Literature Cited
Adrion, J. R., P. S. White, and K. L. Montooth. 2016. The roles of
compensatory evolution and constraint in aminoacyl tRNA synthetase
evolution. Mol. Biol. Evol. 33:152–161.
Arnold, S. 2012. The power of life—cytochrome c oxidase takes center
stage in metabolic control, cell signalling and survival. Mitochondrion
12:46–56.
Avise, J. C. 2004. Molecular Markers, Natural History, and Evolution.
Baker, A. J., E. S. Tavares, and R. F. Elbourne. 2009. Countering
criticisms of single mitochondrial DNA gene barcoding in birds. Mol.
Ecol. Resour. 9:257–268.
Ballard, J. W. O., and M. Kreitman. 1995. Is mitochondrial DNA a
strictly neutral marker? Trends Ecol. Evol. 10:485–488.
Ballard, J. W. O., and N. Pichaud. 2014. Mitochondrial DNA: More than an
evolutionary bystander. Funct. Ecol. 28:218–231.
Ballard, J. W. O., and M. C. Whitlock. 2004. The incomplete natural
history of mitochondria. Mol. Ecol. 13:729–744.
Bar-Yaacov, D., A. Blumberg, and D. Mishmar. 2012. Mitochondrial-nuclear
co-evolution and its effects on OXPHOS activity and regulation. Biochim.
Biophys. Acta - Gene Regul. Mech. 1819:1107–1111.
Barr, C. M., M. Neiman, and D. R. Taylor. 2005. Inheritance and
recombination of mitochondrial genomes in plants, fungi and animals. New
Phytol. 168:39–50.
Barreto, F. S., and R. S. Burton. 2013. Evidence for compensatory
evolution of ribosomal proteins in response to rapid divergence of
mitochondrial rRNA. Mol. Biol. Evol. 30:310–314.
Barreto, F. S., E. T. Watson, T. G. Lima, C. S. Willett, S. Edmands, W.
Li, and R. S. Burton. 2018. Genomic signatures of mitonuclear
coevolution across populations of Tigriopus californicus. Nat. Ecol.
Evol. 2:1250–1257.
Barrientos, A., L. Kenyon, and C. T. Moraes. 1998. Human
xenomitochondrial cybrids. J. Biol. Chem. 273:14210.
Barrowclough, G. F., and R. M. Zink. 2009. Funds enough, and time:
mtDNA, nuDNA and the discovery of divergence. Mol. Ecol. 18:2934–2936.
Barshad, G., A. Blumberg, T. Cohen, and D. Mishmar. 2018. Human
primitive brain displays negative mitochondrial-nuclear expression
correlation of respiratory genes. Genome Res. 28:952–967.
Barton, N. H. 2000. Genetic hitchhiking. Philos. Trans. R. Soc. B Biol.
Sci. 355:1553–1562.
Bazin, E., S. Glémin, and N. Galtier. 2006. Population Size Does Not
Influence Mitochondrial Genetic Diversity in Animals. Science (80-. ).
312:570–572.
Berlin, S., and H. Ellegren. 2004. Chicken W: A genetically uniform
chromosome in a highly variable genome. Proc. Natl. Acad. Sci. U. S. A.
101:15967–15969.
Berlin, S., D. Tomaras, and B. Charlesworth. 2007. Low mitochondrial
variability in birds may indicate Hill-Robertson effects on the W
chromosome. Heredity (Edinb). 99:389–396.
Blount, Z. D., R. E. Lenski, and J. B. Losos. 2018. Contingency and
determinism in evolution: Replaying life’s tape. Science 362.
Bonnet, T., R. Leblois, F. Rousset, and P.-A. Crochet. 2017. A
reassessment of explanations for discordant introgressions of
mitochondrial and nuclear genomes. Evolution (N. Y). 71:2140–2158.
Boore, J. L. 1999. Animal mitochondrial genomes. Nucleic Acids Res.
27:1767–1780.
Brockman, S. A., and C. S. McFadden. 2012. The mitochondrial genome of
Paraminabea aldersladei (Cnidaria: Anthozoa: Octocorallia) supports
intramolecular recombination as the primary mechanism of gene
rearrangement in octocoral mitochondrial genomes. Genome Biol. Evol.
4:994–1006.
Bucklin, A., D. Steinke, and L. Blanco-Bercial. 2011. DNA Barcoding of
Marine Metazoa. Ann. Rev. Mar. Sci. 3:471–508.
Burton, R. S., and F. S. Barreto. 2012. A disproportionate role for
mtDNA in Dobzhansky-Muller incompatibilities? Mol. Ecol. 21:4942–4957.
Calvo, E., S. Cogliati, P. Hernansanz-Agustin, M. Loureiro-Lopez, A.
Guaras, R. A. Casuso, F. Garcia-Marques, R. Acin-Perez, Y. Marti-Mateos,
J. C. Silla-Castro, M. Carro-Alvarellos, J. R. Huertas, J. Vazquez, and
J. A. Enriquez. 2019. Functional role of respiratory supercomplexes in
mice: segmentation of the Qpool and SCAF1. bioRxiv 826115.
Charlesworth, D., M. T. Morgan, and B. Charlesworth. 1993. Mutation
accumulation in finite outbreeding and inbreeding populations. Genet.
Res. 61:39–56.
Chase, M. W., N. Salamin, M. Wilkinson, J. M. Dunwell, R. P.
Kesanakurthi, N. Haidar, and V. Savolainen. 2005. Land plants and DNA
barcodes: Short-term and long-term goals. Philos. Trans. R. Soc. B Biol.
Sci. 360:1889–1895.
Chinnery, P. F., G. A. Taylor, N. Howell, D. T. Brown, T. J. Parsons,
and D. M. Turnbull. 2002. Point Mutations of the mtDNA Control Region in
Normal and Neurodegenerative Human Brains. Am. J. Hum. Genet.
68:529–532.
Chou, J. Y., and J. Y. Leu. 2010. Speciation through cytonuclear
incompatibility: Insights from yeast and implications for higher
eukaryotes. BioEssays 32:401–411.
Christy, S. F., R. I. Wernick, M. J. Lue, G. Velasco, D. K. Howe, D. R.
Denver, and S. Estes. 2017. Adaptive Evolution under Extreme Genetic
Drift in Oxidatively Stressed Caenorhabditis elegans. Genome Biol. Evol.
9:3008–3022.
Clare, E. L., B. K. Lim, M. D. Engstrom, J. L. Eger, and P. D. N.
Hebert. 2007. DNA barcoding of Neotropical bats: species identification
and discovery within Guyana. Mol. Ecol. Notes 7:184–190. Wiley Online
Library.
Coddington, J. A., I. Agnarsson, R. C. Cheng, K. Čandek, A. Driskell, H.
Frick, M. Gregorič, R. Kostanjšek, C. Kropf, M. Kweskin, T. Lokovšek, M.
Pipan, N. Vidergar, and M. Kuntner. 2016. DNA barcode data accurately
assign higher spider taxa. PeerJ 2016:1–25.
Costa, F. O., and G. R. Carvalho. 2010. New insights into molecular
evolution: Prospects from the barcode of life initiative (BOLI). Theory
Biosci. 129:149–157.
Cowan, R. S., M. W. Chase, W. J. Kress, and V. Savolainen. 2006. 300,000
Species to identify: Problems, progress, and prospects in DNA barcoding
of land plants. Taxon 55:611–616.
da Fonseca, R. R., W. E. Johnson, S. J. O’Brien, M. J. Ramos, and A.
Antunes. 2008. The adaptive evolution of the mammalian mitochondrial
genome. BMC Genomics 9:119.
Dasmahapatra, K. K., and J. Mallet. 2006. Taxonomy: DNA barcodes: recent
successes and future prospects. Heredity (Edinb). 97:254–255.
Dobzhansky, T. G. 1937. Genetics and the Origin of Species. Columbia
University Press, New York.
Dowling, D. K., U. Friberg, and J. Lindell. 2008. Evolutionary
implications of non-neutral mitochondrial genetic variation. Trends
Ecol. Evol. 23:546–554.
Dupuis, J. R., A. D. Roe, and F. A. H. Sperling. 2012. Multi-locus
species delimitation in closely related animals and fungi: One marker is
not enough.
Edwards, S. V., S. B. Kingan, J. D. Calkins, C. N. Balakrishnan, W. B.
Jennings, W. J. Swanson, and M. D. Sorenson. 2005. Speciation in birds:
Genes, geography, and sexual selection. Proc. Natl. Acad. Sci.
102:6550–6557.
Ellegren, H. 2013. The Evolutionary Genomics of Birds. Annu. Rev. Ecol.
Evol. Syst. 44:239–259.
Ellison, C. K., and R. S. Burton. 2010. Cytonuclear conflict in
interpopulation hybrids: The role of RNA polymerase in mtDNA
transcription and replication. J. Evol. Biol. 23:528–538.
Ellison, C. K., and R. S. Burton. 2008a. Genotype-dependent variation of
mitochondrial transcriptional profiles in interpopulation hybrids. Proc.
Natl. Acad. Sci. 105:15831–15836.
Ellison, C. K., and R. S. Burton. 2008b. Interpopulation hybrid
breakdown maps to the mitochondrial genome. Evolution (N. Y).
62:631–638.
Eyre-Walker, A. 2006. Size Does Not Matter for Mitochondrial DNA.
Science (80-. ). 312:537–538.
Garvin, M. R., J. P. Bielawski, and A. J. Gharrett. 2011. Positive
darwinian selection in the piston that powers proton pumps in Complex I
of the mitochondria of Pacific salmon. PLoS One 6.
Garvin, M. R., J. P. Bielawski, L. A. Sazanov, and A. J. Gharrett. 2014.
Review and meta-analysis of natural selection in mitochondrial complex I
in metazoans. J. Zool. Syst. Evol. Res. 53:1–17.
Gaspari, M., M. Falkenberg, N.-G. Larsson, and C. M. Gustafsson. 2004.
The mitochondrial RNA polymerase contributes critically to promoter
specificity in mammalian cells. EMBO J. 23:4606–4614.
Gershoni, M., L. Levin, O. Ovadia, Y. Toiw, N. Shani, S. Dadon, N.
Barzilai, A. Bergman, G. Atzmon, J. Wainstein, A. Tsur, L. Nijtmans, B.
Glaser, and D. Mishmar. 2014. Disrupting mitochondrial-nuclear
coevolution affects OXPHOS complex i integrity and impacts human health.
Genome Biol. Evol. 6:2665–2680.
Gershoni, M., A. R. Templeton, and D. Mishmar. 2009. Mitochondrial
bioenergetics as a major motive force of speciation. Bioessays
31:642–650.
Gillespie, J. H. 2000. Genetic drift in infinite populations. Genetics
155:909–919.
Gissi, C., F. Iannelli, and G. Pesole. 2008. Evolution of the
mitochondrial genome of Metazoa as exemplified by comparison of
congeneric species. Heredity (Edinb). 101:301–320.
Gray, M. W. 1999. Evolution of organellar genomes. Curr. Opin. Genet.
Dev. 9:678–687.
Hebert, P. D. N., A. Cywinska, S. L. Ball, and J. R. deWaard. 2003a.
Biological identifications through DNA barcodes. Proc. R. Soc. B Biol.
Sci. 270:313–321.
Hebert, P. D. N., S. Ratnasingham, and J. Waard. 2003b. Barcoding animal
life : cytochrome c oxidase subunit 1 divergences among closely related
species Barcoding animal life : cytochrome c oxidase subunit 1
divergences among closely related species. Proc. R. Soc. Lond. B
270:S96–S99.
Hickerson, M. J., C. P. Meyer, and C. Moritz. 2006. DNA barcoding will
often fail to discover new animal species over broad parameter space.
Syst. Biol. 55:729–739.
Hill, G. E. 2016. Mitonuclear coevolution as the genesis of speciation
and the mitochondrial DNA barcode gap. Ecol. Evol. 6:5831–5842.
Hill, G. E. 2020. Mitonuclear Compensatory Coevolution. Trends Genet.
Hill, G. E. 2019a. Mitonuclear Ecology. Oxford University Press, Oxford,
UK.
Hill, G. E. 2018. Mitonuclear Mate Choice: A Missing Component of Sexual
Selection Theory? BioEssays 40:1700191.
Hill, G. E. 2019b. Reconciling the Mitonuclear Compatibility Species
Concept with Rampant Mitochondrial Introgression. Integr. Comp. Biol.
59:912–924.
Hill, G. E. 2017. The mitonuclear compatibility species concept. Auk
134:393–409.
Hill, G. E., J. C. Havird, D. B. Sloan, R. S. Burton, C. Greening, and
D. K. Dowling. 2019. Assessing the fitness consequences of mitonuclear
interactions in natural populations. Biol. Rev. 94:1089–1104.
Hoekstra, L. A., M. A. Siddiq, and K. L. Montooth. 2013. Pleiotropic
effects of a mitochondrial-nuclear incompatibility depend upon the
accelerating effect of temperature in Drosophila. Genetics
195:1129–1139.
Huang, D., R. Meier, P. A. Todd, and L. M. Chou. 2008. Slow
mitochondrial COI sequence evolution at the base of the metazoan tree
and its implications for DNA barcoding. J. Mol. Evol. 66:167–174.
James, J. E., G. Piganeau, and A. Eyre-Walker. 2016. The rate of
adaptive evolution in animal mitochondria. Mol. Ecol. 25:67–78.
Janzen, D. H., W. Hallwachs, P. Blandin, J. M. Burns, J. M. Cadiou, I.
Chacon, T. Dapkey, A. R. Deans, M. E. Epstein, B. Espinoza, J. G.
Franclemont, W. A. Haber, M. Hajibabaei, J. P. W. Hall, P. D. N. Hebert,
I. D. Gauld, D. J. Harvey, A. Hausmann, I. J. Kitching, D. Lafontaine,
J. F. ??ois Landry, C. Lemaire, J. Y. Miller, J. S. Miller, L. Miller,
S. E. Miller, J. Montero, E. Munroe, S. R. Green, S. Ratnasingham, J. E.
Rawlins, R. K. Robbins, J. J. Rodriguez, R. Rougerie, M. J. Sharkey, M.
A. Smith, M. A. Solis, J. B. Sullivan, P. Thiaucourt, D. B. Wahl, S. J.
Weller, J. B. Whitfield, K. R. Willmott, D. M. Wood, N. E. Woodley, and
J. J. Wilson. 2009. Integration of DNA barcoding into an ongoing
inventory of complex tropical biodiversity. Mol. Ecol. Resour. 9:1–26.
Kazancioǧlu, E., and G. Arnqvist. 2014. The maintenance of mitochondrial
genetic variation by negative frequency-dependent selection. Ecol. Lett.
17:22–27.
Kern, A. D., and M. W. Hahn. 2018. The neutral theory in light of
natural selection. Mol. Biol. Evol. 1–6.
Kerr, K. C. R. 2011. Searching for evidence of selection in avian DNA
barcodes. Mol. Ecol. Resour. 11:1045–1055.
Kerr, K. C. R., M. Y. Stoeckle, C. J. Dove, L. A. Weigt, C. M. Francis,
and P. D. N. Hebert. 2007. Comprehensive DNA barcode coverage of North
American birds. Mol. Ecol. Notes 7:535–543.
Kivisild, T., P. Shen, D. P. Wall, B. Do, R. Sung, K. Davis, G.
Passarino, P. A. Underhill, C. Scharfe, A. Torroni, R. Scozzari, D.
Modiano, A. Coppa, P. De Knijff, M. Feldman, L. L. Cavalli-Sforza, and
P. J. Oefner. 2006. The role of selection in the evolution of human
mitochondrial genomes. Genetics 172:373–387.
Kress, W. J., K. J. Wurdack, E. A. Zimmer, L. A. Weigt, and D. H.
Janzen. 2005. Use of DNA barcodes to identify flowering plants. Proc.
Natl. Acad. Sci. 102:8369–8374.
Kwong, S., A. Srivathsan, G. Vaidya, and R. Meier. 2012. Is the COI
barcoding gene involved in speciation through intergenomic conflict?
Mol. Phylogenet. Evol. 62:1009–1012.
Lane, N. 2009a. Biodiversity: On the origin of bar codes. Nature
462:272–274.
Lane, N. 2014. Bioenergetic constraints on the evolution of complex
life. Cold Spring Harb. Perspect. Biol. 6.
Lane, N. 2008. Mitochondria and the W chromosome: Low variability on the
W chromosome in birds is more likely to indicate selection on
mitochondrial genes. Heredity (Edinb). 100:444–445.
Lane, N. 2011. Mitonuclear match: Optimizing fitness and fertility over
generations drives ageing within generations. Bioessays 33:860–869.
Lane, N. 2009b. On the origin of bar codes. Nature 462:272–274.
Lanza, R. P., B. L. Dresser, and P. Damiani. 2000. Cloning Noah’s Ark.
Sci. Am. 283:84–89.
Latorre-Pellicer, A., R. Moreno-Loshuertos, A. V. Lechuga-Vieco, F.
Sánchez-Cabo, C. Torroja, R. Acín-Pérez, E. Calvo, E. Aix, A.
González-Guerra, A. Logan, M. L. Bernad-Miana, E. Romanos, R. Cruz, S.
Cogliati, B. Sobrino, Á. Carracedo, A. Pérez-Martos, P. Fernández-Silva,
J. Ruíz-Cabello, M. P. Murphy, I. Flores, J. Vázquez, and J. A.
Enríquez. 2016. Mitochondrial and nuclear DNA matching shapes metabolism
and healthy ageing. Nature 535:561–565.
Lee, H. Y., J. Y. Chou, L. Cheong, N. H. Chang, S. Y. Yang, and J. Y.
Leu. 2008. Incompatibility of Nuclear and Mitochondrial Genomes Causes
Hybrid Sterility between Two Yeast Species. Cell 135:1065–1073.
Elsevier Ltd.
Luo, Y., X. Yang, and Y. Gao. 2013. Mitochondrial DNA response to high
altitude: A new perspective on high-altitude adaptation. Mitochondrial
DNA 24:313–319.
Lynch, M., B. Koskella, and S. Schaack. 2006. Mutation Pressure and the
Evolution of Organelle Genomic Architecture. Science (80-. ).
311:1727–1730.
Marais, G. A. B. 2007. Sex chromosomes and mitochondrial DNA
polymorphism in birds: The Hill-Robertson effects extend from nucleus to
mitochondria. Heredity (Edinb). 99:357–358.
Maynard Smith, J., and J. Haigh. 1974. The hitch-hiking effect of a
favourable gene. Genet. Res. 23:23–35.
Meiklejohn, C. D., M. A. Holmbeck, M. A. Siddiq, D. N. Abt, D. M. Rand,
and K. L. Montooth. 2013. An Incompatibility between a Mitochondrial
tRNA and Its Nuclear-Encoded tRNA Synthetase Compromises Development and
Fitness in Drosophila. PLoS Genet. 9:e1003238.
Meiklejohn, C. D., K. L. Montooth, and D. M. Rand. 2007. Positive and
negative selection on the mitochondrial genome. Trends Genet
23:259–263.
Meyer, C. P., and G. Paulay. 2005. DNA barcoding: Error rates based on
comprehensive sampling. PLoS Biol. 3:1–10.
Morinière, J., L. Hendrich, M. Balke, A. J. Beermann, T. König, M. Hess,
S. Koch, R. Müller, F. Leese, P. D. N. Hebert, A. Hausmann, C. D.
Schubart, and G. Haszprunar. 2017. A DNA barcode library for Germany′s
mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and
Trichoptera). Mol. Ecol. Resour., doi: 10.1111/1755-0998.12683.
Moritz, C., T. E. Dowling, and W. M. Brown. 1987. Evolution of animal
mitochondrial DNA: relevance for population biology and systematics.
Annu. Rev. Ecol. Syst. 18:269–292. Annual Reviews 4139 El Camino Way,
PO Box 10139, Palo Alto, CA 94303-0139, USA.
Nabholz, B., S. Glemin, and N. Galtier. 2009. The erratic mitochondrial
clock: variations of mutation rate, not population size, affect
{{}mtDNA{}} diversity across birds and mammals. Bmc Evol. Biol.
9:13.
Naro‐Maciel, E., B. Reid, N. N. Fitzsimmons, M. Le, R. O. B. Desalle,
and G. Amato. 2010. DNA barcodes for globally threatened marine turtles:
a registry approach to documenting biodiversity. Mol. Ecol. Resour.
10:252–263. Wiley Online Library.
Oliveira, D. C. S. G., R. Raychoudhury, D. V. Lavrov, and J. H. Werren.
2008. Rapidly evolving mitochondrial genome and directional selection in
mitochondrial genes in the parasitic wasp Nasonia (Hymenoptera:
Pteromalidae). Mol. Biol. Evol. 25:2167–2180.
Osada, N., and H. Akashi. 2012. Mitochondrial-nuclear interactions and
accelerated compensatory evolution: Evidence from the primate cytochrome
c oxidase complex. Mol. Biol. Evol. 29:337–346.
Pacelli, C., D. Latorre, T. Cocco, F. Capuano, C. Kukat, P. Seibel, and
G. Villani. 2011. Tight control of mitochondrial membrane potential by
cytochrome c oxidase. Mitochondrion 11:334–341.
Palumbi, S. R., F. Cipriano, and M. P. Hare. 2001. Predicting Nuclear
Gene Coalescence From Mitochondrial Data: the Three-Times Rule.
Evolution (N. Y). 55:859.
Papadopoulou, A., J. Bergsten, T. Fujisawa, M. T. Monaghan, T. G.
Barraclough, and A. P. Vogler. 2008. Speciation and DNA barcodes:
testing the effects of dispersal on the formation of discrete sequence
clusters. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 363:2987–2996.
Pazhenkova, E. A., and V. A. Lukhtanov. 2019. Nuclear genes (but not
mitochondrial DNA barcodes) reveal real species: Evidence from the
Brenthis fritillary butterflies (Lepidoptera, Nymphalidae). J. Zool.
Syst. Evol. Res. 57:298–313.
Petit, R. J., and L. Excoffier. 2009. Gene flow and species
delimitation. Trends Ecol. Evol. 24:386–393.
Pett, W., and D. Lavrov. 2015. Mito-nuclear interactions in the
evolution of animal mitochondrial tRNA metabolism. Genome Biol. Evol.
7:2089–2101.
Pfenninger, M., H. Lerp, M. Tobler, C. Passow, J. L. Kelley, E. Funke,
B. Greshake, U. K. Erkoc, T. Berberich, and M. Plath. 2014. Parallel
evolution of cox genes in H2S-tolerant fish as key adaptation to a toxic
environment. Nat. Commun. 5:3873.
Pierron, D., D. E. Wildman, M. Hüttemann, G. C. Markondapatnaikuni, S.
Aras, and L. I. Grossman. 2012. Cytochrome c oxidase: Evolution of
control via nuclear subunit addition. Biochim. Biophys. Acta - Bioenerg.
1817:590–597. Elsevier B.V.
Popadin, K. Y., S. I. Nikolaev, T. Junier, M. Baranova, and S. E.
Antonarakis. 2013. Purifying selection in mammalian mitochondrial
protein-coding genes is highly effective and congruent with evolution of
nuclear genes. Mol. Biol. Evol. 30:347–355.
Rand, D. M., M. Dorfsman, and L. M. Kann. 1994. Neutral and non-neutral
evolution of Drosophila mitochondrial DNA. Genetics 138:741–756.
Rand, D. M., R. A. Haney, and A. J. Fry. 2004. Cytonuclear coevolution:
the genomics of cooperation. Trends Ecol. Evol. 19:645–653.
Ratnasingham, S., and P. D. N. Hebert. 2013. A DNA-Based Registry for
All Animal Species: The Barcode Index Number (BIN) System. PLoS One,
doi: 10.1371/journal.pone.0066213.
Rokas, A., E. Ladoukakis, and E. Zouros. 2003. Animal mitochondrial DNA
recombination revisited. Trends Ecol. Evol. 18:411–417.
Rubinoff, D., S. Cameron, and K. Will. 2006. A genomic perspective on
the shortcomings of mitochondrial DNA for “barcoding” identification.
J. Hered. 97:581–594.
Ruiz‐Pesini, E., and D. C. Wallace. 2006. Evidence for adaptive
selection acting on the tRNA and rRNA genes of human mitochondrial DNA.
Hum. Mutat. 27:1072–1081. Wiley Online Library.
Saccone, C., C. Gissi, C. Lanave, A. Larizza, G. Pesole, and A. Reyes.
2000. Evolution of the mitochondrial genetic system: An overview. Gene
261:153–159.
Scheel, B. M., and B. Hausdorf. 2014. Dynamic evolution of mitochondrial
ribosomal proteins in Holozoa. Mol. Phylogenet. Evol. 76:67–74.
Elsevier Inc.
Scheper, G. C., M. S. van der Knaap, and C. G. Proud. 2007. Translation
matters: protein synthesis defects in inherited disease. Nat. Rev.
Genet. 8:711–723.
Scott, G. R., P. M. Schulte, S. Egginton, A. L. M. Scott, J. G.
Richards, and W. K. Milsom. 2011. Molecular evolution of cytochrome c
oxidase underlies high-altitude adaptation in the bar-headed goose. Mol.
Biol. Evol. 28:351–363.
Shtolz, N., and D. Mishmar. 2019. The Mitochondrial Genome–on Selective
Constraints and Signatures at the Organism, Cell, and Single
Mitochondrion Levels. Frontiers Media S.A.
Sloan, D. B., J. C. Havird, and J. Sharbrough. 2017. The on-again,
off-again relationship between mitochondrial genomes and species
boundaries. Mol. Ecol. 26:2212–2236.
Sloan, D. B., J. M. Warren, A. M. Williams, Z. Wu, S. E. Abdel-Ghany, A.
J. Chicco, and J. C. Havird. 2018. Cytonuclear integration and
co-evolution. Nat. Rev. Genet. 19:635–648.
Smeds, L., V. Warmuth, P. Bolivar, S. Uebbing, R. Burri, A. Suh, A.
Nater, S. Bureš, L. Z. Garamszegi, S. Hogner, J. Moreno, A. Qvarnström,
M. Ruzic, S. A. Sæther, G. P. Sætre, J. Török, and H. Ellegren. 2015.
Evolutionary analysis of the female-specific avian W chromosome. Nat.
Commun. 6.
Smith, D. R. 2016. The mutational hazard hypothesis of organelle genome
evolution: 10 years on. Mol. Ecol. 25:3769–3775.
Smith, M. A., B. L. Fisher, and P. D. N. Hebert. 2005. DNA barcoding for
effective biodiversity assessment of a hyperdiverse arthropod group: The
ants of Madagascar. Philos. Trans. R. Soc. B Biol. Sci., doi:
10.1098/rstb.2005.1714.
Smith, M. A., J. J. Rodriguez, J. B. Whitfield, A. R. Deans, D. H.
Janzen, W. Hallwachs, and P. D. N. Hebert. 2008. Extreme diversity of
tropical parasitoid wasps exposed by iterative integration of natural
history, DNA barcoding, morphology, and collections. Proc. Natl. Acad.
Sci. 105:12359 LP – 12364.
Stewart, J. B., C. Freyer, J. L. Elson, and N.-G. Larsson. 2008.
Purifying selection of mtDNA and its implications for understanding
evolution and mitochondrial disease. Nat Rev Genet 9:657–662.
Stoeckle, M. Y., and D. S. Thaler. 2014. DNA barcoding works in practice
but not in neutral theory. PLoS One 9:e100755.
Sunnucks, P., H. E. Morales, A. M. Lamb, A. Pavlova, and C. Greening.
2017. Integrative approaches for studying mitochondrial and nuclear
genome co-evolution in oxidative phosphorylation. Front. Genet. 8:25.
Suzuki, T., A. Nagao, and T. Suzuki. 2011. Human Mitochondrial tRNAs:
Biogenesis, Function, Structural Aspects, and Diseases. Annu. Rev.
Genet. 45:299–329.
Tavares, E. S., and A. J. Baker. 2008. Single mitochondrial gene
barcodes reliably identify sister-species in diverse clades of birds.
Bmc Evol. Biol. 8:14.
Teske, P. R., T. R. Golla, J. Sandoval-Castillo, A. Emami-Khoyi, C. D.
Van Der Lingen, S. Von Der Heyden, B. Chiazzari, B. Jansen Van Vuuren,
and L. B. Beheregaray. 2018. Mitochondrial DNA is unsuitable to test for
isolation by distance. Sci. Rep. 8:1–9. Springer US.
Thornlow, B. P., J. Hough, J. M. Roger, H. Gong, T. M. Lowe, and R. B.
Corbett-Detig. 2018. Transfer RNA genes experience exceptionally
elevated mutation rates. Proc. Natl. Acad. Sci. 115:8996–9001.
Tobe, S. S., A. C. Kitchener, and A. M. T. Linacre. 2010. Reconstructing
mammalian phylogenies: a detailed comparison of the cytochrome b and
cytochrome oxidase subunit I mitochondrial genes. PLoS One 5:e14156.
Tobler, M., N. Barts, and R. Greenway. 2019. Mitochondria and the origin
of species: bridging genetic and ecological perspectives on speciation
processes. Integr. Comp. Biol.
Toews, D. P. L., and A. Brelsford. 2012. The biogeography of
mitochondrial and nuclear discordance in animals. Mol. Ecol.
21:3907–3930.
Toews, D. P. L., S. A. Taylor, R. Vallender, A. Brelsford, B. G.
Butcher, P. W. Messer, and I. J. Lovette. 2016. Plumage Genes and Little
Else Distinguish the Genomes of Hybridizing Warblers. Curr. Biol.
26:2313–2318. Elsevier Ltd.
Tomasco, I. H., and E. P. Lessa. 2014. Two mitochondrial genes under
episodic positive selection in subterranean octodontoid rodents. Gene
534:371–378. Elsevier B.V.
Vences, M., M. Thomas, R. M. Bonett, and D. R. Vieites. 2005.
Deciphering amphibian diversity through DNA barcoding: chances and
challenges. Philos. Trans. R. Soc. London B Biol. Sci. 360:1859–1868.
The Royal Society.
Vonlanthen, P., D. Bittner, A. G. Hudson, K. A. Young, R. Müller, B.
Lundsgaard-Hansen, D. Roy, S. Di Piazza, C. R. Largiadèr, and O.
Seehausen. 2012. Eutrophication causes speciation reversal in whitefish
adaptive radiations. Nature 482:357. Nature Publishing Group.
Wallace, D. C. 2010. Bioenergetics, the origins of complexity, and the
ascent of man. Proc. Natl. Acad. Sci. 107:8947–8953.
Wang, Z. O., and D. D. Pollock. 2007. Coevolutionary patterns in
cytochrome c oxidase subunit I depend on structural and functional
context. J. Mol. Evol. 65:485–495.
Ward, R. D., and B. H. Holmes. 2007. An analysis of nucleotide and amino
acid variability in the barcode region of cytochrome c oxidase I (cox1)
in fishes. Mol. Ecol. Notes 7:899–907. Wiley Online Library.
Wei, W., S. Tuna, M. J. Keogh, K. R. Smith, T. J. Aitman, P. L. Beales,
D. L. Bennett, D. P. Gale, M. A. K. Bitner-Glindzicz, and G. C. Black.
2019. Germline selection shapes human mitochondrial DNA diversity.
Science (80-. ). 364. American Association for the Advancement of
Science.
White, D. J., J. N. Wolff, M. Pierson, and N. J. Gemmell. 2008.
Revealing the hidden complexities of mtDNA inheritance. Mol. Ecol.
17:4925–4942.
Whitworth, T. L., R. D. Dawson, H. Magalon, and E. Baudry. 2007. DNA
barcoding cannot reliably identify species of the blowfly genus
Protocalliphora (Diptera: Calliphoridae). Proc. R. Soc. B Biol. Sci.
274:1731–1739.
Wilson, A. C., R. L. Cann, S. M. Carr, M. George, U. B. Gyllensten, K.
M. Helm‐Bychowski, R. G. Higuchi, S. R. Palumbi, E. M. Prager, R. D.
Sage, and M. Stoneking. 1985. Mitochondrial DNA and two perspectives on
evolutionary genetics. Biol. J. Linn. Soc. 26:375–400.
Wolff, J. N., E. D. Ladoukakis, J. A. Enríquez, and D. K. Dowling. 2014.
Mitonuclear interactions: evolutionary consequences over multiple
biological scales. Philos. Trans. R. Soc. B Biol. Sci. 369:20130443.
Wright, S. 1942. Genetics and the origin of species. J. Hered.
33:283–284.
Xu, J. 2016. Fungal DNA barcoding. Genome 59:913–932.
Zahiri, R., J. D. Lafontaine, B. C. Schmidt, J. R. DeWaard, E. V
Zakharov, and P. D. N. Hebert. 2014. A transcontinental challenge - A
test of DNA barcode performance for 1,541 species of Canadian Noctuoidea
(Lepidoptera). PLoS One 9:1–12.
Zaidi, A. A., and K. D. Makova. 2019. Investigating mitonuclear
interactions in human admixed populations. Nat. Ecol. Evol. 3:213–222.
Nature Publishing Group.
Zhu, C. T., P. Ingelmo, and D. M. Rand. 2014. GxGxE for Lifespan in
Drosophila: Mitochondrial, Nuclear, and Dietary Interactions that Modify
Longevity. PLoS Genet. 10:e1004354.
Zink, R. M., and G. F. Barrowclough. 2008. Mitochondrial DNA under siege
in avian phylogeography. Mol. Ecol. 17:2107–2121.