Juntao Hu

Rapid environmental change poses unprecedented challenges for species persistence, threatening not only population size but the genomic adaptive variation required for evolutionary responses. Understanding this adaptive potential is crucial for effective management and conservation strategies, as it determines a population's capacity to cope with current and future climate shifts, habitat loss, emerging diseases and other environmental pressures. This Special Issue is therefore timely in the context of advancing genetic diversity monitoring recommendations (e.g., UN Convention on Biological Diversity Target 4), bringing together 40 original papers, perspectives and reviews that link genomic insights to conservation status and practice. The contributions span empirical studies, mechanistic investigations, theoretical frameworks and applied case studies. Together, these studies highlight how genomic approaches can illuminate the mechanisms and distribution of adaptive variation and inform strategies to maintain population resilience and guide effective management under environmental change.

Seasonal migration represents one of the most fascinating behaviours observed throughout the animal kingdom. Understanding the spatial ecological and evolutionary dynamics of seasonally migratory animals is important to predict their responses to anthropogenic climate change. Unlike the directional and closed‐circuit round‐trip migratory pattern in most seasonally migratory animal species, many migratory insects exhibit a tangled reticular movement instead of a simple transition between sites. Consequently, the interplay between gene flow and natural selection in seasonal dispersal of insects may display a unique pattern and affect the potential of migratory insects to climate change. To characterise such pattern and evaluate the adaptive potential of seasonally migratory insects to future climate, we used genomic data from 32 populations of the seasonal dispersal and invasive oriental fruit fly ( Bactrocera dorsalis ) sampled across year‐round and seasonal areas in the mountains of southwest China (MSWC). Despite significant ecological niche differences between populations of year‐round and seasonal areas, we found no significant population structure both within and across areas. In addition, genomic landscape and vulnerability analyses suggested that the northwestern and northeastern populations possessed distinct genetic compositions and reduced adaptive potential compared to the southern populations. Finally, we predicted the migration distance and direction that may allow the current populations to persist under future climates. Our findings demonstrate that gene flow plays a predominant role in homogenising genetic variation at genome‐wide scale while natural selection shapes genetic variation patterns at specific loci possibly involved in adaptation in seasonally migratory insects.

Anthropogenic salinisation of freshwater ecosystems represents a major threat to biodiversity. While the ecological consequences of freshwater salinisation have received extensive investigation, our knowledge of the evolutionary responses to projected salinisation is more limited. Phenotypic plasticity can be an important first step to facilitate population persistence in stressful environments. Here, we combined high‐resolution environmental data with a laboratory‐based experiment to investigate the time‐course of gene expression plasticity in response to projected salinisation in two populations of the western mosquitofish ( Gambusia affinis ) with different histories of salt exposure. We found significant differences in transcriptional plasticity between populations as well as a general tendency for non‐parallel expression change in salinity‐responsive genes identified in both populations. Despite this pattern, we identified a core set of genes that showed parallel responses to salinity in both populations across all time points. However, these parallel responses in gene expression were putatively regulated by largely non‐overlapping sets of microRNAs in each population. Finally, we found that genes expressed in parallel showed greater nucleotide diversity than genes with non‐parallel responses, possibly providing standing genetic variation to facilitate population persistence under changing salinity conditions. Our results provide insights into the evolutionary consequences of freshwater salinisation and demonstrate the potential of freshwater fish to cope with projected salinisation.

Climate change imposes a significant threat to global biodiversity. Evolutionary processes, including adaptation and migration, have been integrated to study vulnerability to changing environments. However, the role of plasticity as a source of variation in fitness‐related traits remains less explored when assessing climate change vulnerability. Epigenetic modifications can mediate both evolved and plastic responses to environmental change, thereby contributing crucially to species persistence. Here, we estimated the influence of epigenetic plasticity on the responses of threespine stickleback (Gasterosteus aculeatus) to climate change. We showed that vulnerability to projected climates was the greatest if only plastic loci were available to populations; however, the increased vulnerability could be mitigated by short‐distance migration. Our study advances beyond current range modelling by incorporating plasticity into predictions of species' responses to climate change and demonstrates the contrasting roles of different evolutionary processes in shaping responses to projected environments.

Populations colonizing contrasting environments are likely to undergo adaptive divergence and evolve ecotypes with locally adapted phenotypes. While diverse molecular mechanisms underlying ecotype divergence have been identified, less is known about their interplay and degree of divergence. Here we integrated epigenomic and transcriptomic data to explore the interactions among gene expression, alternative splicing, DNA methylation, and microRNA expression to gauge the extent to which patterns of divergence at the four molecular levels are aligned in a case of postglacial divergence between marine and freshwater ecotypes of nine-spined sticklebacks (Pungitius pungitius). Despite significant genome-wide associations between epigenomic and transcriptomic variation, we found largely non-parallel patterns of ecotype divergence across epigenomic and transcriptomic levels, with predominantly nonoverlapping (ranging from 43.40 to 87.98%) sets of differentially expressed, spliced and methylated genes, and candidate genes targeted by differentially expressed miRNA between the ecotypes. Furthermore, we found significant variation in the extent of ecotype divergence across different molecular mechanisms, with differential methylation and differential splicing showing the highest and lowest extent of divergence between ecotypes, respectively. Finally, we found a significant enrichment of genes associated with ecotype divergence in differential methylation. Our results suggest a nuanced relationship between epigenomic and transcriptomic processes, with alignment at the genome-wide level masking relatively independent effects of different molecular mechanisms on ecotype divergence at the gene level.

Repeatability of adaptation to similar environments provides opportunity to evaluate the predictability of natural selection. While many studies have investigated gene expression differences between populations adapted to contrasting environments, the role of post‐transcriptional processes such as alternative splicing has rarely been evaluated in the context of parallel adaptation. To address the aforementioned knowledge gap, we reanalysed transcriptomic data from three pairs of threespine stickleback (Gasterosteus aculeatus) ecotypes adapted to marine or freshwater environment. First, we identified genes with repeated expression or splicing divergence across ecotype pairs, and compared the genetic architecture and biological processes between parallelly expressed and parallelly spliced loci. Second, we analysed the extent to which parallel adaptation was reflected at gene expression and alternative splicing levels. Finally, we tested how the two axes of transcriptional variation differed in their potential for evolutionary change. Although both repeated differential splicing and differential expression across ecotype pairs showed tendency for parallel divergence, the degree of parallelism was lower for splicing than expression. Furthermore, parallel divergences in splicing and expression were likely to be associated with distinct cis‐regulatory genetic variants and functionally unique set of genes. Finally, we found that parallelly spliced genes showed higher nucleotide diversity than parallelly expressed genes, indicating splicing is less susceptible to genetic variation erosion during parallel adaptation. Our results provide novel insight into the role of splicing in parallel adaptation, and underscore the contribution of splicing to the evolutionary potential of wild populations under environmental change.

Climate change is intensifying the frequency and severity of extreme temperatures. Understanding the molecular mechanisms underlying the ability to cope with acute thermal stress is key for predicting species' responses to extreme temperature events. While many studies have focused on the individual roles of gene expression, post‐transcriptional processes and epigenetic modifications in response to acute thermal stress, the relative contribution of these molecular mechanisms remains unclear. The wide range of thermal limits of western mosquitofish (Gambusia affinis) provides an opportunity to explore this interplay. Here, we quantified changes in gene expression, alternative splicing, DNA methylation and microRNA (miRNA) expression in muscle tissue dissected from mosquitofish immediately after reaching high (CTmax) or low thermal limit (CTmin). Although the numbers of genes showing expression and splicing changes in response to acute temperature stress were small, we found a possibly larger and non‐redundant role of splicing compared to gene expression, with more genes being differentially spliced (DSGs) than differentially expressed (DEGs), and little overlap between DSGs and DEGs. We also identified a small proportion of CpGs showing significant methylation change (i.e. differentially methylated cytosines, DMCs) in fish at thermal limits; however, there was no overlap between DEGs and genes annotated with DMCs in both CTmax and CTmin experiments. The weak interplay between epigenetic modifications and gene expression was further supported by our discoveries of no differentially expressed miRNAs. These findings provide novel insights into the relative role of different molecular mechanisms underlying immediate responses to extreme temperatures and demonstrate non‐concordant responses of epigenetic and transcriptional mechanisms to acute temperature stress.

Many studies have documented the average body size of animals declining over time. Compared to mean body size, less is known about long-term changes in intraspecific trait variation (ITV), which is also important to understanding species’ ability to cope with environmental challenges. On the basis of 393,499 specimen records from 380 species collected in North America between 1880 and 2020, we found that body size ITV increased by 9.59% for mammals (n = 302) and 30.67% for birds (n = 78); human-harvested species had higher probability of ITV increase. The observed increasing ITV in many species suggests possible niche expansion and potential buffering effects against downsizing but it risks increased maladaptation to rapidly changing environments. The results demonstrate that trait mean and variance do not necessarily respond in similar ways to anthropogenic pressures and both should be considered.

Repeated phenotypic patterns among populations undergoing parallel evolution in similar environments provide support for the deterministic role of natural selection. Epigenetic modifications can mediate plastic and evolved phenotypic responses to environmental change and might make important contributions to parallel adaptation. While many studies have explored the genetic basis of repeated phenotypic divergence, the role of epigenetic processes during parallel adaptation remains unclear. The parallel evolution of freshwater ecotypes of threespine stickleback fish (Gasterosteus aculeatus) following colonization of thousands of lakes and streams from the ocean is a classic example of parallel phenotypic and genotypic adaptation. To investigate epigenetic modifications during parallel adaptation of threespine stickleback, we reanalysed three independent data sets that investigated DNA methylation variation between marine and freshwater ecotypes. Although we found widespread methylation differentiation between ecotypes, there was no significant tendency for CpG sites associated with repeated methylation differentiation across studies to be parallel versus nonparallel. To next investigate the role of plastic versus evolved changes in methylation during freshwater adaptation, we explored if CpG sites exhibiting methylation plasticity during salinity change were more likely to also show evolutionary divergence in methylation between ecotypes. The directions of divergence between ecotypes were generally in the opposite direction to those observed for plasticity when ecotypes were challenged with non‐native salinity conditions, suggesting that most plastic responses are likely to be maladaptive during colonization of new environments. Finally, we found a greater number of CpG sites showing evolved changes when ancestral marine ecotypes are acclimated to freshwater environments, whereas plastic changes predominate when derived freshwater ecotypes transition back to their ancestral marine environments. These findings provide evidence for an epigenetic contribution to parallel adaptation and demonstrate the contrasting roles of plastic and evolved methylation differences during adaptation to new environments.