Supplemental Material for Clark et al., 2021

File S1 is a figure from FastQ Screen analysis. File S2 is a tarball containing the reference-guided assemblies for BA_411 and WI_6. Assembly files with "clean" appended to the name have been filtered for scaffolds without reference coverage. File S3 is a tarball containing Blobtools output. File S4 is a tarball containing BUSCO outputs.

Supplementary Figure 1: FastQC Screen Analysis Indicates the Expected Composition of Reads Based on Screened Genomes. Read subsets from each D. pulicaria library were mapped against several common and selected sequencing contaminants using bowtie2. Plots indicate that majority of the reads are mapping uniquely to the bait genome PA42 (“Daphnia”), as expected. For other genomes in the search library, the reads did not map uniquely and likely represent low-complexity regions. There is a significant proportion of the read subset that does not map to any represented sequences represented with grey bars.

Supplementary Figure 2: Sourmash Distance Estimates Indicate Higher Similarity Between D. pulicaria Strains (BA411 & WI6), Relative to the D. pulex (PA42) Reference. Dendrograms on the top and left recapitulate the relationship between samples in the distance analysis that is also visualized by the matrix. The color gradient indicates the sourmash distance estimate, where darker colors indicate high similarity between samples and lighter colors indicate more divergent samples. The D. pulicaria assemblies only vary by 0.1 when compared to each other.