(A) Genomic PCR fragments. The L1MB3 element is present in all boreotherian species. The element is located between exon 20 and 21 of the human AP4E1 gene on human Chromosome 15 (q21.2). Small-size variations are due to random indels. The larger fragment for human is due to an additional insertion of an Alu Sx element. Smaller fragments in afrotherians and xenarthrans indicate the absence situation prior to insertion of the element (plesiomorph condition).
(B) A schematic representation of the presence/absence loci of various taxa after sequence determination. Direct repeats and the unoccupied target sites are shaded gray.
(C) A phylogenetic interpretation of the presence/absence pattern. The L1MB3 element is present (+) in representatives of boreotherians and absent (−) in afrotherians and xenarthrans. The ball indicates the integration time of the L1MB3 element prior to the common ancestor of all recent boreotherians, but after this lineage separated from other placentals. The relative time of this integration is represented by node 3 in Figure 2; ten other integrations confirm the boreotherian hypothesis.
(D) Genomic PCR fragments. The L1MB5 element, in addition to its presence in all boreotherian species is also found in the afrotherian species. The smaller fragments in xenarthrans indicate its absence in these species. Its integration site corresponds to the human locus on Chromosome 15 (q23).
(E) A schematic representation of the presence/absence loci of various taxa after sequence determination. Direct repeats and the unoccupied target sites are shaded gray.
(F) The L1MB5 element is present (+) in representatives of boreotherians and afrotherians, grouping them in the clade Epitheria, and is absent (−) in xenarthrans. The ball indicates the integration time of the L1MB5 element prior to the common ancestor of all Epitheria, but after this lineage separated from other placentals. This integration time is the same as node 2 in Figure 2, and we have so far recovered one additional retroposon integration to support the Epitheria hypothesis.
DR, direct repeats.