Jones Lab Publications

Also see Adam Jones’ publications on: Research Gate or Google Scholar.

Books:

front_cover copy

C++ for Biologists: Evolutionary Models. This book is a tutorial that focuses on developing individual-based simulation models (like those used in the Jones, Arnold, and Bürger models featured in the papers below) using the C++ programming language. No prior programming experience is necessary. A hard copy can be purchased from Amazon (just search for C++ for Biologists in books) or you can click here to download the C_for_Biologists_Free_Version.

Peer-Reviewed Publications: 

1. Jones, A. G. and J. C. Avise. 1997. Microsatellite analysis of maternity and the mating system in the Gulf pipefish (Syngnathus scovelli), a species with male pregnancy and sex-role reversal. Molecular Ecology 6:203-213.

2. Jones, A. G. and J. C. Avise. 1997. Polygynandry in the dusky pipefish Syngnathus floridae revealed by microsatellite DNA markers. Evolution 51:1611-1622.

3. Jones, A. G., S. Östlund-Nilsson and J. C. Avise. 1998. A microsatellite assessment of sneaked fertilizations and egg thievery in the fifteenspine stickleback. Evolution 52:848-858.

4. Jones, A. G., C. A. Stockwell, D. Walker and J. C. Avise. 1998. The molecular basis of a microsatellite null allele from the White Sands pupfish. Journal of Heredity 89:339-342.

5. Stockwell, C. A., M. Mulvey, and A. G. Jones. 1998. Genetic evidence for two evolutionarily significant units of White Sands pupfish. Animal Conservation 1:213-225.

6. Jones, A. G., C. Kvarnemo, G. I. Moore, L. W. Simmons, and J. C. Avise. 1998. Microsatellite evidence for monogamy and sex-biased recombination in the Western Australian seahorse, Hippocampus angustus. Molecular Ecology 7:1497-1505.

7. Zane, L., W. S. Nelson, A. G. Jones and J. C. Avise. 1999. Microsatellite assessment of multiple paternity in natural populations of a live-bearing fish, Gambusia holbrooki. Journal of Evolutionary Biology 12:61-69.

8. Jones, A. G., G. Rosenqvist, A. Berglund, and J. C. Avise. 1999. Clustered microsatellite mutations in the pipefish Syngnathus typhle. Genetics 152:1057-1063.

9. Jones, A. G., G. Rosenqvist, A. Berglund, and J. C. Avise. 1999. The genetic mating system of a sex-role-reversed pipefish (Syngnathus typhle): a molecular inquiry. Behavioral Ecology and Sociobiology 46:357-365.

10. Jones, A. G., G. Rosenqvist, A. Berglund, S. J. Arnold, and J. C. Avise. 2000. The Bateman gradient and the cause of sexual selection in a sex-role-reversed pipefish. Proceedings of the Royal Society of London B: Biological Sciences 267:677-680.

11. Jones, A. G., G. Rosenqvist, A. Berglund, and J. C. Avise. 2000. Mate quality influences multiple maternity in the sex-role-reversed pipefish Syngnathus typhle. Oikos 90:321-326.

12. Kvarnemo, C., G. I. Moore, A. G. Jones, W. S. Nelson, and J. C. Avise. 2000. Monogamous pair bonds and mate switching in the Western Australian seahorse Hippocampus subelongatus. Journal of Evolutionary Biology 13:882-888.

13. Jones, A. G. and J. C. Avise. 2001. Mating systems and sexual selection in male-pregnant pipefishes and seahorses: insights from microsatellite-based studies of maternity. Journal of Heredity 92: 150-158.

14. Jones, A. G., D. Walker, K. Lindström, C. Kvarnemo, and J. C. Avise. 2001. Surprising similarity of sneaking rates and genetic mating patterns in two populations of the sand goby experiencing disparate sexual selection regimes. Molecular Ecology 10:461-469.

15. Jones, A. G. 2001. GERUD1.0: A computer program for the reconstruction of parental genotypes from progeny arrays using multi-locus DNA data. Molecular Ecology Notes 1:215-218.

16. McCoy, E. E., A. G. Jones, and J. C. Avise. 2001. The genetic mating system and tests for cuckoldry in a pipefish species in which males fertilize eggs and brood offspring externally. Molecular Ecology 10:1793-1800.

17a. Arnold, S. J., M. E. Pfrender, and A. G. Jones. 2001. The adaptive landscape as a conceptual bridge between micro- and macro-evolution. Genetica 112/113:9-32.

17b. Arnold, S. J., M. E. Pfrender, and A. G. Jones. 2001. The adaptive landscape as a conceptual bridge between micro- and macro-evolution. Pp. 9-32 in Microevolution — Rate, Pattern, Process (A.P. Hendry, M.T. Kinnison, Eds.) Kluwer Academic Publishers. (reprinting of publication 17a)

18. Jones, A. G., M. S. Blouin, and S. J. Arnold. 2001. Genetic variation in two populations of the rough-skinned newt (Taricha granulosa) assessed using novel tetranucleotide microsatellite loci. Molecular Ecology Notes 1:293-296.

19. Jones, A. G., D. Walker, C. Kvarnemo, K. Lindström, and J. C. Avise. 2001. How cuckoldry can decrease the opportunity for sexual selection: data and theory from a genetic parentage analysis of the sand goby, Pomatoschistus minutus. Proceedings of the National Academy of Sciences USA 98:9151-9156.

20. Jones, A. G., D. Walker, and J. C. Avise. 2001. Genetic evidence for extreme polyandry and extraordinary sex-role reversal in a pipefish. Proceedings of the Royal Society of London B: Biological Sciences 268:2531-2535.

21. Jones, A. G., E. M. Adams, and S. J. Arnold. 2002. Topping off: a mechanism of first-male sperm precedence in a vertebrate. Proceedings of the National Academy of Sciences USA 99:2078-2081.

22. Jones, A. G. 2002. The evolution of alternative cryptic female choice strategies in age-structured populations. Evolution 56: 2530-2536.

23. Jones, A. G., J. R. Arguello, and S. J. Arnold. 2002. Validation of Bateman’s principles: a genetic study of sexual selection and mating patterns in the rough-skinned newt. Proceedings of the Royal Society of London B: Biological Sciences 269:2533-2539.

24. Avise, J. C., A. G. Jones, D. Walker, J. A. DeWoody, and collaborators. 2002. Genetic mating systems and reproductive natural histories of fishes: Lessons for ecology and evolution. Annual Review of Genetics 36:19-45.

25. Jones, A. G., G. I. Moore, C. Kvarnemo, D. Walker, and J. C. Avise. 2003. Sympatric speciation as a consequence of male pregnancy in seahorses. Proceedings of the National Academy of Sciences USA 100:6598-6603.

26. Jones, A. G., S. J. Arnold, and R. Bürger. 2003. Stability of the G-matrix in a population experiencing pleiotropic mutation, stabilizing selection, and genetic drift. Evolution 57:1747-1760.

27. Jones, A. G. and W. R. Ardren. 2003. Methods of parentage analysis in natural populations. Molecular Ecology 12:2511-2523.

28. Pampoulie, C., E. Gysels, B. Hellemans, G. E. Maes, V. Leentjes, A. G. Jones, and F. A. M. Volckaert. 2004. Evidence for fine scale genetic structure and estuarine colonisation in a high gene flow marine goby (Pomatoschistus minutus). Heredity 92:434-445.

29. Watts, R. A., C. A. Palmer, R. C. Feldhoff, P. W. Feldhoff, L. D. Houck, A. G. Jones, M. E. Pfrender, S. M. Rollman, and S. J. Arnold. 2004. Stabilizing selection on behavior and morphology masks positive selection on the signal in a pheromone signaling complex. Molecular Biology and Evolution 21:1032-1041.

30. Hoffman, E. A., J. R. Arguello, N. Kolm, A. Berglund, and A. G. Jones. 2004. Eleven polymorphic microsatellite loci in a coral reef fish, Pterapogon kauderni. Molecular Ecology Notes 4:342-344.

31. Jones, A. G., S. J. Arnold, and R. Bürger. 2004. Evolution and stability of the G-matrix on a landscape with a moving optimum. Evolution 58:1639-1654.

32. Jones, A. G., J. R. Arguello, and S. J. Arnold. 2004. Molecular parentage analysis in experimental newt populations: the response of mating system measures to variation in the operational sex ratio. The American Naturalist 164:444-456.

33. Jones, A. G. 2004. Male pregnancy and the formation of seahorse species. The Biologist 51:216-221.

34. Hoffman, E. A., N. Kolm, A. Berglund, J. R. Arguello, and A. G. Jones. 2005. Genetic structure in the coral-reef-associated Bangaii cardinalfish, Pterapogon kauderni. Molecular Ecology 14:1367-1375.

35. Kolm, N., E. A. Hoffman, J. Olsson, A. Berglund, and A. G. Jones. 2005. Group stability and homing behavior but no kin group structures in a coral reef fish. Behavioral Ecology 16:521-527.

36. Adams, E. M., A. G. Jones, and S. J. Arnold. 2005. Multiple paternity in a natural population of a salamander with long-term sperm storage. Molecular Ecology 14:1803-1810.

37. Jones, A. G. 2005. GERUD2.0: a computer program for the reconstruction of parental genotypes from half-sib progeny arrays with known or unknown parents. Molecular Ecology Notes 5:708-711.

38. Jones, A. G., G. Rosenqvist, A. Berglund, and J. C. Avise. 2005. The measurement of sexual selection using Bateman’s principles: an experimental test in the sex-role-reversed pipefish Syngnathus typhle. Integrative and Comparative Biology 45:874-884.

39. Hoffman, E. A., K. B. Mobley, and A. G. Jones. 2006. Male pregnancy and the evolution of body segmentation in seahorses and pipefishes. Evolution 60:404-410.

40. Hoffman, E. A., F. W. Schueler, A. G. Jones, and M. S. Blouin. 2006. An analysis of selection on a colour polymorphism in the northern leopard frog. Molecular Ecology 15:2627-2641.

41. Harlin-Cognato, A., E. A. Hoffman, and A. G. Jones. 2006. Gene cooption without duplication during the evolution of a male-pregnancy gene in pipefish. Proceedings of the National Academy of Sciences 103:19407-19412.

42. Kvarnemo, C., G. I. Moore, and A. G. Jones. 2007. Sexually selected females in the monogamous Western Australian seahorse. Proceedings of the Royal Society of London B 274:521-525.

43. Jones, A. G., S. J. Arnold, and R. Bürger. 2007. The mutation matrix and the evolution of evolvability. Evolution 61:727-745.

44. Mobley, K. B. and A. G. Jones. 2007. Geographical variation in the mating system of the dusky pipefish (Syngnathus floridae). Molecular Ecology 16:2596-2606.

45. Jones, A. G. 2008. A theoretical quantitative genetic study of negative ecological interactions and extinction times in changing environments. BMC Evolutionary Biology 8:119.

46. Arnold, S. J., R. Bürger, P. A. Hohenlohe, B. C. Ajie, and A. G. Jones. 2008. Understanding the evolution and stability of the G-matrix. Evolution 62:2451-2461.

47. Partridge, C., I. Ahnesjö, C. Kvarnemo, K. Mobley, A. Berglund, and A. G. Jones. 2009. The effect of perceived female parasite load on post-copulatory male choice in a sex-role-reversed pipefish. Behavioral Ecology and Sociobiology 63:345-354.

48. Coleman, S. W., A. Harlin-Cognato, and A. G. Jones. 2009. Reproductive isolation, reproductive mode, and sexual selection: tests of the viviparity-driven conflict hypothesis. The American Naturalist 173:291-303.

49. Mobley, K. B., T. Amundsen, E. Forsgren, P. A. Svensson, and A. G. Jones. 2009. Multiple mating and a low incidence of cuckoldry for nest-holding males in the two-spotted goby, Gobiusculus flavescens. BMC Evolutionary Biology 9:6.

50. Mobley, K. B. and A. G. Jones. 2009. Environmental, demographic, and genetic mating system variation among five geographically distinct dusky pipefish (Syngnathus floridae) populations. Molecular Ecology 18:1476-1490.

51. Ratterman, N. L., G. G. Rosenthal, and A. G. Jones. 2009. Sex recognition via chemical cues in the sex-role-reversed Gulf pipefish (Syngnathus scovelli). Ethology 115:339-346.

52. Jones, A. G. 2009. On the opportunity for sexual selection, the Bateman gradient and the maximum intensity of sexual selection. Evolution 63:1673-1684.

53. Jones, A. G. and N. L. Ratterman. 2009. Mate choice and sexual selection: What have we learned since Darwin? Proceedings of the National Academy of Sciences USA 106:10001-10008.

54. Small, C. M., G. E. Carney, Q. Mo, M. Vannucci, and A. G. Jones. 2009. A microarray analysis of sex- and gonad-biased gene expression in the zebrafish: Evidence for masculinization of the transcriptome. BMC Genomics 10:579.

55. Jones, A. G., C. M. Small, K. A. Paczolt, and N. L. Ratterman. 2010. A practical guide to methods of parentage analysis. Molecular Ecology Resources 10:6-30.

56. Paczolt, K. A. and A. G. Jones. 2010. Postcopulatory sexual selection and sexual conflict in the evolution of male pregnancy. Nature 464:401-404.

57. Braga Goncalves, I., K. B. Mobley, I. Ahnesjö, G. Sagebakken, A. G. Jones, and C. Kvarnemo. 2010. Reproductive compensation in broad-nosed pipefish females. Proceedings of the Royal Society of London B 277:1581-1587.

58. Mobley, K. B., C. M. Small, N.K. Jue, and A. G. Jones. 2010. Population structure of the dusky pipefish (Syngnathus floridae) from the Atlantic and Gulf of Mexico, as revealed by mitochondrial DNA and microsatellite analyses. Journal of Biogeography 37:1363-1377.

59. Partridge, C., A. Boettcher, and A. G. Jones. 2010. Short-term exposure to a synthetic estrogen disrupts mating dynamics in a pipefish. Hormones and Behavior 58:800-807.

60. Coleman, S. W. and A. G. Jones. 2011. Patterns of multiple paternity and maternity in fishes. Biological Journal of the Linnean Society 103:735-760.

61. Mobley, K. B., C. M. Small, and A. G. Jones. 2011. The genetics and genomics of Syngnathidae: pipefishes, seahorses and seadragons. Journal of Fish Biology 78:1624-1646.

62. Mobley, K. B., I. Ahnesjö, C. Kvarnemo, C. Partridge, A. Berglund, and A. G. Jones. 2011. The effect of maternal body size on embryo survivorship in the broods of pregnant male pipefish. Behavioral Ecology 65:1169-1177.

63. Kvarnemo, C., K. B. Mobley, C. Partridge, A. G. Jones, and I. Ahnesjö. 2011. Evidence of paternal nutrient provisioning to embryos in broad-nosed pipefish Syngnathus typhle. Journal of Fish Biology 78:1725-1737.

64. Krakauer, A. H., M. S. Webster, E. H. DuVal, A. G. Jones, and S. M. Shuster. 2011. The opportunity for sexual selection: not mismeasured, just misunderstood. Journal of Evolutionary Biology 24:2064-2071.

65. Jones, A. G., N. L. Ratterman, and K. A. Paczolt. 2012. The adaptive landscape in sexual selection research. In: The Adaptive Landscape in Evolutionary Biology (E. Svensson, R. Calsbeek, eds.), pp. 110-125. Oxford University Press, Oxford.

66. Partridge, C., A. Boettcher, and A. G. Jones. 2012. Population structure of the Gulf pipefish in and around Mobile Bay and the Northern Gulf of Mexico. Journal of Heredity 103:821-830.

67. Jones, A. G., R. Bürger, S. J. Arnold, P. A. Hohenlohe, and J. C. Uyeda. 2012. The effects of stochastic and episodic movement of the optimum on the evolution of the G-matrix and the response of the mean to selection. Journal of Evolutionary Biology 25:2210-2231.

68. Mobley, K. B. and A. G. Jones. 2013. Overcoming statistical bias to estimate genetic mating system parameters in open populations: A comparison of Bateman’s principles between the sexes in a sex-role-reversed pipefish. Evolution 67:646-660.

69. Rose, E., K. A. Paczolt, and A. G. Jones. 2013. The contributions of pre-mating and post-mating episodes to total selection in sex-role-reversed Gulf pipefish. The American Naturalist 182:410-420.

70. Partridge, C., A. Boettcher, and A. G. Jones. 2013. The role of courtship behavior and size in mate preference in the sex-role reversed Gulf pipefish, Syngnathus scovelli. Ethology 119:692-701.

71. Rose, E., K. A. Paczolt, and A. G. Jones. 2013. The effects of synthetic estrogen exposure on pre-mating and post-mating selection episodes in sex-role-reversed Gulf pipefish. Evolutionary Applications 6:1160-1170.

72. Small, C. M., A. Harlin-Cognato, and A. G. Jones. 2013. Functional similarity and molecular divergence of a novel reproductive transcriptome in two male-pregnant Syngnathus pipefish species. Ecology and Evolution 3:4092-4108.

73. Monteiro, N. M., R. M. Silva, M. Cunha, A. Antunes, A. G. Jones, and M. N. Vieira. 2014. Validating the use of coloration patterns for individual recognition in the worm pipefish using a novel set of microsatellite markers. Molecular Ecology Resources 14:150-156.

74. Ratterman, N. L., G. G. Rosenthal, G. E. Carney, and A. G. Jones. 2014. Genetic variation and covariation in male attractiveness and female mating preferences in Drosophila melanogaster. G3: Genes, Genomes, Genetics 4:79-88.

75. Mobley, K. B., M. Abou Chakra, and A. G. Jones. 2014. No evidence for size-assortative mating in the wild despite mutual mate choice in sex-role-reversed pipefishes. Ecology and Evolution 4:67-78.

76. Jones, A. G., R. Bürger, and S. J. Arnold. 2014. Epistasis and natural selection shape the mutational architecture of complex traits. Nature Communications 5:3709.

77. Rose, E., C. M. Small, H. A. Saucedo, C. Harper, and A. G. Jones. 2014. Genetic evidence for monogamy in the dwarf seahorse, Hippocampus zosterae. Journal of Heredity 105:828-833.

78. Flanagan, S. P., J. B. Johnson, E. Rose, and A. G. Jones. 2014. Sexual selection on female ornaments in the sex-role-reversed Gulf pipefish (Syngnathus scovelli). Journal of Evolutionary Biology 27:2457-2467.

79. Paczolt, K. A., C. N. Passow, P. J. Delclos, H. K. Kindsvater, A. G. Jones, and G. G. Rosenthal. 2015. Multiple mating and reproductive skew in parental and introgressed females of the live-bearing fish Xiphophorus birchmani. Journal of Heredity 106:57-66.

80. Braga Goncalves, I., K. B. Mobley, I. Ahnesjö, Gry Sagebakken, A. G. Jones, and C. Kvarnemo. 2015. Effects of mating order and male size on embryo survival in a pipefish. Biological Journal of the Linnean Society 114:639-645.

81. Jones, A. G. 2015. BATEMANATER: A computer program to estimate and bootstrap mating system variables based on Bateman’s principles. Molecular Ecology Resources 15:1396-1402.

82. Paczolt, K. A. and A. G. Jones. 2015. The effects of food limitation on life-history tradeoffs in pregnant male Gulf pipefish. PLOS One 10:e0124147.

83. Flanagan, S. P. and A. G. Jones. 2015. Identifying signatures of sexual selection using genomewide selection components analysis. Ecology and Evolution 5:2722-2744.

84. Rose, E., S. P. Flanagan, and A. G. Jones. 2015. The effects of synthetic estrogen exposure on the sexually dimorphic liver transcriptome of the sex-role-reversed Gulf pipefish. PLOS One 10:e0139401.

85. Paczolt, K. A., W. E. Martin, N. L. Ratterman, and A. G. Jones. 2016. A low rate of multiple maternity for pregnant male northern pipefish, Syngnathus fuscus. Journal of Fish Biology 88:1614-1619.

86. Jones, A. G. 2016. Theory of sexual selection. In: Encyclopedia of Evolutionary Biology, vol. 4 (R. M. Kliman, ed.), pp. 119-127. Academic Press, Oxford.

87. Flanagan, S. P., E. Rose, and A. G. Jones. 2016. Population genomics reveals multiple drivers of population differentiation in a sex-role-reversed pipefish. Molecular Ecology 25:5043-5072.

88. Rose, E., H. D. Masonjones, and A. G. Jones. 2016. A DNA-based assessment of the phylogenetic position of a morphologically distinct, anchialine-lake-restricted seahorse. Journal of Heredity 107:553-558.

89. Small, C. M., S. Bassham, J. Catchen, A. Amores, A. M. Fuiten, R. S. Brown, A. G. Jones, and W. A. Cresko. 2016. The genome of the Gulf pipefish enables understanding of evolutionary innovations. Genome Biology 17:258.

90. Monteiro, N., D. Carneiro, A. Antunes, N. Queiroz, M. N. Vieira, and A. G. Jones. 2017. The lek mating system of the worm pipefish (Nerophis lumbriciformis): A molecular maternity analysis and test of the phenotype-linked fertility hypothesis. Molecular Ecology 26:1371-1385.

91. Flanagan, S. P., G. Rosenqvist, and A. G. Jones. 2017. Mate quality and the temporal dynamics of breeding in a sex-role-reversed pipefish, Syngnathus typhle. Behavioral Ecology and Sociobiology 71:28.

92. Flanagan, S. P. and A. G. Jones. 2017. Genome-wide selection components analysis in a fish with male pregnancy. Evolution 71:1096-1105.

93. Monteiro, N., M. Cunha, L. Ferreira, N. Vieira, A. Antunes, D. Lyons, and A. G. Jones. 2017. Parabolic variation in sexual selection intensity across the range of a cold-water pipefish: Implications for susceptibility to climate change. Global Change Biology 23:3600-3609.

94. Flanagan, S. P. and A. G. Jones. 2017. Constraints on the Fst – heterozygosit outlier approach. 108:561-573.

Other publications:
95. Jones, A. G. and J. C. Avise. 2003. Quick guide: Male pregnancy. Current Biology 13:R791-R791.

96. Jones, A. G. 2004. Sea turtles: Old viruses and new tricks. Current Biology 14:R842-R843.

97. Paczolt, K. A. and A. G. Jones. 2010. Evidence for male allocation in pipefish? Reply. Nature 466:E12-E12.

98. Jones, A. G. 2013. Parental care in the 21st century. Evolution 67:3379-3380.

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