Demographic history was reconstructed based on a Hidden Markov Model (HMM) approach using PSMC30 (link). Briefly, the genomic sequences generated from each diploid channel catfish were aligned to the channel catfish reference assembly using BWA mem (version 0.7.12-r1039) with default settings. The consensus sequences were called using SAMtools (version 0.1.19). The ‘fq2psmcfa' tool was used to create the input file for PSMC modelling, with the option -q20. The consensus sequences were divided into non-overlapping 100 bp bins, with a bin scored as heterozygous if there was a heterozygote in the bin, otherwise it was scored as homozygous. The resultant bin sequences were used as the input for the PSMC estimates using ‘psmc' with the options -N25 -t15 -r5 -p ‘4+25*2+4+6'. The reconstructed population history was plotted using ‘psmc_plot.pl' with the options -u 2.5e-08 -g 7. Because plotting the results required input of generation time (-g 7) and mutation rate (-u 2.5e-08), generation time was calculated as: g=a+[s/(1-s)], where s is the expected adult survival rate which is recorded as 80% in channel catfish, and a is the sexual maturation age that is 3-year for channel catfish. Therefore, the generation time used in this PSMC model was determined as: g=3+[0.80/(1-0.80)]=7. The mutation rate was set following the rate described in a previous study in medaka64 (link).
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