Eulaemus, Girard, 1857

Olave, Melisa, Avila, Luciano J., Sites Jr, Jack W. & Morando, Mariana, 2015, Model-based approach to test hard polytomies in the Eulaemus clade of the most diverse South American lizard genus Liolaemus (Liolaemini, Squamata), Zoological Journal of the Linnean Society 174 (1), pp. 169-184 : 175

THE EULAEMUS PHYLOGENY (FULL MATRIX)

We recovered nine main clades using both concatenated and MDC analyses ( Fig. 3A, B ; main clade names: anomalus group, boulengeri complex, darwinii group, donosobarrosi complex, fitzingerii complex, lineomaculatus section, montanus group, rothi complex, wiegmannii group), but relationships amongst these main clades are discordant between methods.

1. Concatenated analysis ( Fig. 3A ). The MrBayes analysis of the complete concatenated matrix (188 taxa, 14 loci) recovered all of the traditionally recognized main Eulaemus groups with high posterior probabilities (PP = 1). The lineomaculatus section was recovered as sister clade of the montanus section. The montanus section had the following topology: ( montanus group + ( anomalus group + wiegmannii group)), and its sister clade was resolved as ( darwinii group + ( rothi complex, boulengeri complex + ( donosobarrosi group + fitzingerii group))). Almost all of these relationships were well supported (PP> 0.95) with the exception of the unresolved positions of the rothi and boulengeri complexes (PP = 0.77).

2. MDC ( Fig. 3B ). Our MDC analysis was also based on the complete data set, and although it recovered the main traditional groups of Eulaemus as clades, the majority of relationships amongst these clades are different from those recovered with the concatenation approach. We again recovered the lineomaculatus section as the sister group to all other clades; the anomalus group was still recovered as the sister clade of the wiegmannii group, and this clade is sister to a larger clade with the following topology: (( donosobarrosi group + fitzingerii group) + (( darwinii group + rothi complex) + ( montanus group + boulengeri complex))).

Figures

Figure 3. Empirical Eulaemus phylogenetic hypotheses. Phylogenetic results using the full matrix of 188 taxa (A, B) and a reduced set of 40 taxa chosen to subsample the largest clades (C to F). A, topology recovered from the concatenated matrix; B, species tree recovered by the minimizing deep coalescence (MDC) approach; C, *BEAST results of partial matrix with representatives of largest clades; values on branches are estimated divergences times (upper) and posterior probability values estimated (lower) or separated by a slash; bold branches represent nodal support> 0.90; D, BEST result; E, MDC result of partial matrix; and F, partial concatenated matrix. In (A), (D), and (F) nodes with support <0.90 were collapsed. The calibration point for estimation of divergence times is shown with a white circle in the node corresponding to the divergence of the Eulaemus and Liolaemus clades.