148-7-116)

18. Gokaydin, D., Oliveira-Martins, J. B., Gordo, I. & Gomes, M. G. 2007 The reinfection threshold regulates pathogen diversity: the case of influenza. J. R. Soc. Interface 4,137-142

17. Dionisio, F. & Gordo, I. 2007 Controlling excludability in the evolution of cooperation. Evol. Ecol. Res. 9, 365–373

16. Combadao, J., Campos, P. R. A., Dionisio, F. & Gordo, I. 2007 Small-world networks decrease the speed of Muller’s ratchet. Genet. Res. 89, 7–18. (doi:10.1017/S0016672307008658)

15. Campos, P. R. A. & Gordo, I. 2006 Pathogen genetic variation in small-world host contact structures. J. Stat. Mech.-Theory Exp. (doi:10.1088/1742-5468/2006/12/L12003)

14. Campos, P. R. A., Combadao, J., Dionisio, F. & Gordo, I. 2006 Muller’s ratchet in random graphs and scale-free networks. Phys. Rev. E 74 (doi:10.1103/PhysRevE.74.042901)

13. Faro, J., Combadao, J. & Gordo, I. 2006 Did Germinal Centers evolve under differential effects of diversity vs. affinity? Lecture Notes in Computer Science. 4163: 1-8 (doi:10.1007/11823940_1)

12. Perfeito, L., Gordo, I. & Campos, P. R. A. 2006 The effect of spatial structure in adaptive evolution. Eur. Phys. J. B 51, 301–306. (doi:10.1140/epjb/e2006-00222-x)

11. Gordo, I. & Campos, P. R. A. 2006 Adaptive evolution in a spatially structured asexual population. Genetica 127, 217–229. (doi:10.1007/s10709-005-4012-9)

10. Dionisio, F. & Gordo, I. 2006 The tragedy of the commons, the public goods dilemma, and the meaning of rivalry and excludability in evolutionary biology. Evol. Ecol. Res. 8, 321–332.

9. Rosas, A., Gordo, I. & Campos, P. R. A. 2005 Scaling, genetic drift, and clonal interference in the extinction pattern of asexual population. Phys. Rev. E 72. (doi:10.1103/PhysRevE.72.012901)

8. Dionisio, F., Conceicao, I. C., Marques, A. C. R., Fernandes, L. & Gordo, I. 2005 The evolution of a conjugative plasmid and its ability to increase bacterial fitness. Biol. Lett. 1, 250–252. (doi:10.1098/rsbl.2004.0275)

7.  Gordo, I. & Dionisio, F. 2005 Nonequilibrium model for estimating parameters of deleterious mutations. Phys. Rev. E 71. (doi:10.1103/PhysRevE.71.031907)

6. Bachtrog, D. & Gordo, I. 2004 Adaptive evolution of asexual populations under Muller’s ratchet. Evolution 58, 1403–1413. (doi:10.1554/03-595)

5. Gordo, I., Navarro, A. & Charlesworth, B. 2002 Muller’s ratchet and the pattern of variation at a neutral locus. Genetics 161, 835–848. 

4. Gordo, I. & Charlesworth, B. 2001 The speed of Muller’s ratchet with background selection, and the degeneration of Y chromosomes. Genet. Res. 78, 149–161.

3. Gordo, I. & Charlesworth, B. 2001 Genetic linkage and molecular evolution. Curr. Biol. 11, R684–R686. (doi:10.1016/S0960-9822(01)00408-0)

2. Gordo, I. & Charlesworth, B. 2000 On the speed of Muller’s ratchet. Genetics 156, 2137–2140. 

1. Gordo, I. & Charlesworth, B. 2000 The degeneration of asexual haploid populations and the speed of Muller’s ratchet. Genetics 154, 1379–1387.