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.