Putative orthologs and conversion lists from Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality

BLAST reciprocal best hit results between <i>Megalopta genalis</i> and <i>Apis mellifera</i>, as well as between <i>M. genalis</i> and <i>Bombus terrestris</i>. Conversion lists used to translate between two <i>A. mellifera</i> microarrays, an older (OGSv2.0) and current (OGSv3.2) annotation of the honey bee genome are also provided

Gene Ontology enrichment results from Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality

PANTHER pathways and GO-Slim Biological Processes overrepresented in DEGs for each pairwise comparison of groups. Only categories with a Bonferroni-corrected p-value of less than 0.05 are shown. In addition to pairwise lists, results from the comparison between workers and long-term reproductive groups (queens and solitary reproductive females) as shown in Figure 2 are given

Gene expression results from Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality

For each tissue, logFC and FDR-corrected p-values are given for each pairwise comparison of groups for all <i>Megalopta genalis</i> contigs expressed in the tissue. Along with contig ID, putative orthologs to <i>Apis mellifera</i> and <i>Bombus terrestris</i> based on BLAST reciprocal best hits and PANTHER annotations are provided

Sample information from Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality

Information for each sample, including sample ID, caste, tissue, emergence and collection dates, age, head width and ovary information

Overlapping gene lists and representation factor results for gene expression studies from Caste-biased gene expression in a facultatively eusocial bee suggests a role for genetic accommodation in the evolution of eusociality

For each study comparison, gene lists are provided for the study, the shared universe between studies, as well as direction-specific lists for each comparison. Also provided are the numbers of overlapping genes, the representation factor, and the p-value for each test

Table_S4_large_table_of_expression_data_-_checked_-_final

Table_S4_large_table_of_expression_data_-_checked_-_fina

Microbial Ecology of the Hive and Pollination Landscape: Bacterial Associates from Floral Nectar, the Alimentary Tract and Stored Food of Honey Bees (<i>Apis mellifera</i>)

<div><p>Nearly all eukaryotes are host to beneficial or benign bacteria in their gut lumen, either vertically inherited, or acquired from the environment. While bacteria core to the honey bee gut are becoming evident, the influence of the hive and pollination environment on honey bee microbial health is largely unexplored. Here we compare bacteria from floral nectar in the immediate pollination environment, different segments of the honey bee (<i>Apis mellifera</i>) alimentary tract, and food stored in the hive (honey and packed pollen or “beebread”). We used cultivation and sequencing to explore bacterial communities in all sample types, coupled with culture-independent analysis of beebread. We compare our results from the alimentary tract with both culture-dependent and culture-independent analyses from previous studies. Culturing the foregut (crop), midgut and hindgut with standard media produced many identical or highly similar 16S rDNA sequences found with 16S rDNA clone libraries and next generation sequencing of 16S rDNA amplicons. Despite extensive culturing with identical media, our results do not support the core crop bacterial community hypothesized by recent studies. We cultured a wide variety of bacterial strains from 6 of 7 phylogenetic groups considered core to the honey bee hindgut. Our results reveal that many bacteria prevalent in beebread and the crop are also found in floral nectar, suggesting frequent horizontal transmission. From beebread we uncovered a variety of bacterial phylotypes, including many possible pathogens and food spoilage organisms, and potentially beneficial bacteria including <i>Lactobacillus kunkeei</i>, Acetobacteraceae and many different groups of Actinobacteria. Contributions of these bacteria to colony health may include general hygiene, fungal and pathogen inhibition and beebread preservation. Our results are important for understanding the contribution to pollinator health of both environmentally vectored and core microbiota, and the identification of factors that may affect bacterial detection and transmission, colony food storage and disease susceptibility.</p></div

Venn diagrams depicting unique and shared OTU's.

<p>Diagrams comparing cultured isolates and cloned sequences derived from beebread and the gut (mid and hind gut). Operational taxonomic units (OTU's) are defined at 99% and 97%. Percent relative abundance of shared OTUs across all libraries is shown in parentheses.</p

Neighbor joining phylogenetic tree of Firmicutes.

<p>Tree based on 1076 positions of the 16S-rDNA bacterial sequence from beebread, honey, alimentary tract and flowers visited by <i>A. mellifera</i>, and comparison with related microorganisms (GenBank accessions). Abbreviated taxon labels refer to clones (C), or isolates (I), and symbols mapped to the right of the topology represent the sampled niche. Bootstrap values (n = 1000) are given at the branching points.</p

PCoA analysis of bacterial communities from <i>Apis mellifera</i> associated niches.

<p>Analysis based on unweighted UniFrac distances. Positions of the bacterial communities for each sampled niche along the first three principal coordinate axes are illustrated, along with the percentage of variation explained by each axis. The simulated gut community was composed of cloned sequences specific to the midgut and hindgut. Symbols are colored by general niche; yellow: alimentary tract, red: food stores and black: flowers. Sample size shown in parentheses.</p