Fig. 3 Gene flow signals for baleen whales inferred by the D statistic, DFOIL, and PhyloNet. Gene flow signals for baleen whales inferred by the D statistic,

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Fig. 3 Gene flow signals for baleen whales inferred by the D statistic, DFOIL, and PhyloNet. Gene flow signals for baleen whales inferred by the D statistic, DFOIL, and PhyloNet. (A) The species tree of baleen whales with gene flow signals detected by the D statistic and DFOIL indicated by dashed lines. Signals I to IV were inferred by the D statistic, and signals V, VI, and VII were detected by DFOIL and were partially corroborated by the D statistic. Note that DFOIL cannot infer gene flow involving the minke whale. (B to D) Rooted networks for the Balaenopteridae sensu lato phylogeny with reticulations inferred from PhyloNet based on 34,192 20-kbp GFs. Reticulations are shown as blue arrows with inheritance probability denoted above or below. Log-likelihood scores are shown below the networks. Notably, inheritance probability around 33% resembles the distribution of quartet scores and the phylogenetic signals from GFs (Fig. 1). (B) The three best networks indicated a reticulation originating at the circled three branches to minke whale. Similar likelihood scores do not allow the identification of a single origin of gene flow; therefore, the networks were merged, and a range of inheritance probabilities is given. (C) The fourth best network has only a marginally poorer likelihood score and indicates a reticulation between the ancestor of the fin and humpback whale and that of the minke whale. (D) The fifth best network has the same likelihood as (C) and finds an alternative placement of gray whale (blue branch) and reticulation from the ancestor of the blue and sei whale to that of the minke whale. Úlfur Árnason et al. Sci Adv 2018;4:eaap9873 Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).