Reasonably correct phylogenies are fundamental to the testing of evolutionary hypotheses. Here, we present phylogenetic findings based on analyses of 67 complete mammalian mitochondrial (mt) genomes. The analyses, irrespective of whether they were performed at the amino acid (aa) level or on nucleotides (nt) of first and second codon positions, placed Erinaceomorpha (hedgehogs and their kin) as the sister group of remaining eutherians. Thus, the analyses separated Erinaceomorpha from other traditional lipotyphlans (e.g., tenrecs, moles, and shrews), making traditional Lipotyphla polyphyletic. Both the aa and nt data sets identified the two order-rich eutherian clades, the Cetferungulata (comprising Pholidota, Carnivora, Perissodactyla, Artiodactyla, and Cetacea) and the African clade (Tenrecomorpha, Macroscelidea, Tubulidentata, Hyracoidea, Proboscidea, and Sirenia). The study corroborated recent findings that have identified a sister-group relationship between Anthropoidea and Dermoptera (flying lemurs), thereby making our own order, Primates, a paraphyletic assembly. Molecular estimates using paleontologically well-established calibration points, placed the origin of most eutherian orders in Cretaceous times, 70–100 million years before present (MYBP). The same estimates place all primate divergences much earlier than traditionally believed. For example, the divergence between Homo and Pan is estimated to have taken place ≈10 MYBP, a dating consistent with recent findings in primate paleontology.   

1.
Adachi J, Hasegawa, M: Improved dating of the human-chimpanzee separation in the mitochondrial DNA tree: heterogeneity among amino acid sites. J molec Evol 40:622–628 (1995).
2.
Adachi J, Hasegawa M: MOLPHY, version 2.3: programs for molecular phylogenetics based on maximum likelihood. Comp Sci Monogr 28:1 (Institute of Statistical Mathematics, Tokyo 1996).
3.
Anderson S, Bankier AT, Barrell BG, de Bruijn MHL, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJH, Staden R, Young IG: Sequence and organization of the human mitochondrial genome. Nature 290:457–465 (1981).
4.
Anderson S, de Bruijn MH, Coulson AR, Eperon IC, Sanger F, Young IG: Complete sequencer of bovine mitochondrial DNA: conserved features of the mammalian mitochondrial genome. J molec Biol 156:683–717 (1982).
5.
Archibald JD: Fossil evidence for a late Cretaceous origin of “hoofed” mammals. Science 272:1150–1153 (1996).
6.
Archibald JD, Averianov AO, Ekdale EG: Late Cretaceous relatives of rabbits, rodents, and other extant eutherian mammals. Nature 414:62–65 (2001).
7.
Arnason U: The karyotype of the grey seal (Halichoerus grypus). Hereditas 64:237–242 (1970).
8.
Arnason U: The role of chromosomal rearrangement in mammalian speciation with special reference to Cetacea and Pinnipedia. Hereditas 70:113–118 (1972).
9.
Arnason U: Comparative chromosome studies in Cetacea. Hereditas 77:1–36 (1974a).
10.
Arnason U: Comparative chromosome studies in Pinnipedia. Hereditas 76:179–226 (1974b).
11.
Arnason U: The relationship between the four principal pinniped karyotypes. Hereditas 87:227–242 (1977).
12.
Arnason U, Adegoke JA, Bodin K, Born EW, Esa YB, Gullberg A, Nilsson M, Short RV, Xu X, Janke A: Mammalian mitogenomic relationships and the root of the eutherian tree. Proc natl Acad Sci, USA 99:8151–8156 (2002).
13.
Arnason U, Gullberg A: Comparison between the complete mtDNA sequences of the blue and the fin whale, two species that can hybridize in nature. J molec Evol 37:312–322 (1993).
14.
Arnason U, Gullberg A: Cytochrome b nucleotide sequences and the identification of five primary lineages of extant cetaceans. Mol Biol Evol 13:407–417 (1996).
15.
Arnason U, Gullberg A, Gretarsdottir S, Ursing B, Janke A: The complete mitochondrial genome of the sperm whale and the establishment of a new molecular reference for estimating eutherian divergence dates. J molec Evol 50:569–578 (2000a).
16.
Arnason U, Gullberg A, Janke A: Molecular timing of primate divergences as estimated by two non-primate calibration points. J molec Evol 47:718–727 (1998).
17.
Arnason U, Gullberg A, Janke A: The mitochondrial DNA molecule of the aardvark, Orycteropus afer, and the position of the Tubulidentata in the eutherian tree. Proc R Soc Lond B 266:339–345 (1999).
18.
Arnason U, Gullberg A, Janke A, Xu, X: Pattern and timing of evolutionary divergences among hominoids based on analyses of complete mtDNAs. J molec Evol 43:650–661 (1996a).
19.
Arnason U, Gullberg A, Schweizer Burguete A, Janke A: Molecular estimates for primate dispersal and the origin of modern humans. Hereditas 133:217–228 (2000b).
20.
Arnason U, Gullberg A, Widegren B: The complete nucleotide sequence of the mitochondrial DNA of the fin whale, Balaenoptera physalus. J molec Evol 33:556–568 (1991).
21.
Arnason U, Johnsson E: The complete mitochondrial DNA sequence of the harbor seal, Phoca vitulina. J molec Evol 34:493–505 (1992).
22.
Arnason U, Widegren B: Pinniped phylogeny enlightened by molecular hybridizations using highly repetitive DNA. Mol Biol Evol 3:356–365 (1986).
23.
Arnason U, Xu X, Gullberg A: Comparison between the complete mitochondrial DNA sequences of human and the common chimpanzee. J molec Evol 42:145–152 (1996b).
24.
Barroso CML, Schneider H, Schneider MPC, Sampaio I, Harada ML, Czelusniak J, Goodman M: Update on the phylogenetic systematics of New World monkeys: further DNA evidence for placing the pygmy marmoset (Cebuella) within the genus Callithrix. Int J Primatol 18:651–674 (1997).
25.
Beard KC: Phylogenetic systematics of the Primatomorpha, with special reference to Dermoptera, in Szalay FS, Novacek MJ, McKenna MC (eds): Mammal Phylogeny, Vol 2: Placentals, pp 129–150 (Springer-Verlag, Berlin/Heidelberg/New York 1993).
26.
Benton MJ: Early origins of modern birds and mammals: molecules vs. morphology. BioEssays 21:1043–1051 (1999).
27.
Bibb MJ, Van Etten RA, Wright CT, Walberg MW, Clayton DA: Sequence and gene organization of mouse mitochondrial DNA. Cell 26:167–180 (1981).
28.
Butler PM: Phylogeny of the insectivores, in Benton MJ (ed): The Phylogeny and Classification of the Tetrapods, Vol. 2: Mammals, pp 117–141 (Clarendon Press, Oxford 1988).
29.
Cifelli RL: Early Cretaceous mammal from North America and the evolution of marsupial dental characters. Proc natl Acad Sci, USA. 90:9413–9416 (1993).
30.
D’Erchia AM, Gissi C, Pesole G, Saccone C, Arnason U: The guinea pig is not a rodent. Nature 381:597–600 (1996).
31.
Eisenberg JF: The Mammalian Radiations (University of Chicago Press, Chicago 1981).
32.
Gadaleta G, Pepe G, De Candia G, Quagliariello C, Sbisa E, Saccone C: The complete nucleotide sequence of the Rattus norvegicus mitochondrial genome: cryptic signals revealed by comparative analysis between vertebrates. J molec Evol 28:497–516 (1989).
33.
Gagneux P, Wills C, Gerloff U, Tautz D, Morin PA, Boesch C, Fruth B, Hohmann G, Ryder OA, Woodruff DS: Mitochondrial sequences show diverse evolutionary histories of African hominoids. Proc natl Acad Sci, USA 96:5077–5082 (1999).
34.
Gatesy J, O’Leary MA: Deciphering whale origins with molecules and fossils. Trends Ecol Evol 16:562–570 (2001).
35.
Gibbons A: In search of the first hominids. Science 295:1214–1219 (2002).
36.
Gingerich PD, ul Haq M, Zalmout IS, Kahn IH, Malkani MS: Origin of whales from early artiodactyls: hands and feet of Eocene Protocetidae from Pakistan. Science 293:2239–2242 (2001).
37.
Godinot M, Mahboubi M: Earliest known simian primate found in Algeria. Nature 357:324–326 (1992).
38.
Goodman M: Epilogue: a personal account of the origins of a new paradigm. Mol Phylogenet Evol 5:269–285 (1996).
39.
Goodman M, Porter CA, Czelusniak J, Page SL, Schneider H, Shoshani J, Gunnell G, Groves CP: Toward a phylogenetic classification of primates based on DNA evidence complemented by fossil evidence. Mol Phylogenet Evol 9:585–598 (1998).
40.
Graur D, Hide AH, Li WH: Is the guinea-pig a rodent? Nature 351:649–652 (1991).
41.
Haile-Selassie Y: Late Miocene hominids from the Middle Awash, Ethiopia. Nature 412:178–181 (2001).
42.
Hammer MF, Karafet T, Rasanayagam A, Wood, ET, Altheide TK, Jenkins T, Griffiths RC, Templeton AR, Zegura SL: Out of Africa and back again: nested cladistic analysis of human Y chromosome variation. Mol Biol Evol 15:427–441 (1998).
43.
Hiendleder S, Lewalski H, Wassmuth R, Janke A: The complete mitochondrial DNA sequence of the domestic sheep (Ovis aries) and comparison with the other major ovine haplotype. J molec Evol 47:441–448 (1998).
44.
Ingman M, Kaessmann H, Pääbo S, Gyllensten U: Mitochondrial genome variation and the origin of modern humans. Nature 408:708–713 (2000).
45.
Irwin DM, Arnason U: Cytochrome b gene of marine mammals: phylogeny and evolution. Mammal Evol 2:37–55 (1994).
46.
Janke A, Feldmaier-Fuchs G, Thomas WK, von Haeseler A, Pääbo S: The marsupial mitochondrial genome and the evolution of placental mammals. Genetics 137:243–256 (1994).
47.
Kaessmann H, Wiebe V, Weiss G, Pääbo S: Great ape DNA sequences reveal a reduced diversity and an expansion in humans. Nature Genet 27:155–156 (2001).
48.
Kielan-Jaworowska Z, Dashzeveg D: Eutherian mammals from the Early Cretaceous of Mongolia. Zool Scripta 18:347–355 (1989).
49.
Krettek A, Gullberg A, Arnason U: Sequence analysis of the complete mitochondrial DNA molecule of the hedgehog, Erinaceus europaeus, and the phylogenetic position of the Lipotyphla. J molec Evol 41:952–957 (1995).
50.
Ledje C, Arnason U: Phylogenetic analyses of complete cytochrome b sequences of the order Carnivora with particular emphasis on the Caniformia. J molec Evol 42:135–144 (1996a).
51.
Ledje C, Arnason U: Phylogenetic relationships within caniform carnivores based on the analyses of the mitochondrial 12S rRNA gene. J molec Evol 43:641–649 (1996b).
52.
Le Gros Clark WE, Sonntag CF: A monograph of Orycteropus afer. Proc zool Soc 30:445–485 (1926).
53.
Madsen O, Scally M, Douady CJ, Kao DJ, DeBry RW, Adkins R, Amrine HM, Stanhope MJ, de Jong WW, Springer MS: Parallel adaptive radiations in two major clades of placental mammals. Nature 409:610–614 (2001).
54.
McKenna MC, Bell SK: Classification of Mammals Above the Species Level (Columbia University Press, New York 1997).
55.
Montgelard C, Catzeflis FM, Douzery E: Phylogenetic relationships of artiodactyls and cetaceans as deduced from the comparison of cytochrome b and 12S rRNA mitochondrial sequences. Mol Biol Evol 14:550–559 (1997).
56.
Mouchaty SK, Catzeflis F, Janke A, Arnason U: Molecular evidence of an African Phiomorpha–South American Caviomorpha clade and support for Hystricognathi based on the complete mitochondrial genome of the cane rat (Thryonomys swinderianus). Mol Phylogenet Evol 18:127–135 (2001).
57.
Mouchaty SK, Gullberg A, Janke A, Arnason U: Phylogenetic position of the tenrecs (Mammalia: Tenrecidae) of Madagascar based on analysis of the complete mitochondrial genome sequence of Echinops telfairi. Zool Scr 29:307–317 (2000a).
58.
Mouchaty SK, Gullberg A, Janke A, Arnason U: The phylogenetic position of the Talpidae within eutheria based on analysis of complete mitochondrial sequences. Mol Biol Evol 17:60–67 (2000b).
59.
Muizon, C de: Rev. Téc. Yaciminetos petroliferos fiscales bolivianos 12:575 (as cited by Archibald, 1996).
60.
Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryder OA, O’Brien SJ: Molecular phylogenetics and the origins of placental mammals. Nature 409:614–618 (2001a).
61.
Murphy WJ, Eizirik E, O’Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, Springer MS: Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294:2348–2351 (2001b).
62.
Nessov LA: Novyye mlyekopitayushchiye myela Kyzylkumov [New mammals from the Cretaceous of the Kyzylkum Desert]. Vyestn Lening Univ Ser 7 17:8–18 (1985).
63.
Novacek MJ: Mammalian phylogeny: shaking the tree. Nature 356:121–125 (1992).
64.
Pickford M, Senut B: The geological and faunal context of the Late Miocene hominid remains from Lukeino, Kenya. C R Acad Sci, Paris 332:145–152 (2001).
65.
Reyes A, Pesole G, Saccone C: Long-branch attraction phenomenon and the impact of among-site rate variation on rodent phylogeny. Gene 259:177–187 (2000).
66.
Reyment R, Dingle RV: Palaeogeography of Africa during the Cretaceous period. Palaeogeogr Palaeoclimat Palaeoecol 59:93–116 (1987).
67.
Rosenberg MS, Kumar S: Incomplete taxon sampling is not a problem for phylogenetic inference. Proc natl Acad Sci, USA 98:10751–10756 (2001).
68.
Sarich VM: Primate systematics with special reference to Old World monkeys, in Napier JR, Napier PH (eds): Old World Monkeys: Evolution, Systematics and Behaviour, pp 175–266 (Academic Press, New York 1970).
69.
Sarich VM: Mammalian systematics: twenty-five years among their albumins and transferrins, in Szalay FS, Novacek MJ, McKenna MC (eds): Mammal Phylogeny, Vol 2: Placentals, pp 103–114 (Springer-Verlag, Berlin/Heidelberg/New York 1993).
70.
Sarich VM, Wilson AC: Immunological time scale for human evolution. Science 158:1200–1203 (1967).
71.
Sclater JG, Hellinger S, Tapscott C: The paleobathymetry of the Atlantic Ocean from the Jurassic to the present. J Geol 85:509–552 (1977).
72.
Senut B, Pickford M, Gommery D, Mein P, Cheboi K, Coppens Y: First hominid from the Miocene (Lukeino Formation, Kenya). C R Acad Sci, Paris 332:137–144 (2001).
73.
Sibley CG, Ahlquist JE: DNA hybridization evidence of hominoid phylogeny: results from an expanded data set. J molec Evol 26:99–121 (1987).
74.
Stanhope MJ, Waddell VG, Madsen O, de Jong W, Hedges SB, Cleven GC, Kao D, Springer MS: Molecular evidence for multiple origins of Insectivora and for a new order of endemic African insectivore mammals. Proc natl Acad Sci, USA 95:9967–9972 (1998).
75.
Stauffer RL, Walker A, Ryder OA, Lyons-Weiler M, Hedges SB: Human and ape molecular clocks and constraints on paleontological hypotheses. J Hered 92:469–474 ( 2001).
76.
Stewart C-B, Disotell TR: Primate evolution—in and out of Africa. Curr Biol 8:582–588 (1998).
77.
Tavaré S, Marshall CR, Will O, Soligo C, Martin RD: Using the fossil record to estimate the age of the last common ancestor of extant primates. Nature 416:726–729 (2002).
78.
Templeton AR: The “Eve” hypothesis: a genetic critique and reanalysis. Am Anthropol 95:51–72 (1993).
79.
Templeton AR: Out of Africa again and again. Nature 416:45–51 (2002).
80.
Thewissen JGM, Williams EM, Roe LJ, Hussain ST: Skeletons of terrestrial cetaceans and the relationship of whales to artiodactyls. Nature 413:277–281 (2001).
81.
Ursing BM, Arnason U: Analyses of mitochondrial genomes strongly support a hippopotamus-whale clade. Proc R Soc Lond B 265:2251–2255 (1998).
82.
Vigilant L, Stoneking M, Harpending H, Hawkes K, Wilson AC: African populations and the evolution of human mitochondrial-DNA. Science 253:1503–1507 (1991).
83.
Wyss AR, Flynn J: A phylogenetic analysis and definition of the Carnivora, in Szalay FS, Novacek MJ, McKenna MC (eds): Mammal Phylogeny, Vol 2: Placentals, pp 32–52 (Springer-Verlag, Berlin/Heidelberg/New York 1993).
84.
Xu X, Arnason U: The complete mitochondrial DNA sequence of the horse, Equus caballus: extensive heteroplasmy of the control region. Gene 148:357–362 (1994).
85.
Xu X, Arnason U: The complete mitochondrial DNA sequence of the white rhinoceros, Ceratotherium simum, and comparison with the mtDNA sequence of the Indian rhinoceros, Rhinoceros unicornis. Mol Phylogenet Evol 7:189–194 (1997).
86.
Xu X, Gullberg A, Arnason U: The complete mitochondrial DNA (mtDNA) of the donkey and mtDNA comparisons among four closely related mammalian species-pairs. J molec Evol 43:438–446 (1996a).
87.
Xu X, Janke A, Arnason U: The complete mitochondrial DNA sequence of the greater Indian rhinoceros, Rhinoceros unicornis, and the phylogenetic relationship among Carnivora, Perissodactyla, and Artiodactyla (+ Cetacea). Mol Biol Evol 13:1167–1173 (1996b).
88.
Yoder AD, Yang ZH: Estimation of primate speciation dates using local molecular clocks. Mol Biol Evol 17:1081–1090 (2000).
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