The strict orthology of mitochondrial (mt) coding sequences has promoted their use in phylogenetic analyses at different levels. Here we present the results of a mitogenomic study (i.e., analysis based on the set of protein-coding genes from complete mt genomes) of 60 mammalian species. This number includes 11 new mt genomes. The sampling comprises all but one of the traditional eutherian orders. The previously unrepresented order Dermoptera (flying lemurs) fell within Primates as the sister group of Anthropoidea, making Primates paraphyletic. This relationship was strongly supported. Lipotyphla (''insectivores'') split into three distinct lineages: Erinaceomorpha, Tenrecomorpha, and Soricomorpha. Erinaceomorpha was the basal eutherian lineage. Sirenia (dugong) and Macroscelidea (elephant shrew) fell within the African clade. Pholidota (pangolin) joined the Cetferungulata as the sister group of Carnivora. The analyses identified monophyletic Pinnipedia with Otariidae (sea lions, fur seals) and Odobenidae (walruses) as sister groups to the exclusion of Phocidae (true seals).Dermosimii ͉ Eutheria ͉ Mammalia ͉ phylogeny ͉ primate paraphyly M itogenomic (mtg) phylogenetics has contributed considerably to resolving evolutionary relationships among mammals. However, relatively few genomes have been sequenced for some orders and others are still unrepresented. The first eutherian mtg study (1) included five orders: Rodentia, Primates, Artiodactyla, Cetacea, and Carnivora. This study identified a sister group relationship between Artiodactyla and Cetacea and close affinities between these two orders and Carnivora. Because of the absence of an unequivocal outgroup (OG), the relationships relative to Primates and Rodentia could not be resolved, however. The first mtg rooting of the eutherian tree (2), using a marsupial as OG, reconstructed the relationship OG(Rodentia,(Primates,(Carnivora,(Artiodactyla,Cetacea)))), a topology that has been generally identified in subsequent mtg analyses. These two studies also showed that individual mitochondrial (mt) genes did not obligatorily reconstruct the same topology, underlining the necessity of using the concatenated sequences of different genes for maximizing the reliability of the analyses.Most taxonomic schemes recognize 18 orders of extant eutherians (Table 1). It is likely, however, that this number is an underestimate because most molecular studies, both mtg (3, 4) and mt͞nuclear (5-7), split Lipotyphla into separate lineages. Similarly, if Rodentia is nonmonophyletic (8-11), the number of eutherian orders may be still greater than suggested by only lipotyphlan polyphyly.Five eutherian orders are previously not represented by complete mtDNAs. To further complete the picture of eutherian mtg relationships we have added 11 complete mtDNAs to the eutherian data set, including four of these orders: Pholidota, Dermoptera, Sirenia, and Macroscelidea.The phylogenetic position of Pholidota has been a matter of debate. A sister group relationship between Xenarthra and Pholidota in a...
