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Full size imageHowever, a network analysis27 gained from the same 18,621 GFs identifies conflicting phylogenetic signal (Fig. 2B). The square and cuboid-like structures indicate alternative phylogenetic signals, particularly among brown and polar bears, but also among the Asiatic bears. The brown bear from the Admiralty, Baranof, and Chichagof (ABC) islands groups in different arrangements with other brown and polar bears, consistent with gene flow between the two species7,8,23. When the threshold level for depicting conflicting branches is reduced in the network analysis, the signal becomes increasingly complex, illustrating the conflict among 18,621 ML-trees (Supplementary Fig. 9). Still, the network analysis agrees with the species tree when the spectacled bear is the outgroup. The phylogenetic conflict can be caused by incomplete lineage sorting (ILS) or gene flow, but less likely from lack of resolution due to the strong phylogenetic signal of each GF (Supplementary Figs 6 and 7). Analyses of 8,050 protein coding sequences (10,303,323 bp) and GFs from scaffolds previously identified as X chromosomal (total 74 Mb)22, conform to the species tree and networks (Supplementary Fig. 10). Finally, the paternal side of bear evolution based on Y chromosome sequences28 for available genomes is consistent with the inferred species tree (Supplementary Fig. 11).
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The Bayesian mtDNA tree (Fig. 3, Supplementary Fig. 12) conforms to previous studies2,15, making this the hitherto largest taxonomic sampling of 38 complete bear mt genomes. However, several nodes of the mtDNA tree differ notably from the coalescent species tree (Fig. 2A). In the mtDNA tree, the brown bears are paraphyletic, because the brown bear mt genome introgressed into the polar bear population8. The extinct cave bear (Ursus spelaeus) is the sister group to polar and brown bears. The American black bear is the sister group to the Asiatic black bear, and the sloth bear is the sister group to all ursine bears. The topological agreement of the mtDNA tree to previous studies and placement of the new individuals corroborates that the studied individuals are representative for their species.
