A named list (the same structure returned by read_trees()) of five
phylogenetic trees from a dung beetle phylogenomic study, Montanaro,
Lopes et al. (2026), pruned to 15 taxa for compact demonstration of
the phylorug workflow. The trees are already rooted, outgroup-removed, and
tip labels translated from museum codes to species names. Users can select a
backbone tree and comparison trees, then pass them directly to
check_taxa(), node_presence_matrix() and plot_phylorug().
Format
A named list of 5 objects of class "phylo", each with 15 tips. Node
labels contain support values: SH-aLRT/UFBoot2 for IQ-TREE trees and local
posterior probability for ASTRAL trees.
Source
Montanaro, G., Lopes, F., Gunter, N.L., et al. (2026). Phylogenomics resolves a 200-year-old puzzle: a revised tribal classification of Afro-Eurasian dung beetles (Coleoptera: Scarabaeinae). bioRxiv. doi:10.64898/2026.07.22.740134
Details
The five trees represent independent phylogenomic analyses of the same set of taxa using different inference methods and data types:
- 70p_uce
IQ-TREE maximum likelihood analysis of ultraconserved element (UCE) data. Recommended as the backbone tree.
- 70p_partition_entropy
IQ-TREE maximum likelihood analysis of partitioned sequence data.
- 70p_ghost
IQ-TREE GHOST heterotachous model on partitioned data.
- 70p_ASTRAL_uce
ASTRAL coalescent analysis of UCE gene trees.
- 70p_ASTRAL_partition_entropy
ASTRAL coalescent analysis of partitioned gene trees.
Examples
# Core pipeline:
backbone <- sample_trees[["70p_uce"]]
others <- sample_trees[names(sample_trees) != "70p_uce"]
# Optional: diagnose taxon overlap
check_taxa(backbone, others)
#> All 4 comparison trees share the same 15 taxa as the backbone.
#> [1] TRUE
#> attr(,"diagnostics")
#> comparison status n_taxa missing extra
#> 1 70p_ASTRAL_partition_entropy identical 15
#> 2 70p_ASTRAL_uce identical 15
#> 3 70p_ghost identical 15
#> 4 70p_partition_entropy identical 15
npm <- node_presence_matrix(backbone, others, support_col = c(1, 2))
tmp <- tempfile(fileext = ".pdf")
plot_phylorug(backbone, npm, file = tmp)
unlink(tmp)