UCE phylogenomics, biogeography, and classification of long-horned bees (Hymenoptera: Apidae: Eucerini), with insights on using specimens with extremely degraded DNA

Long-horned bees (Apidae, Eucerini) are found in different biomes worldwide and include some important crop pollinators. In the New World, Eucerini has received extensive taxonomic study during the twentieth century, resulting in several revisions of its genera. In contrast, progress on eucerine phylogenetic research and genus-level classification has been slow, primarily due to the relatively homogeneous external morphology within the tribe and the rarity of many of its species in collections. Notable exceptions have been analyses based on molecular data of a few loci, which have shed light on the initial diversification of Eucerini and clarified relationships among some lineages of eucerine bees. Here, we present a comprehensive phylogenetic study of Eucerini based on ultraconserved elements including 153 species from nearly all genera and subgenera and from all biogeographic regions where they occur. We recovered seven main lineages and found most of the genera and subgenera to be reciprocally monophyletic. Using the updated phylogenetic framework, we: (1) propose taxonomic changes, including a new subtribal classification, and reorganized generic and subgeneric limits; (2) estimate divergence times; and (3) conduct a detailed exploration of historical biogeography of long-horned bees. We find that eucerine lineages expanded their range onto most continents only after its initial diversification in southern South America during the Eocene. Finally, we discuss the challenges of working with specimens with highly degraded DNA, present insights into how to improve phylogenetic results for both species-tree and concatenation approaches and introduce a new pipeline for UCE curation (Curation of UltraconseRved Elements).