Fig. 3

Distinct phylogenetic signals in Cupressaceae plastomes. a Difference in site log likelihoods for the two major tree topologies recovered in Fig. 1. Sites supporting the Juniperus + Cupressus topology are shown in blue, while sites supporting the CaHX + Cupressus topology are shown in gray. b Sliding window analysis (window size = 5000; step size = 100) showing the sum of the difference in site log likelihoods in segments of the genome. c Linear map of the X. vietnamensis plastome. Genes placed above or below the map indicate that they are on opposite strands of the genome sequence. Red dotted lines demark the segment of the genome that exhibits an anomalous phylogenetic signal relative to the rest of the genome