Rowan D. H. Barrett

The evolution of genotypic parallelism under shared environmental conditions provides strong evidence for the role of natural selection. However, analyses typically examine genomic signatures of selection long after the putative selection event and only assess the repeatability of responses across spatial population replicates. This impedes our ability to attribute a particular response to a given selection pressure and to distinguish non‐parallel responses caused by stochastic processes from those caused by local selection. As such, the consistency of natural selection over space and time is unknown, and the role of persistent local selection pressures is unclear. Here, we leveraged the natural bar‐built estuary system of Santa Cruz, California, to examine the repeatability of seasonal genomic change in threespine stickleback ( Gasterosteus aculeatus ) over space and time. By comparing allele‐frequency shifts that are shared across locations (spatial repeatability) with those that are shared across years within locations (temporal repeatability), we identified both spatially shared and local components of putative selection. We found that repeated seasonal outlier responses occurred more often than expected under a neutral null model. Although repeatability declined as the number of estuaries sharing an outlier increased, enrichment above neutral expectations increased with broader spatial sharing, particularly for outliers repeated across both years. While the precise outlier SNPs varied across years, estuary‐specific patterns of responses were broadly consistent, suggesting an important role for local conditions. Together, our findings show that temporal sampling can reveal components of putative selection that would be missed from spatial comparisons alone. More broadly, they highlight the importance of examining repeatability over both space and time to understand the parallel and non‐parallel components of adaptive genomic change.

The coral microbiome is highly complex, and interactions between microbiome members have been proposed as an important component of coral thermotolerance. However, establishing causal links among specific microbiome members remains difficult in corals because these communities are diverse and difficult to manipulate experimentally. We used Aiptasia, an emerging coral model system, to test how algal symbiont identity influences the structure and dynamics of the prokaryotic microbiome during heat stress. We generated clonal Aiptasia lines hosting two well-defined strains of photosynthetic algae in the family Symbiodiniaceae. We exposed these animals to an acute thermal stress assay while tracking prokaryotic dynamics with 16S sequencing. Among heat-stressed animals, algal strain was the strongest driver of prokaryotic community composition. We also identified line-associated indicator taxa that may be linked to differences in bleaching resistance. Finally, the more thermally sensitive host-algal association showed greater inter-sample dissimilarity in prokaryotic community structure under heat stress, suggesting that sustained microbiome variability may characterize more stress-sensitive cnidarian holobionts. These results suggest algal symbionts may shape bleaching responses not only through effects on host physiology, but also through their influence on prokaryotic microbiome dynamics.

The threespine stickleback (Gasterosteus aculeatus) is a key model in evolutionary genetics, particularly for studies of parallel evolution, yet most genomic insights derive from populations on the west coast of North America and in Europe. Here, we use restriction site-associated DNA sequencing (RAD-seq) of pooled samples to examine genomic differentiation between marine and freshwater stickleback populations from Atlantic Canada. Our analyses reveal substantial heterogeneity in the extent and genomic distribution of marine–freshwater differentiation, with some freshwater populations showing strong divergence consistent with long-term isolation and drift, and others exhibiting patterns consistent with ongoing gene flow and admixture. Despite this demographic variation, we identify genomic regions that are repeatedly differentiated between marine and freshwater habitats, including loci near dopamine receptor genes (Drd4a and Drd2l). Gene ontology analyses of candidate regions show enrichment for functions related to nervous system development and dopamine receptor activity. Together, these results indicate that freshwater-associated genomic differentiation in Atlantic Canadian stickleback occurs across contrasting demographic contexts and suggest a potential role for neurological and behavioural pathways in adaptation to freshwater environments.

Ecological speciation is now regarded as one of the primary processes by which new species are generated. Adaptive divergence in allopatry begins this process, but it is often unclear when and how mechanisms that promote reproductive isolation, such as assortative mating and selection against hybrids, evolve. Here, we test for evidence of these mechanisms across replicated secondary contact experiments in natural settings. We introduced four to eight allopatric populations of threespine stickleback ( Gasterosteus aculeatus ), in both single-ecotype and mixed-ecotype treatments, into nine natural lakes, after which we inferred mating patterns by genotyping the resulting F1 generation. Contrary to expectations from the literature, we found no evidence of assortative mating or partial reproductive isolation among the introduced source populations. Instead, we detected evidence of disassortative mating by source population in three lakes and some evidence of disassortative mating by ecotype in one lake. These mating patterns were both context-dependent and population-dependent, varying substantially across lakes receiving the same source populations, and with some source populations generally displaying greater tendencies for disassortment. The absence of positive assortative mating in any replicate demonstrates that adaptive divergence in allopatry alone might be insufficient to generateassortative mating in many cases, while the possibility of disassortative mating in these contexts poses an additional hurdle on the path toward speciation.

Background: Disentangling the drivers structuring microbiomes can help predict organisms’ responses to rapid environmental change. However, despite microbial communities being important for both host and environmental health, large gaps remain in our understanding of how host-associated microbiomes are structured and respond to different stimuli, especially in marine environments. Here, we leverage a seasonal upwelling gradient in Panama’s Tropical Eastern Pacific, investigating how the diversity and composition of ten coral reef fish species’ skin microbiomes compare between regions and seasons that experience different environmental conditions. Results: Fish skin microbiomes varied greatly within and among host species and were distinct from the microbiomes of the surrounding seawater. All species had diverse skin microbiomes, with a dominance of Proteobacteria (65%), Bacteroidota (13%), and Cyanobacteria (6%). Host species and trophic group played a greater role in determining fish skin microbiome structure than seasonal and regional environmental variation, despite water microbiomes responding strongly to both season and region. Nevertheless, three out of five trophic groups: the herbivores, carnivores, and planktivore, also displayed significant changes in their microbiomes during upwelling, albeit to a lesser extent than water samples, whereas the invertivores’ and omnivore’s microbiomes did not change significantly. We performed differential abundance (DA) analyses on these fish and compared microbial taxa that changed between seasons and regions in fish versus water samples. While water communities had thousands of significant DA taxa, fish had around 40 times fewer ( n = 17 to 73) and only shared 47 DA taxa with the water samples. Differences between these microbial communities likely arise from both host selection via fishes’ immune system and the skin mucus serving as an environmental filter. However, neither host-associated nor environmental predictors fully explained the variation in microbiome composition, highlighting its complexity. Conclusions: Our results show how ecological differences between host species may elicit distinct microbiome responses to environmental changes, with potential cascading effects on ecosystem dynamics under global climate change. Further characterization of marine microbial communities, as well as additional physicochemical and host-related parameters, will be key to monitoring and predicting how these communities will respond to the increasingly rapid and widespread environmental changes our oceans are facing.

Predicting the distance between an individual's release point into a new environment and their subsequent location (‘displacement’) could be useful during biological ‘introduction’ events (e.g., invasions/translocations) because variation in displacement could lead to spatially‐structured ecological and evolutionary effects, as well as implications for efforts to control introduction outcomes (e.g., establishment success). Two challenges limit our ability to predict post‐introduction displacement. First, displacement is shaped by individual movement, and many factors affect movement. As such, considerable recent effort has focused on finding particularly influential factors, including bold and exploratory behaviour. Second, movement patterns often differ between environments. Predicting post‐introduction displacement therefore benefits from assessments in the most relevant environment—that in which the introduction is occurring. Conservation translocations provide a rare opportunity to overcome both challenges by allowing assessment of how behaviour might be associated with post‐introduction displacement in the new environment. Our study leveraged a conservation translocation where threespine stickleback ( Gasterosteus aculeatus ) from seven source populations were introduced into one ‘recipient’ lake. Our study focused on comparisons of the genetics (source population ancestry) and behaviour (bold and exploratory) of individuals subsequently showing lower displacement (captured at the release site) versus greater displacement (captured farthest from the release site). Bold behaviour was assessed as latency to emerge from shelter, whereas exploratory behaviour was the number of unique sections crossed in an open field. Fish from the different source populations showed different bold and exploratory behaviours; yet those population‐level differences were not associated with post‐introduction displacement. At the individual level in the recipient lake, however, fish showing greater displacement 1 month after release were less exploratory than those showing lower displacement. This association between capture location and exploratory behaviour was no longer evident a year later, implying that the original association was related to initial post‐release displacement. Our work highlights how exploratory behaviour might be associated with displacement following introduction into a new environment. More broadly, our study provides rare insights into the extent to which post‐introduction displacement is predictable in a real‐world setting, and it also underscores the value of conducting experimental manipulations in nature.

Species introductions and transplants offer powerful contexts to understand evolutionary patterns and processes, and they are increasingly critical for conservation. However, introduction success varies widely, and predicting outcomes remains challenging. Introducing multiple source populations should increase the chance of success, while also providing an opportunity to explore the factors that predict success of individual source populations in the same environment. We used replicated, mixed-population introductions of >12,000 threespine stickleback ( Gasterosteus aculeatus ) to test whether source population success could be predicted by environmental matching between source and recipient environments and/or by intrinsic source population characteristics. We introduced four to eight source populations of stickleback into each of nine natural lakes and tracked their relative success over the following two years (up to two generations). Source population success was largely consistent across lakes, despite divergent environmental conditions. These results point to the importance of intrinsic source population characteristics rather than environmental matching in predicting introduction success in natural settings. Source populations that were consistently successful tended to have greater stress tolerance (mortality rate during translocation) and higher genetic diversity, though these relationships were not conclusive. Our study highlights the value of considering factors that generate fitness differences independent of environmental contexts in predicting ecological and evolutionary dynamics and planning conservation programs. Significance Statement: Predicting which populations will succeed when introduced to new environments is a central challenge in ecology, evolution, and conservation. Environmental conditions are often assumed to be crucial in determining which populations succeed, given the expectation that populations preadapted to local conditions should perform best. We test this assumption by introducing >12,000 threespine stickleback fish from up to eight source populations into nine natural lakes spanning diverse environmental conditions. We show that the relative success of individual source populations was remarkably consistent across lakes and environmental conditions, indicating that some populations are intrinsically better suited to introductions. Our findings underscore the importance of considering intrinsic population characteristics alongside environmental conditions when predicting ecological and evolutionary outcomes and guiding conservation efforts.

The persistence of populations facing severe environmental disturbance can be enabled by natural selection on heritable phenotypic variation—a process known as evolutionary rescue. Few studies have documented this process or its long-term consequences in complex natural environments. Here, we used copepod resting eggs of Leptodiaptomus minutus from three time periods of lake ecological history, spanning approximately 200 generations (100 years) in two populations impacted by historical acidification. Whole genome sequencing of the resting eggs revealed significant allele frequency shifts associated with the acidification, followed by pH recovery. We used a resurrection ecology approach to retrace adaptive shifts concomitant with environmental transitions. Copepods from the pre-acidification period showed sensitivity to acidity, while individuals from the acidification period were adapted to acidic pH. This tolerance was subsequently lost during pH recovery, implying an adaptive reversal. Demographic models indicated a decline during the acidification process, followed by population recovery based on historical data, suggesting that selection led to evolutionary rescue. This study fills a critical knowledge gap about the long-term implications of evolutionary rescue in the wild.

Bacterial populations evolve rapidly in the lab when faced with experimentally applied selective pressures. Yet how bacteria evolve in nature, in more complex multi-species communities, is both challenging to study and essential to our understanding of ecosystem responses to rapid anthropogenic change. To track bacterial evolution in a semi-natural context, we applied Roundup, a glyphosate-based herbicide (GBH) that interferes with aromatic amino acid synthesis, as a selective pressure to 1000 L ponds containing bacterioplankton communities from a pristine lake. We show that both ecological and evolutionary changes can occur on short timescales after a strong selective pressure. Using metagenome-assembled genomes as a proxy for species, we found that GBH treatment substantially affected community diversity but did not purge within-species genetic diversity over the 4 weeks of the experiment. We identified several functional categories of genes consistently targeted by GBH selection across seven different species of bacteria. Genes involved in amino acid transport and metabolism were more likely to experience GBH-driven changes in allele frequency, including the gene aroA targeted by glyphosate, along with other potentially novel targets of selection. Together, these results show how environmental change can rapidly affect bacterial community structure and select for specific genetic targets without purging genetic diversity genome-wide.