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Table 1 Gene flow detected by the DFOIL analyses that is based on a five taxon analysis.Full size tablePhyloNet32 has been developed to detect hybridization events in genomic data while accounting for ILS. We applied the ML approach implemented in PhyloNet32 to detect hybridization among bear species. Due to computational constraints we sampled 4,000 ML trees from putatively independent GFs using one individual representing per species. The ABC island brown bear was chosen as another representative for brown bears and positive control, because its population hybridized with polar bears7,8,28. The outgroup, the spectacled bears were removed to reduce the computational complexity and, because previous analyses using D-statistics and DFOIL did not detect gene flow between tremarctine and ursine bears. The complex phylogeny requires exceptional computational time so we analyzed only networks with up to two reticulations. The resulting PhyloNet network with the highest likelihood (Supplementary Fig. 15) shows reticulations between ABC island brown bear and polar bears, and also between the Asiatic black bear and the ancestral branch to American black, brown and polar bears. It is noteworthy, that the second reticulation has a high inheritance probability (41.8%), which agrees with the strongest gene flow signal identified by DFOIL analyses (Fig. 4, Table 1). Due to computational limits so far only two reticulations that represent the strongest hybridization signals were identified. For three and more reticulations the network-space becomes extremely large.

Cat If You See Me With A Seam Ripper Now Is Not The Time Shirt

dditional analysis using CoalHMM33 supports the findings of gene flow from D-, DFOIL, and PhyloNet analyses (Supplementary Fig. 16). It shows that a migration model fits most pair wise comparisons significantly better than ILS, and is robust under a broad range of parameters (Supplementary Figs 17 and 18). Thus, gene flow among bears throughout most of their history is the major factor for generating conflicting evolutionary signals.Estimation of divergence times and population splits(Supplementary Table 7). The amount of heterozygous sites differs among species and individuals, and is highest in the Asiatic black bear genome and, as expected2 lowest in the polar bears and spectacled bears (Supplementary Fig. 4). It is noteworthy that the average numbers of heterozygous sites differ among the two sun bears, which may reflect different population histories.