Supplemental Material for Brand, Lin, and Johnson, 2018

Supplemental Figure 1 Phylogenetic tree of the pectinase gene family. All phasmatodea pectinases cluster within the gammaproteobacteria and form a highly supported monophyletic clade, supporting a single horizontal gene transfer event in the ancestor of the three insect lineages analyzed. Pectinases detected in the B. germanica genome cluster within bacteria as well, but do not form a monophyletic clade. It is likely that the pectinases identified are due to bacterial contamination of the genome assembly (see main text). Known chrysomelid beetle pectinases cluster within fungi, representing independent horizontal gene transfer events of pectinases from fungi to insects (Pauchet et al. 2010) Orange: M. extradentata, Blue: C. hookeri, Purple: D. australis, Red: B. germanica. Bootstrap support of 100 replicates is indicated for each branch. Gene models of the four newly annotated species with insect or bacterial genes in the 20kb flanking regions are indicated.<br> <br>Supplemental Figure 2 Phylogenetic tree of the cellulase gene family. All identified cellulase genes cluster within other known bacterial cellulase genes. Orange: M. extradentata, Blue: C. hookeri, Purple: D. australis, Red: B. germanica, Brown: Z. nevadensis, Pink: T. cristinae. Bootstrap support of 100 replicates is indicated for each branch

Probability of sampling zero AHBs for all counties sampled without AHB presence using the binomial distribution.

<p>For Yolo, for example, there was over 80% chance of sampling zero AHBs assuming AHBs are present at 2.5%. Yolo, Sutter, Placer, and Butte were sampled with insufficient depth to rule out significant AHB presence.</p

Africanized bees extend their distribution in California

<div><p>Africanized honey bees (<i>Apis mellifera</i>) arrived in the western hemisphere in the 1950s and quickly spread north reaching California in the 1990s. These bees are highly defensive and somewhat more difficult to manage for commercial purposes than the European honey bees traditionally kept. The arrival of these bees and their potentially replacing European bees over much of the state is thus of great concern. After a 25 year period of little systematic sampling, a recent small scale study found Africanized honey bees in the Bay Area of California, far north of their last recorded distribution. The purpose of the present study was to expand this study by conducting more intensive sampling of bees from across northern California. We found Africanized honey bees as far north as Napa and Sacramento. We also found Africanized bees in all counties south of these counties. Africanized honey bees were particularly abundant in parts of the central valley and Monterey. This work suggests the northern spread of Africanized honey bees may not have stopped. They may still be moving north at a slow rate, although due to the long gaps in sampling it is currently impossible to tell for certain. Future work should routinely monitor the distribution of these bees to distinguish between these two possibilities.</p></div

Current distribution of AHBs in California.

<p>Percentage of AHBs in each county sampled by the present study only are shown. Counties highlighted in red have been found to be inhabited by AHBs. Counties in pink had no AHBs, but had poor sampling.</p

Percentage Africanized and European bees by county.

<p>Percentage Africanized and European bees by county.</p

Gene ontology analysis of differentially expressed genes between nurse and forager digestive tracts.

<p>Top panel shows the distribution of GO functional categories for all DEGs found (565 in total), while the bottom panel shows the same for the genes with the 50 highest probabilities of being differentially expressed (the 50 genes with the most robust patterns of differential expression).</p

Number of differentially expressed genes found with increasing sequencing depth in comparisons of (A) the sting gland between nurses and foragers, and (B) the whole digestive tract between nurses and foragers.

<p>Two different normalization techniques were used in the NOISeq package: upper quartile normalization (UQ), and RPKM. </p

Number of differentially expressed genes found with increasing sequencing depth in comparisons of the sting gland and digestive tract.

<p>Nurse sting gland is compared to nurse digestive tract in part A, and forager sting gland is compared to forager digestive tract in part B.</p

Effect of increasing read depth on the strength of the difference between DEGs measured as M (absolute value of the fold difference in expression) and D (the raw difference in expression).

<p>Effect of increasing read depth on the strength of the difference between DEGs measured as M (absolute value of the fold difference in expression) and D (the raw difference in expression).</p

Mean expression levels for all genes and all expressed transcription factors in the sting gland and digestive tract of nurses and foragers.

<p>Values are from the 12 million read depth NOISeq analysis.</p