Fig. 5

Outcomes of full MSC (StarBEAST2) analyses for a focal clade of 9 taxa of rainbow skinks, using three different ‘treatments’ for the assignment of alleles to each taxon. a The phylogeny, as estimated using a concatenated alignment (also shown in Fig. 1), illustrates the level of divergence between lineages in the species (C. amax, C. gracilis, C. munda and C. rufilatus) whose sampling was manipulated in the experimental treatments (1S, 2S1L, 2S2L; described in text). Support values (on the nodes of A) show the support, across the 9 replicate posterior distributions, in the species trees estimated using the 1S, 2S1L, 2S2L treatments (respectively). b The level of discordance (unrooted Robinson-Foulds distance) is shown among trees estimated with the 9 replicates of the tree treatments (maximum clade credibility trees), as well as the concatenation tree (A), and the topology estimated with ASTRAL (and shown in Fig. 2). c The tree height and N _e values estimated by each of the replicates, shown as the mean (± s.d.) of 100 samples from the posterior distribution of each chain. Here treatment 1S shown in blue, 2S1L in black, and 2S2L in green