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Copepods, small aquatic crustaceans, are one of the most abundant zooplankton in the world. These animals play a critical ecological role in aquatic ecosystems such as oceans, streams, or, as in this study, alpine lakes. In these ecosystems, copepods have adapted to stressful and dynamic environments, a process which can be investigated via comparative transcriptomics. An assembled transcriptome is a pre-requisite to applying transcriptomic tools in physiological research, but there are few transcriptome assemblies available for copepods. To address this gap, we assembled a de novo transcriptome of Cyclops abyssorum tatricus by merging Pacific Bioscience long reads from copepods collected in two lakes at two different time points. The final assembly consisted of 52,521 contigs with a BUSCO score of 80.7%. We annotated a total of 26,255 (49.99%) protein sequences using the eggNOG database. Gene ontology analyses revealed that most gene annotations were involved in cellular processes and signaling (34.61%). Comparisons with two other copepod species showed that the transcriptome assembly of C. abyssorum tatricus is enriched for cold acclimation genes, consistent with its long-term adaptation to cold water environments. This de novo transcriptome will enable comparative transcriptomic studies in this species, allowing us to investigate physiological adaptations to alpine environments.

The extent to which acclimation and genetic adaptation might buffer natural populations against climate change is largely unknown. Most models predicting biological responses to environmental change assume that species' climatic envelopes are homogeneous both in space and time. Although recent discussions have questioned this assumption, few empirical studies have characterized intraspecific patterns of genetic variation in traits directly related to environmental tolerance limits. We test the extent of such variation in the broadly distributed tidepool copepod Tigriopus californicus using laboratory rearing and selection experiments to quantify thermal tolerance and scope for adaptation in eight populations spanning more than 17° of latitude. Tigriopus californicus exhibit striking local adaptation to temperature, with less than 1 per cent of the total quantitative variance for thermal tolerance partitioned within populations. Moreover, heat-tolerant phenotypes observed in low-latitude populations cannot be achieved in high-latitude populations, either through acclimation or 10 generations of strong selection. Finally, in four populations there was no increase in thermal tolerance between generations 5 and 10 of selection, suggesting that standing variation had already been depleted. Thus, plasticity and adaptation appear to have limited capacity to buffer these isolated populations against further increases in temperature. Our results suggest that models assuming a uniform climatic envelope may greatly underestimate extinction risk in species with strong local adaptation.

Theory suggests that evolutionary changes in phenotypic plasticity could either hinder or facilitate evolutionary rescue in a changing climate. Nevertheless, the actual role of evolving plasticity in the responses of natural populations to climate change remains unresolved. Direct observations of evolutionary change in nature are rare, making it difficult to assess the relative contributions of changes in trait means versus changes in plasticity to climate change responses. To address this gap, this review explores several proxies that can be used to understand evolving plasticity in the context of climate change, including space for time substitutions, experimental evolution and tests for genomic divergence at environmentally responsive loci. Comparisons among populations indicate a prominent role for divergence in environmentally responsive traits in local adaptation to climatic gradients. Moreover, genomic comparisons among such populations have identified pervasive divergence in the regulatory regions of environmentally responsive loci. Taken together, these lines of evidence suggest that divergence in plasticity plays a prominent role in adaptation to climatic gradients over space, indicating that evolving plasticity is also likely to play a key role in adaptive responses to climate change through time. This suggests that genetic variation in plastic responses to the environment (G × E) might be an important predictor of species' vulnerabilities to climate-driven decline or extinction. This article is part of the theme issue ‘The role of plasticity in phenotypic adaptation to rapid environmental change’.

1. Ocean acidification, caused by the uptake of atmospheric CO 2 , is a threat to marine biodiversity, potentially rivalling the threat imposed by rising temperatures in some marine ecosystems. Although a growing body of literature documents negative effects of acidification on marine organisms, the majority of this work has focused on the effects of future conditions on modern populations, ignoring the potential effects of adaptation and physiological acclimatization. 2. We review current literature on the potential for adaptation to elevated pCO 2 in marine organisms. Although this body of work is currently quite small, we argue that data on the physiological effects of acidification, natural variation in pH and lessons learned from previous work on thermal adaptation can all inform predictions and priorities for future research. 3. Spatially varying selection is one of the most important forces maintaining intraspecific genetic variation. Unlike temperature, pH lacks a strong and persistent global gradient, and so selection may maintain less adaptive variation for pH than for temperature. On the other hand, we are only beginning to amass long-term data sets for pH variation in natural habitats, and thus, pH gradients may be more common than previously observed. 4. Two of the most important effects of elevated pCO 2 are reduced calcification and changes in metabolism. We discuss the ways that a detailed understanding of the physiological mechanisms underlying these effects is key to predicting the capacity for acclimatization and adaptation. 5. Important priorities for future research will be to assess local adaptation to pH conditions and to measure the capacity for adaptation to future acidified conditions in natural populations. Tools for this work include traditional quantitative genetics, transcriptomics and the adaptation of ion-sensitive field-effect transistor (ISFET) technology for use in continuous seawater pH monitoring in the field.

Neophobia (aversion to new objects, food, and environments) is a personality trait that affects the ability of wildlife to adapt to new challenges and opportunities. Despite the ubiquity and importance of this trait, the molecular mechanisms underlying repeatable individual differences in neophobia in wild animals are poorly understood. We evaluated wild-caught house sparrows ( Passer domesticus ) for neophobia in the lab using novel object tests. We then selected a subset of neophobic and non-neophobic individuals (n = 3 of each, all females) and extracted RNA from four brain regions involved in learning, memory, threat perception, and executive function: striatum, caudal dorsomedial hippocampus, medial ventral arcopallium, and caudolateral nidopallium (NCL). Our analysis of differentially expressed genes (DEGs) used 11,889 gene regions annotated in the house sparrow reference genome for which we had an average of 25.7 million mapped reads/sample. PERMANOVA identified significant effects of brain region, phenotype (neophobic vs. non-neophobic), and a brain region by phenotype interaction. Comparing neophobic and non-neophobic birds revealed constitutive differences in DEGs in three of the four brain regions examined: hippocampus (12% of the transcriptome significantly differentially expressed), striatum (4%) and NCL (3%). DEGs included important known neuroendocrine mediators of learning, memory, executive function, and anxiety behavior, including serotonin receptor 5A, dopamine receptors 1, 2 and 5 (downregulated in neophobic birds), and estrogen receptor beta (upregulated in neophobic birds). These results suggest that some of the behavioral differences between phenotypes may be due to underlying gene expression differences in the brain. The large number of DEGs in neophobic and non-neophobic birds also implies that there are major differences in neural function between the two phenotypes that could affect a wide variety of behavioral traits beyond neophobia.

Populations may respond to environmental heterogeneity via evolutionary divergence or phenotypic plasticity. While evolutionary divergence occurs through DNA sequence differences among populations, plastic divergence among populations may be generated by changes in the epigenome. Here, we present the results of a genome‐wide comparison of DNA methylation patterns and genetic structure among four populations of Eastern oyster (Crassostrea virginica) in the northern Gulf of Mexico. We used a combination of restriction site‐associated DNA sequencing (RADseq) and reduced representation bisulfite sequencing (RRBS) to explore population structure, gene‐wide averages of FST, and DNA methylation differences between oysters inhabiting four estuaries with unique salinity profiles. This approach identified significant population structure despite a moderately low FST (0.02) across the freshwater boundary of the Mississippi river, a finding that may reflect recent efforts to restore oyster stock populations. Divergence between populations in CpG methylation was greater than for divergence in FST, likely reflecting environmental effects on DNA methylation patterns. Assessment of CpG methylation patterns across all populations identified that only 26% of methylated DNA was intergenic; and, only 17% of all differentially methylated regions (DMRs) were within these same regions. DMRs within gene bodies between sites were associated with genes known to be involved in DNA damage repair, ion transport, and reproductive timing. Finally, when assessing the correlation between genomic variation and DNA methylation between these populations, we observed population‐specific DNA methylation profiles that were not directly associated with single nucleotide polymorphisms or broader gene‐body mean FST trends. Our results suggest that C. virginica may use DNA methylation to generate environmentally responsive plastic phenotypes and that there is more divergence in methylation than divergence in allele frequencies.

Triploid oysters are commonly used as the basis for production in the aquaculture of eastern oysters along the USA East and Gulf of Mexico coasts. While they are valued for their rapid growth, incidents of triploid mortality during summer months have been well documented in eastern oysters, especially at low salinity sites. We compared global transcriptomic responses of diploid and triploid oysters bred from the same three maternal source populations at two different hatcheries and outplanted to a high (annual mean salinity = 19.4 ± 6.7) and low (annual mean salinity = 9.3 ± 5.0) salinity site. Oysters were sampled for gene expression at the onset of a mortality event in the summer of 2021 to identify triploid‐specific gene expression patterns associated with low salinity sites, which ultimately experienced greater triploid mortality. We also examined chromosome‐specific gene expression to test for instances of aneuploidy in experimental triploid oyster lines, another possible contributor to elevated mortality in triploids. We observed a strong effect of hatchery conditions (cohort) on triploid‐specific mortality (field data) and a strong interactive effect of hatchery, ploidy, and outplant site on gene expression. At the low salinity site where triploid oysters experienced high mortality, we observed downregulation of transcripts related to calcium signaling, ciliary activity, and cell cycle checkpoints in triploids relative to diploids. These transcripts suggest dampening of the salinity stress response and problems during cell division as key cellular processes associated with elevated mortality risk in triploid oysters. No instances of aneuploidy were detected in our triploid oyster lines. Our results suggest that triploid oysters may be fundamentally less tolerant of rapid decreases in salinity, indicating that oyster farmers may need to limit the use of triploid oysters to sites with more stable salinity conditions.

Imidacloprid (IMD) is a neonicotinoid pesticide soil-drenched to many crops to control piercing-sucking insects such as the Asian citrus psyllid (ACP). Neonicotinoids are persistent in the environment and transport analyses are helpful estimate leaching potential from soils that could result in groundwater pollution. The objective of this study was to analyze IMD breakthrough under saturated water flow in soil columns packed with three horizons (A, E, Bh) of Immokalee Fine Sand (IFS). Also, we used the dimensionless form of the convective-dispersive model (CD-Model) to compare the optimized transport parameters from each column experiment (retardation factor, R; fraction of instantaneous-to-total retardation, β; and mass transfer coefficient, ω) with the parameters obtained from sorption batch equilibria and sorption kinetics. The tracer (Cl-) breakthrough curves (BTCs) were symmetrical and properly described by the CD-Model. IMD BTCs from A, Bh, and multilayered [A+E+Bh] soil columns showed steep fronts and tailing that were well described by the one-site nonequilibrium (OSNE) model, which was an evidence of non-ideal transport due to IMD mass transfer into the soil organic matter. In general, IMD was weakly-sorbed in the A and Bh horizons (R values of 3.72 ± 0.04 and 3.08 ± 0.07, respectively), and almost no retardation was observed in the E horizon (R = 1.20 ± 0.02) due to its low organic matter content (0.3%). Using the HYDRUS-1D package, optimized parameters (R, β, ω) from the individual columns successfully simulated IMD transport in a multilayered column mimicking an IFS soil profile. These column studies and corresponding simulations agreed with previous findings from batch sorption equilibria and kinetics experiments, where IMD showed one-site kinetic mass transfer between soil surfaces and soil solution. Ideally, sandy soils should be maintained unsaturated by crop irrigation systems and rainfall monitoring during and after soil-drench application. The unsaturated soil will increase IMD retardation factors and residence time for plant uptake, lowering leaching potential from soil layers with low sorption capacity, such as the E horizon.

Background Digital technologies such as wearables, websites and mobile applications are increasingly used in interventions targeting physical activity (PA). Increasing access to such technologies makes an attractive prospect for helping individuals of low socioeconomic status (SES) in becoming more active and healthier. However, little is known about their effectiveness in such populations. The aim of this systematic review was to explore whether digital interventions were effective in promoting PA in low SES populations, whether interventions are of equal benefit to higher SES individuals and whether the number or type of behaviour change techniques (BCTs) used in digital PA interventions was associated with intervention effects. Methods A systematic search strategy was used to identify eligible studies from MEDLINE, Embase, PsycINFO, Web of Science, Scopus and The Cochrane Library, published between January 1990 and March 2020. Randomised controlled trials, using digital technology as the primary intervention tool, and a control group that did not receive any digital technology-based intervention were included, provided they had a measure of PA as an outcome. Lastly, studies that did not have any measure of SES were excluded from the review. Risk of Bias was assessed using the Cochrane Risk of Bias tool version 2. Results Of the 14,589 records initially identified, 19 studies were included in the final meta-analysis. Using random-effects models, in low SES there was a standardised mean difference (SMD (95%CI)) in PA between intervention and control groups of 0.06 (− 0.08,0.20). In high SES the SMD was 0.34 (0.22,0.45). Heterogeneity was modest in both low (I 2  = 0.18) and high (I 2  = 0) SES groups. The studies used a range of digital technologies and BCTs in their interventions, but the main findings were consistent across all of the sub-group analyses (digital interventions with a PA only focus, country, chronic disease, and duration of intervention) and there was no association with the number or type of BCTs. Discussion Digital interventions targeting PA do not show equivalent efficacy for people of low and high SES. For people of low SES, there is no evidence that digital PA interventions are effective, irrespective of the behaviour change techniques used. In contrast, the same interventions in high SES participants do indicate effectiveness. To reduce inequalities and improve effectiveness, future development of digital interventions aimed at improving PA must make more effort to meet the needs of low SES people within the target population.