Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 103 (26), 9929-34

Pegasoferae, an Unexpected Mammalian Clade Revealed by Tracking Ancient Retroposon Insertions


Pegasoferae, an Unexpected Mammalian Clade Revealed by Tracking Ancient Retroposon Insertions

Hidenori Nishihara et al. Proc Natl Acad Sci U S A.


Despite the recent large-scale efforts dedicated to comprehensive phylogenetic analyses using mitochondrial and nuclear DNA sequences, several relationships among mammalian orders remain controversial. Here, we present an extensive application of retroposon (L1) insertion analysis to the phylogenetic relationships among almost all mammalian orders. In addition to demonstrating the validity of Glires, Euarchontoglires, Laurasiatheria, and Boreoeutheria, we demonstrate an interordinal clade that links Chiroptera, Carnivora, and Perissodactyla within Laurasiatheria. Re-examination of a large DNA sequence data set yielded results consistent with our conclusion. We propose a superordinal name "Pegasoferae" for this clade of Chiroptera + Perissodactyla + Carnivora + Pholidota. The presence of a single incongruent L1 locus generates a tree in which the group of Carnivora + Perissodactyla associates with Cetartiodactyla but not with Chiroptera. This result suggests that incomplete lineage sorting of an ancestral dimorphism occurred with regard to the presence or absence of retroposon alleles in a common ancestor of Scrotifera (Pegasoferae + Cetartiodactyla), which was followed by rapid divergence into the extant orders over an evolutionarily short period. Accordingly, Euungulata (Cetartiodactyla + Perissodactyla) and Fereuungulata (Carnivora + Pholidota + Perissodactyla + Cetartiodactyla) cannot be validated as natural groups. The interordinal mammalian relationships presented here provide a cornerstone for future studies in the reconstruction of mammalian classifications, including extinct species, on evolution of large genomic sequences and structure, and in developmental analysis of morphological diversification.

Conflict of interest statement

Conflict of interest statement: No conflicts declared.


Fig. 1.
Fig. 1.
The in silico screening of genomic data for L1 sequences in introns performed in this study by using the databases available from University of California Santa Cruz Genome Bioinformatics ( The number of L1 insertions found and the number of loci used in interexonic PCR are shown for each species. The L1MA and L1MB are L1 subfamilies used for insertion comparison in this study. hg16, mm4, canFam1, and bosTau1 denote the database versions of human, mouse, dog, and cow, respectively.
Fig. 2.
Fig. 2.
An interordinal mammalian phylogeny reconstructed by our retroposon insertion analysis. Downward arrows denote insertions of retroposons into each lineage. Locus INT283, denoted by a dashed arrow, supports the monophyly of Cetartiodactyla, Perissodactyla, and Carnivora. The loci surrounded by dashed lines in Afrotheria were identified in our previous study (22). Asterisks below the branches denote that the monophylies are statistically significant (∗, P < 0.05; ∗∗, P < 0.01; ∗∗∗, P < 0.001).
Fig. 3.
Fig. 3.
An example of INT391 locus suggesting Pegasoferae clade. (A) An electrophoretic profile of PCR products of locus INT391, in which L1 is present in horse, cat, and bat, but not other mammals. The larger size of the mouse PCR product is caused by species-specific insertions of another retrotransposon (database position chr19:55196706–55197619 in mm7). M, size markers (øX174/HincII digest). (B) An alignment of locus INT391 sequences. Thick and thin lines denote the L1 and the direct repeat sequences, respectively, that were generated during integration. The central region of the inserted L1 sequence is omitted.

Similar articles

See all similar articles

Cited by 71 PubMed Central articles

See all "Cited by" articles

Publication types

Associated data

LinkOut - more resources