Phylogenetic tree construction
Within the core taxa identified above, we constructed phylogenies to compare our sequences to previously characterized bacteria from bees or other related habitats. Previously published 16S rDNA sequences were downloaded from NCBI’s 16S rRNA RefSeq database. Our strain list was comprised of previous studies of solitary and social bee-associated bacteria with published full-length16S sequences or genomes, as well as related strains within these groups (Lugli et al. 2017, Zheng et al. 2020).
To build trees, sequences were first alignied using AlignSeqs(Wright 2015). Pairwise distances of aligned sequences were calculated and used in the construction of neighbor joining trees optimized using internal maximum likelihood estimation (Schliep 2011) and visualized using ggtree (Yu et al. 2017).