Results
Screening DNA methylation using the epiRADseq method on the Ion Torrent PGM in house sparrows generated a pseudo-reference of 17,532,684 bases. At the individual-level, between 5,095 and 89,777 CCGG sites were resolved. We constructed a dataset of all individuals at 0- and 8-hours, and a dataset of the magnitude of change between temporally paired individual samples at 0- and 8-hours.
House sparrows from introduced populations had more significant differences in DNA methylation between 0- and 8-hour samples, with a stronger magnitude of change, compared to house sparrows from native populations (Table 1, Figure 1). We detected 9 differently methylated CpG sites among all samples with a magnitude of change ranging between -2.01 and 4.37 (Figure 2). In this comparison, the individuals from introduced populations had a magnitude of change ranging between -5.24 and 11.41, and the individuals from native populations had a magnitude of change ranging between -0.63 and 0.08 (Figure 2). The individuals from introduced populations had significantly higher mean change in DNA methylation (introduced 4.61, native -0.1; t-test P = 0.01) and significantly greater variance in change of DNA methylation (introduced 32.10, native 0.07; f-test P < 0.001).
We detected a qualitatively similar, but quantitively stronger, pattern when we analyzed individuals from introduced and native populations separately. We detected 35 differently methylated CpG sites among only individuals from introduced populations with a magnitude of change ranging between -9.31 and 11.41 (Figure 1). We detected only 1 differently methylated CpG site among only individuals from native populations with a magnitude of change of -0.38 (Figure 1). We were not able to directly compare the numerical results between native and introduced, due to the separate analyses. However, we detected more significant CpG sites in the individuals from introduced populations and found higher magnitude and variance in change among the individuals from introduced populations.
Further, house sparrows from introduced populations had more uniquely differently methylated CpG sites. Among all significant tests, there were 4 differently methylated CpG sites shared between the “all individuals” and the “introduced” analysis; and there were 5 unique differently methylated CpG sites for “all individuals” analysis, 31 unique differently methylated CpG sites for the “introduced” analysis, and only 1 unique differently methylated CpG site for the “native” analysis.