Conclusion
Clearly, our study raises more questions than it answers. Several
drivers of expression were identified, but in a direction opposite of
predictions (e.g., tissue, temperature predictability, native/non
status, urbanization). Likewise, factors expected to have some
explanatory power on expression (e.g., sex of bird, precipitation
predictability) had little to none. There are a few next steps that
could be particularly enlightening to understand the role of DNMTs and
TET2 in this or related systems. First, experiments involving
transcriptional repression of DNMT expression or exclusion of DNMTs from
nuclei so methyl marks naturally degrade (Law and Jacobsen 2010) could
reveal both the role of DNMTs in phenotypic plasticity in various cells
of house sparrows but also the success of individual birds in new
ecological contexts (Luo et al. 2012). Genetically-modified animals
cannot ethically be released from captivity, but creative approaches to
studying sparrow domestication or the colonization of captive spaces
could be insightful. Relatedly, DNMT/TET expression could be studied in
embryonic and nestling birds (Wilks et al. 2023, Siller Wilks et al.
2024). Our bias to studying adults here probably missed important among
and within population differences, but the study of adults is justified
from other work (Sun et al. 2021). It will also be important to consider
alternative, functional roles for DNMTs besides plasticity. InDaphnia magna (Agrelius et al. 2023), DNMT3 expression was higher
in calorically-restricted individuals, altering the life history
trajectories faced by individuals depending on the environments in which
they were reared (Nguyen et al. 2021).
A final lens through which to view DNMT/TET expression relates to the
concept of epigenetic potential (Kilvitis et al. 2017), genetic
variation among individuals in the propensity for their genomes to be
methylated. Originally, we proposed genetic polymorphisms in DNMTs as a
possible, ecologically relevant form of epigenetic potential, but
neither we nor others have yet to search for DNMT genetic variants in
invaders. One recent study of great tits (Sepers et al. 2023) revealed
nine SNPs in DNMT3a, two of which were associated with methylation of
two distant CpGs. One of these CpGs occurred in an exon of the gene,
SELPLG, and another intronically in CTNNA3. Whether these SNPs affect
expression of these genes, the expression of DNMT3 itself, or the
physiological functions any of these genes was not considered.
Nevertheless, in future work, it would be valuable to determine whether
different DNMT forms are directionally selected, just as the CpG content
of gene promoters was in the Kenyan house sparrow range expansion
(Kilvitis et al. 2017).
It is an exciting time for ecological epigenetics, as the technical
toolkit it requires is expanding rapidly (Loughland et al. 2021). We are
also becoming better able to ‘iteratively measure plastic traits’
(Dupont et al. 2024) and distinguish plasticity via epigenetic processes
as the outcome of ‘directional induction or bet-hedging stochasticity’
(Vogt 2021). We are only just beginning to appreciate, though, that
plasticity is probably important to so many biological processes because
it underpins organismal agency (Mitchell 2023, Kirchhoff et al. 2018,
Friston 2010, Ball 2023). Strong eco-evolutionary roles of plasticity
are well known across biological systems (Wade and Sultan 2023), but as
we come to understand how methylating enzymes help sculpt the
epigenotype in nature, we could be taking a small but important step to
revealing how organisms use a variety of entangled, cognitive
plasticities (Watson and Szathmáry 2016) to achieve resilience through
antifragility (Taleb 2014) and thus endure natural and ongoing
anthropogenic change.