3.6 Phylogenetic relationship and evolutionary history ofC. japonica
We compared the C. japonica genome with seven other model species, includingA. amphitrite , which is also a desiccation-tolerant species to analyze the desiccation-adaptive evolution of C. japonica . Of all the genes (30,900) of C. japonica , 23,684 genes were assigned to 12,396 gene families (Figure.5). Compared with the seven other species, 1,138 gene families were unique to C. japonica (Table 8, Figure 6). Using ORTHOMCL software, we identified a set of 968 single-copy orthologous genes shared by eight species (Figure 6). Phylogenetic analysis based on single-copy orthologous genes clustered C. japonica and P. trituberculatus into one branch, and the differentiation time between C. japonica and P. trituberculatus was 42.1–135.5 Mya (Figure 7). Compared with seven other species, we identified 2,417 expanded and 2,709 contracted gene families in C. japonica (Figure 7). The expanded gene families ofC. japonica were significantly enriched in 1,375 GO terms and 85 KEGG pathways (corrected P < 0.05).
We applied the PSMC method to estimate the demographic history ofC. japonica . The historical demographic pattern (Figure 8) shows that C. japonica maintained a relatively stable population size, followed by an obvious expansion, and reached their maximum effective population size about 0.5×105 years ago.