Hypothetical scenarios of interspersed ancestry of placentals. (A) Hybridization/introgression scenario: Initially, the three placental lineages diverged and separated from an Eomaia-like (Eomaia scansoria) common ancestor. Alternate gene flow between the lineages led to a mosaic pattern of relationships among the current species. The sequence of genetic flow leading to significant support for Exafroplacentalia, Epitheria, and Atlantogenata was chosen randomly and not meant to indicate a specific time course. The lineages leading to Boreotheria, Afrotheria, and Xenarthra are shown in red, green, and blue, respectively. Gray circles represent diagnostic retroposon insertions for Exafroplacentalia, orange circles for Epitheria, and black circles for Atlantogenata. (B) Geographic transitions at the time of separation of the three lineages during the Cretaceous. (Left terrestrial globe) Possible overlapping geographical distribution of the three placental lineages before continental drift, the expected period of genetic flow between the lineages; (right terrestrial globe) separation of the continents and divergence of placental lineages possibly prohibiting further gene flow (Murphy et al. 2001b; Wildman et al. 2007). Roman numerals indicate exchanges of genetic material between the species shown in A. (C) Randomly sorted ancestral alleles: Fixation of retroposon alleles was not completed in the ancestral population before the separation of lineages. After the proliferation of inserted retroposon alleles, the distributions to different lineages occurred randomly (broken lines). After fixation of the alleles in the terminal lineages, a mosaic pattern of relatedness remains. (I) Five orthologous markers represent Exafroplacentalia, (II) 9 markers (plus an additional marker previously described in Kriegs et al. 2006 that was undetected here) represent Epitheria, and (III) 8 markers represent Atlantogenata. Open circles represent alleles without retroelements.
