Demographic history
Based on short reads generated for whole genome sequencing, using
next-generation technology, demographic histories for two T.
dalaica were deduced following the PSMC pipeline (H. Li & Durbin,
2011), and subsequently compared. Briefly, after cleaning and filtering
using fastp (Chen et al., 2018), all short reads were mapped to the de
novo assembly using BWA-mem, with default settings applied (H. Li &
Durbin, 2009). Based on both mapping results and the assembly, SAMtools
(H. Li et al., 2009), followed by BCFtools (Danecek & McCarthy, 2017),
were used to generate a consensus sequence of the heterozygous genome.
This was then used to deduce the demographic history using PSMC, with
parameters set as follows: -N25 -t15 -r5 -p “4+25*2+4+6”. A previously
reported cyprinid mutation rate of 4.13e-9 (Fu, Chen, Zou, Long, & He,
2010), and a 2-year generation time, were used to infer the effective
population size (EPS) of T. dalaica .