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Cat If You See Me With A Seam Ripper Now Is Not The Time Shirt
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.ues for pā<ā1.0 and accession numbers.Full size imageFinally, a consensus analysis based on GF ML-trees (Supplementary Fig. 13) produces a tree that is identical to the coalescent species tree, but highlights that numerous individual GF trees support alternative topologies (Supplementary Table 3). Inspection of the individual 18,621 GF ML topologies shows that 38.1% (7,086) support a topology where Asiatic black bear is the sister group to the American black/brown/polar bear clade. The Asiatic black bear groups in different arrangements with the two other Asiatic bears: 18.7% (3,474) of the branches support a grouping with the sun bear, and 7.5% (1,394) with the sloth bear.
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Gene flow among bears is commonSeemingly conflicting phylogenetic signals in evolutionary analyses can be explained by incomplete lineage sorting (ILS) or gene flow among species. In contrast to the largely random process of ILS, gene flow produces a bias in the phylogenetic signal, because it is a directed process. The D-statistic measures the excess of shared polymorphisms of two closely related lineages with respect to a third lineage18 and can thus discriminate between gene flow and ILS. The test assumes that the ancestral population of the in-group taxa was randomly mating and recently diverged29. These assumptions might be compromised in wide-spread, structured species like bears. However, speciation is rarely instantaneous, but is rather preceded by a period of population divergence. This should not compromise the test as long as there was a panmictic population ancestral to the progenitor populations of the eventual daughter species at some point in time, which is a reasonable assumption.
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