Mitochondrial genomes of parasitic arthropods: Implications for studies of population genetics and evolution

Parasitology

Volumn 134, Issue 2, 2007, Pages 153-167

  Shao, R ^a   Barker, S C ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Gene order; Gene rearrangement; Mitochondrial genome; Parasitic arthropod; Phylogenetics; Population genetics; Systematics

Indexed keywords

TRANSFER RNA;

AMINO ACID SEQUENCE; ARTHROPOD; GENE DUPLICATION; GENE EXPRESSION; GENE ORDER; GENE REARRANGEMENT; GENETIC ANALYSIS; GENETIC RECOMBINATION; INHERITANCE; MITOCHONDRIAL GENE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POPULATION GENETICS; PRIORITY JOURNAL; REVIEW; RNA STRUCTURE; SEQUENCE ANALYSIS;

ANIMALS; ARTHROPODS; BASE SEQUENCE; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENETICS, POPULATION; GENOME; MITOCHONDRIA; PHYLOGENY;

ANIMALIA; ARTHROPODA;

EID: 33846016261     PISSN: 00311820     EISSN: 14698161     Source Type: Journal    
DOI: 10.1017/S0031182006001429     Document Type: Review

References (117)

1. Adler, P. H. (2005). Black flies, the Simuliidae. In Biology of Disease Vectors (ed. Marquardt, W. C.), pp. 127-140. Elsevier Academic Press, Boston.
2. Almeida, W. D. and Christoffersen, M. L. (1999). A cladistic approach to relationships in Pentastomida. Journal of Parasitology 85, 695-704.
3. Andersson, S. G., Zomorodipour, A., Andersson, J. O., Sicheritz-Ponten, T., Alsmark, U. C., Podowski, R. M., Naslund, A. K., Eriksson, A. S., Winkler, H. H. and Kurland, C. G. (1998). The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature, London 396, 133-140.
4. Aranishi, F. and Okimoto, T. (2005). Sequence polymorphism in a novel noncoding region of Pacific oyster mitochondrial DNA. Journal of Applied Genetics 46, 201-206.
5. Arnason, U., Adegoke, J. A., Bodin, K., Born, E. W., Esa, Y. B., Gullberg, A., Nilsson, M., Short, R. V., Xu, X. F. and Janke, A. (2002). Mammalian mitogenomic relationships and the root of the eutherian tree. Proceedings of the National Academy of Sciences, USA 99, 8151-8156.
6. Avise, J. C. (2004). Molecular Markers, Natural History, and Evolution, 2nd Edn. Sinauer Associates, Sunderland, Mass.
7. Azeredo-Espin, A. M. and Lessinger, A. C. (2006). Genetic approaches for studying myiasis-causing flies: molecular markers and mitochondrial genomics. Genetica 126, 111-131.
8. Bae, J. S., Kim, I., Sohn, H. D. and Jin, B. R. (2004). The mitochondrial genome of the firefly, Pyrocoelia rufa: complete DNA sequence, genome organization, and phylogenetic analysis with other insects. Molecular Phylogenetics and Evolution 32, 978-985.
9. Barker, S. C. and Murrell, A. (2004). Systematics and evolution of ticks with a list of valid genus and species names. Parasitology 129 (Suppl.), S15-S36.
10. Beard, C. B. (2005). Kissing bugs and bedbugs, the Hemiptera. In Biology of Disease Vectors (ed. Marquardt, W. C.), pp. 57-65. Elsevier Academic Press, Boston.
11. Beard, C. B., Hamm, D. M. and Collins, F. H. (1993). The mitochondrial genome of the mosquito Anopheles gambiae: DNA sequence, genome organization, and comparisons with mitochondrial sequences of other insects. Insect Molecular Biology 2, 103-124.
12. Beati, L. and Keirans, J. E. (2001). Analysis of the systematic relationships among ticks of the genera Rhipicephalus and Boophilus (Acari: Ixodidae) based on mitochondrial 12S ribosomal DNA gene sequences and morphological characters. Journal of Parasitology 87, 32-48.
13. Bergstrom, J. (1979). Morphology of fossil arthropods as a guide to phylogenetic relationships. In Arthropod Phylogeny (ed. Gupta, A. P.), pp. 3-56. Van Nostrand Reinhold, New York.
14. Black, W. C. and Kondratieff, B. C. (2005). Evolution of arthropod disease vectors. In Biology of Disease Vectors (ed. Marquardt, W. C.), pp. 9-23. Elsevier Academic Press, Boston.
15. Black, W. C. T. and Piesman, J. (1994). Phylogeny of hard- and soft-tick taxa (Acari: Ixodida) based on mitochondrial 16S rDNA sequences. Proceedings of the National Academy of Sciences, USA 91, 10034-10038.
16. Black, W. C. T. and Roehrdanz, R. L. (1998). Mitochondrial gene order is not conserved in arthropods: prostriate and metastriate tick mitochondrial genomes. Molecular Biology and Evolution 15, 1772-1785.
17. Boore, J. L. and Brown, W. M. (1998). Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Current Opinion in Genetics and Development 8, 668-674.
18. Boore, J. L. and Brown, W. M. (2000). Mitochondrial genomes of Galathealinum, Helobdella, and Platynereis: Sequence and gene arrangement comparisons indicate that Pogonophora is not a phylum and Annelida and Arthropoda are not sister taxa. Molecular Biology and Evolution 17, 87-106.
19. Boore, J. L. and Staton, J. L. (2002). The mitochondrial genome of the sipunculid Phascolopsis gouldii supports its association with Annelida rather than Mollusca. Molecular Biology and Evolution 19, 127-137.
20. Boore, J. L., Lavrov, D. V. and Brown, W. M. (1998). Gene translocation links insects and crustaceans. Nature, London 392, 667-668.
21. Borkent, A. (2005). The biting midges, the Ceratopogonidae (Diptera). In Biology of Disease Vectors (ed. Marquardt, W. C.), pp. 113-126. Elsevier Academic Press, Boston.
22. Brinkmann, H., Denk, A., Zitzler, J., Joss, J. J. and Meyer, A. (2004). Complete mitochondrial genome sequences of the South american and the Australian lungfish: testing of the phylogenetic performance of mitochondrial data sets for phylogenetic problems in tetrapod relationships. Journal of Molecular Evolution 59, 834-848.
23. Brown, W. M., George, M., Jr. and Wilson, A. C. (1979). Rapid evolution of animal mitochondrial DNA. Proceedings of the National Academy of Sciences, USA 76, 1967-1971.
24. Campbell, N. J. H. and Barker, S. C. (1998). An unprecedented major rearrangement in an arthropod mitochondrial genome. Molecular Biology and Evolution 15, 1786-1787.
25. Cockburn, A. F., Mitchell, S. E. and Seawright, J. A. (1990). Cloning of the mitochondrial genome of Anopheles quadrimaculatus. Archives of Insect Biochemistry and Physiology 14, 31-36.
26. Colless, D. H. and McAlpine, D. K. (1991). Diptera (Flies). In The Insects of Australia (ed. CSIRO), pp. 717-789. Melbourne University Press, Melbourne.
27. Covacin, C., Shao, R., Cameron, S. and Barker, S. C. (2006). Extraordinary number of gene rearrangements in the mitochondrial genomes of lice (Phthiraptera: Insecta). Insect Molecular Biology 15, 63-68.
28. Crozier, R. H. and Crozier, Y. C. (1993). The mitochondrial genome of the honeybee Apis mellifera: complete sequence and genome organization. Genetics 133, 97-117.
29. Davis, C. S., Delisle, I., Stirling, I., Siniff, D. B. and Strobeck, C. (2004). A phylogeny of the extant Phocidae inferred from complete mitochondrial DNA coding regions. Molecular Phylogenetics and Evolution 33, 363-377.
30. Dimauro, S. and Davidzon, G. (2005). Mitochondrial DNA and disease. Annals of Medicine 37, 222-232.
31. Dong, S. and Kumazawa, Y. (2005). Complete mitochondrial DNA sequences of six snakes: phylogenetic relationships and molecular evolution of genomic features. Journal of Molecular Evolution 61, 12-22.
32. Dotson, E. M. and Beard, C. B. (2001). Sequence and organization of the mitochondrial genome of the Chagas disease vector, Triatoma dimidiata. Insect Molecular Biology 10, 205-215.
33. Dowton, M., Castro, L. R. and Austin, A. D. (2002). Mitochondrial gene rearrangements as phylogenetic characters in the invertebrates: the examination of genome 'morphology'. Invertebrate Systematics 16, 345-356.
34. Drovetski, S. V. (2002). Molecular phylogeny of grouse: individual and combined performance of W-linked, autosomal, and mitochondrial loci. Systematic Biology 51, 930-945.
35. Dudaniec, R. Y. and Kleindorfer, S. (2006). Effects of the parasitic flies of the genus Philornis (Diptera: Muscidae) on birds. Emu 106, 13-20.
36. Durden, L. A. and Musser, G. G. (1994). The sucking lice (Insecta, Anoplura) of the world - a taxonomic checklist with records of mammalian hosts and geographical distributions. Bulletin of the American Museum of Natural History 218, 1-90.
37. Eldridge, B. F. (2005). Mosquitoes, the Culicidae. In Biology of Disease Vectors (ed. Marquardt, W. C.), pp. 95-111. Elsevier Academic Press, Boston.
38. Elmerot, C., Arnason, U., Gojobori, T. and Janke, A. (2002). The mitochondrial genome of the pufferfish, Fugu rubripes, and ordinal teleostean relationships. Gene 295, 163-172.
39. Evans, J. D. and Lopez, D. L. (2002). Complete mitochondrial DNA sequence of the important honey bee pest, Varroa destructor (Acari: Varroidae). Experimental and Applied Acarology 27, 69-78.
40. Flook, P. K., Rowell, C. H. and Gellissen, G. (1995). The sequence, organization, and evolution of the Locusta migratoria mitochondrial genome. Journal of Molecular Evolution 41, 928-941.
41. Goddard, J. M. and Wolstenholme, D. R. (1980). Origin and direction of replication in mitochondrial DNA molecules from the genus Drosophila. Nucleic Acids Research 8, 741-757.
42. Gray, M. W. (1989). Origin and evolution of mitochondrial DNA. Annual Review of Cell Biology 5, 25-50.
43. Gray, M. W., Burger, G. and Lang, B. F. (1999). Mitochondrial evolution. Science 283, 1476-1481.
44. Haring, E., Kruckenhauser, L., Gamauf, A., Riesing, M. J. and Pinsker, W. (2001). The complete sequence of the mitochondrial genome of Buteo buteo (Aves, Accipitridae) indicates an early split in the phylogeny of raptors. Molecular Biology and Evolution 18, 1892-1904.
45. Hassanin, A. (2006). Phylogeny of Arthropoda inferred from mitochondrial sequences: strategies for limiting the misleading effects of multiple changes in pattern and rates of substitution. Molecular Phylogenetics and Evolution 38, 100-116.
46. Holt, R. A., Subramanian, G. M., Halpern, A., Sutton, G. G., Charlab, R., Nusskern, D. R., Wincker, P., Clark, A. G., Ribeiro, J. M., Wides, R., Salzberg, S. L., Loftus, B., Yandell, M., Majoros, W. H., Rusch, D. B., Lai, Z., Kraft, C. L., Abril, J. F., Anthouard, V., Arensburger, P., Atkinson, P. W., Baden, H., De Berardinis, V., Baldwin, D., Benes, V., Biedler, J., Blass, C., Bolanos, R., Boscus, D., Barnstead, M., Cai, S., Center, A., Chaturverdi, K., Christophides, G. K., Chrystal, M. A., Clamp, M., Cravchik, A., Curwen, V., Dana, A., Delcher, A., Dew, I., Evans, C. A., Flanigan, M., Grundschober- Freimoser, A., Friedli, L., Gu, Z., Guan, P., Guigo, R., Hillenmeyer, M. E., Hladun, S. L., Hogan, J. R., Hong, Y. S., Hoover, J., Jaillon, O., Ke, Z., Kodira, C., Kokoza, E., Koutsos, A., Letunic, I., Levitsky, A., Liang, Y., Lin, J. J., Lobo, N. F., Lopez, J. R., Malek, J. A., McIntosh, T. C., Meister, S., Miller, J., Mobarry, C., Mongin, E., Murphy, S. D., O'brochta, D. A., Pfannkoch, C., Qi, R., Regier, M. A., Remington, K., Shao, H., Sharakhova, M. V., Sitter, C. D., Shetty, J., Smith, T. J., Strong, R., Sun, J., Thomasova, D., Ton, L. Q., Topalis, P., Tu, Z., Unger, M. F., Walenz, B., Wang, A., Wang, J., Wang, M., Wang, X., Woodford, K. J., Wortman, J. R., Wu, M., Yao, A., Zdobnov, E. M., Zhang, H., Zhao, Q., Zhao, S., Zhu, S. C., Zhimulev, I., Coluzzi, M., Della Torre, A., Roth, C. W., Louis, C., Kalush, F., Mural, R. J., Myers, E. W., Adams, M. D., Smith, H. O., Broder, S., Gardner, M. J., Fraser, C. M., Birney, E., Bork, P., Brey, P. T., Venter, J. C., Weissenbach, J., Kafatos, F. C., Collins, F. H. and Hoffman, S. L. (2002). The genome sequence of the malaria mosquito Anopheles gambiae. Science 298, 129-149.
47. Hu, M. and Gasser, R. B. (2006). Mitochondrial genomes of parasitic nematodes-progress and perspectives. Trends in Parasitology 22, 78-84.
48. Hu, M., Chilton, N. B., Abs El-Osta, Y. G. and Gasser, R. B. (2003). Comparative analysis of mitochondrial genome data for Necator americanus from two endemic regions reveals substantial genetic variation. International Journal for Parasitology 33, 955-963.
49. Ingman, M. and Gyllensten, U. (2003). Mitochondrial genome variation and evolutionary history of Australian and New Guinean aborigines. Genome Research 13, 1600-1606.
50. Ingman, M., Kaessmann, H., Paabo, S. and Gyllensten, U. (2000). Mitochondrial genome variation and the origin of modern humans. Nature, London 408, 708-713.
51. Janke, A., Erpenbeck, D., Nilsson, M. and Arnason, U. (2001). The mitochondrial genomes of the iguana (Iguana iguana) and the caiman (Caiman crocodylus): implications for amniote phylogeny. Proceedings of the Royal Society of London, B 268, 623-631.
52. Jordan, A. M. (1993). Tsetse flies (Glossinidae). In Medical Insects and Arachnids (ed. Lane, R. P. and Crosskey, R. W.), pp. 333-388. Chapman and Hall, London.
53. Junqueira, A. C. M., Lessinger, A. C., Torres, T. T., Da Silva, F. R., Vettore, A. L., Arruda, P. and Espin, A. M. L. A. (2004). The mitochondrial genome of the blowfly Chrysomya chloropyga (Diptera: Calliphoridae). Gene 339, 7-15.
54. Kittler, R., Kayser, M. and Stoneking, M. (2003). Molecular evolution of Pediculus humanus and the origin of clothing. Current Biology 13, 1414-1417.
55. Kumazawa, Y. and Nishida, M. (1993). Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. Journal of Molecular Evolution 37, 380-398.
56. Kumazawa, Y. and Nishida, M. (1995). Variations in mitochondrial tRNA gene organization of reptiles as phylogenetic markers. Molecular Biology and Evolution 12, 759-772.
57. Kumazawa, Y. and Nishida, M. (1999). Complete mitochondrial DNA sequences of the green turtle and blue-tailed mole skink: statistical evidence for archosaurian affinity of turtles. Molecular Biology and Evolution 16, 784-792.
58. Lang, B. F., Gray, M. W. and Burger, G. (1999). Mitochondrial genome evolution and the origin of eukaryotes. Annual Review of Genetics 33, 351-397.
59. Lavrov, D. V. and Brown, W. M. (2001). Trichinella spiralis mtDNA: a nematode mitochondrial genome that encodes a putative ATP8 and normally structured tRNAS and has a gene arrangement relatable to those of coelomate metazoans. Genetics 157, 621-637.
60. Lavrov, D. V., Brown, W. M. and Boore, J. L. (2004). Phylogenetic position of the Pentastomida and (pan)crustacean relationships. Proceedings of the Royal Society of London, B 271, 537-544.
61. Le, T. H., Blair, D. and McManus, D. P. (2002). Mitochondrial genomes of parasitic flatworms. Trends in Parasitology 18, 206-213.
62. Leo, N. P., Campbell, N. J., Yang, X., Mumcuoglu, K. and Barker, S. C. (2002). Evidence from mitochondrial DNA that head lice and body lice of humans (Phthiraptera: Pediculidae) are conspecific. Journal of Medical Entomology 39, 662-666.
63. Lessinger, A. C., Junqueira, A. C. M., Conte, F. F. and Espin, A. M. L. A. (2004). Analysis of a conserved duplicated tRNA gene in the mitochondrial genome of blowflies. Gene 339, 1-6.
64. Lessinger, A. C., Martins Junqueira, A. C., Lemos, T. A., Kemper, E. L., Da Silva, F. R., Vettore, A. L., Arruda, P. and Azeredo-Espin, A. M. (2000). The mitochondrial genome of the primary screwworm fly Cochliomyia hominivorax (Diptera: Calliphoridae). Insect Molecular Biology 9, 521-529.
65. Lewis, R. E. and Lewis, J. H. (1985). Notes on the geographical-distribution and host preferences in the order Siphonaptera. Part 7. New taxa described between 1972 and 1983, with a supraspecific classification of the order. Journal of Medical Entomology 22, 134-152.
66. Liu, Y. P., Wu, G. S., Yao, Y. G., Miao, Y. W., Luikart, G., Baig, M., Beja-Pereira, A., Ding, Z. L., Palanichamy, M. G. and Zhang, Y. P. (2006). Multiple maternal origins of chickens: out of the Asian jungles. Molecular Phylogenetics and Evolution 38, 12-19.
67. Macaulay, V., Hill, C., Achilli, A., Rengo, C., Clarke, D., Meehan, W., Blackburn, J., Semino, O., Scozzari, R., Cruciani, F., Taha, A., Shaari, N. K., Raja, J. M., Ismail, P., Zainuddin, Z., Goodwin, W., Bulbeck, D., Bandelt, H. J., Oppenheimer, S., Torroni, A. and Richards, M. (2005). Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science 308, 1034-1036.
68. Macey, J. R., Papenfuss, T. J., Kuehl, J. V., Fourcade, H. M. and Boore, J. L. (2004). Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences. Molecular Phylogenetics and Evolution 33, 22-31.
69. Macey, J. R., Schulte, J. A. and Larson, A. (2000). Evolution and phylogenetic information content of mitochondrial genomic structural features illustrated with acrodont lizards. Systematic Biology 49, 257-277.
70. Macey, J. R., Wang, Y. Z., Ananjeva, N. B., Larson, A. and Papenfuss, T. J. (1999). Vicariant patterns of fragmentation among gekkonid lizards of the genus Teratoscincus produced by the Indian collision: A molecular phylogenetic perspective and an area cladogram for Central Asia. Molecular Phylogenetics and Evolution 12, 320-332.
71. Mangold, A. J., Bargues, M. D. and Mas-Coma, S. (1998). Mitochondrial 16S rDNA sequences and phylogenetic relationships of species of Rhipicephalus and other tick genera among Metastriata (Acari: Ixodidae). Parasitology Research 84, 478-484.
72. Masta, S. E. and Boore, J. L. (2004). The complete mitochondrial genome sequence of the spider Habronattus oregonensis reveals rearranged and extremely truncated tRNAs. Molecular Biology and Evolution 21, 893-902.
73. May, R. M. (1990). How many species? Philosophical Transactions of the Royal Society of London, B 330, 293-304.
74. McCosker, P. J. (1979). Global aspects of the management and control of ticks of veterinary importance. In Recent Advances in Acarology (ed. Rodriguez, J.), pp. 45-53. Academic Press, New York.
75. McFadden, C. S., Tullis, I. D., Hutchinson, M. B., Winner, K. and Sohm, J. A. (2004). Variation in coding (NADH dehydrogenase subunits 2, 3, and 6) and noncoding intergenic spacer regions of the mitochondrial genome in Octocorallia (Cnidaria: Anthozoa). Marine Biotechnology 6, 516-526.
76. Mirabello, L. and Conn, J. E. (2006). Molecular population genetics of the malaria vector Anopheles darlingi in Central and South America. Heredity 96, 311-321.
77. Mitani, H., Talbert, A. and Fukunaga, M. (2004). New World relapsing fever Borrelia found in Ornithodoros porcinus ticks in central Tanzania. Microbiology and Immunology 48, 501-505.
78. Morrison, C. L., Harvey, A. W., Lavery, S., Tieu, K., Huang, Y. and Cunningham, C. W. (2002). Mitochondrial gene rearrangements confirm the parallel evolution of the crab-like form. Proceedings of the Royal Society of London, B 269, 345-350.
79. Mueller, R. L., Macey, J. R., Jaekel, M., Wake, D. B. and Boore, J. L. (2004). Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes. Proceedings of the National Academy of Sciences, USA 101, 13820-13825.
80. Munstermann, L. E. (2005). Phlebotomine sand flies, the Psychodidae. In Biology of Disease Vectors (ed. Marquardt, W. C.), pp. 141-151. Elsevier Academic Press, Boston.
81. Murrell, A., Campbell, N. J. and Barker, S. C. (1999). Mitochondrial 12S rDNA indicates that the Rhipicephalinae (Acari: Ixodida) is paraphyletic. Molecular Phylogenetics and Evolution 12, 83-86.
82. Mustafa, A., Rankaduwa, W. and Campbell, P. (2001). Estimating the cost of sea lice to salmon aquaculture in eastern Canada. Canadian Veterinary Journal 42, 54-56.
83. Nardi, F., Spinsanti, G., Boore, J. L., Carapelli, A., Dallai, R. and Frati, F. (2003). Hexapod origins: monophyletic or paraphyletic? Science 299, 1887-1889.
84. Nass, M. M. and Nass, S. (1962). Fibrous structures within the matrix of developing chick embryo mitochondria. Experimental Cell Research 26, 424-427.
85. Navajas, M., Le Conte, Y., Solignac, M., Cros-Arteil, S. and Cornuet, J. M. (2002). The complete sequence of the mitochondrial genome of the honeybee ectoparasite mite Varroa destructor (Acari: Mesostigmata). Molecular Biology and Evolution 19, 2313-2317.
86. Nikaido, M., Harada, M., Cao, Y., Hasegawa, M. and Okada, N. (2000). Monophyletic origin of the order Chiroptera and its phylogenetic position among mammalia, as inferred from the complete sequence of the mitochondrial DNA of a Japanese megabat, the Ryukyu flying fox (Pteropus dasymallus). Journal of Molecular Evolution 51, 318-328.
87. Norris, D. E., Klompen, J. S., Keirans, J. E. and Black, W. C. T. (1996). Population genetics of Ixodes scapularis (Acari: Ixodidae) based on mitochondrial 16S and 12S genes. Journal of Medical Entomology 33, 78-89.
88. Okimoto, R., Macfarlane, J. L., Clary, D. O. and Wolstenholme, D. R. (1992). The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum. Genetics 130, 471-498.
89. Philippe, H. and Laurent, J. (1998). How good are deep phylogenetic trees? Current Opinion in Genetics and Development 8, 616-623.
90. Philippe, H., Delsuc, F., Brinkmann, H. and Lartillot, N. (2005). Phylogenomics. Annual Review of Ecology, Evolution and Systematics 36, 541-562.
91. Price, R. D., Hellenthal, R. A., Palma, R. L., Johnson, K. P. and Clayton, D. H. (2003). The Chewing Lice: World Checklist and Biological Overview. Illinois Natural History Survey.
92. Rajkumar, R., Banerjee, J., Gunturi, H. B., Trivedi, R. and Kashyap, V. K. (2005). Phylogeny and antiquity of M macrohaplogroup inferred from complete mt DNA sequence of Indian specific lineages. BMC Evolutionary Biology 5, 26.
93. Rand, D. M., Haney, R. A. and Fry, A. J. (2004). Cytonuclear coevolution: the genomics of cooperation. Trends in Ecology and Evolution 19, 645-653.
94. Reed, D. L., Smith, V. S., Hammond, S. L., Rogers, A. R. and Clayton, D. H. (2004). Genetic analysis of lice supports direct contact between modern and archaic humans. PLoS Biology 2, e340.
95. Reyes, A., Gissi, C., Catzeflis, F., Nevo, E., Pesole, G. and Saccone, C. (2004). Congruent mammalian trees from mitochondrial and nuclear genes using Bayesian methods. Molecular Biology and Evolution 21, 397-403.
96. Rokas, A. and Holland, P. W. (2000). Rare genomic changes as a tool for phylogenetics. Trends in Ecology and Evolution 15, 454-459.
97. Ryckman, R. R., Bentley, D. G. and Archbold, E. F. (1981). The Cimicidae of the Americas and Oceanic islands, a checklist and bibliography. Bulletin of the Society of Vector Ecology 6, 93-142.
98. Saito, S., Tamura, K. and Aotsuka, T. (2005). Replication origin of mitochondrial DNA in insects. Genetics 171, 1695-1705.
99. San Mauro, D., Garcia-Paris, M. and Zardoya, R. (2004). Phylogenetic relationships of discoglossid frogs (Amphibia : Anura : Discoglossidae) based on complete mitochondrial genomes and nuclear genes. Gene 343, 357-366.
100. Scouras, A., Beckenbach, K., Arndt, A. and Smith, M. J. (2004). Complete mitochondrial genome DNA sequence for two ophiuroids and a holothuroid: the utility of protein gene sequence and gene maps in the analyses of deep deuterostome phylogeny. Molecular Phylogenetics and Evolution 31, 50-65.
101. Shao, R. and Barker, S. C. (2003). The highly rearranged mitochondrial genome of the plague thrips, Thrips imaginis (Insecta: Thysanoptera): convergence of two novel gene boundaries and an extraordinary arrangement of rRNA genes. Molecular Biology and Evolution 20, 362-370.
102. Shao, R., Aoki, Y., Mitani, H., Tabuchi, N., Barker, S. C. and Fukunaga, M. (2004). The mitochondrial genomes of soft ticks have an arrangement of genes that has remained unchanged for over 400 million years. Insect Molecular Biology 13, 219-224.
103. Shao, R., Barker, S. C., Mitani, H., Aoki, Y. and Fukunaga, M. (2005a). Evolution of duplicate control regions in the mitochondrial genomes of Metazoa: a case study with Australasian Ixodes ticks. Molecular Biology and Evolution 22, 620-629.
104. Shao, R., Barker, S. C., Mitani, H., Takahashi, M. and Fukunaga, M. (2006). Molecular mechanisms for the variation of mitochondrial gene content and gene arrangement among chigger mites of the genus Leptotrombidium (Acari: Acariformes). Journal of Molecular Evolution 63, 251-261.
105. Shao, R., Campbell, N. J. H. and Barker, S. C. (2001). Numerous gene rearrangements in the mitochondrial genome of the wallaby louse, Heterodoxus macropus (Phthiraptera). Molecular Biology and Evolution 18, 858-865.
106. Shao, R., Mitani, H., Barker, S. C., Takahashi, M. and Fukunaga, M. (2005b). Novel mitochondrial gene content and gene arrangement indicate illegitimate inter-mtDNA recombination in the chigger mite, Leptotrombidium pallidum. Journal of Molecular Evolution 60, 764-773.
107. Skerratt, L. F., Campbell, N. J., Murrell, A., Walton, S., Kemp, D. and Barker, S. C. (2002). The mitochondrial 12S gene is a suitable marker of populations of Sarcoptes scabiei from wombats, dogs and humans in Australia. Parasitology Research 88, 376-379.
108. Sprinzl, M., Hartmann, T., Weber, J., Blank, J. and Zeidler, R. (1989). Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Research 17 (Suppl.), 1-172.
109. Staton, J. L., Daehler, L. L. and Brown, W. M. (1997). Mitochondrial gene arrangement of the horseshoe crab Limulus polyphemus L: Conservation of major features among arthropod classes. Molecular Biology and Evolution 14, 867-874.
110. Taanman, J. W. (1999). The mitochondrial genome: structure, transcription, translation and replication. Biochimica et Biophysica Acta 1410, 103-123.
111. Taylor, S. W., Fahy, E. and Ghosh, S. S. (2003). Global organellar proteomics. Trends in Biotechnology 21, 82-88.
112. Thangaraj, K., Chaubey, G., Kivisild, T., Reddy, A. G., Singh, V. K., Rasalkar, A. A. and Singh, L. (2005). Reconstructing the origin of Andaman Islanders. Science 308, 996.
113. Thao, M. L., Baumann, L. and Baumann, P. (2004). Organization of the mitochondrial genomes of whiteflies, aphids, and psyllids (Hemiptera, Sternorrhyncha). BMC Evolutionary Biology 4, 25.
114. Tjensvoll, K., Hodneland, K., Nilsen, F. and Nylund, A. (2005). Genetic characterization of the mitochondrial DNA from Lepeophtheirus salmonis (Crustacea; Copepoda). A new gene organization revealed. Gene 353, 218-230.
115. Wallace, D. C. (2002). Animal models for mitochondrial disease. Methods in Molecular Biology 197, 3-54.
116. Wolstenholme, D. R. (1992). Animal mitochondrial DNA: structure and evolution. International Review of Cytology 141, 173-216.
117. Yamazaki, N., Ueshima, R., Terrett, J. A., Yokobori, S., Kaifu, M., Segawa, R., Kobayashi, T., Numachi, K., Ueda, T., Nishikawa, K., Watanabe, K. and Thomas, R. H. (1997). Evolution of pulmonate gastropod mitochondrial genomes: Comparisons of gene organizations of Euhadra, Cepaea and Albinaria and implications of unusual tRNA secondary structures. Genetics 145, 749-758.