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.