Understanding the molecular mechanisms of thermal adaptation is crucial to predict the impacts of global warming. However, there is still a lack of research on the effects of rising temperatures over time, and of studies involving different populations from the same species. The present study focuses on these two aspects, which have been shown to be of great importance in understanding how organisms cope and adapt to ongoing changes in their environment. This study investigates the impact of global warming on the gene expression patterns of Drosophila subobscura populations from two different latitudinal locations after 23 generations of thermal evolution. Our results indicate that transcriptomic changes due to selection are contingent on the genetic background of the populations, with the high-latitude population exhibiting more pronounced changes. We found an interplay between plasticity and selection, with the high latitude population showing fewer initial plastic genes and lower levels of adaptive plasticity, but a greater magnitude of change in both plastic and selective responses during evolution under warming conditions compared to its low latitude counterpart. A substantial proportion of the transcriptome was observed to be subject to selection, despite the lack of observable response at the higher level of organisation. The interplay between plasticity and selection may prove to be an essential component in shaping species' evolutionary responses to climate change. Furthermore, the value of conducting studies on multiple populations of the same species is emphasised, given the identification of differences between populations with different backgrounds in several contexts.

Artificial propagation and wild release may influence the genetic integrity of wild populations. This practice has been prevalent in fisheries for millennia and is often termed “stocking”. In the Laurentian Great Lakes, walleye populations faced declines from the 1950s to the 1970s, prompting extensive stocking efforts for restoration. By the mid-2010s, walleye populations showed signs of recovery, but the genetic legacy of stocking on population structure at the genomic level remains unclear. Using a dataset of 45,600 genome-aligned SNP loci genotyped in 1,075 walleye individuals, we investigated the genetic impacts of over 50 years of stocking across the Great Lakes. Natural geographic barriers shaped walleye population structure, but pairwise comparisons revealed changes in genetic structure due to stocking from non-native sources also significantly contribute to population structure. Admixture between Lake Erie walleye and walleye from the re-populated Tittabawassee River indicate that stocking may have re-distributed putatively adaptive alleles around the Great Lakes. Genome scans identified FST outliers and evidence of selective sweeps, indicating local adaptation of spawning populations is likely. Notably, one genomic region showed strong differentiation between Muskegon River and walleye from the Tittabawassee River which was re-populated by Muskegon Strain walleye, suggesting admixture and selection both impact the observed genetic diversity. Overall, our study underscores how artificial propagation and translocations can significantly alter the evolutionary trajectory of populations. The findings highlight the complex interplay between stocking practices and genetic diversity, emphasizing the need for careful management strategies to preserve the genetic integrity of wild populations amidst conservation efforts.

Species without dimorphic secondary sex characteristics easily visible to humans, such as difference in size or morphology, are expected to experience low levels of sex-specific selection. However, monomorphism in classic visible traits could be a result of genetic or physiological constraints that prevent the sexes from reaching divergent fitness optima. Additionally, biochemical and molecular work has revealed a variety of less easily observed phenotypes that none-the-less exhibit profound dimorphism. Sex-specific selection could act on these more subtle, less visible, traits. We investigate sex-specific selection in the polygynandrous dusky pipefish (Syngnathus floridae), which lacks size, color, and morphological dimorphism. Using experimental breeding populations, we revealed that although males and females have similar opportunities for sexual selection, only males experience significant sexual selection pressures on body size. We also investigated patterns of sex-biased and sex-specific gene expression in gonads, livers, and gills, and tested whether genes with highly divergent expression patterns between the sexes are more likely to be tissue specific, and therefore relieved of genetic constraints. We. Sex-bias in gene expression was widespread, although the reproductive organs had the most sex-biased and sex-specific genes. Sex-specific selection on gene expression in gills was primarily related to immune response, whereas the liver and gonads had a wide variety of cellular processes, as well as reproductive proteins, showing sex-biased expression. These sex-biased genes are likely less constrained by pleiotropy, as they were more organ-specific in their expression patterns. Altogether, we find evidence for ongoing and historical sex-specific selection in the dusky pipefish.

Priority effects, where the order and timing of species arrival influence the assembly of ecological communities, have been observed in a variety of taxa and habitats. However, the genetic and molecular basis of priority effects remains unclear, hindering the mechanistic understanding of priority effects. We sought to gain such an understanding for the nectar yeast Metschnikowia reukaufii, commonly found in the nectar of our study plant, the hummingbird-pollinated Diplacus (Mimulus) aurantiacus. In this plant, M. reukaufii experiences strong priority effects when it reaches flowers after other nectar yeasts, such as M. rancensis. After inoculation into two contrasting types of synthetic nectar simulating early arrival of M. rancensis, we conducted whole-transcriptome sequencing of 108 strains of M. reukaufii. We found that several genes were differentially expressed in M. reukaufii strains when the nectar had been conditioned by growth of M. rancensis. Many of these genes were associated with amino acid metabolism, consistent with our previous finding that early-arriving species limit late-arriving species’ growth by reducing amino acid availability. Furthermore, investigation of expression quantitative trait loci (eQTLs) revealed that genes involved in amino acid transport and resistance to antifungal compounds were enriched in genetic variants, with differing effects on gene expression caused by M. rancensis. We also found that gene expression was associated with population growth rate, particularly when amino acids were limited. These results suggest that intraspecific genetic variation in the ability of nectar yeasts to respond to nutrient limitation and direct fungal competition underpins the molecular mechanisms of priority effects.

Invasive species with native ranges spanning strong environmental gradients that establish in new habitats are particularly well-suited for examining the roles of selection and population history in rapid environmental adaptation, providing insight into potential evolutionary responses to climate change. The Atlantic oyster drill (Urosalpinx cinerea) is a marine snail with a native range spanning the strongest marine thermal gradient in the world that has established invasive populations on the U.S. Pacific coast. Here, we leverage this system using genome-wide SNPs and environmental data to examine invasion history and identify genotype-environment associations indicative of local adaptation across its native range, and then assess evidence for predicted allelic frequency shifts signaling rapid adaptation in invasive populations. We demonstrate strong genetic structuring among native regions aligned with life history expectations and identify southern New England as the source of invasive populations. We also identify putatively thermally adaptive loci across the native range, for which two invasive populations show significant divergence from source populations. However, we find no evidence of directional shifts in allele frequencies as would be predicted by environmental selection, suggesting that divergence is likely due to genetic drift rather than rapid adaptation. Alternatively, the success of new populations in environments differing from their origin may be due to relaxed selection pressures associated with more benign conditions, and/or standing capacity for phenotypic plasticity. This demonstrates the utility of invasive species for understanding evolutionary responses to changing environments, and the importance of considering population history and environmental selection pressures when evaluating adaptative capacity.

Demographic processes can substantially affect a species’ response to changing ecological conditions, necessitating the combined consideration of genetic responses to environmental variables and neutral genetic variation. Using a seascape genomics approach combined with population demographic modelling, we explored the interplay of demographic and environmental factors that shaped the current population structure in Indo-Pacific bottlenose dolphins (Tursiops aduncus) along most of the western Australian coastline. We combined large-scale environmental data gathered via remote sensing with RADseq genomic data from 138 individuals at 19 sampling sites. Using population genetic and outlier detection anaylses, we identified three distinct genetic clusters, coinciding with tropical, subtropical and temperate provincial bioregions. In contrast to previous studies, our demographic models indicated that populations occupying the paleo-shoreline split into two demographically independent lineages before the last glacial maximum (LGM). A subsequent split after the LGM at 8.5 kya gave rise to the Shark Bay population, thereby creating the three currently observed clusters. Although multi-locus heterozygosity declined from north to south, dolphins from the southernmost cluster inhabiting temperate waters had higher heterozygosity in potentially adaptive loci, compared to dolphins from subtropical and tropical waters. These findings suggest ongoing adaptation to cold temperate waters in the southernmost cluster, possibly linked to distinct selective pressures between the different bioregions. Our study demonstrated that in the marine realm, without apparent physical boundaries, only a combined approach can fully elucidate the intricate environmental and genetic interactions shaping the evolutionary trajectory of marine mammals.

Social insects form complex societies with division of labor between different female castes. In most species, a single queen heads the colony; in others, several queens share the task of reproduction. These different social organizations are often associated with distinct queen morphologies and life history strategies and occur in different environments. In the ant Temnothorax rugatulus, two queen morphs - macrogynes and microgynes - exist associated with mono- and polygynous colonies, respectively, which occur at lower and higher elevations. We analyzed plastic changes in brain transcriptomes in response to the social environment in these queen morphs and their workers. We manipulated the number of queens over several weeks to investigate whether transcriptional activity is influenced by queen morph, social environment, or their interaction. Changes in gene expression in the queens’ brains in response to our manipulations were subtle and largely influenced by the interaction between social environment and queen morph, rather than independently by these factors. Macrogynes and microgynes thus adjust differently to their social environment. Similarly, worker transcriptomes were influenced by an interaction between behavioral type, i.e., nurses or foragers, and queen morph. Nurses differentially regulated genes related to nutrition depending on queen morph, suggesting a link between social environment and metabolic dynamics in ant colonies. Overall, our study shed light on how the social environment influences the molecular physiology of social insects. Furthermore, we demonstrate that in this ant with two queen morphs, worker physiology depends on queen morph and their role in the colony.

Symbiotic marine bacteria that are transmitted through the environment are susceptible to possible abiotic factors (salinity, temperature, physical barriers) that separates them from their hosts. Given that many symbioses are driven by host specificity, environmentally transmitted symbionts can alter symbiont preference depending on conditions over space and time. In order to determine whether the population structure of environmentally transmitted beneficial associations reflect host specificity or biogeography, we analyzed the genetic structure of Sepiola atlantica (Cephalopoda: Sepiolidae) and their Vibrio symbionts (V. fischeri and V. logei) in four Galician Rías (Spain). This geographical location is characterized by a jagged coastline with a deep-sea entrance into the land, ideal for testing whether such population barriers exist due to genetic isolation. We used haplotype estimates combined with nested clade analysis to determine the genetic relatedness for both S. atlantica and Vibrio bacteria. Analyses of molecular variance (AMOVA) were used to estimate variation within and between populations for both host and symbiont genetic data. Our analyses reveal a low percentage of variation among host populations, suggesting that these populations are panmictic, whereas between host population variation does exist due to geographical distance. In contrast, Vibrio symbionts are panmictic among and between populations, demonstrating that the hydrology of the rias are driving bacterial distribution (and not host specificity). Thus, for environmentally transmitted symbioses such as the sepiolid squid-Vibrio association, abiotic factors can be major selective force for determining population structure for one of the partners.

Hymenopteran queens are collectively highly fecund, often long-lived individuals that undergo dramatic physiological changes after they mate and establish a nest. However, the degree to which these changes are conserved among species with different life histories is not well-defined. We conducted a comparative proteomic study investigating differences between reproductive stages (virgins, mated, and established queens) of Apis mellifera, Bombus impatiens, B. terrestris, and Lasius niger. We identified conserved upregulation of proteins involved in anatomical and system development as queens transition to establishing a nest in all species except B. terrestris. We also identified conserved patterns of vitellogenin, vitellogenin receptor, and immune responsive protein (IRP)30, all of which are proteins typically associated with oviposition. However, expression patterns of other immune proteins, heat-shock proteins (HSPs), detoxification enzymes, and antioxidant enzymes were more dissimilar, with some species exhibiting similar trends and coregulation through reproductive stages, while others exhibited variable or opposite patterns. These conserved and unique profiles likely in part reflect similarities and differences in selective pressure on reproductive stages of each species and may indicate differing abilities to respond to emergent pathogens or environmental change.

Climate change and human influence are transforming mountain ecosystems, significantly impacting species distributions and biodiversity. Among these changes, the upward migration of lowland species into mountain regions stands out. This study examines the ecogeographical niche overlap and genetic diversity among three Leucanthemum species in the Carpathian Mountains distributed along an altitudinal gradient: the lowland L. ircutianum (4x), the montane L. rotundifolium (2x), and the alpine L. gaudinii (2x). By genotyping over 600 individuals using SNP analysis, followed by Principal Coordinate Analysis (PCoA), Neighbor-Net Network, and Structure clustering, we reveal not just distinct genetic groups but also hybridization across all species, suggesting the potential for triple hybrids. Genetic admixture is further supported by environmental background and niche overlap analyses that reveal substantial overlap among species, particularly in line with their vertical distribution. Climate envelope plots indicate a likely reduction in available habitat for mountainous species due to climate change, leading to an increase in competition and an intensification of hybridization. Anthropogenic influences are further intensifying these hybridization trends. Among the studied species, L. gaudinii is most at risk of overwhelming hybridization, whereas L. ircutianum may experience habitat expansion. By providing a comprehensive genetic and ecological overview, our research highlights the significance of hybridization in biodiversity conservation and the challenges posed by environmental changes and anthropogenic activities in mountain environments. This study not only contributes to the understanding of genetic diversity in the Carpathians but also underscores the broader implications for molecular ecology and conservation strategies in mountain ecosystems.

The predictive link between the spatial demographic changes of a species and its environment is complex and difficult to detect without detailed models and data from multiple sources. Integrative distributional, demographic, and coalescent modeling (iDDC) integrates simulation-based spatial population genetic and species distribution models (SDMs) to enable testing eco-evolutionary hypotheses given geo-referenced genetic data. Integral to iDDC is the transformation between habitat suitability values and local deme sizes, a key parameter that has not been thoroughly explored or used to test eco-evolutionary hypotheses. In this study, we investigate this parameter’s influence on spatiotemporal demographic inference in two Enyalius lizard species in the Brazilian Atlantic Forest, one with a high-elevation distribution, Enyalius iheringii, and another having a low-elevation distribution, Enyalius catenatus. Since environmental tolerances in high-elevation species are generally broader than in low-elevation species, we test two hypotheses: (1) E. iheringii has higher effective migration compared to E. catenatus; and (2) the relationship between habitat suitability and local deme size is non-linear for E. iheringii and linear for E. catenatus. We find support for (1) and mixed support for (2), where we find strong model support for a non-linear transformation for E. iheringii but also find support (although weak) for a non-linear transformation for E. catenatus. We also generate landscape-wide maps of predicted genetic diversity for both target species. We find that genetic diversity predictions for the E. iheringii correspond with predicted patterns of range stability, while predictions for E. catenatus are distinct from predictions of range-wide stability.