Fig. 5
Discordant phylogenetic signals in the nuclear genome. Unrooted Neighbour-Net trees and species trees inferred for the three lineages of North American ravens—Chihuahuan Ravens (CHI, black), pure Holarctic (HOL, purple) and California (CAL, orange)—estimated from three nuclear data sets: a autosomal introns, b all genome-wide SNPs, c high FST SNPs between California and Holarctic lineages (n = 131 SNPs with FST > 0.2). For species trees, we show the maximum clade credibility (MCC) species tree inferred from all post-stationarity trees, and the percentage of trees matching each topology contained within the 95% HPD set of trees in each data set
