Linear regression of logit proportion of UCE loci captured verses specimen age.

<p>Number of UCE loci and specimen age for; <i>Xylocopa</i> (carpenter bees) from Blaimer et al. 2016, <i>Aphelocoma</i> (scrub-jays) from McCormack et al. 2016, Eupholini (smurf weevils) from this study. Specimen age is in years from when individual was first collected and preserved. Regressions show a decline in the number of UCE loci captured as specimen age increases, the rate of decline is similar between studies.</p

Linear regression of logit proportion of UCE loci captured verses specimen age.

<p>Number of UCE loci and specimen age for; <i>Xylocopa</i> (carpenter bees) from Blaimer et al. 2016, <i>Aphelocoma</i> (scrub-jays) from McCormack et al. 2016, Eupholini (smurf weevils) from this study. Specimen age is in years from when individual was first collected and preserved. Regressions show a decline in the number of UCE loci captured as specimen age increases, the rate of decline is similar between studies.</p

Shows approximate position of character sets used for each locus in PartitionFinder 2 for ASTRAL analyses, overlaid on the frequency of PIS in the final UCE data set.

<p>UCE Core refers to the section of the locus that corresponds to the length of UCE probe. Numbers 1–5 on left of UCE Core correspond to matching characters sets on the right, such that e.g. both sections 5 are the same character set. Character sets 1–5 correspond to one fifth of the length of the locus (left and right of UCE Core) minus the sites from the UCE Core.</p

Phylogenetic tree results of the Eupholini weevils, branch colors correspond to species clades: LEFT: SVDQuartets species tree.

<p>Dashed lines denote nodes that differ between trees. Node values indicate bootstrap support values. RIGHT: ASTRAL species tree, input trees derived from multi-partitioned MrBayes analyses of individual gene trees. Node values indicate support values of MrBayes posterior (minus burn-in) used as ASTRAL bootstrap replicates.</p

LEFT: ASTRAL species tree derived from multi-partitioned RAxML trees.

<p>Node values indicate bootstrap support values. RIGHT: ASTRAL species tree, input trees derived from multi-partitioned MrBayes analyses of individual gene trees. Node values are derived from posterior distribution of MrBayes trees (minus burn-in) where each sample of the MCMC generation represents a bootstrap sample to ASTRAL.</p

ASTRAL species tree, input trees derived from multi-partitioned MrBayes analyses of individual gene trees (i.e. using the 6 character in sets in Fig 2 to inform the partitioning strategy).

<p>Node values indicate support values of MrBayes posterior used as ASTRAL bootstrap replicates, branch colors correspond to species clades. Weevils from top clockwise: <i>Eupholus azureus</i> Macleay, <i>Eupholus schoenherrii schoenherrii</i> (Guérin-Méneville), <i>Celebia arrogans</i> (Boisduval), <i>Rhinoscapha sp</i>. “Large-brown Mt.Wilhelm 2700m”, <i>Gymnopholus (Symbiopholus) acarifer</i> Gressitt, <i>Gymnopholus regalis</i> Gressitt, <i>Eupholus cuvierii</i> (Guérin-Méneville), <i>Rhinoscapha tricolor</i> Faust, <i>Rhinoscapha doriae</i> Pascoe, <i>Gymnopholus nitidus</i> Gressitt & Sedlacek.</p

Left: Boxplot of number of UCEs by preservation type.

<p>Average number of UCEs for modern ethanol preserved specimens was higher than for museum pinned specimens. Right: Plot of number of UCEs vs their date of collection. Plot shows general trend of fewer UCEs captured for the older the specimens, however the exact rate of decrease would require more specimens systematically sampled by precise preservation type.</p

Phylogenetic tree results of the Eupholini weevils, branch colors correspond to species clades: LEFT: ASTRAL species tree, input trees derived from single-partitioned MrBayes analyses (each gene tree reconstructed using a single partition), of individual gene trees.

<p>RIGHT: ASTRAL species tree, input trees derived from multi-partitioned MrBayes analyses of individual gene trees. Node values indicate support values of MrBayes posterior used as ASTRAL bootstrap replicates.</p

Pairwise comparisons of topological distances between different tree reconstruction methods used.

<p>Tree to tree topological distance metrics used the subtree prune and regraft distance (SPR_DIST), Robinson-Foulds distance (RF_DIST), path distance metric between pairs of taxa (PATH.DIFF_DIST). The ASTRAL trees based on multiple partitions are the ASTRAL RAxML tree using six character-sets (astral_raxmltree), ASTRAL RAxML tree based on single character-sets/partitions (astral_singlepart_raxmltree), ASTRAL MrBayes tree using six character-sets (astral_mrbtree) and ASTRAL MrBayes tree based on single character-sets/partitions (astral_singlepart_mrbtree). Results of lower triangle shown.</p

Phylogenetic tree results of the Eupholini weevils, branch colors correspond to species clades: LEFT: SVDQuartets species tree.

<p>Dashed lines denote nodes that differ between trees. Node values indicate bootstrap support values. RIGHT: ASTRAL species tree, input trees derived from multi-partitioned MrBayes analyses of individual gene trees. Node values indicate support values of MrBayes posterior (minus burn-in) used as ASTRAL bootstrap replicates.</p