Mitonuclear ecology

Molecular Biology and Evolution

Volumn 32, Issue 8, 2015, Pages 1917-1927

  Hill, Geoffrey E ^a  

^a AUBURN UNIVERSITY   (United States)

Author keywords

Adaptation; Coadaptation; Genomic conflict; Sexual reproduction; Sexual selection; Speciation

Indexed keywords

ECOLOGY; ELECTRON TRANSPORT; ENERGY YIELD; EUKARYOTE EVOLUTION; MITOCHONDRIAL GENE; MITOCHONDRIAL GENOME; OXIDATIVE PHOSPHORYLATION; PROKARYOTE; REPRODUCTION; SEXUAL SELECTION; SPECIES DIFFERENTIATION; ANIMAL; CELL NUCLEUS; GENETICS; HUMAN; MITOCHONDRION; MOLECULAR EVOLUTION; PHYSIOLOGY;

ANIMALS; CELL NUCLEUS; EVOLUTION, MOLECULAR; GENES, MITOCHONDRIAL; GENOME, MITOCHONDRIAL; HUMANS; MITOCHONDRIA;

EID: 84942058525     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msv104     Document Type: Article

References (127)

1. Allen JF. 2003a. Why chloroplasts and mitochondria contain genomes. Comp Funct Genomics. 4:31-36.
2. Allen JF. 2003b. The function of genomes in bioenergetic organelles. Philos Trans R Soc Lond B Biol Sci. 358:19-38.
3. Andersson M. 1994. Sexual selection. Princeton (NJ): Princeton University Press.
4. Andersson M, Simmons LW. 2006. Sexual selection and mate choice. Trends Ecol Evol. 21:296-302.
5. Arnold S. 2012. The power of life - cytochrome c oxidase takes center stage inmetabolic control, cell signalling and survival. Mitochondrion 12:46-56.
6. Arnold SJ. 1983. Sexual selection: the interface of theory and empiricism. In: Bateson PPG, editor. Mate choice. Cambridge: Cambridge University Press. p. 67-107.
7. Arnqvist G, Dowling DK, Eady P, Gay L, Tregenza T, Tuda M, Hosken DJ. 2010. Genetic architecture of metabolic rate: environment specific epistasis between mitochondrial and nuclear genes in an insect. Evolution 64:3354-3363.
8. Baker AJ, Tavares ES, Elbourne RF. 2009. Countering criticisms of single mitochondrial DNA gene barcoding in birds. Mol Ecol Resour. 9:257-268.
9. Ballard JWO, Kreitman M. 1995. Is mitochondrial DNA a strictly neutral marker? Trends Ecol Evol 10:485-488.
10. Bar-Yaacov D, Blumberg A, Mishmar D. 2012. Mitochondrial-nuclear co-evolution and its effects on OXPHOS activity and regulation. Biochim Biophys Acta-Gene Reg Mech. 1819:1107-1111.
11. Barreto FS, Burton RS. 2013a. Elevated oxidative damage is correlated with reduced fitness in interpopulation hybrids of a marine copepod. Proc R Soc Lond B Biol Sci. 280:20131521.
12. Barreto FS, Burton RS. 2013b. Evidence for compensatory evolution of ribosomal proteins in response to rapid divergence of mitochondrial rRNA. Mol Biol Evol. 30:310-314.
13. Barton NH, Charlesworth B. 1998. Why sex and recombination? Science 281:1986-1990.
14. Bolnick DI, Turelli M, Lopez-Fernández H,Wainwright PC, Near TJ. 2008. Accelerated mitochondrial evolution and "Darwin's corollary": asymmetric viability of reciprocal F1 hybrids in Centrarchid fishes. Genetics 178:1037-1048.
15. Brand M, Nicholls D. 2011. Assessing mitochondrial dysfunction in cells. Biochem J. 435:297-312.
16. Bucklin A, Steinke D, Blanco-Bercial L. 2011. DNA barcoding of marine metazoa. Ann Rev Mar Sci. 3:471-508.
17. Burton RS, Barreto FS. 2012. A disproportionate role for mtDNA in Dobzhansky-Muller incompatibilities? Mol Ecol 21:4942-4957.
18. Burton RS, Ellison CK, Harrison JS. 2006. The sorry state of F-2 hybrids: consequences of rapid mitochondrial DNA evolution in allopatric populations. Am Nat. 168:S14-S24.
19. Burton RS, Pereira RJ, Barreto FS. 2013. Cytonuclear genomic interactions and hybrid breakdown. Ann Rev Ecol Evol Syst. 44:281-302.
20. Calvo SE, Mootha VK. 2010. The mitochondrial proteome and human disease. Annu Rev Genomics Hum Genet. 11:25-44.
21. Castoe TA, Jiang ZJ, Gu W, Wang ZO, Pollock DD. 2008. Adaptive evolution and functional redesign of core metabolic proteins in snakes. PLoS One 3:e2201.
22. Cheviron Z, Brumfield R. 2011. Genomic insights into adaptation to high-altitude environments. Heredity 108:354-361.
23. Chou JY, Leu JY. 2010. Speciation through cytonuclear incompatibility: insights from yeast and implications for higher eukaryotes. Bioessays 32:401-411.
24. Cotton JA, McInerney JO. 2010. Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function. Proc Natl Acad Sci U S A. 107:17252-17255.
25. Coyne JA, Orr HA. 2004. Speciation. New York: Sinauer Associates, Inc.
26. Crespi B, Nosil P. 2013. Conflictual speciation: species formation via genomic conflict. Trends Ecol Evol. 28:48-57.
27. Crespi B, Schwander T. 2012. Asexual evolution: do intragenomic parasites maintain sex? Mol Ecol 21:3893-3895.
28. Dalrymple RL, Hui FK, Flores-Moreno H, Kemp DJ, Moles AT. 2015. Roses are red, violets are blue-so how much replication should you do? An assessment of variation in the colour of flowers and birds. Biol J Linn Soc Lond. 114:69-81.
29. Dean R, Zimmer F, Mank JE. 2014. The potential role of sexual conflict and sexual selection in shaping the genomic distribution of mitonuclear genes. Genome Biol Evol. 6:1096-1104.
30. Dean R, Zimmer F, Mank JE. 2015. Deficit of mito-nuclear genes on the human X chromosome predates sex chromosome formation. Genome Biol Evol. 7:636-641.
31. Denver DR, Morris K, Lynch M, Vassilieva LL, Thomas WK. 2000. High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans. Science 289:2342-2344.
32. Dobzhansky T. 1946. Genetics of natural populations. XIII. Recombination and variability in populations of Drosophila pseudoobscura. Genetics 31:269.
33. Dowling DK, Friberg U, Hailer F, Arnqvist G. 2007. Intergenomic epistasis for fitness: within-population interactions between cytoplasmic and nuclear genes in Drosophila melanogaster. Genetics 175:235-244.
34. Dowling DK, Friberg U, Lindell J. 2008. Evolutionary implications of nonneutral mitochondrial genetic variation. Trends Ecol Evol. 23:546-554.
35. Drown DM, Preuss KM, Wade MJ. 2012. Evidence of a paucity of genes that interact with the mitochondrion on the x in mammals. Genome Biol Evol. 4:875-880.
36. Ellison C, Niehuis O, Gadau J. 2008. Hybrid breakdown and mitochondrial dysfunction in hybrids of Nasonia parasitoid wasps. J Evol Biol. 21:1844-1851.
37. Ellison CK, Burton RS. 2006. Disruption of mitochondrial function in interpopulation hybrids of Tigriopus californicus. Evolution 60:1382-1391.
38. Ellison CK, Burton RS. 2008. Genotype-dependent variation of mitochondrial transcriptional profiles in interpopulation hybrids. Proc Natl Acad Sci U S A. 105:15831-15836.
39. Fisher RA. 1958. The genetical theory of natural selection. New York: Dover.
40. Foley B, Rose C, Rundle D, Leong W, Edmands S. 2013. Postzygotic isolation involves strong mitochondrial and sex-specific effects in Tigriopus californicus, a species lacking heteromorphic sex chromosomes. Heredity 111:391-401.
41. Frank S. 1996. Mitochondria and male disease. Nature 383:224.
42. Galtier N, Nabholz B, Glémin S, Hurst G. 2009. Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Mol Ecol. 18:4541-4550.
43. Garvin MR, Bielawski JP, Sazanov LA, Gharrett AJ. 2015. Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. J Zool Syst Evol Res. 53:1-17.
44. Gemmell NJ, Metcalf VJ, Allendorf FW. 2004. Mother's curse: the effect of mtDNA on individual fitness and population viability. Trends Ecol Evol. 19:238-244.
45. Gerber AS, Loggins R, Kumar S, Dowling TE. 2001. Does nonneutral evolution shape observed patterns of DNA variation in animal mitochondrial genomes? Annu Rev Genet 35:539-566.
46. Gershoni M, Templeton AR, Mishmar D. 2009. Mitochondrial bioenergetics as a major motive force of speciation. Bioessays 31:642-650.
47. Greiner S, Sobanski J, Bock R. 2014. Why are most organelle genomes transmitted maternally? Bioessays 37:80-94
48. Gyllensten U, Wharton D, Josefsson A, Wilson AC. 1991. Paternal inheritance of mitochondrial DNA in mice. Nature 352:255-257.
49. Hadjivasiliou Z, Lane N, Seymour RM, Pomiankowski A. 2013. Dynamics of mitochondrial inheritance in the evolution of binary mating types and two sexes. Proc R Soc Lond B Biol Sci. 280:20131920.
50. Hadjivasiliou Z, Pomiankowski A, Seymour RM, Lane N. 2012. Selection for mitonuclear co-adaptation could favour the evolution of two sexes. Proc R Soc Lond B Biol Sci. 279:1865-1872.
51. Hahn MW. 2008. Toward a selection theory of molecular evolution. Evolution 62:255-265.
52. Hamilton WD, Zuk M. 1982. Heritable true fitness and bright birds: a role for parasites? Science 218:384-386.
53. Havird JC, Hall MD, Dowling DK. 2015. Mitochondria, mutations and sex: a new hypothesis for the evolution of sex based on mitochondrial mutational erosion. bioRxiv doi: http://dx.doi.org/10.1101/019125.
54. Hebert PD, Gregory TR. 2005. The promise of DNA barcoding for taxonomy. Syst Biol. 54:852-859.
55. Hebert PD, Ratnasingham S, de Waard JR. 2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Lond B Biol Sci. 270:S96-S99.
56. Hill GE. 2011. Condition-dependent traits as signals of the functionality of vital cellular processes. Ecol Lett. 14:625-634.
57. Hill GE. 2014a. Sex linkage of nuclear-encoded mitochondrial genes. Heredity 112:469-470.
58. Hill GE. 2014b. Cellular respiration: the nexus of stress, condition, and ornamentation. Integr Comp Biol. 54:645-657.
59. Hill GE, Johnson JD. 2013. The mitonuclear compatibility hypothesis of sexual selection. Proc R Soc Lond B Biol Sci. 280:20131314.
60. Hoekstra RF. 2000. Evolutionary origin and consequences of uniparental mitochondrial inheritance. Hum Reprod. 15:102-111.
61. HoranMP, Gemmell NJ,Wolff JN. 2013. From evolutionary bystander to master manipulator: the emerging roles for the mitochondrial genome as a modulator of nuclear gene expression. Eur J Hum Genet. 21:1335.
62. Hurst LD, Hamilton WD. 1992. Cytoplasmic fusion and the nature of sexes. Proc R Soc Lond B Biol Sci. 247:189-194.
63. Innocenti P, Morrow EH, Dowling DK. 2011. Experimental evidence supports a sex-specific selective sieve in mitochondrial genome evolution. Science 332:845-848.
64. James AC, Ballard JWO. 2003. Mitochondrial genotype affects fitness in Drosophila simulans. Genetics 164:187-194.
65. Johnson JD, Hill GE. 2013. Is carotenoid ornamentation linked to the inner mitochondria membrane potential? A hypothesis for the maintenance of signal honesty. Biochimie 95:436-444.
66. Keightley PD, Otto SP. 2006. Interference among deleterious mutations favours sex and recombination in finite populations. Nature 443:89-92.
67. Kuijper B, Lane N, Pomiankowski A. 2015. Can paternal leakagemaintain sexually antagonistic polymorphism in the cytoplasm? J Evol Biol 28:468-480.
68. Kuijper B, Pen I, Weissing FJ. 2012. A guide to sexual selection theory. Annu Rev Ecol Evol Syst. 43:287-311.
69. Kurbalija NovičićZ, Immonen E, JelićM, An-DelkovićM, Stamenković-Radak M, Arnqvist G. 2015. Within-population genetic effects of mtDNA on metabolic rate in Drosophila subobscura. J Evol Biol. 28:338-346.
70. Lane N. 2005. Power, sex, suicide: mitochondria and the meaning of life. Oxford: Oxford University Press.
71. Lane N. 2009. On the origin of bar codes. Nature 462:272-274.
72. Lane N. 2011a. Energetics and genetics across the prokaryote-eukaryote divide. Biol Direct. 6:35.
73. Lane N. 2011b. Mitonuclear match: optimizing fitness and fertility over generations drives ageing within generations. Bioessays 33:860-869.
74. Lane N. 2011c. The costs of breathing. Science 334:184-185.
75. Lane N. 2012. The problem with mixing mitochondria. Cell 151:246-248.
76. Lane N. 2014. Bioenergetic constraints on the evolution of complex life. Cold Spring Harb Perspect Biol. 6:a015982.
77. Lane N, Martin W. 2010. The energetics of genome complexity. Nature 467:929-934.
78. Lee C, Yen K, Cohen P. 2013. Humanin: a harbinger of mitochondrialderived peptides? Trends Endocrinol Metab 24:222-228.
79. Lee C, Zeng J, Drew BG, Sallam T, Martin-Montalvo A, Wan J, Kim S-J, Mehta H, Hevener AL, de Cabo R. 2015. The mitochondrial-derived peptide MOTS-c promotes metabolic homeostasis and reduces obesity and insulin resistance. Cell Metab. 21:443-454.
80. Levin L, Blumberg A, Barshad G, Mishmar D. 2014. Mito-nuclear co-evolution: the positive and negative sides of functional ancient mutations. Front Genet. 5:448.
81. Ligon JD. 1999. The evolution of avian breeding systems. Oxford: Oxford University Press.
82. Lively CM, Craddock C, Vrijenhoek RC. 1990. Red Queen hypothesis supported by parasitism in sexual and clonal fish. Nature 344:864-866.
83. Lynch M. 1997. Mutation accumulation in nuclear, organelle, and prokaryotic transfer RNA genes. Mol Biol Evol. 14:914-925.
84. Martin W, Koonin EV. 2006. Introns and the origin of nucleus-cytosol compartmentalization. Nature 440:41-45.
85. Martin W, Müller M. 1998. The hydrogen hypothesis for the first eukaryote. Nature 392:37-41.
86. Maynard Smith J. 1978. The evolution of sex. Cambridge: Cambridge University Press.
87. McCauley DE. 2013. Paternal leakage, heteroplasmy, and the evolution of plant mitochondrial genomes. New Phytol. 200:966-977.
88. McGaugh SE, Heil CS, Manzano-Winkler B, Loewe L, Goldstein S, Himmel TL, Noor MA. 2012. Recombination modulates how selection affects linked sites in Drosophila. PLoS Biol. 10:e1001422.
89. Meiklejohn CD, Holmbeck MA, Siddiq MA, Abt DN, Rand DM, Montooth KL. 2013. An incompatibility between a mitochondrial tRNA and its nuclear-encoded tRNA synthetase compromises development and fitness in Drosophila. PLoS Genet. 9:e1003238.
90. Mendelson TC, Shaw KL. 2012. The (mis)concept of species recognition. Trends Ecol Evol. 27:421-427.
91. Morales HE, Pavlova A, Joseph L, Sunnucks P. 2015. Positive and purifying selection in mitochondrial genomes of a bird with mitonuclear discordance. Mol Ecol.
92. Orr HA. 2005a. The genetic basis of reproductive isolation: insights from Drosophila. Proc Natl Acad Sci U S A. 102:6522-6526.
93. Orr HA. 2005b. The genetic theory of adaptation: a brief history. Nat Rev Genet. 6:119-127.
94. Osada N, Akashi H. 2012. Mitochondrial-nuclear interactions and accelerated compensatory evolution: evidence from the primate cytochrome c oxidase complex. Mol Biol Evol. 29:337-346.
95. Otto SP, Barton NH. 2001. Selection for recombination in small populations. Evolution 55:1921-1931.
96. Otto SP,Michalakis Y. 1998. The evolution of recombination in changing environments. Trends Ecol Evol. 13:145-151.
97. Parker GA. 2014. The sexual cascade and the rise of pre-ejaculatory (Darwinian) sexual selection, sex roles, and sexual conflict. Cold Spring Harb Perspect Biol. 6:a017509.
98. Pereira RJ, Barreto FS, Burton RS. 2014. Ecological novelty by hybridization: experimental evidence for increased thermal tolerance by transgressive segregation in Tigriopus californicus. Evolution 68:204-215.
99. Pierron D, Wildman DE, Huttemann M, Markondapatnaikuni GC, Aras S, Grossman LI. 2012. Cytochrome c oxidase: evolution of control via nuclear subunit addition. Biochim Biophys Acta Bioenerg. 1817:590-597.
100. Price T. 2007. Speciation in birds. London: Roberts and Company Publishers.
101. Rand DM, Haney RA, Fry AJ. 2004. Cytonuclear coevolution: the genomics of cooperation. Trends Ecol Evol. 19:645-653.
102. Reeve HK, Pfennig DW. 2003. Genetic biases for showy males: are some genetic systems especially conducive to sexual selection? Proc Natl Acad Sci U S A. 100:1089-1094.
103. Ritchie MG. 2007. Sexual selection and speciation. Annu Rev Ecol Evol Syst. 38:79-102.
104. Rogell B, Dean R, Lemos B, Dowling DK. 2014. Mito-nuclear interactions as drivers of gene movement on and off the X-chromosome. BMC Genomics 15:330.
105. Roy SW, Gilbert W. 2006. The evolution of spliceosomal introns: patterns, puzzles and progress. Nat Rev Genet. 7:211-221.
106. Ryan MJ, Rand AS. 1993. Species recognition and sexual selection as a unitary problem in animal communication. Evolution 47:647-657.
107. Sackton TB, Haney RA, Rand DM. 2003. Cytonuclear coadaptation in Drosophila: disruption of cytochrome c oxidase activity in backcross genotypes. Evolution 57:2315-2325.
108. Safran RJ, Scordato ES, Symes LB, Rodriguez RL, Mendelson TC. 2013. Contributions of natural and sexual selection to the evolution of premating reproductive isolation: a research agenda. Trends Ecol Evol. 28:643-650.
109. Schmidt TR, Wu W, Goodman M, Grossman LI. 2001. Evolution of nuclear-and mitochondrial-encoded subunit interaction in cytochrome c oxidase. Mol Biol Evol. 18:563-569.
110. Scott GR, Hawkes LA, Frappell PB, Butler PJ, Bishop CM, Milsom WK. 2015. How bar-headed geese fly over the Himalayas. Physiology 30:107-115.
111. Scott GR, Schulte PM, Egginton S, Scott AL, Richards JG, Milsom WK. 2011. Molecular evolution of cytochrome c oxidase underlies high-altitude adaptation in the bar-headed goose. Mol Biol Evol. 28:351-363.
112. Servedio MR. 2001. Beyond reinforcement: the evolution of premating isolation by direct selection on preferences and postmating, prezygotic incompatibilities. Evolution 55:1909-1920.
113. Shen Y-Y, Liang L, Zhu Z-H, Zhou W-P, Irwin DM, Zhang Y-P. 2010. Adaptive evolution of energy metabolism genes and the origin of flight in bats. Proc Natl Acad Sci U S A. 107:8666-8671.
114. Stoeckle MY, Thaler DS. 2014. DNA barcoding works in practice but not in (neutral) theory. PLoS One 9:e100755.
115. Toews DP, Brelsford A. 2012. The biogeography of mitochondrial and nuclear discordance in animals. Mol Ecol. 21:3907-3930.
116. Toews DP, Mandic M, Richards JG, Irwin DE. 2014. Migration, mitochondria, and the yellow-rumped warbler. Evolution 68:241-255.
117. Trier CN, Hermansen JS, Sætre G-P, Bailey RI. 2014. Evidence for mito-nuclear and sex-linked reproductive barriers between the hybrid Italian sparrow and its parent species. PLoS Genet. 10:e1004075.
118. Turelli M, Moyle LC. 2007. Asymmetric postmating isolation: Darwin's corollary to Haldane's rule. Genetics 176:1059-1088.
119. Wallace AR. 1889. Darwinism. London: Macmillan.
120. Wallace DC. 2007. Why do we still have a maternally inherited mitochondrial DNA? Insights from evolutionary medicine. Annu Rev Biochem. 76:781-821.
121. Wallace DC. 2010a. Mitochondrial DNA mutations in disease and aging. Environ Mol Mutagen. 51:440-450.
122. Wallace DC. 2010b. Bioenergetics, the origins of complexity, and the ascent of man. Proc Natl Acad Sci U S A. 107:8947-8953.
123. Wallace DC. 2013. Bioenergetics in human evolution and disease: implications for the origins of biological complexity and the missing genetic variation of common diseases. Philos Trans R Soc Lond B Biol Sci. 368:20120267.
124. Williams TA, Foster PG, Cox CJ, Embley TM. 2013. An archaeal origin of eukaryotes supports only two primary domains of life. Nature 504:231-236.
125. Wilson RE, Peters JL, McCracken KG. 2013. Genetic and phenotypic divergence between low - and high - altitude populations of two recently diverged cinnamon teal subspecies. Evolution 67:170-184.
126. Wolff JN, Ladoukakis ED, Enríquez JA, Dowling DK. 2014. Mitonuclear interactions: evolutionary consequences over multiple biological scales. Philos Trans R Lond B Biol Sci. 369:20130443.
127. Woodson JD, Chory J. 2008. Coordination of gene expression between organellar and nuclear genomes. Nat Rev Genet. 9:383-395.