Evolutionary Applications

Protecting populations and genetic diversity within them is critical to conserving the resilience and adaptive potential of species. Fisheries management has long had the ambition of managing species at the population level, but mainly define "fish stocks" based on geographical limits, which can lead to overfishing of sensitive populations in areas where many different populations coexist. Modern genetic methods are now sufficiently cost-effective, fast, and accurate to be integrated into fisheries management, enabling genetic identification and monitoring of fish populations. Here, we establish a genetic baseline for the commercially important fish Atlantic cod (Gadus morhua) in the waters surrounding Sweden, by using standardised sampling procedures and developing a genetic panel of 4000 single nucleotide polymorphisms (SNPs) for cost-effective assignment of population-of-origin and inversion genotypes. Using the SNP panel, we resolve the geographical distribution of three genetically distinct cod populations in the region: offshore, coastal/Western Baltic, and Eastern Baltic cod. While there is considerable spatial overlap between the three populations, they are genetically differentiated across the entire genome, as well as in genomic regions associated with chromosomal inversions. In addition, heterozygosity and effective population size estimates suggest differences in genetic diversity and rates of genetic erosion, underscoring the need to monitor the genetic diversity within each population separately. Repeating this methodology across years provides a first suggestion for establishing spatiotemporally resolved genetic monitoring of Atlantic cod in Sweden - simultaneously accounting for both population structure within the species and the genetic diversity within populations.

AimTo assess how biogeographic barriers and environmental heterogeneity shape connectivity and local adaptation in the striped Venus clam (Chamelea gallina), a commercially exploited bivalve in the Mediterranean Sea. LocationNortheast Atlantic (Gulf of Cadiz) and Mediterranean Sea (Alboran, Balearic, Tyrrhenian and Adriatic regions). TaxonChamelea gallina (Bivalvia: Veneridae). MethodsWe analysed genome-wide single nucleotide polymorphisms (SNPs) from 226 individuals sampled across six regions (Gulf of Cadiz, Alboran Sea, Balearic Sea, Ebro Delta, Tyrrhenian Sea and Adriatic Sea) using a seascape genomic framework. Population structure was inferred using both putatively neutral and adaptive loci. Genotype-environment associations were tested against key oceanographic variables, including sea surface temperature, salinity and nutrient availability. ResultsNeutral loci revealed weak genetic differentiation, consistent with substantial gene flow across most of the species range. In contrast, putatively adaptive loci uncovered pronounced genetic structure that corresponded closely to major Mediterranean biogeographic regions, particularly the Adriatic Sea, the Gulf of Cadiz and western-central Mediterranean basins. Significant associations were detected between genetic variation and environmental gardients, with several candidate adaptive SNPs located within coding regions, suggesting functional responses to spatially heterogeneous conditions. Main conclusionsOur results demonstrate that local adaptation can generate biologically meaningful population structure in C. gallina despite high levels of connectivity inferred from neutral markers. This decoupling between neutral and adaptive variation highlights the importance of integrating adaptive genomic information into biogeographic inference. Recognizing environmentally driven genetic differentiation is essential for defining robust management units and for improving the long-term sustainability and resilience of C. gallina fisheries under increasing anthropogenic pressure and climate change.

Accurate detection of hybridization and introgression is critical for both evolutionary research and applied conservation. In many systems, however, hybrid ancestry is difficult to detect beyond the F1 generation, especially when based on limited genetic markers. In European waters, hybridization between the native Homarus gammarus and the invasive H. americanus poses a direct risk to the integrity of native stocks and effective fishery management, yet detection methods are often limited to morphological traits or first-generation hybrids. A set of 79 SNPs previously developed to distinguish species between American and European lobsters and F1 individuals has shown promise, but its capacity to resolve later-generation backcrosses remains untested. Here, we present a resampling-based evaluation of this panels performance under realistic introgression scenarios, using individual-based population genetic models informed by empirical data. We show that the panel retains discriminatory power across multiple hybrid classes, with diminishing accuracy in second-generation backcrosses. These findings validate the panels utility for applied monitoring and highlight the broader potential of resumpling-anchored frameworks to benchmark hybrid detection tools in a wide range of species. Article summaryThis study tests how well a reduced panel of genetic markers can detect hybridization across multiple generations. Using empirical genetic data of a 79-SNP panel from European and American lobsters, the authors generated individuals with known ancestry proportions through a resampling framework that preserves observed genetic variation. These data were analysed using model-based genetic assignment and ordination. The results show that the marker panel reliably identifies pure species and first-generation hybrids, but has reduced power to distinguish later backcross generations, mainly between adjacent hybrid classes. The study provides a practical benchmark for evaluating reduced marker panels used in applied monitoring and conservation genetics.

Assessing genetic diversity is essential for conserving endangered populations, yet comprehensive genomic evaluations remain limited for many declining species. Here, we investigated inbreeding levels and effective population sizes (Ne) of caribou (Rangifer tarandus) in western Canada, where populations have experienced pronounced declines over the past centuries due to anthropogenic pressures and climate change. We analyzed 33,346 Single Nucleotide Polymorphisms (SNPs) from 759 individuals representing 45 subpopulations within six metapopulations to: (1) assess inbreeding using runs of homozygosity (ROHs), (2) estimate contemporary and historical Ne, and (3) evaluate relationships between census size (Nc), inbreeding, and Ne. Small and endangered subpopulations, predominantly in southern regions, generally exhibited high inbreeding (FROH > 0.1), although some larger populations also showed elevated levels. Most subpopulations displayed a mixture of short and long ROHs, indicating both ancient shared ancestry and recent inbreeding. Twelve subpopulations had Ne <50, and 28 subpopulations and all metapopulations had Ne < 500, suggesting compromised short-term viability and long-term adaptive potential. Nc significantly predicted inbreeding (R{superscript 2} = 0.25), whereas contemporary Ne did not. Historical Ne reconstructions revealed a north-to-south gradient in bottleneck timing: northern populations declined in [~]1700-1780, central populations in [~]1780-1860, and southern populations in [~]1860-1940, likely driven by sequential impacts of climate shifts and anthropogenic disturbances. Our findings identify at-risk populations requiring urgent genetic intervention and demonstrate that integrating inbreeding and Ne estimates provides a robust framework for caribou recovery and the management of fragmented wildlife populations.

Restoration and management of natural populations often assume that local genotypes are best suited for transplantation to their local environment. Prioritizing a single local genotype, however, contrasts with the framework of maximizing intraspecific diversity to increase population resilience to environmental change. Local populations may also become maladapted to a rapidly changing environment, motivating alternative frameworks that instead minimize environmental distance between source and transplantation sites. Here, we tested the predictive power of the local is best, maximize intraspecific diversity, and minimize environmental distance frameworks on the survival and growth of Eastern oyster (Crassostrea virginica) genotypes in field common gardens that differed in salinity and disease pressure. Although a genome scan revealed patterns of adaptation to disease, heat stress, and salinity among source populations, we did not find strong support for the local is best framework: geographically distant southern genotypes performed comparably to local selection lines and a local wild population. Higher genetic diversity within monocultures was associated with higher survival, yet highly diverse polycultures survived at lower rates than the best-performing monocultures, providing mixed support for the maximize intraspecific diversity framework. Temperature and salinity of the environments-of-origin of parents predicted the survival of their offspring in common gardens, but the relationship between survival and environmental distance was context-dependent, leading to mixed support for the minimize environmental distance framework. Together, these results demonstrate that no single framework reliably predicted transplantation success, suggesting that effective management strategies may need to integrate genomic and environmental lines of evidence to guide genotype selection.

AO_SCPLOWBSTRACTC_SCPLOWMigration events can act as strong selective filters by spatially sorting individuals according to their migration ability, behaviour, and associated functional traits. The European eel, a panmictic and threatened fish, presents various estuarine migration patterns at juvenile stage (glass eel), ranging from sedentarization in brackish/saltwater of the estuary (non-migrant phenotype) to upstream colonisation of freshwater ecosystems (migrant phenotype). We hypothesize that migration propensity is partly genetically determined in glass eel, and that migration-related genotypes are spatially sorted during estuarine migration. To test these hypotheses, we first collected six pools of individuals over three years at two extreme sites along a gradient from ocean to Adour River tidal limit (Ocean vs. Upstream). Secondly, we collected additional glass eels and phenotypically sorted migrant vs. non-migrant individuals using an experimental device mimicking alternating tidal currents, producing two other pools. Whole genome pool sequencing and analysis of these eight pools generated 18.99 106 SNP variants. Controlling for linked selection through a local score approach, we found five best outlier SNPs with a significant genetic differentiation between Ocean vs. Upstream sites (average FST = 0.21) compared to the pangenomic estimate (FST = 0.0086). These five SNPs were all found in the same gene (gpb2), involved in interferon-mediated antiviral immune responses. We also found 28 best outlier SNPs with a significant genetic differentiation between migrant vs. non-migrant phenotypes (average FST = 0.51). They were located in genes mainly involved in neuronal development, cell migration and tissue remodelling, transcriptional regulation, and metabolic or stress-related processes. Our results support that variation in eel migration propensity is partly genetically determined and that, while panmixia maintains high level of genetic diversity, spatial sorting could promote intra-generational genetic divergence between habitats of European eels. However, the absence of shared genes among the best outliers between in-situ and experimental contrasts suggests a complex and context-dependent genetic control of migration.

O_LIMontane and specialist insects are particularly vulnerable to habitat loss and climate change. The Spanish Moon Moth (Actias isabellae), a rare and protected species, hosts an isolated Alpine population (subspecies galliaegloria) whose conservation status remains unclear. C_LIO_LIWe combined Restriction-site Associated DNA sequencing (RADseq) and Ecological Niche Modelling (ENM) to assess its genetic diversity, population structure, and environmental vulnerability. C_LIO_LIGenomic analyses revealed extremely low genetic diversity and inbreeding in the Alpine subspecies, consistent with a historical bottleneck, reducing adaptive potential. C_LIO_LISpecies distribution models predict a major contraction of suitable habitat by 2050 due to rising temperatures and declines in its primary host, Scots pine (Pinus sylvestris). C_LIO_LIThese findings highlight the compounded risks posed by genetic impoverishment and habitat loss, emphasizing the urgent need for targeted conservation measures. C_LIO_LIOur study demonstrates the value of integrating genomic and ecological approaches to evaluate extinction risk and guide management strategies for montane specialist insects under rapid environmental change. C_LI

Climate warming alters the thermal environment experienced by ectotherms, whose physiological performance and fitness are constrained by temperature. Early life stages are often the temperature-sensitive phases of the life cycle, with potential consequences for population persistence, particularly in freshwater stenotherms such as the Arctic charr (Salvelinus alpinus). The persistence of populations will partly depend on the adaptive potential of critical life stages to environmental changes. In this study, we used a common garden approach to compare the response and phenotypic plasticity of four charr populations to warmer conditions. These populations inhabit thermally contrasted lakes and differ in origin (native/introduced) and management history. We reared embryos at either an optimal (5{degrees}C) temperature for larval development or a warmer but realistic (8.5 {degrees}C) temperature. We tested adaptive divergence among populations in four traits (survival, incubation duration, body length and yolk sac volume), using Qst - Fst comparisons. We report negative effects of temperature on body size, survival and earlier hatching. Thermal reaction norms differed among populations, indicating adaptive divergence. Contrary to expectations, populations originating from warmer environments did not consistently exhibit higher trait values under elevated temperatures. In contrast, the unmanaged and colder high-altitude population exhibited higher survival rates and lower yolk reserves for a given size under heat stress than the other populations. Our results suggested that evolutionary trajectories specific to each population are shaped by factors related to the populations history, including introductions, demographic fluctuations and long-term repopulation practices, which can jointly influence the potential for adaptation to heat stress.

Trait-selective harvesting by fisheries can impose strong selective pressures on fish populations, driving changes in life history traits affecting fisheries productivity and ecosystem functioning. While the genetic consequences of harvesting have been extensively studied, the extent to which phenotypic variation reflects genomic evolution versus environmentally-induced plasticity remains unclear. Epigenetic mechanisms, such as DNA methylation, may mediate between these processes, serving as a rapid and reversible response to the selective pressures imposed by harvesting. In this study, we implemented an improved laboratory and bioinformatics protocol, epiGBS3, to examine genomic variation and DNA methylation patterns in the marine fish Xyrichtys novacula. The study spanned three replicated geographical areas each comprising two adjacent locations: an intensively exploited fishery and a no-take Marine Protected Area (ntMPA). A nested analysis design across the three areas revealed strong gene flow and no evidence of genetic structure. Nevertheless, nucleotide diversity was significantly reduced in fisheries relative to ntMPAs. We also found that DNA methylation levels differed between protected and exploited sites after controlling for age, suggesting that fishing may influence epigenetic changes independently of fisheries-induced age-truncation effects. This represents one of the first lines of evidence that fisheries can potentially shape epigenetic variation, supporting DNA methylation as contributor to local adaptation under high gene flow and strong anthropogenic selection.

Selective breeding in aquaculture is necessary to establish food security and meet demand for sustainably produced protein. An informed selective breeding program requires understanding how population structure, environmental adaptation, and human activities shape natural genetic variation in wild conspecifics. Unfortunately, wild variation remains poorly characterized for many commercially important aquaculture species. Here, we conduct the first range-wide study of genomic population structure for the eastern oyster (Crassostrea virginica) across thousands of miles (Texas, USA to Eastern Canada) using a 200K SNP array. We integrate population structure analyses, genotype-environmental associations, and structural variant detection to identify adaptive loci and quantify human-mediated genetic impacts. Our data confirms two ancestral clusters with a phylogeographic break between the Gulf and Atlantic (FST = 0.06) and highlights patterns of substructure within each region. We find evidence of unexpected patterns of genomic variation in two locations: evidence of Gulf ancestry in a mid-Atlantic estuary (Chesapeake Bay), and evidence of Atlantic ancestry in a Gulf estuary (Apalachicola Bay). While we cannot definitively determine the causes of these unexpected patterns, we show that they are consistent with direct and indirect human impacts in these estuaries. Genotype-environment association analyses with in situ temperature and salinity measurements were used to identify putatively adaptive loci, including SNPs within large structural variants (>1Mb). Our results identified genomic targets for aquaculture breeding programs aimed at climate resilience, reveal complex patterns of human impacts in managed systems, and demonstrate how seascape genomics can be used to improve aquaculture outcomes.

Pacific cod is a key species in North Pacific fisheries, and its stock assessment and management units are separated according to biological, geographical, and administrative information. Understanding the fine-scale genetic population structure of this species is crucial for effective management, particularly in regions such as Japan, where complex coastal geography and localised fisheries management prevail. Therefore, in this study, we analysed genome-wide single nucleotide polymorphisms (SNPs; 6,035 loci) in 496 individuals of Pacific cod sampled from 33 sites around the Japanese archipelago via genotyping by random amplicon sequencing-direct (GRAS-Di) analysis. Our analyses revealed three major genetic groups: Japanese Broad Range, Northernmost Honshu-Hokkaido (NHH), and Western Sea of Japan groups. These groups exhibited significant genetic differentiation (global FST = 0.056), distinct levels of nucleotide diversity, and group-specific genome-wide patterns of Tajimas D. Moreover, demographic history reconstruction based on whole-genome sequencing of three representative individuals revealed that each genetic group followed distinct demographic trajectories since the last glacial period. Importantly, the NHH group, related to the Mutsu Bay spawning aggregation and previously shown to exhibit strong natal homing in tagging surveys, was genetically identified for the first time in this study. Isolation-by-distance was observed across Japanese waters and within the Japanese Broad Range group, but not within the NHH group, suggesting that gene flow is generally restricted by geographic distance, except within the NHH group. To evaluate the potential for genetic stock identification, we extended a resampling-based cross-validation framework by incorporating outlier detection to assess marker selection strategies. Over 500 background SNPs were required to achieve >90% assignment accuracy for genetic stock identification, whereas only eight or more outlier SNPs showed comparable performance. These findings suggest that carefully selected SNP panels, particularly those including outlier loci, substantially improve stock discrimination. Overall, our study demonstrates the fine-scale genetic structure and demographic history of Pacific cod in Japanese waters and highlights the utility of practical marker strategies for enhancing the biological realism of fisheries assessment and supporting sustainable fisheries management.

Animal translocations are becoming increasingly popular as a tool for conservationists. Demographic factors can be crucial determinants dictating translocation viability in the short term. Translocated populations pass through artificial bottlenecks and can suffer from founder effects. Reduction in genetic variation relative to their source populations is likely, limiting their adaptive potential. Founder events can increase frequencies of deleterious alleles due to elevated rates of inbreeding and inbreeding depression. Here, we describe the effects of human-driven, serial population translocations on the genetic diversity of critically endangered Anegada iguanas (Cyclura pinguis) in the British Virgin Islands. Though founding populations were extremely small (N=8, N=4), the census sizes of translocated iguana populations increased dramatically over the first twenty years. This implies that these translocations were successful from a demographic perspective despite the small number of animals used, indicating a genetic paradox. To quantify genetic signatures in these bottlenecked populations, blood samples were collected from the source population and two translocated populations and genotyped at 21 microsatellite loci. We found that allele frequencies in translocated populations differed significantly from those of the source, with the translocated populations having less genetic diversity. However, common methods for estimating presence of genetic bottlenecks were non-significant. Estimates of internal relatedness by age class suggest that inbreeding depression may be elevated after translocation, likely reflecting the small initial population sizes associated with these translocation events. Anecdotally, our work shows that translocations may result in subtle genetic erosion that has long-term population viability impacts, even when census size indicates success.

Climate change is a growing threat to biodiversity, and the persistence of populations largely depends on their capacity to adapt to changing environmental conditions. Although there is an urgent need to forecast population adaptive potential, it is unclear how such predictions are affected by the genomic architectures underlying local adaptation across a species range. In this study, we examine the genomic basis of local adaptation of the short-distance dispersing coral Stylophora pistillata, sampled at forty-six sites across eight reefs of the Great Barrier Reef, Australia. Our results show that thermal adaptation for this species involves hundreds of genomic loci with combinations that differ across regions. Although adaptive loci were largely region-specific, genotype-environment relationships estimated across the range provided sensible predictions of regional-level local adaptation. Additionally, predicted shifts in genotype-environment associations under increased projected warming were highly spatially variable, both between and within geographic regions. While some Great Barrier Reef S. pistillata populations might be well-adapted for near-future (2050) and moderate (SSP1-2.6 and SSP2-4.5) climate warming, up to 30% may face severe maladaptation risk by 2100 under a high-emission (SSP5-8.5) scenario. Collectively, these findings offer new insights into the spatial distribution of adaptive potential in coral populations and how it might shape their resilience in a warming ocean.

It is commonplace in East Africa for 100% of cassava fields to be infected with Cassava mosaic disease (CMD) and/or Cassava brown streak disease (CBSD), resulting in annual losses of more than US$1.25 billion and reduced food and economic security for farming households. The vector of both diseases is the African cassava species of the whitefly Bemisia tabaci. Since the late 1990s, there has been an unprecedented increase in whitefly populations, to the extent that they are referred to as "super-abundant". Research efforts since the late 1990s has focused mainly on developing plant resistance to the viral pathogens and paid scant attention to understanding the root causes of disease epidemics or the control of whitefly infestation. Here, we aimed at developing long-term whitefly-control solutions using an in-planta RNA interference (RNAi) approach. First, transcriptome analysis identified candidate genes that play key roles in whitefly biology: osmoregulation, sugar metabolism and transport, symbiosis with endosymbiotic bacteria and detoxification of phytotoxins. Then, fifteen RNAi inverted repeat constructs were produced, designed to target the candidate genes and 140 independent transgenic lines were generated in cassava variety NASE 13. Whole plant bioassays showed insecticidal activity of transgenic plants, reaching 58% lethality for adults within 7 days and 75-90% lethality of nymphs after 25 days, compared to control plants. Target genes were confirmed to be downregulated by up to 2.5-fold in adult whiteflies and nymphs. We used population dynamics modelling to predict the potential of the RNAi technology to control whiteflies under field conditions in East Africa.

Significant debate has revolved around the delimitation of subspecific boundaries relative to conservation policy, and specifically how best to maximize limited resources. The conservation of subspecies captures intraspecific genetic diversity and aids in the long-term preservation of adaptive potential. Here, we evaluate patterns of neutral and adaptive genomic variation across the eastern lineage of the American black bear. We specifically assess the relative impact of phylogeographic history and local adaptation on differentiation of subpopulations in Louisiana, which were federally protected as a subspecies from 1992-2016. Despite high values of genetic differentiation (Fst >0.127) of these focal populations, we show that serial founder events during range expansion into eastern North America and multiple bottlenecks drove patterns of diversity within Louisiana. While we attribute initial population divergence between Louisiana subpopulations to east-west shifts of the Mississippi River between 6.2 - 2.7kya, drift accelerated following bottlenecks that were likely due to indigenous societies cultural and land-use changes and later to impacts of European fur traders. We further show that local adaptation has had a smaller impact (4.6%) than phylogeography (30.1%) on the distribution of genomic variation across this lineage. The strongest drivers of adaptive variation include mean annual temperature and monthly precipitation variation, where northern populations have substantial derived variation. Our genomic assessment, in conjunction with weak phenotypic data, does not support the continued recognition of Ursus americanus luteolus as a subspecies of American black bear. Continued genetic conservation efforts should focus on maintaining or increasing diversity, while supporting ongoing successes of demographic recovery.

Successful establishment of a species in a new range is a useful way to understand the impact of demography and selection on the evolution of globally distributed species. In particular, introductions influence genetic diversity and population structure in the introduced range in unpredictable ways. Additionally, introgressive hybridization is often associated with successful establishment in new ranges. In this study, we explore the impact of introgressive hybridization on the polyploid Capsella bursa-pastoris in the New York City metropolitan area. We find Capsella bursa-pastoris in the New York City metropolitan area likely originated from multiple introductions from northern Eurasia, and that populations across the New York City metropolitan area are generally panmictic. As with Capsella bursa-pastoris in Eurasia, we discover evidence of introgression from the diploid Capsella rubella in this population. By evaluating ancestry in regions across the genome, we find introgressed regions are rich in gene content and contribute to genetic diversity in this population. These results suggest that introgressive hybridization before introductions may buffer species from the negative effects of population bottlenecks and allow for successful establishment.

Foodborne non-typhoidal Salmonella remains a major public health concern, yet routine surveillance recovers large numbers of isolates from food that are not associated with human illness. Studies have shown foodborne isolates can be genetically linked to clinical cases, highlighting a critical challenge for risk assessment and outbreak prioritisation. This study aimed to determine whether genomic markers can distinguish foodborne Salmonella strains with an increased likelihood of causing infection. Whole-genome sequencing data from over 900 Salmonella isolates recovered from food and the environment through UK Health Security Agency surveillance were analysed using hierarchical clustering to define genetically related groups. These clusters were expanded using the global EnteroBase database to provide broader epidemiological context. Genome-wide association analyses identified genetic markers associated with clusters containing clinical isolates, including phage-associated regions. A highly conserved 7 kb marker identified in S. Agona demonstrated strong predictive performance at a global scale, with high sensitivity and specificity for infection-associated lineages and strict serovar restriction. Comparative genomic analysis revealed that all markers localised to a shared chromosomal hotspot corresponding to a prophage integration site. The 7 kb risk-associated marker formed part of a larger prophage closely related to the well-characterised S. Typhimurium Fels-2 phage, which encodes a DNA invertase linked to phase variation, a mechanism known to promote phenotypic heterogeneity and host adaptation. As these S. Agona isolates are monophasic, our findings indicate that our genome-wide association approach has rediscovered this DNA invertase known to contribute to infection risk but in a different serovar via an alternative regulatory mechanism. Overall, this work demonstrates the potential to move beyond treating all foodborne Salmonella isolates as equivalent hazards, towards a genomics-informed framework for risk stratification. This approach provides a foundation for improved risk-based decision-making, enhance outbreak investigations and enable earlier prioritisation of public health responses during Salmonella surveillance and control. Author summaryFoodborne Salmonella infections remain a major public health concern, but not all strains pose the same risk to human health. Here we investigated whether genetic differences could explain why some foodborne strains are more likely to cause human infection. We analysed over 900 genomes from food and environmental sources, grouping closely related strains before placing them in a global context using EnteroBase. By combining pangenome and genome-wide association analyses, we identified distinct lineages within several serovars that differed in their association with human cases. In Salmonella Agona, all clinical isolates belonged to a single lineage carrying a highly conserved 7 kb marker that was absent from low-risk strains. This marker demonstrated strong sensitivity and specificity across global datasets and was located within a prophage closely related to the well-characterised Fels-2 phage. This region encodes a DNA invertase previously linked to phase variation, a mechanism that promotes bacterial adaptability. Our findings indicate that infection risk can be structured at the lineage level and influenced by mobile genomic elements, particularly prophages, that enhance environmental persistence and host adaptation. This work advances genomic surveillance from retrospective linkage towards mechanistic and predictive risk assessment, with direct relevance for supporting risk-based decision-making during outbreak investigations.

Gene drives allow pest populations to be genetically modified to reduce their harm on agriculture and human health. The genetic modification, or payload, spreads within a target population at rates exceeding normal Mendelian inheritance. While gene drives have demonstrated immense potential in laboratory populations, they present unique challenges. Foremost among these challenges is spatial confinement, or ensuring that the payload remains confined to target populations. However, there is an inherent tension between gene drive spread and spatial confinement: increasing the spreading efficiency of a gene drive increases the risk of escape, while engineering confinement mechanisms increases the risk of gene drive extinction. In this work, we explore spatial outcomes in gene drives designed for spatial confinement and the dependence of these outcomes on target organism dispersal and payload fitness cost. We use a stochastic spatial model to compute the probability of failure for each gene drive, and use techniques from global sensitivity analysis to quantify the contribution of dispersal and fitness cost to variance in gene drive performance. Our findings reveal how spatial outcomes are affected by key parameters, and how this sensitivity varies tremendously between different gene drives. These spatial properties can be used to classify gene drive behavior and are useful to determine suitability for a particular application.

Sea star wasting disease has caused widespread mortality in the kelp forest predator, the sunflower sea star (Pycnopodia helianthoides). Wild populations have declined by up to 99% in parts of their native range along the western North American coast. In response, a multi-institutional conservation breeding and rearing program has been initiated to support future reintroduction efforts for the species. We split a full-sibling cohort across four larval density treatments (1 larva/ml, 2 larvae/ml, 5 larvae/ml, and 15-20 larvae/ml) to assess the effects on larval settlement, juvenile survival, and juvenile fitness at 12 months old. Stars raised in the highest density treatment displayed a lower settlement rate and were significantly smaller than the other density groups at 12 months old, but showed no significant difference in flip time, a measure of fitness. Additionally, measurements of diameter, weight, and arm count across modern and historical juvenile and adult stars indicate that P. helianthoides experience exponential weight gain as they grow in length, with corresponding asymptotic growth in arm count. These findings will inform best practices for the aquarium propagation of P. helianthoides and will contribute to broader efforts aimed at reestablishing populations in the wild.

The plant-beneficial bacterium Pseudomonas protegens CHA0 (CHA0) is widely studied for the biological control of soil-borne plant diseases. Beyond its root-colonising capabilities, CHA0 can also infect and kill insect larvae and thus exhibits a multi-host lifestyle shared with other plant- and insect-colonising bacteria. To better understand the robustness of this multi-host lifestyle, we subjected CHA0 to ten consecutive passages through larvae of the pest insect Plutella xylostella via repeated cycles of insect colonisation and killing forcing it into an insect-only lifestyle. Overall, serial passaging did not result in consistent changes in insect killing speed, larval or root colonisation, plant protection efficiency, microbial antagonism or in vitro growth. This suggests that its multi-host lifestyle was conserved following serial passage. Nonetheless, a few independently passaged lines showed an increase in larval killing speed, which in one case might be linked to choline uptake. To disentangle changes specific to the insect host from those arising due to the experimental system itself, we conducted parallel serial passages through the same system while omitting the insect host. In some of these lines, exposure to the background of the system led to changes in microbial antagonism and in in vitro growth, which likely are associated with mutations in regions encoding for regulatory systems. Our findings indicate that P. protegens CHA0 remains phenotypically stable in complex environments such as an insect host, suggesting that the multi-host lifestyle might also be conserved when applied in the field and supporting CHA0s potential for reliable biocontrol performance against both plant diseases and insect pests. Author summaryControlling insect pests with living organisms, known as biological control, offers an environmentally friendly alternative to chemical pesticides. The plant-beneficial bacterium Pseudomonas protegens CHA0 is a promising biocontrol candidate that not only colonizes plant roots but also infects and kills certain insect larvae. This ability to colonize different hosts appears to be a conserved trait also observed in other bacteria. To better understand the robustness of this multi-host lifestyle, we repeatedly exposed CHA0 to larvae of the insect pest Plutella xylostella and assessed the resulting physiological and genetic changes. Surprisingly, after ten cycles, CHA0 largely retained its insect-killing and plant-protective traits. Although a few populations showed minor changes, including slightly faster insect killing and traits associated with aspects of the experimental system, these changes were limited in scope. Overall, our findings suggest that P. protegens CHA0 does not change rapidly in complex environments such as an insect host, supporting its potential for reliable biocontrol performance in the field.