63. Zwonitzer KD, Tressel LG, Wu Z, Kan SL, Broz AK, Mower JP, Ruhlman TA, Jansen RK, Sloan DB, Havird JC. 2024. Genome copy number predicts extreme evolutionary rate variation in plant mitochondrial DNA. Proceedings of the National Academy of Sciences of the United States of America 121: e2317240121.
62. Moran BM, Payne CY, Powell DL, Iverson ENK, Banerjee SM, Langdon QK, Gunn TR, Liu F, Matney R, Singhal K, Leib RD, Hernandez-Perez O, Corbett-Detig R, Schartl M, Havird JC, Schumer M. 2024. A Lethal Genetic Incompatibility between Naturally Hybridizing Species in Mitochondrial Complex I. Nature 626: 119-127.
61. Smith CH, Mejia-Trujillo R, Breton S, Pinto BJ, Kirkpatrick M, Havird JC. 2023. Mitonuclear sex determination in bivalves? Empirical evidence from freshwater mussels. Molecular Biology and Evolution 40(11):msad240.
60. Zwonitzer KD*, Iverson ENK*, Sterling JJ, Weaver RJ, Maclaine BA, Havird JC. 2023. Disentangling positive vs. relaxed selection in animal mitochondrial genomes. The American Naturalist 202: E121-E129. *these authors contributed equally to this work
59. Pinto BJ, Gamble T, Smith CH, Keating SE, Havird JC, Chiari Y. 2023. The revised reference genome of the leopard gecko (Eublepharis macularius) provides insight into the considerations of genome phasing and assembly. Journal of Heredity 114:513-520.
58. Smith CH, Pinto BJ, Kirkpatrick M, Hillis DM, Pfeiffer JM, Havird JC. 2023. A tale of two paths: The evolution of mitochondrial recombination in bivalves with doubly uniparental inheritance. Journal of Herediity 114:199-206.
57. Weaver RJ, Rabinowitz S, Thueson K, Havird JC. 2022. Genomic signatures of mitonuclear coevolution in mammals. Molecular Biology and Evolution 39(11): msac233.
56. Havird JC, Brannock PM, Yoshioka RM, Vaught RC, Carlson K, Edwards C, Tracy A, Twining CW, Zheng Y, Wilson AE, Hairston Jr. NG, Santos SR. 2022. Grazing by an endemic atyid shrimp controls microbial communities in the Hawaiian anchialine ecosystem. Limnology and Oceanography 67: 2012-2027.
55. Sterling JJ, Sakihara TS, Brannock PM, Pearson Z, Maclaine KD, Santos SR, Havird JC. 2022. Primary microbial succession in the anchialine ecosystem. Integrative and Comparative Biology 62: 275-287. *Featured cover article
54. Breton S, Stewart DT, Brémaud J, Havird JC, Smith CH, Hoeh WR. 2022. Did doubly uniparental inheritance (DUI) of mtDNA originate as a cytoplasmic male sterility (CMS) system? BioEssays 44, e2100283.
53. Xu R, Iannello M, Havird JC, Milani L, Ghiselli F. 2022. Lack of transcriptional coordination between mitochondrial and nuclear oxidative phosphorylation genes in the presence of two divergent mitochondrial genomes. Zoological Research 43: 111−128.
52. Maclaine KD, Stebbings KA, Llano DA, Havird JC. 2021. The mtDNA mutation spectrum in the PolG mutator mouse reveals germline and somatic selection. BMC Genomic Data 22:52.
51. Maeda G*, Iannello M*, McConie HJ, Ghiselli F, Havird JC. 2021. Relaxed selection on male mitochondrial genes in DUI bivalves eases the need for mitonuclear coevolution. Journal of Evolutionary Biology, 34, 1722– 1736. *these authors contributed equally to this work. *Featured cover article.
50. Waneka G, Svendsen JM, Havird JC, Sloan DB. 2021. Mitochondrial mutations in Caenorhabditis elegans show signatures of oxidative damage and an AT-bias. Genetics 219(2). doi:10.1093/genetics/iyab116
49. Zhang B*, Havird JC*, Wang E, Lv J, Xu X. 2021. Massive gene rearrangement in mitogenomes of phytoseiid mites. International Journal of Biological Macromolecules 186: 33–39. *these authors contributed equally to this work
48. Piccinini G, Iannello M, Puccio G, Plazzi F, Havird JC, Ghiselli F. 2021. Mitonuclear coevolution, but not nuclear compensation, drives evolution of OXPHOS complexes in bivalves. Molecular Biology and Evolution 38: 2597–2614.
47. Shah A, Woods H, Havird JC, Encalada A, Flecker A, Funk W, Guayasamin JM, Kondratieff B, Poff NL, Thomas S, Zamudio K, Ghalambor C. 2020. Temperature-dependence of metabolic rate in tropical and temperate aquatic insects: support for the Climate Variability Hypothesis in mayflies but not stoneflies. Global Change Biology 21: 297–311.
46. Weaver RJ, Carrion G, Nix R, Maeda G, Rabinowitz S, Iverson ENK, Thueson K, Havird JC. 2020. High mitochondrial mutation rates in Silene are associated with nuclear-mediated changes in mitochondrial physiology. Biology Letters 16: 20200450.
45. Iverson ENK, Nix R, Abebe A, Havird JC. 2020. Thermal responses differ across levels of biological organization. Integrative and Comparative Biology 60: 361–374.
44. Hoffman SK, Seitz KW, Havird JC, Weese DA, Santos SR. 2020. Phenotypic comparability from genotypic variability among physically structured microbial consortia. Integrative and Comparative Biology 60: 288–303.
43. Weaver RJ, Gonzalez B, Santos SR, Havird JC. 2020. Red coloration in an anchialine shrimp: carotenoids, genetic variation, and candidate genes. Biological Bulletin 238: 119–130. *Featured cover article.
42. Havird JC, Neuwald JL, Shah AA, Mauro A, Marshall CA, Ghalambor CK. 2020. Distinguishing between active plasticity due to thermal acclimation and passive plasticity due to Q10 effects: Why methodology matters. Functional Ecology 34: 1015-1028.
41. Havird JC, Meyer E, Fujita Y, Vaught RC, Henry RP, Santos SR. 2019. Disparate physiological and transcriptomic responses to variability in environmental salinity among shrimps representing independent invasions of the anchialine ecosystem. Journal of Experimental Biology 222(Pt 24). pii: jeb211920.
40. Havird JC, Shah AA, Chicco AJ. 2019. Powerhouses in the cold: Mitochondrial function during thermal acclimation in montane mayflies. Philosophical Transactions of the Royal Society B: Biological Sciences 375: 20190181.
39. Forsythe ES, Sharbrough J, Havird JC, Warren JM, Sloan DB. 2019. CyMIRA: The Cytonuclear Molecular Interactions Reference for Arabidopsis. Genome Biology and Evolution 11: 2194–2202.
38. Havird JC, Noe GR, Logan D, Link L, Torres A, Sloan DB, Chicco AJ. 2019. Do angiosperms with highly divergent mitochondrial genomes have altered mitochondrial function? Mitochondrion 49:1-11.
37. Havird JC, Weaver RJ, Milani L, Ghiselli F, Greenway R, Ramsey AJ, Jimenez AG, Dowling DK, Hood WR, Montooth KL, Estes S, Schulte PM, Sokolova IM, Hill GE. 2019. Beyond the powerhouse: integrating mitonuclear evolution, physiology, and theory in comparative biology. Integrative and Comparative Biology 59: 856–863.
36. Havird JC, McConie HJ. 2019. Sexually antagonistic mitonuclear coevolution in duplicate oxidative phosphorylation genes. Integrative and Comparative Biology 59(4):864-874.
35. Havird JC, Forsythe ES, Williams AM, Werren JH, Dowling DK, Sloan DB. 2019. Selfish mitonuclear conflict. Current Biology 29: R496-R511.
34. Hill GE, Havird JC, Sloan DB, Burton RS, Greening C, Dowling DK. 2019. Assessing the fitness consequences of mitonuclear interactions in natural populations. Biological Reviews 94: 1089-1104.
33. Sloan DB, Warren J, Abdel-Ghany S, Chicco A, Williams A, Wu Z, Havird JC. 2018. Cytonuclear integration and coevolution. Nature Reviews Genetics 19: 635-648.
32. Hoffman SK, Seitz KW, Havird JC, Weese DA, Santos SR. 2018. Seasonal influences on diversity and community structure of Bacteria and micro-Eukarya from the Hawaiian anchialine ecosystem. Aquatic Microbial Ecology 82: 87-104.
31. Hoffman SK, Seitz KW, Havird JC, Weese DA, Santos SR. 2018. Diversity and the environmental drivers of spatial variation in Bacteria and micro-Eukarya communities from the Hawaiian anchialine ecosystem. Hydrobiologia 806:265-282.
30. Sharbrough J*, Havird JC*, Noe GR, Warren JM, Sloan DB. 2017. The mitonuclear dimension of Neanderthal and Denisovan ancestry in modern human genomes. Genome Biology and Evolution 9:1567-1581. *these authors contributed equally to this work
29. Havird JC, Trapp P, Miller C, Bazos I, Sloan DB. 2017. Causes and consequences of rapidly evolving mtDNA in a plant lineage. Genome Biology and Evolution 9:323-336.
28. Sloan DB, Havird JC, Sharborough J. 2017. The on-again, off-again relationship between mitochondrial genomes and species boundaries. Molecular Ecology 26:2212-2236.
27. Rockenbach K, Havird JC, Monroe JG, Triant DA, Taylor DR, Sloan DB. 2016. Positive selection in rapidly evolving plastid-nuclear enzyme complexes. Genetics 204:1507-1522.
26. Havird JC, Sloan DB. 2016. The roles of mutation, selection, and expression in determining relative rates of evolution in mitochondrial vs. nuclear genomes. Molecular Biology and Evolution 33:3042-3053.
25. Havird JC, Santos SR. 2016. Here we are, but where do we go? A systematic review of crustacean transcriptomic studies from 2014-2015. Integrative and Comparative Biology 56:1055-1066.
24. Havird JC, Santos SR. 2016. Developmental transcriptomics of the Hawaiian anchialine shrimp Halocaridina rubra Holthuis, 1963 (Crustacea: Atyidae). Integrative and Comparative Biology 56:1170-1182. *Featured cover article.
23. Havird JC, Mitchell RT, Henry RP, Santos SR. 2016. Salinity-induced changes in gene expression from anterior and posterior gills of Callinectes sapidus(Crustacea: Portunidae) with implications for crustacean ecological genomics. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 19:34-44.
22. Havird JC, Fitzpatrick SW, Kronenberger JA, Angeloni LM, Funk WC, Sloan DB. 2016. Sex, mitochondria, and genetic rescue. Trends in Ecology and Evolution 31:96-99.
21. Havird JC, Whitehill NS, Snow CD, Sloan DB. 2015. Conservative and compensatory evolution in oxidative phosphorylation complexes of angiosperms with highly divergent rates of mitochondrial genome evolution. Evolution 69:3069-3081.
20. Havird JC, Vaught RC, Weese DA, Santos SR. 2015. Reproduction and development in Halocaridina rubra (Crustacea: Atyidae) clarifies larval ecology in the Hawaiian anchialine ecosystem. Biological Bulletin 229:134-142.
19. Sloan DB, Fields PD, Havird JC. 2015. Mitonuclear linkage disequilibrium in human populations. Proceedings of the Royal Society B 282:20151704.
18. Havird JC, Hall M, Dowling DK. 2015. The evolution of sex: A new hypothesis based on mitochondrial mutational erosion. BioEssays 37:951-958.
17. Havird JC, Kocot KM, Brannock PM, Cannon JT, Waits DS, Weese DA, Santos SR, Halanych KM. Reconstruction of cyclooxygenase evolution in animals suggests variable, lineage-specific duplications and homologs with low sequence identity.Journal of Molecular Evolution 80:193-208.
16. Havird JC, Henry RP, Fujita Y, Hidaka M, Santos SR. Taking their breath away: Metabolic adaptations to low-oxygen levels in anchialine shrimps (Crustacea: Atyidae and Alpheidae). Comparative Biochemistry and Physiology A: Molecular and Integrative Physiology 178:109-120.
15. Havird JC, Santos SR. Transcriptomic resources for five shrimp (Crustacea: Atyidae and Alpheidae) species from the anchialine ecosystem. Molecular Ecology Resources 14:1322.
14. Vaught RC, Havird JC, Santos SR. Genetic lineage and environmental conditions as drivers of chromatosome variation in the anchialine shrimp Halocaridina rubra Holthuis 1963 (Atyidae: Decapoda). Journal of Crustacean Biology 34:647-657.
13. Havird JC, Henry RP, Santos SR. 2014. Osmoregulatory adaptations in the Hawaiian anchialine shrimp Halocaridina rubra (Crustacea: Atyidae): expression of ion transporters, mitochondria-rich cell proliferation, and hemolymph osmolality during salinity transfers. Journal of Experimental Biology 217:2309-2320.
12. Havird JC, Santos SR. 2014. Performance of single and concatenated sets of mitochondrial genes at inferring metazoan relationships relative to full mitogenome data. PLoS One 9:e84080.
11. Havird JC, Weeks JR, Hau S, Santos SR. 2013. Invasive species in the Hawaiian anchialine ecosystem: investigating potential predation on endemic organisms.Hydrobiologia 716:189-201. *Featured cover article
10. Havird JC, Henry RP, Wilson AE. 2013. Altered expression of Na+/K+-ATPase and other osmoregulatory genes in the gills of euryhaline animals in response to salinity transfer: A meta-analysis of 59 quantitative PCR studies over 10 years.Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 8:131-140.
9. Parker JK, Havird JC, De La Fuente L. 2012. Differentiation of Xylella fastidiosastrains via multi-locus sequence analysis of environmentally-mediated genes (MLSA-E). Applied and Environmental Microbiology 76:1385–1396.
8. Havird JC, Parker JK, Connery B. 2011. Fishes of the Streams of Acadia National Park, Maine. Northeastern Naturalist 18:217–228.
7. Havird JC, Tangjitjaroen W, Vidthayanon C, Grudpan C, Udduang S, Page LM. 2010. A new species of Lepidocephalichthys with a highly distinctive lamina circularis and comments on sexual dimorphism and relationships in southern lineages of Cobitidae. Zootaxa 2557:1–18. *Most accessed Zootaxa paper during August 2010.
6. Havird JC, Miyamoto MM. 2010. The importance of taxon sampling in genomic studies: An example from the cyclooxygenases of teleost fishes. Molecular Phylogenetics and Evolution 56:451–455.
5. Havird JC, Page LM. 2010. A revision of Lepidocephalichthys (Teleostei: Cobitidae) with descriptions of two new species from Thailand and Myanmar. Copeia2010(1):137–159.
4. Havird JC, Miyamoto MM, Choe KP, Evans DH. 2008. Gene duplications and losses within the cyclooxygenase family of teleosts and other chordates.Molecular Biology and Evolution 25:2349–59.
3. Claiborne JB, Choe KP, Morrison–Shetlar AI, Weakley JC, Havird J, Freiji A, Evans DH, Edwards SL. 2008. Molecular detection and immunological localization of gill Na+/H+ exchanger in the dogfish (Squalus acanthias). American Journal of Physiology 294:R1092–R1102.
2. Hyndman KA, Choe KP, Havird JC, Rose RE, Piermarini PM, Evans DH. 2006. Neuronal nitric oxide synthase in the gill of the killifish, Fundulus heteroclitus.Comparative Biochemistry and Physiology 144B:510–9.
1. Choe KP, Havird J, Rose RE, Hyndman KH, Piermarini P, Evans DH. 2006. COX2 in a euryhaline teleost, Fundulus heteroclitus: primary sequence, distribution, localization, and potential function in gills during salinity acclimation. Journal of Experimental Biology 209(9):1696–708.
Short communications/Other publications
10. Havird JC. 2016. Zombified caterpillars forced to carb-load by parasitoid wasps. Newswise Press Release for Society for Integrative and Comparative Biology.
9. Havird JC. 2015. It takes two… but why? Blame an ancient hook-up. New Scientist19 September 2015: 28-29.
8. Havird JC. 2015. Being a couch potato could have led to marital bliss in mantis shrimps. Newswise Press Release for Society for Integrative and Comparative Biology.
7. Havird JC. 2014. Vertebrate reproductive evolution is laid bare by the ever-erect, spring-loaded alligator penis. Society for Integrative and Comparative Biology: Science News (journalism piece; http://www.sicb.org/students/havirdj.php)
6. Havird JC. 2008. Freshwater fishes of Sumatra: from rivers to research. Tropical Fish Hobbyist. April 2008:104–110 (not peer reviewed).
5. Havird JC, Choe KP, Evans DH. 2007. Expression of cyclooxygenase in the killifish (Fundulus heteroclitus) and longhorn sculpin (Myoxocephalus octodecemspinosus). Bulletin Mount Desert Island Biological Laboratory 46:45–46.
4. Havird JC, Choe KP, Evans DH. 2007. Phylogenetic analysis reveals at least 3 duplications of cyclooxygenase in the chordates. Bulletin Mount Desert Island Biological Laboratory 46:43–44.
3. Havird JC, Choe KP, Evans DH. 2006. The evolution of Cyclooxygenase in ancestral chordates. Bulletin Mount Desert Island Biological Laboratory 45:33–34.
2. Havird JC, Galardi-Este O, Kreh RL, Choe KP, Evans DH. 2006. The gill of the killifish, Fundulus heteroclitus, expresses two different EP1 receptors. Bulletin Mount Desert Island Biological Laboratory 45:35–36.
1. Choe KP, Havird JC, Claiborne JB, Evans DH. 2005. Branchial expression of COX–2, nNOS and transporters following rapid transfer of Fundulus heteroclitus from fresh water to seawater. Bulletin Mount Desert Island Biological Laboratory 44:57–58.
