<p>(A) Neighbor-net [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.ref031" target="_blank">31</a>] analysis of 2,118 RE presence/absence patterns suggests that Neoaves diversification may be more accurately visualized as a largely bifurcating tree with highly reticulate structures at the base of the core landbird radiation and across most of the initial super-radiation. Within the latter, red-brown reticulations highlight bifurcate relationships (cf. <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.g001" target="_blank">Fig 1A and 1B</a>) with limited conflict if stretched boxes are longer than they are wide. In contrast, the core waterbird radiation exhibits limited conflict and appears fully bifurcating (cf. <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.g001" target="_blank">Fig 1A and 1B</a>). (B–D) Distribution of frequencies of RE markers without and with ILS (i.e., persistence across ≥two speciation events) for each of the three adaptive radiations (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002224#pbio.1002224.s009" target="_blank">S3 Table</a>). (B) Core waterbird radiation with 18% total ILS, mostly across two speciation events. (C) Core landbird radiation with 27% total ILS, most of which led to weak or moderate conflict via ILS across two to three speciation events. (D) The initial super-radiation exhibits 73% total ILS, almost exclusively with strong discordances caused by persistence of ILS across five or more speciation events.</p
