2.5 | Phylogenetic relationship, genetic structure and admixture
Principal component analysis (PCA) was carried out using EIGENSOFT (Nick et al., 2006) software base on the SNP dataset, and the population clustering analysis was conducted in PLINK (v1.90b6.10) (Purcell et al., 2007). We used genome-wide SNPs to construct the maximum likelihood (ML)phylogenetic tree with 1000 bootstraps using iqtree (v1.6.12) (Lam-Tung, Schmidt, Arndt, & Quang, 2015). The genome sequence ofBaylisascaris schroederi was selected as an outgroup. Population structure was analyzed using the ADMIXTURE (v1.3.0) program with a block-relaxation algorithm. To explore the convergence of individuals, we predefined the number of genetic clusters of K from 2 to 4.
We investigated the relationships within Parascaris spp. populations in a coalescent framework with SNAPP implemented in BEAST v2.6.3 (Bouckaert et al., 2014). We performed two independent runs with a chain length of 10,000,000 generations, sampling every 1,000 generations. We examined convergence using TRACER v1.7.1 and created a maximum clade credibility tree after a burn-in of 20% via TREEANNOTATOR (Helfrich, Rieb, Abrami, Lücking, & Mehler, 2018). According to epidemiological investigation, we assumed that the average generation time of Parascaris spp. was 0.17 years, and converted the SNAPP analyses into units of real-time using a mutation rate (μ ) of 9×10-9 per generation per site.