Evolutionary Applications

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.

Understanding population structure is critical for effective fisheries management in species with complex life histories and variable recruitment. Southern flounder (Paralichthys lethostigma) is a valuable flatfish species with declining populations in the Southeast United States. Improved management may depend on a better understanding of fine-scale and temporal population genetic structure in this region; however, such structure remains poorly characterized. To address our lack of understanding of the spatial and temporal population structure of this important species, we used double digest reduced-representation genome sequencing (ddRADSeq) on juveniles from estuaries in North Carolina and Texas between 2014 and 2023. We found significant genetic differentiation between the Gulf of Mexico and Atlantic populations, supporting the management of these regions as distinct stocks. By contrast, we detected significant variance in genetic structure within Texas and North Carolina populations that was not consistent across sampling years between estuaries in close proximity. The population genetic structure of southern flounder suggests significant, temporally variable genetic differences within estuarine locations that may result from variation in larval dispersal and recruitment patterns. Our findings highlight the value of integrating fine-scale, multi-year genetic data to capture temporal dynamics and avoid misleading conclusions based on single-year or broad-scale sampling.

1Effective population size (Ne) is a critical parameter for evaluating the evolutionary and persistence potential of endangered populations and for designing sustainable conservation strategies. Captive breeding and release programs are widely used across taxa to reduce risk of extinction when natural reproduction is insufficient or no longer possible, making it essential to assess their consequences. We used the case study of the landlocked Saimaa salmon (Salmo salar), one of the most critically en-dangered salmonid populations in Europe, with unique evolutionary significance due to its isolation from other populations since the last glaciation. Using long-term demographic data (1969-2024) from wild-caught founders of a captive breeding and release program, we estimated the effective population size under multiple scenarios of variance in reproductive success. Across scenarios, Ne ranged from 33 to 81 individuals, representing 32%-75% of the census size. Captive breeding practices aimed at equalizing parental contributions during fertilization and early life stages increased Ne by 12% compared to natural reproductive conditions. However, variation in survival after early developmental stages, typically beyond direct management control, remained a key determinant of Ne. Despite recent increases in the number of founders, the population remains genetically vulnerable due to historical bottlenecks. These results highlight that while captive breeding programs can partially mitigate genetic risks, their effectiveness depends critically on both controlled and uncontrolled sources of variance in reproductive success. Strengthening such programs may require combining breeding management with habitat restoration and, where appropriate, genetic rescue to ensure the long-term evolutionary potential of such unique and endangered 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.

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.

Populations of the Caribbean reef-building coral, Acropora palmata, have declined sharply since their population genetic structure was first characterized in the early 2000s. Previous analyses comprehensively sampled coral colonies across the Caribbean and western North Atlantic but genomic resolution was limited by the number of loci assayed. These analyses indicated extensive asexual reproduction via fragmentation, high outcrossing at the genet level, and a distinct east-west population split. To advance basic research and inform genetic management of this endangered species, we present an updated population genomic assessment using a species-specific microarray to analyze over 4,000 samples representing [~]1,500 genets from 12 geographic regions. Data were contributed by more than 30 research and restoration groups. Our analysis identifies nine spatially structured genetic clusters, with low average pairwise FST values of between 0.01 to 0.125. Interestingly, legacy genets from the Florida Reef Tract were admixed between two clusters, one dominant in the Mesoamerican Reef Tract on the western flank and the other cluster appearing in genets from Cuba to the south. Migration surface analyses highlight the influence of major current systems on gene flow. Isolation by distance was evident along the Greater Antilles but weak along the Florida Reef Tract. Kinship among wild genets was low across sites, suggesting limited local relatedness; however, assisted sexual reproduction in restoration efforts may disrupt natural kinship patterns. These findings refine our understanding of A. palmatas genetic architecture and underscore the importance of incorporating genomic data into conservation strategies.

Conservation interventions are increasingly required for species threatened by population declines and isolation due to anthropogenic pressures. Small, isolated populations are particularly vulnerable to the loss of genetic diversity, increased inbreeding, and the accumulation of deleterious mutations. Translocations or supplementation of allopatric individuals for genetic rescue may be the only way to increase genetic diversity to increase population persistence via increased adaptive potential. Here, we use an experimentally admixed population of sand lizards on a small island in Sweden as a valuable model of genetic rescue. This population was established approximately 20 years ago (5-6 generations) resulting in increased fecundity and hatchling viability. This population was founded from crossings between individuals from an inbred population from the nearby mainland and individuals sourced from populations in southern Sweden. Low-coverage whole-genome sequencing revealed elevated genetic diversity and reduced realized genetic load in this admixed population relative to the source populations. Ancestry analyses indicated a greater contribution of southern Swedish genetic variation, potentially reflecting contribution of beneficial adaptive variation from this region that may underlie the positive population effects. This system provides valuable empirical insights into the long-term genomic consequences of genetic rescue in this model vertebrate population.

Genomic erosion as a manifestation of small effective population size (Ne) and consanguinity subverts long-term perpetuation of threatened species by compromising their adaptive potential; however, the integration of genomics remains limited in applied conservation efforts to guide priorities. This study combines non-invasive sampling, double-digest Restriction site-associated DNA sequencing (ddRAD), and population-genomic analyses to assess genetic health in two vulture assemblages-mixed wild enclosure and captive breeding cohorts. Both the geographical locations exhibit signs of populations in distress: low genetic diversity and abundant intermediate-length runs of homozygosity (RoH), consistent with long-term reduced Ne plus recent demographic isolation. Our demographic model runs favoured ancient migration (AM) topology characterised by an ephemeral window of gene flow, taken over by a prolonged population separation period. The mutation quantification results from approximately 59,000 outgroup-polarised SNPs reveal higher additive burden and more homozygous-derived sites in BKN. However, this was later traced to low-impact and non-coding variants rather than a surge in the loss-of-function (LoF) alleles. The data support a genomic profile that carries an elevated risk from polygenic/aggregate deleterious burden in BKN despite a scarcity of high-impact mutations. By highlighting the disconnect between genetic resilience and demographic recovery, our results accentuate the need to incorporate genomics-informed inbreeding and monitoring programs, while also focusing on reducing anthropogenic mortality with genetic augmentation.

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.

Genetic resistance to anticoagulant rodenticides is a world-wide evolutionary phenomenon among invasive commensal rodents, that has not been investigated in Canada. We sequenced exon 3 of the VKORC1 gene of house mouse Mus musculus samples obtained from pest management professionals in Ontario and Quebec, to search for mutations known to confer resistance. Sanger sequencing was used alongside a novel qPCR assay for codons 128 and 139. We detected high prevalence (99%) of two non-synonymous single nucleotide polymorphisms in house mice, previously found in the USA and Europe, known to cause extreme resistance to first and some second-generation anticoagulants (L128S & Y139C). Homozygous resistant mice were more common in high population density areas. L128S alleles were more common in Southwestern Ontario, and Y139C in Central Ontario, despite high linkage disequilibrium. Detection success was far greater with qPCR than with Sanger sequencing. We conclude that uncoordinated rodenticide usage has selected for extreme resistance in mice throughout Ontario. Therefore, chemical control of the house mouse may be ineffective with first-generation anticoagulants throughout Ontario. This suggests that the evolution of wild urban mice is influenced by pest management practices, which may vary by region within the province.

Global climate change has increased the frequency and severity of stressful temperatures that freshwater fishes experience, necessitating rapid and sensitive methods to monitor wild populations. Tissues used to measure transcriptional responses traditionally involved invasive or lethal sampling, which may be undesirable for imperilled species. Epidermal mucus offers a non-lethal and minimally invasive alternative, but whether thermal thresholds can be detected in mucus to identify fish experiencing thermal stress is unclear. Bull trout (Salvelinus confluentus) are a legally protected salmonid and cold-water specialist, generally occupying waters 12 {degrees}C and below, with higher temperatures resulting in cellular stress. Therefore, we measured a suite of 56 genes using high-throughput qPCR to compare machine learning classifiers developed with transcriptional profiles of epidermal mucus, gill, liver, and muscle to classify laboratory reared juvenile bull trout as below (9 {degrees}C, 12 {degrees}C) or above (15 {degrees}C, 18 {degrees}C) cellular thermal thresholds. Mucus profiles most resembled gills but represented an intermediate transcriptional response to all tissues. A reduced biomarker panel of 10 genes in mucus assigned fish to stress categories with 94.1% (95% CI = 71.3-99.9%) accuracy, which was comparable to gill (100.0%, CI = 82.4- 100%), liver (95.0%, CI = 75.1-99.9%), and muscle (100.0%, CI = 80.5-100.0%). Sex-specific temperature effects were evident in all tissues, but less pronounced in mucus and gill than in liver and muscle. Our findings demonstrate that transcriptional profiling of mucus can reliably identify individuals experiencing thermal stress, highlighting the promise of this non-lethal approach for monitoring at-risk species.

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.

Ash dieback caused by Hymenoscyphus fraxineus threatens European ash (Fraxinus excelsior L.) across its range, yet natural populations retain heritable, polygenic variation in disease response. A major challenge for genomic prediction in long-lived trees is reduced transferability across heterogeneous environments, where genotype-by-environment (GxE) interactions may influence phenotypic expression. Here, we combined nationwide sampling across Poland (320 trees from 107 populations), whole-genome SNP data, and climate-derived predictors to test whether modelling environmental similarity and GxE can improve the prediction of ash dieback severity, quantified using a synthetic tree damage index (Syn). Environmental ordination identified a primary hydroclimatic gradient as a key driver of Syn (PC1env: {beta} = 0.45 {+/-} 0.14, p = 0.0016), although broad-scale environmental predictors explained only a modest proportion of phenotypic variance. Genome-wide association analyses revealed substantial additive genetic signal (SNP-based heritability h{superscript 2}SNP = 0.63; extreme-phenotype h{superscript 2}SNP = 0.81) and identified 414 suggestive loci (p < 1 x 10-), consistent with a broadly polygenic architecture of resistance, but with pronounced local enrichment of association signals in two candidate regions on chromosomes 2 and 4. In genomic prediction, trait-enriched SNP panels consistently outperformed random panels across marker densities. Predictive ability reached r {approx} 0.89 in internal validation for a 500-SNP panel and remained robust (r {approx} 0.80) in an independent external validation set (n = 64). Incorporating GxE in a multi-kernel framework yielded modest but consistent gains over main-effect models, particularly under environmental extrapolation, with REML variance partitioning supported a non-zero interaction component (VGxE {approx} 14.9% and 20.9%). Our results demonstrate that ash dieback resistance is predictably polygenic and that accounting for environmental heterogeneity enhances the robustness and transferability of genomic prediction, supporting environment-aware selection and assisted migration strategies for European ash restoration.

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.

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 sugar kelp Saccharina latissima is a promising candidate for sustainable aquaculture in the North Atlantic and North-East Pacific but genetic improvement has been hindered by limited understanding of the genetic basis of economically important traits. We conducted the first genome-wide association study (GWAS) for this species using 202 self-fertilised pseudo-F1 individuals derived from 12 populations spanning northern and southern European genetic clusters. Individuals were genotyped with ddRAD-seq-derived SNP markers and phenotyped in a common garden experiment for four morphological traits (blade length, blade width, blade area, stipe length) and six metabolic traits related to nitrogen metabolism. We identified 26 significant marker-trait associations, with phenotypic variance explained (PVE) ranging from 0.65% to 52.44%. Major-effect loci were detected for blade width (52.44% PVE) and blade area (45.22% PVE) and a locus on chromosome 17 influenced both blade length and blade area. Marker-based heritability estimates ranged from 0.75 to 0.99 for morphological traits and from 0.00 to 0.99 for metabolic traits, though with large standard errors. Cross-validation of genomic selection models yielded predictive abilities of 0.21-0.59 across traits. Our findings reveal a mixed genetic architecture with major-effect loci suitable for marker-assisted selection and polygenic traits amenable to genomic selection, providing a foundation for genomics-assisted breeding programs in kelp aquaculture.

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.

Although malaria prevalence in Vietnam has markedly declined and the country presses closer to elimination, a highly focal reservoir of Plasmodium vivax malaria persists in its forested and border regions, threatening the countrys 2030 elimination targets. Genomic surveillance of malaria parasites can be a vital tool to produce fine-scale insights into the changing population dynamics of parasite populations, especially in population decline. Here, we analysed the genomic diversity of 18 newly sequenced P. vivax isolates from the Central Highlands, South Central Coast, and Southeastern regions of Vietnam collected in 2019, analysing them alongside 115 publicly available sequences from Vietnam collected between 2009-2016. Over these 10 years, infections became increasingly monoclonal, transmission remained highly focal, and the overall population structure was weak. Geographic factors, and not temporal factors, were a major driver of genetic substructure. Identity-by-descent (IBD) analyses revealed pockets of inbreeding in transmission hotspots, and high relatedness in parasites from within the same or adjacent provinces. Whilst within-population haplotype-based testing revealed minimal selection pressures on the 2009-2016 and 2019 populations, we observed multiple signals of differential selection of genetic variants involved in life-cycle specific processes. Overall, our work provides the most recent assessment of the genomic diversity of P. vivax in Vietnam, revealing relics of evolution in a parasite population in decline. Continued genomic surveillance, especially in outbreak contexts, and with more recent samples will be a crucial strategy to inform malaria elimination activities. Author SummaryPlasmodium vivax is the most geographically widespread malaria parasite and the predominant species in the Greater Mekong Subregion. In Vietnam, P. vivax malaria continues to persist in remote forested settings and along its international borders. Using genomic approaches, we analysed 133 P. vivax genomes from the Central Highlands, South Central Coast, and Southeastern regions of Vietnam, including 18 newly sequenced isolates collected in 2019 and 115 publicly available genomes sampled between 2009 and 2016. Our work describes the evolutionary and genetic consequences of intensive control efforts that have led to decreasing transmission and population decline. We found decreasing infection complexity and increasing clonal inbreeding, which suggests localised transmission of clonal lineages in transmission hotspots. Over the 10-year sampling period, we observed consistent allele frequencies in putative drug resistance loci, suggesting an absence of drug-driven directional selection. Our findings highlight the importance of genomic surveillance in monitoring parasite persistence, which will be critical for guiding public health decisions to sustain progress towards malaria elimination.