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

Additional file 2: Supplementary Figures S1-S5. of Rapid evolution of chemosensory receptor genes in a pair of sibling species of orchid bees (Apidae: Euglossini)

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Additional file 1: Supplementary Tables S1-S6. of Rapid evolution of chemosensory receptor genes in a pair of sibling species of orchid bees (Apidae: Euglossini)

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Hits of nuclear genes against KEGG BRITE Ontology database using the KAAS pipeline for the 16 genomic libraries.

<p>The number of hits is listed below the species name. Colours assigned according to the highest level of KEGG Orthology hierarchy (different organismal/cellular pathway groups/ecosystem processes).</p

Characteristics of contigs with homology to viral protein sequences in the libraries.

<p>Characteristics of contigs with homology to viral protein sequences in the libraries.</p

Correlation between genomic library size (y-axis) and total length of mitochondrial genome recovered (x-axis).

<p>A significantly positive linear correlation (Pearson r = 0.6049, P = 0.0219) between the number of base pairs sequenced and the proportion of the mitochondrial genome recovered was found.</p

Bacterial hits found in four genomic libraries.

<p>Hits for the bacterial species are displayed next to the chart pie for species with ≥4% of the hits. For the three pycnogonid species, Gammaproteobacteria are predominant, whereas for the vent limpet <i>Lepetodrilus</i> sp. nov. different bacterial groups were detected. The colours of the charts relate to the phyla/classes of Bacteria (see legend).</p

rRNA genes found in the different libraries.

<p>The total number of reads, the number of assembled contigs with coverage and the total unique rRNA gene bp are listed.</p

Coverage estimations for the sequenced genomic libraries based upon genome size information of closely related taxa found in the Animal Genome Size database.

*<p>Information on genome size of <i>Euphausia superba</i> is based upon the flow-cytometry estimates listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049202#pone.0049202-Jeffery1" target="_blank">[46]</a>.</p

Total number and genomic density of microsatellites found in the libraries before and after applying stringent filtering criteria (best primers, single read contigs only, see Supporting information S3 for further information).

<p>Results are given for three different sets of search parameters which correspond to search parameters in: Mayer et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049202#pone.0049202-Mayer2" target="_blank">[48]</a> but filtering for perfect microsatellites only, Santana et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049202#pone.0049202-Santana1" target="_blank">[15]</a>, Gardner et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049202#pone.0049202-Gardner1" target="_blank">[4]</a>.</p