UCE Phylogenetics
Current understanding
Ultraconserved elements (UCEs) have emerged as a powerful class of molecular markers for resolving deep and shallow phylogenetic relationships across diverse animal lineages. Their near-universal presence across genomes, combined with flanking regions that carry phylogenetically informative variation, makes UCE-based phylogenomics particularly well-suited for large-scale comparative analyses. Within the Hymenoptera, UCE data have been applied to untangle the complex relationships among bees (Apoidea), a group whose phylogenomics has historically been hampered by taxon sampling gaps and limited genomic resources.
A recent phylogenomic analysis leveraging 119 Apoidea genomes used UCE data to produce a well-resolved tree in which the vast majority of nodes received 100% ultrafast bootstrap support. A notable outcome of this analysis was the placement of Perdita meconis — representing the first Panurginae genome contributed to Apoidea phylogenetic datasets — as the sister lineage to Andrena within family Andrenidae (subfamily Andreninae). This finding helps clarify the internal structure of Andrenidae and demonstrates the utility of UCE-based approaches for integrating newly sequenced genomes into existing phylogenomic frameworks. See Schweizer et al. 2024, Finding 1 for details.
Supporting evidence
- Schweizer et al. 2024, Finding 1: UCE-based phylogenomic analysis of 119 Apoidea genomes resolves Perdita meconis as sister to Andrena within Andrenidae, with most nodes at 100% ultrafast bootstrap support.
Contradictions / open disagreements
The primary open question concerns the robustness of the Perdita–Andrena sister-group relationship. Taxon sampling in the 119-genome dataset is heavily skewed toward social bees in Apidae and Halictidae; Stenotritidae is entirely absent, and only one Andrenidae genus (Andrena) is represented alongside Perdita. Broader sampling of Andrenidae diversity — and inclusion of the missing family Stenotritidae — will be required to confirm the internal topology of Andrenidae using UCE data.
Tealc’s citation-neighborhood suggestions
Readers may wish to consult foundational UCE methodology papers (e.g., Faircloth et al. 2012, Systematic Biology) and broader Apoidea phylogenomic studies that pre-date genome-scale UCE approaches, to contextualize the improvements in resolution that UCE phylogenomics provides.