Introduction
Thermal acclimation allows organisms to overcome periods of extreme climatic conditions (Hoffmann and Sgró, 2011; Overgaard et al., 2011; Anderson et al., 2012), which is essential for maximizing fitness in fluctuating environments (Lande, 2009; Chevin et al., 2010). These types of plastic responses not only occur within the lifespan of an individual through within-generation plasticity (WGP) but also across multiple generations by transgenerational plasticity (TGP) (Mousseau and Fox, 1998; Uller, 2008; Nelson and Nadeau, 2010; Bonduriansky et al., 2011; Heard and Martienssen, 2014). WGP has long been investigated across a diverse number of taxa and a wide range of traits (Hoffmann et al., 2005; Dillon et al., 2007; Bowler and Terblanche, 2008; Fusco and Minelli, 2010). However, the adaptive significance and underlying transcriptional bases of TGP when co-occurring with WGP are less understood.
The interaction between WGP and TGP and their co-occurrence differ across taxa (Walsh et al., 2015, 2016), with some studies reporting the decoupling of WGP and TGP. However, evidence for the co-occurrence of WGP and TGP is rapidly increasing in different organisms (Jablonka et al., 1995; Molinier et al., 2006; Carone et al., 2010; Herman and Sultan, 2011; Herman et al., 2013; Uller et al., 2013; Heckwolf et al., 2018). When co-existing, there is extensive variation in the magnitude and direction of plasticity within and across generations (Galloway and Etterson, 2007; Uller et al., 2013; Walsh et al., 2015; Gillis and Walsh, 2018; Diaz et al., 2020; Rösvik et al., 2020), which reflects different degrees of adaptability, generating cases of silver spoon (Walsh et al., 2024), bet-hedging (Joschinski and Bonte, 2020), or negative carry-over effects (Waite and Sorte, 2022). From these, scenarios of co-existing adaptive plasticity are particularly interesting to understand how evolution simultaneously shapes the transcriptional landscape of these two types of plasticity. For example, current models predict the evolution of adaptive TGP as an anticipatory response to overcome periods of otherwise unfavorable conditions in the offspring when the parent-to-offspring environmental predictability increases (Uller, 2008; Badyaev and Uller, 2009; Bonduriansky et al., 2011; Hoyle and Ezard, 2012; Kuijper and Hoyle, 2015; Proulx and Teotónio, 2017). This hypothesis has been formally tested using thermal tolerance data (Diaz et al., 2020). However, its predictions at the transcriptional level are currently lacking evidence.
When evolving simultaneously, the outcome from adaptive WGP and TGP allows organisms to overcome unfavorable thermal conditions due to a predictive acclimation period in the same or the parental generation (Mousseau and Fox, 1998; Uller, 2008; Nelson and Nadeau, 2010; Bonduriansky et al., 2011; Heard and Martienssen, 2014; Clark et al., 2019). Despite the recent increase in studies comparing multiple acclimation responses, it is still unclear to what extent selection targets the same regulatory networks during the acclimation process in both cases. Selection may modulate the level and direction of expression on different sets of genes during WGP and TGP or the same genes but inducing divergent transcriptional paths (Bell and Stein, 2017; Hales et al., 2017). Only a few studies have addressed this question, and even fewer have considered cases where both WGP and TGP are adaptive. So far, studies of predator-induced plasticity in Daphnia (Bell and Stein, 2017; Hales et al., 2017) and extended Dauer diapause in C. elegans (Webster et al., 2018) suggest independent transcriptional mechanisms for WGP and TGP. Similarly, recent evidence from thermal acclimation in sticklebacks (Shama et al., 2016), sea urchins (Clark et al., 2019), and coral reef fish (Bernal et al., 2022) suggests the decoupling of transcriptional plasticity within and across generations. Another fundamental gap in these studies is the role played by mechanisms of alternative splicing (AS) (Telonis-Scott et al., 2009) or intron retention (IR). Although these mechanisms of transcriptional change are often overlooked, there is substantial evidence connecting AS with thermal plasticity in animals (Anduaga et al., 2019; Steward et al., 2022) and plants (Dikaya et al., 2021; John et al., 2021), including a specific role of IR in the control of gene expression (Yablonovitch et al., 2017; Anduaga et al., 2019). The contribution of these mechanisms to TGP is rarely considered, but there is evidence from the coral reef fish suggesting a small but complementary role of AS in transgenerational acclimation (Ryu et al., 2018).
In this study, we address these fundamental questions by considering a scenario with previous phenotypic evidence of adaptive thermal acclimation within and across generations in the desert endemicDrosophila mojavensis (Diaz et al., 2020). In our previous study, we compared larval and adult plasticity, which allowed us to test predictions on the level of TGP between life stages. We demonstrate that the parental environment is more likely to reflect that of the offspring in the early stages than adulthood, which correlates with differences in TGP between life stages. Here, we take advantage of this scenario to investigate how evolution shapes the transcriptional landscape when adaptive WGP and TGP evolve simultaneously. First, we expand our scope to a more complete view of transcriptional plasticity by investigating the relative contributions of differential expression (DE) and alternative splicing (AS) mechanisms to WGP and TGP. Second, we test if patterns of transcriptional plasticity within and across generations reflect our predictions from heat tolerance data between life stages, where major transcriptional changes are expected in larval TGP due to their higher parent-to-offspring environmental predictability. Third, we estimate the number and transcriptional changes of genes responding to WGP and TGP to investigate differences in the level, direction, and splicing of gene expression associated with thermal acclimation within and across generations. Our results contribute to expanding the understanding of transcriptional evolution when multiple sources of acclimation co-exist and how organisms may adapt to climate change scenarios (Hoffmann and Sgró, 2011; Sgrò et al., 2016; Donelson et al., 2018; Bonamour et al., 2019).