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).