The file contains supplementary text and figures, including the following: Note on monepantel and genes associated with resistance.

Fig A. Comparison of chromosomal scaffolds between tci2_wsi3.0 and DNAZOO genome assemblies. Fig B. Genetic differentiation between all samples. Fig C. Farm mean faecal egg count reduction test results, adjusted by L3 species proportions. Fig D. Distinguishing genetic drift from selection on the UK Farm populations. Fig E. Comparison of genetic variation between technical replicates. Fig F. Relative sequencing coverage ratio along chromosome 5 between Farm 1 post:pre, Farm 2A post:pre and between Farm 1 post:Farm 2A post. Fig G. Gene, BUSCO, and repeat density. Fig H. Proportion of SNPs in 1 Mb windows identified as ‘significant’ by Cochran-Mantel-Haenszel test. Fig I. Genome-wide gene coverage between susceptible and resistant isolates. (DOCX)