Table 1 Differentially methylated genes across natural populations along a salinity cline.

Genes derived from DNA methylation comparisons between natural populations associated with ≥10 pop-DMS [decreased salinity: KIE (20 PSU) versus NYN (6 PSU); increased salinity: KIE (20 PSU) versus SYL (33 PSU)]. Ensembl gene ID and name as well as the position on the chromosome are listed. The numbers refer to the numbers of DMS in the population comparison (wild). These DMS were classified into inducible, inconclusive, and stable sites according to their behavior in a two-generation salinity acclimation experiment with laboratory-bred sticklebacks from the mid-salinity population (20 PSU) exposed to experimental salinity increase or decrease (33 and 6 PSU, respectively). Furthermore, inducible sites were distinguished whether they matched methylation levels of the locally adapted population (expected) or not (opposite). Genes written in bold vary in both population comparisons. We used a Fisher’s exact test to assess whether pop-DMS associated to the same gene are correlated in their response to experimental salinity change (nonrandom distribution among the categories stable, inducible, and inconclusive) and reported corresponding P values. For a full table on all genes associated with one or more pop-DMS, see table S2 (A and B).

Ensembl gene IDChromosomeStart
position
End
position
Gene
name
WildInducibleExpected
inducible
Opposite
inducible
StableInconclusiveFisher’s
exact (P)
Salinity decrease:
ENSGACG00000008328Chr101286014412863850si:dkey-166 k12.1240009150.005
ENSGACG00000019416Chr744518924453656HMX1 ortholog17000980.033
ENSGACG00000013229Chr181532771715352321150003120.011
ENSGACG00000017287Chr31345452713465167mmp16b120001200.001
ENSGACG00000017584Chr31469081414694448CCNY1212120000.001
ENSGACG00000018249Chr41214162512143011si:ch211-153b23.512110380.188
ENSGACG00000008034Chr6936818793809411110100010.014
ENSGACG00000009469Chr191665769173856egln2110001100.001
ENSGACG00000004433Chr1721274572211376igsf21a1010100000.003
ENSGACG00000007343Chr101066699510679875col9a210000640.227
ENSGACG00000018407Chr41382833613837518Sncb10220530.848
Salinity increase:
ENSGACG00000020323Chr7170101601701117623000221<0.001
ENSGACG00000013229Chr1815327717153523211510100140.125
ENSGACG00000013359Chr111296088312968110sec14l1150001230.011
ENSGACG00000019416Chr744518924453656HMX1 ortholog15330570.745
ENSGACG00000002948Chr8218240221355ddx1014000680.077
ENSGACG00000016350Chr143603545360492314101760.277
ENSGACG00000006636Chr1847808934786820ZC3H12D130003100.034
ENSGACG00000004667Chr1242734984286193tti1120001200.001
ENSGACG00000015566Chr290430629051779casc4100001000.003