3.5 | Adaptive evolution in metabolism
In-depth genome scanning and functional annotation helped us to understand the divergence event. Genome-wide nucleotide diversity (π ) was computed for each population with all individuals. Meanwhile, we identified genomic regions as candidate divergent regions (CDRs) among PEc, PEz and PEa populations (Table S6, Fig. S9). We used iHS to detect genes under recent natural selection in the PEc and PEz&PEa populations. A total of 1,046 SNPs in PEc and 1,093 SNPs in PEz&PEa were identified within the top 1% iHS scores (Fig. S10). These positively selected significant SNPs were annotated to 290 and 254 functional genes, respectively. The GO functional enrichment showed that they were mainly enriched in GO terms such as metabolism and regulation of gene expression (Table S7). The results of KEGG enrichment also showed that the two clades have significant selection signals in metabolic-related signaling pathways (Fig. S11). In addition, we also used the XP-EHH method to screen for genes that may have been positively selected by different environmental pressures by comparing the PEc and PEz&PEa populations. The two-side P -value test was used to scan genome regions with selection sweep signals of the two clades. Interestingly, the differences in carbohydrate metabolism and lipid metabolism were extremely significant in the two clades (Fig. S12 – S13, Table S8). PEz&PEa clade has shown significant positive selection for almost all key enzymes in glycolysis and tricarboxylic acid cycle. These loci have aroused our attention and re-examined the selection dynamics of their surrounding regions (Fig. 6). This includes the kinases (E1:hexokinase and E2:6-phosphofructokinase-1) involved in the two most important irreversible reactions in the first stage of the conversion of glucose to pyruvate under anaerobic conditions. Meanwhile, the dehydrogenase (isocitrate dehydrogenase) in the irreversible reaction of isocitrate oxidative decarboxylation to α-ketoglutarate has also been significantly positively selected (P <0.05). The collective selection of enzymes in the glycolysis process and tricarboxylic acid cycle showed that PEz&PEa has a greater demand than PEc in this process. In addition, members of the lipid synthase family which is involved in the uptake of fatty acids are significantly positively selected in PEc. Parasitic helminths contain appreciable quantities of lipids. However, most of the intestinal helminths do not utilize significant amounts of lipids even during starvation and under aerobic conditions(Frayha & Smyth, 1983) largely due to their anaerobic mode of life. The significant selection of these enzymes such as fatty acid CoA synthetase family and long-chain fatty acid CoA ligase 5 suggests that they might be involved in some other processes as well, not just lipid uptake or metabolism. In terms of energy conservation, considering lipids and end products of carbohydrate metabolism for helminths seem unrealistic and uneconomical.