The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds
Fig 4
Phylogenetic network of rare genomic changes reveals three adaptive radiations of Neoaves with varying complexity of genealogical incongruences.
(A) Neighbor-net [31] 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. Fig 1A and 1B) 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. Fig 1A and 1B). (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 (S3 Table). (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.