2.3 Assembly of mitogenomes and phylogenetic analysis
To assess the phylogenetic relationships among individuals, maximum-likelihood phylogenetic trees were constructed for diploids and triploids separately, as well as all individuals together, using the IQ-TREE software version 2.0.3 (Nguyen et al., 2015), based on their complete mitochondrial genome sequences. The mitogenome sequences werede novo assembled from the resequencing data using procedures described in Liu et al. (2016). Briefly, the first 5 M paired-end reads were selected for further analysis to fragmentize the assembly of nuclear sequences. De novo assembly of relatively short sequences (e.g. mitogenomes) was conducted using Spades v3.13.0 (Bankevich et al., 2012). The mitogenome sequence was then captured from the assembly using a probe sequence which is conserved in C. auratus(GCTAGCGTAGCTTAATACAAAGC).