Education

Max Planck Institute for Evolutionary Anthropology, NSF International Postdoctoral Fellow, 2008-2009
University of Arizona, Ph.D., Ecology and Evolutionary Biology, 2007
University of Idaho, M.S., Biology, 2002
University of Idaho, B.S., Zoology, 1999

Research Interests

Speciation, sex chromosome evolution, population genetics, comparative evolutionary genomics, evolution of mammalian reproduction

Field of Study

Mammalian Evolutionary Genetics and Genomics

Publications

79. Kopania EEK, Watson EM, Rathje CC, Skinner BM, Ellis PJI, Larson EL, Good JM. (2022) The contribution of sex chromosome conflict to disrupted spermatogenesis in hybrid house mice. Genetics, In press. Preprint: bioRxiv doi: https://doi.org/10.1101/2022.07.19.499960.

78. Herrera ND, Bell KC, Callahan CM, Sarver BAJ, Sullivan J, Demboski JR, Good JM. Genomic resolution of cryptic species diversity in chipmunks. Evolution, 76:2004-2019. bioRxiv doi: https://doi.org/10.1101/2022.02.28.482304.

77. Moore EC, Thomas GWC, Mortimer SME, Kopania EEK, Hunnicutt KE, Larson EL, Good JM. The evolution of widespread recombination suppression on the dwarf hamster (Phodopus) X chromosome. Genome Biology and Evolution, 14:evac080. bioRxiv doi: https://doi.org/10.1101/2021.11.15.468705.

76. Kopania EEK, Larson EL, Callahan CM, Keeble SM, Good JM. (2022) Molecular evolution across mouse spermatogenesis. Molecular Biology and Evolution, 39:msac023. Preprint: bioRxiv doi: https://doi.org/10.1101/2021.08.04.455131.

75. Beckman EJ, Martins F, Suzuki TA, Bi K, Keeble S, Good JM, Chavez A, Ballinger MA, Agwamba K, Nachman MW. (2022) The genomic basis of high-elevation adaptation in wild house mice (Mus musculus domesticus) from South America. Genetics, iyab226, doi: https://doi.org/10.1093/genetics/iyab226.

74. Larson EL, Kopania EEK, Hunnicutt KE, Vanderpool D, Keeble SM, Good JM. (2022) Stage-specific disruption of X chromosome expression during spermatogenesis in sterile house mouse hybrids. G3 Genes|Genomes|Genetics, jkab407, https://doi.org/10.1093/g3journal/jkab407. bioRxiv doi: https://doi.org/10.1101/2021.11.12.468424.

73. Hunnicutt KE, Good JM, Larson EL. (2022) Unraveling patterns of disrupted gene expression across a complex tissue. Evolution, 76:275-291. https://doi.org/10.1111/evo.14420. Preprint: bioRxiv doi: https://doi.org/10.1101/2021.07.08.451646.

72. Roycroft EJ, Achmadi A, Callahan CM, Esselstyn JA, Good JM, Moussalli A, Rowe KC. (2021) Molecular evolution of ecological specialisation: genomic insights from the adaptive radiation of murine rodents. Genome Biology and Evolution, evab103, https://doi.org/10.1093/gbe/evab103.

71. Brekke* TD, Moore* EC, Campbell-Staton SC, Callahan CM, Cheviron ZA, Good JM. (2021) X chromosome-dependent disruption of placental regulatory networks in hybrid dwarf hamsters. Genetics, 17:218:iyab043. https://doi.org/10.1093/genetics/iyab043. Preprint: bioRxiv doi: 10.1101/2020.09.15.298893  *Equal contribution.

70. Sarver BAJ, Sneddon D, Herrera ND, Hunter SS, Settles ML, Kronenberg Z, Demboski JR, Good JM, Sullivan J. (2021) Diversification, introgression, and rampant cytonuclear discordance in central and southern rocky mountains chipmunks (Sciuridae: Tamias). Systematic Biology, syaa085, https://10.1093/sysbio/syaa085.

69. Ferreira MS, Jones MR, Callahan CM, Farelo L, Tolesa Z, Suchentrunk F, Mills LS, Alves PC, Good JM, Melo-Ferreira J. (2021) The legacy of recurrent introgression during the radiation of hares. Systematic Biology, 70:593-607. https://doi.org/10.1093/sysbio/syaa088. Preprint: bioRxiv doi: 10.1101/2020.06.19.160283.

68. Jones MR, Mills LS, Jensen JD, Good JM. (2020) Convergent evolution of seasonal camouflage to reduced snow cover across the snowshoe hare range. Evolution, 74:2033-2045. doi.org/10.1111/evo.13976. Preprint: bioRxiv doi:10.1101/851766v2.

67. Jones MR, Mills LS, Jensen JD, Good JM. (2020) The origin and spread of locally adaptive seasonal camouflage in snowshoe hares. The American Naturalist, 196:316-332. doi:10.1086/710022. Preprint: bioRxiv doi:10.1101/847616.

66. Ferreira M, Alves P, Callahan C, Giska I, Farelo L, Hannes J, Mills LS, Hackländer K, Good JM, Melo-Ferreira J. (2020) Transcriptomic regulation of seasonal coat color change in hares. Ecology and Evolution, 10:1180-1192. doi:10.1002/ece3.5956

65. Marques JP, Seixas FA, Farelo L, Callahan CM, Good JM, Montgomery WI, Reid N, Alves PC, Boursot P, Melo-Ferreira J. (2020) An annotated draft genome of the mountain hare (Lepus timidus). Genome Biology and Evolution, 12:3656-3662. doi:10.1093/gbe/evz273.

64. Harris RB, Irwin K, Jones MR, Laurent S, Barrett RDH, Nachman MW, Good JM, Linnen CR, Jensen JD, Pfeifer SP. (2019) The population genetics of crypsis in vertebrates: recent insights from mice, hares, and lizards. Heredity, 124:1-14. doi:10.1038/s41437-019-0257-4.

63. Bi K, Linderoth T, Singhal S, Vanderpool D, Patton JL, Nielsen R, Moritz C, Good JM. (2019) Temporal genomic contrasts reveal rapid evolutionary responses in an alpine mammal during recent climate change. PLoS Genetics, 15(5): e1008119. https://doi.org/10.1371/journal.pgen.1008119.

62. Skinner BM, Bacon J, Rathje CC, Larson EL, Kopania EEK, Good JM, Affara NA, Ellis PJI. (2019) Automated nuclear cartography reveals conserved sperm chromosome territory localisation across 2 million years of mouse evolution. Genes, 10:109. doi: 10.3390/genes10020109.

61. Skinner BM, Rathje CC, Bacon J, Johnson EEP, Larson EL, Kopania EEK, Good JM, Yousafzai G, Affara NA, Ellis PJI. (2019) A high-throughput method for unbiased quantitation and categorisation of nuclear morphology. Biology of Reproduction, 100:1250-1260. bioRxiv doi.org/10.1101/312470. 

60. Phifer-Rixey M, Bi K, Ferris KG, Sheehan MJ, Lin D, Mack KL, Keeble SM, Suzuki TA, Good JM, Nachman MW. (2018) The genomic basis of environmental adaptation in house mice. PLoS Genetics, 14(9): e1007672; doi: 10.1371/journal.pgen.1007672.

59. Jones MR, Mills LS, Alves PC, Callahan CM, Alves JM, Lafferty DJR, Jiggins FM, Jensen JD, Melo-Ferreira J,  Good JM. (2018) Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares. Science, 360, 1355-1358.

58. Larson EL, Kopania E, Good JM. (2018) Spermatogenesis and the evolution of mammalian sex chromosomes. Trends in Genetics, doi: 10.1016/j.tig.2018.06.003.

57.  Bracewell RR, Vanderpool D, Good JM, Six DL. (2018) Cascading speciation among mutualists and antagonists in a tree-beetle-fungi interaction. Proceedings of the Royal Society B, 285: 20180694; doi: 10.1098/rspb.2018.0694.

56. Larson EL, Vanderpool D, Sarver BAJ, Callahan C, Keeble S, Provencio LP, Kessler MD, Stewart V, Nordquist E, Dean MD, Good JM. (2018) The evolution of polymorphic hybrid incompatibilities in house mice. Genetics, 209: 845-859; doi: 10.1534/genetics.118.300840mice. 

55. Mills LS, Bragina EV, Kumar AV, Zimova M, Lafferty DJR, Feltner J, Davis BM, Hacklander K, Alves P, Good JM, Melo-Ferreira J, Dietz A, Abramov AV, Lopatina N, Fay K. (2018) Winter color polymorphisms identify global hot spots for evolutionary rescue from climate change. Science, 359, 1033-1036.

54. Zimova M, Hacklaender K, Good JM, Melo-Ferreira J, Alves P, Mills LS. (2018) Function and underlying mechanisms of seasonal colour moulting in mammals and birds: What keeps them changing in a warming world? Biological Reviews, doi: 10.1111/brv.12405.

53. Marques JP, Ferreira M, Farelo L, Callahan C, Hackländer K, Jenny H, Montgomery W, Reid N, Good JM, Alves P, Melo-Ferreira J. (2017) Mountain hare transcriptome and diagnostic markers as resources to monitor hybridization with European hares. Scientific Data, 4:170178. doi: 10.1038/sdata.2017.178. 

52. Bracewell RR, Bentz BJ, Sullivan BT, Good JM. (2017) Rapid neo-sex chromosome evolution and incipient speciation in a major forest pest. Nature Communications, 1593, doi:10.1038/s41467-017-01761-4

51. Chang P, Kopania E, Keeble S, Sarver BAJ, Larson EL, Orth A, Belkhir K, Boursot P, Bonhomme F, Good JM, Dean MD. (2017) Whole exome sequencing of wild-derived inbred strains of mice improves power to link phenotype and genotype. Mammalian Genome, 28:416-425. [Featured cover image]

50. Ferreira MS, Alves PC, Callahan CM, Marques JP, Mills LS, Good* JM, Melo-Ferreira* J. (2017) The transcriptional landscape of seasonal coat color molt in the snowshoe hare. Molecular Ecology, 26: 4173-4185. *Equal contribution.

49. Sarver BAJ, Keeble S, Cosart T, Tucker PK, Dean MD, Good JM. (2017) Phylogenomic insights into mouse evolution using a pseudoreference approach. Genome Biology and Evolution, 9: 726-739, doi: 10.1093/gbe/evx034.

48. Marques JP, Farelo L, Vilela J, Alves PC, Good JM, Boursot P, Melo-Ferreira J. (2017) Range expansion underlies historical introgressive hybridization in the Iberian hare. Scientific Reports, 7:40788, doi: 10.1038/srep40788. 

47. Larson EL, Keeble S, Vanderpool D, Dean MD, Good JM. (2017) The composite regulatory basis of the large X-effect in mouse speciation. Molecular Biology and Evolution, 34 (2): 282-295; doi: 10.1093/molbev/msw243.

46. Sarver BAJ, Demboski JR, Good JM, Forshee N, Hunter SS, Sullivan J. (2017) Comparative phylogenomic assessment of mitochondrial introgression among several species of chipmunks (Tamias). Genome Biology and Evolution, 9:7-19: doi: 10.1093/gbe/evw254. 

45. Brekke TD, Henry LA, Good JM (2016) Genomic imprinting, disrupted placental expression, and speciation. Evolution, 70:2690-2703. 

44. Larson EL, Vanderpool D, Keeble S, Zhou M, Sarver BAJ, Smith AD, Dean MD, Good JM (2016) Contrasting levels of molecular evolution on the mouse X chromosome. Genetics, 10.1534/genetics.116.186825.

43. Abbott RJ, Barton NH, Good JM (2016) Genomics of hybridization and its evolutionary consequences. Molecular Ecology, 10.1111/mec.13685.

42. Andrews KR, Good JM, Miller MR, Luikart G, Hohenlowe PA (2016) Harnessing the power of RADseq for ecological and evolutionary genomics. Nature Reviews Genetics, 17:81-92. 

41. Jones MR, Good JM (2016) Targeted capture in evolutionary and ecological genomics. Molecular Ecology, 85:185-202.

40. Good JM, Vanderpool D, Keeble S, Bi K (2015) Negligible nuclear introgression despite complete mitochondrial capture between two species of chipmunks. Evolution, doi: 10.1111/evo.12712.

39. Mangels R, Young B, Keeble S, Ardekani R, Meslin C, Ferreira Z, Clark NL, Good JM, Dean MD (2015) Genetic and phenotypic influences on copulatory plug survival in mice. Heredity, doi: 10.1038/hdy.2015.50.

38. Crino OL, Prather CT, Driscoll SC, Good JM, Bruener CW (2014) Developmental stress increases reproductive success in male zebra finches. Proceedings of the Royal Society B, 281:20141266.

37. Carneiro M, Rubin CJ, Di Palma,F, Albert FW, Alföldi J, Barrio AM, Pielberg G, Rafati N, Sayyab S, Turner-Maier J, Younis S, Afonso S, Aken B, Alves JM, Barrell D, Bolet G, Boucher S, Burbano HA Campos R, Chang JL, Duranthon V, Fontanesi L, Garreau H, Heiman D, Johnson J, Mage RG, Peng Z, Queney G, Rogel-Gaillard C, Ruffier M, Searle S, Villafuerte R, Xiong A, Young S, Forsberg-Nilsson K, Good JM, Lander ES, Ferrand N, Lindblad-Toh K, Andersson L (2014) Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Science, 345: 1074-1079.

36. Brekke TD, Good JM (2014) Parent-of-origin growth effects and the evolution of hybrid inviability in dwarf hamsters. Evolution, doi:10.1111/evo.12500.

35. Sullivan J, Demboski JR, Bell KC, Hird S, Sarver B, Reid N, Good JM (2014) Divergence-with-gene-flow within the recent chipmunk radiation (Tamias). Heredity, doi: 10.1038/hdy.2014.27.

34. Carneiro M, Albert FW, Afonso S, Pereira RJ, Burbano H, Campos R, Melo-Ferreira J, Blanco-Aguiar JA, Villafuerte R, Nachman MW, Good JM, Ferrand N (2014) The genomic architecture of population divergence between subspecies of the European rabbit. PLoS Genetics, 10(8): e1003519.

33. Bi K, Linderoth T, Vanderpool D, Good JM, Nielsen R, Moritz C (2013) Unlocking the vault: next-generation museum population genomics. Molecular Ecology, 24: 6018-6032.

32. Good JM, Wiebe V, Albert FW, Burbano HA, Kircher M, Green RE, Halbwax M, André C, Atencia R, Fischer A, Pääbo S (2013) Comparative population genomics of the ejaculate in humans and the great apes. Molecular Biology and Evolution, 30:964–976.

31. Campbell P, Good JM, Nachman MD (2013) Meiotic sex chromosome inactivation is disrupted in sterile hybrid male house mice. Genetics, 10.1534/genetics.112.148635.

30. Good JM (2012) The conflict within and the escalating war between the sex chromosomes. PLoS Genetics, 8:e1002955.

29. Bi K, Vanderpool D, Singhal S, Linderoth T, Moritz C, Good JM (2012) Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales. BMC Genomics, 13:403.

28. Campbell P, Good JM, Dean MD, Tucker PK, Nachman MD (2012) The contribution of the Y chromosome to hybrid male sterility in house mice. Genetics, 191: 1271-1281.

27. Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer R, Knight JR, Mullikin JC, Meader SJ, Ponting CP, Lunter G, Higashino S, Hobolth A, Dutheil J, Karakoç E, Alkan C, Sajjadian S, Catacchio CR, Ventura M, Marques-Bonet T, Eichler EE, André C, Atencia R, Mugisha L, Junhold J, Patterson N, Siebauer M, Good JM, Fischer A, Ptak SE, Lachmann M, Symer DE, Mailund T, Schierup MK, Andrés AM, Kelso J, Pääbo S (2012) The bonobo genome compared with the chimpanzee and human genomes. Nature, doi:10.1038/nature11128.

26. Good, J. M. 2011. Reduced representation methods for sub-genomic enrichment and next-generation sequencing. In: Molecular Methods in Evolutionary Genetics (Orgogozo, V., and M. V. Rockman, eds.). Humana Press.

25. Crisci JL, Wong A, Good JM, Jensen JD (2011) On characterizing adaptive events unique to modern humans. Genome Biology and Evolution, 3:791-798.

24. Fischer A, Prüfer K, Good JM, Halbwax M, Wiebe V, André C, Atencia R, Mugisha L, Ptak SE, Pääbo S (2011) Bonobos fall within the genomic variation of chimpanzees. PLoS ONE 6:e21605.

23. Good JM, Vanderpool D, Smith KL, Nachman MW (2011) Extraordinary sequence divergence at Tsga8, an X-linked gene involved in mouse spermiogenesis. Molecular Biology and Evolution, 28(5): 1675-1686.

22. Albert FW, Hodges E, Jensen JD, Besnier F, Xuan Z, Rooks M, Bhattacharjee A, Brizuela L, Good JM, Green RE, Burbano HA, Plyusnina IZ, Trut L, Andersson L, Schöneberg T, Carlborg Ö, Hannon GJ, Pääbo S, (2011) Targeted resequencing of a genomic region influencing tameness and aggression reveals multiple signals of positive selection. Heredity, 107: 205-214.

21. Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PLF, Maricic M, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin JJ, Kelso J, Slatkin M, Pääbo S (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature, 468: 1053-1060.

20. Good JM, Giger T, Dean MD, Nachman MW (2010) Widespread over-expression of the X chromosome in sterile F1 mice. PLoS Genetics, 6(9): e1001148.

19. Green RE, Krause J, Briggs AW, Maricic M, Stenzel U, Kircher M, Patterson N, Li L, Zhai W, Fritz MH-Y, Hansen N, Durand EY, Malaspinas A-S, Jensen JJ, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Z, Guic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, Rasilla M, Fortea J, Rosas A, Schimtz RW, Johnson PLF, Eichler EE, Falush D, Birney E, Mullikan JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S (2010) A draft sequence of the Neandertal genome. Science, 328: 710-722.

18. Burbano HA, Hodges E, Green RE, Briggs AW, Krause J, Meyer M, Good JM, Maricic M, Johnson PLF, Xuan Z, Rooks M, Bhattacharjee A, Brizuela L, Albert FW, de la Rasilla M, Fortea J, Rosas A, Lachmann M, Hannon GJ, Pääbo S (2010) Targeted investigation of the Neandertal genome by array-based sequence capture. Science, 328; 723-725.

17. Krause J, Fu Q, Good JM, Viola B, Shunkov MV, Derevianko AP, Pääbo S (2010) The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature, 464:894-897.

16. Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Pääbo S (2009) Primer Extension Capture: targeted sequence retrieval from heavily degraded DNA sources. Journal of Visualized Experiments, 31. http://www.jove.com/index/details.stp?id=1573, doi: 10.3791/1573.

15. Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Lalueza-Fox C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Schmitz R, Doronichev VB, Golovanova LV, Rasilla M, Fortea J, Rosas A, Pääbo S (2009) Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science, 325: 318-321.

14. Good JM, Dean MD, Nachman MW (2008) A complex genetic basis to X-linked hybrid male sterility between two species of house mice. Genetics, 179: 2213-2228.

13. Green RE, Malaspinas A-S, Krause J, Briggs AW, Johnson PLF, Uhler C, Meyer M, Good JM, Maricic T, Stenzel U, Prufer K, Siebauer M, Burbano HA, Ronan M, Rothberg JM, Egholm M, Rudan P, Brajkovic D, Kucan Z, Gusic I, Wikstrom M, Laakkonen L, Kelso J, Slatkin M, Pääbo S (2008) A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell, 134:416-426.

12. Good JM, Handel MA, Nachman MW (2008) Asymmetry and polymorphism of hybrid male sterility during the early stages of speciation in house mice. Evolution, 62: 50-65.

11. Good JM, Hird S, Reid N, Demboski JR, Steppan SJ, Martin-Nims TR, Sullivan J (2008) Ancient hybridization and mitochondrial capture between two species of chipmunks. Molecular Ecology, 17:1313-1327.

10. Dean MD, Good JM, Nachman MW (2008) Adaptive evolution of proteins secreted during sperm maturation: an analysis of the mouse epididymal transcriptome. Molecular Biology and Evolution, 25: 383-392.

9. Good JM, Hayden CA, Wheeler TJ (2006) Adaptive protein evolution and regulatory divergence in Drosophila. Molecular Biology and Evolution, 23:1101-1103.

8. Saunders MA, Good JM, Lawrence EC, Ferrel RE, Li W-H, Nachman MW (2006) Human adaptive evolution at Myostatin, a regulator of muscle growth. American Journal of Human Genetics, 79:1089-1097.

7. Good JM, Ross CL, Markow TA (2006) Multiple paternity in wild-caught Drosophila mojavensis. Molecular Ecology, 15:2253-2260.

6. Carstens BC, Brunsfeld SJ, Demboski JR, Good JM, Sullivan J (2005) Investigating the evolutionary history of the Pacific Northwest mesic forest ecosystem: hypothesis testing within a comparative phylogeography framework. Evolution, 59:1639-1652.

5.  Good JM, Nachman MW (2005) Rates of protein evolution are positively correlated with timing of expression during mouse spermatogenesis. Molecular Biology and Evolution 22:1044-1052.

4. Cutter AD, Good JM, Pappas CT, Saunders MA, Starrett DM, Wheeler T (2005) Transposable element orientation bias in the Drosophila melanogaster genome. Journal of Molecular Evolution, 61:1-19.

3. Good JM, Demboski JR, Nagorsen D, Sullivan J (2003) Phylogeography and introgressive hybridization: chipmunks (genus Tamias) in the northern Rocky Mountains. Evolution, 57:1900-1916.

2. Cutter AD, Payseur BA, Salcedo T, Estes AM, Good JM, Wood E, Hartl T, Maughan H, Strempel J, Wang B, Bryan AC, Dellos M (2003) Molecular correlates of genes exhibiting RNAi phenotypes in Caenorhabditis elegans. Genome Research, 13:2651-2657.

1. Good JM, Sullivan J (2001) Phylogeography of the red-tailed chipmunk (Tamias ruficaudus), a northern Rocky Mountain endemic. Molecular Ecology, 10:2683-2696.