Limitations and future directions for ADH research
Although the patterns of gene-expression decoupling we observed inN. lecontei are consistent with the ADH, additional data are
needed to: (1) verify that decoupled gene-expression phenotypes are
independent at the genetic level, (2) demonstrate that decoupled
gene-expression traits contribute to stage-specific adaptations, and (3)
establish that metamorphosis is an adaptation for trait decoupling.
Here, we discuss strategies for evaluating each of these additional ADH
predictions.
First, if stage-specific levels of expression for a particular gene are
genetically independent, alleles that contribute to expression variation
in one life stage should not have pleiotropic effects on expression in
another life stage (and vice versa). One way to evaluate this prediction
is to perform quantitative trait locus (QTL) mapping on gene-expression
traits at different life stages. Genetic independence would be supported
if QTL for gene-expression traits measured at different stages are
non-overlapping (e.g., (Freda et al., 2017; Saenko et al., 2012)). One
example of this approach is a 2017 study that investigated genetic
decoupling of thermal hardiness between larval and adult D.
melanogaster (Freda et al., 2017). Whereas D. melanogasterlarvae live in thermally stable rotting fruits and are only present in
the warm months, flying adults experience a more variable thermal
environment and are exposed to low temperatures during the overwintering
generation. Consistent with these strong opposing selection pressures,
thermal hardiness is completely decoupled across metamorphosis in this
species. Moreover, decoupling of the thermal-hardiness phenotype is
mirrored at a genetic level: loci that contribute to cold hardiness in
larvae do not appear to have pleiotropic effects on adults, and vice
versa (Freda et al., 2017). Interpreted in light of fruit-fly ecology,
decoupled thermal hardiness phenotypes and alleles provide strong
support for the ADH.
Second, the prediction that decoupled gene-expression traits contribute
to stage-specific adaptation could be evaluated using multiple
complementary approaches. For example, if decoupled genes contribute
disproportionately to adaptation, genes exhibiting the most stage-biased
expression patterns should also reveal a history of positive selection
(e.g., evidence of recent selective sweeps or elevated rates of
non-synonymous substitutions relative to the rest of the genome) (Vitti,
Grossman, & Sabeti, 2013). Although this prediction has been confirmed
by several studies for sex-biased genes (Assis et al., 2012; Drosophila
12 Genomes et al., 2007; Mank, Nam, Brunstrom, & Ellegren, 2010;
Proschel et al., 2006; L. Yang, Zhang, & He, 2016), it has rarely been
tested in the context of stage-biased expression across metamorphic
boundaries (but see (Perry et al., 2014)). An alternative approach would
be to use experimental genomics to connect genetic variants directly to
fitness at different life stages (e.g., (Egan et al., 2015; Gloss,
Groen, & Whiteman, 2016; Gompert et al., 2019; Ingvarsson, Hu, Lei, &
de Meaux, 2017)). Following exposure to a selection regime that favors
different traits at different ontogenetic stages, the ADH predicts that
genes with the most decoupled expression will exhibit the most
pronounced allele frequency shifts.
Third, to more directly test the hypothesis that metamorphosis itself is
an adaptation for optimizing trait decoupling, comparative data can be
used two evaluate two additional predictions: (1) metamorphosis is
favored under ecological conditions that result in pervasive
antagonistic pleiotropy across the life cycle and (2) metamorphosis
facilitates trait decoupling. To disentangle the ecological and genetic
correlates of metamorphosis from shared phylogenetic history,
comparative tests of the ADH should focus on lineages that contain
multiple independent origins of particular metamorphic phenotypes. For
example, within holometabolous insects, hypermetamorphosis has evolved
multiple times (Belles, 2011). Likewise, gains and losses of complex
life cycles have been demonstrated in numerous taxa and are particularly
well documented in insects and amphibians (Badets & Verneau, 2009;
Bonett & Blair, 2017; Emmanuelle, Gwenaelle, & Armelle, 2010; Moran,
1994; Poulin & Cribb, 2002; Wiens, Kuczynski, Duellman, & Reeder,
2007).