Joshua A. Thia

The evolutionary transition from free-living bacteria to host-adapted symbionts is typically accompanied by substantial genomic changes. Within the genus Serratia , this transition has so far been documented only in the aphid-associated species, Serratia symbiotica , whereas all other Serratia species are free-living. In this study, we identify a putatively new Serratia taxon using metagenomic approaches in the trombidiform mite, Halotydeus destructor . We provide genomic evidence for a possible transition to a host-adapted lifestyle in this new Serratia sp., which sits phylogenetically within a clade of free-living Serratia species. The genomic signatures of evolving toward a host-adapted lifestyle include a reduced genome size and coding capacity, an elevated transposase fraction, and detectable chromosomal rearrangements, relative to other free-living Serratia species. However, the species does not show the same structure of genome reduction as S. symbiotica . Functional gene content analyses including COG categories and virulence factor repertoires also showed that our new Serratia sp. had a distinct gene profile from both free-living Serratia and S. symbiotica . Additional genomic screening suggests that infections of the new Serratia sp. are common in wild populations of H. destructor across its invasive Australian range, warranting future investigations on the possible role this symbiont plays in the evolutionary ecology of its mite host. Our work not only highlights a potential parallel transition to a host-adapted lifestyle in the Serratia genus, but also represents the first characterisation of a possible host-adapted Serratia taxon in a trombidiform mite.

The redlegged earth mite, Halotydeus destructor , is an invasive pest of grain and pasture crops in Australia. Australian populations are increasingly developing resistance to broad‐spectrum pesticides. Here, we assembled a chromosome‐level genome for H. destructor , comprising nine chromosomes and totalling approximately 46 Mb. We also generated a genomic dataset from 190 populations collected across thousands of kilometres of its invasive Australian range and across 4 years (2018, 2021, 2022 and 2023), and used this dataset to develop KASP (Kompetitive allele‐specific PCR) markers for identifying resistance mutations. We combined pooled whole‐genome sequencing with resistance testing for organophosphate pesticides, chlorpyrifos and omethoate, and the pyrethroid pesticide, bifenthrin. Target‐site resistance to chlorpyrifos was strongly associated with the common ace G119S mutation. A second mutation, ace A201S, was also common, although its association with chlorpyrifos or omethoate resistance was less clear. Target‐site resistance to bifenthrin was strongly associated with the common para L1024F mutation. We also detected several rare target‐site mutations that likely contribute to resistance in specific populations, including F331Y in ace , and M918T, M918V, L925I, F1020S and F1538I in para . Copy number variation in ace showed mixed associations with resistance, potentially reflecting the co‐occurrence of variable gene copies and target‐site mutations segregating within and among populations. Finally, we observed putative compositional and structural differences in genomic regions containing carboxylesterases with high ace ‐like homology, a group of genes that might be involved in organophosphate metabolism. This study advances the genomic and molecular resources available for H. destructor , and represents the most comprehensive investigation to date of resistance mechanisms and their spatiotemporal distribution in this invasive pest. Our data showed that pesticide resistance in H. destructor likely involves many genes. Nevertheless, target‐site mutations are likely to remain key markers for rapid resistance diagnostics, for which our KASP markers will provide valuable tools.

BACKGROUND: Range expansion is often accompanied by reduced genetic diversity and increased environmental stress in populations at range edges, potentially constraining adaptive evolution despite strong selection. This study aimed to investigate these processes during the northward range expansion of the fruit fly Zeugodacus tau , an important agricultural pest. We sampled 217 individuals from 11 geographical populations spanning the species' current distribution across China and genotyped them using double‐digest restriction‐site‐associated DNA sequencing (ddRAD‐seq). RESULTS: The surveyed populations were genetically differentiated into southwestern and southeastern groups, with an admixed group located in the longitudinal transition zone between them. Northern populations generally exhibited lower genetic diversity than southern populations, whereas populations with admixed ancestry tended to retain higher genetic diversity than non‐admixed populations at comparable latitudes. TreeMix supported two historical migration events, and all populations except Shanghai exhibited broadly similar demographic histories. Environmental variables independently explained more genomic variation than geographic variables, both across all populations (53.01% vs 27.28%) and within the admixed group (50.64% vs 17.25%). Genome scans identified candidate SNPs in the admixed group that were potentially associated with responses to environmental stress. CONCLUSIONS: Our findings show that the northward range expansion of Z. tau is accompanied by a general decline in genetic diversity, while admixture among differentiated lineages may partially offset this loss. These results highlight the joint roles of demographic history and admixture in shaping genomic variation during range expansion, although the adaptive consequences of admixture remain unresolved. © 2026 Society of Chemical Industry.

Some bacterial endosymbionts of aphids can reduce mummification rates following attack by parasitoids, yet these endosymbionts can remain at a low frequency in populations even when parasitoids are present. The endosymbiont Regiella insecticola is uncommon in the major pest aphid Myzus persicae despite providing apparent protection against parasitoid attack. Here, we consider population-level effects associated with Regiella in its native M. persicae host as well as Regiella transinfected into pest Rhopalosiphum padi (oat aphids) and Diuraphis noxia (Russian wheat aphids), focusing on two parasitoids (Diaeretiella rapae, Aphidius colemani). We consider their impact not only on mummification rates but also on fecundity of non-mummified aphids that have been stung by wasps as detected by a qPCR assay to detect parasitoid DNA, with experiments simulating a single parasitoid attack event. Regiella produced a sharp decrease in mummification rates of their native and transinfected hosts, but aphids with Regiella that were stung (successful oviposition confirmed by molecular analysis) and not mummified showed low reproduction. The combination of these effects meant we did not detect major differences in the population size of infected and uninfected aphids. These results highlight the importance of considering multi-trait effects when assessing the impacts of endosymbiont infections and predicting the outcome of endosymbiont–host–parasitoid interactions.

Symbiotic bacteria are of increasing interest as new, alternative biological control candidates for managing insect pests. Previous work has found that a novel, self-spreading, transinfection of the endosymbiont, Rickettsiella viridis, can induce fitness costs in the globally invasive aphid pest, Myzus persicae (Sulzer). Endosymbiont transinfections could be used in broad scale management if they do not interfere with other common control options that are compatible with integrated pest management at local scales. In this work, we studied the effect of a novel Rickettsiella transinfection on chemical and entomopathogen responses in M. persicae. Our experiments used 4 different clonal genotypes that varied in their resistance to chemical insecticides, allowing us to capture the potential genetic variability in the response of aphid hosts to the Rickettsiella infection. These aphid genotypes were exposed to 3 chemical insecticides registered for aphid control in Australian agriculture (bifenthrin, a pyrethroid; dimethoate, an organophosphate; and imidacloprid, a neonicotinoid), as well as the fungal entomopathogen, Beauveria bassiana (Balsamo). Mortality following chemical insecticide exposure varied considerably among aphid genotypes but was unaffected by the Rickettsiella infection. Mortality and fecundity following fungal entomopathogen exposure exhibited interactions between genotype and Rickettsiella infection status, with some possible transgenerational effects. However, there was no evidence that the efficacy of Beauveria was compromised by Rickettsiella. These results support the potential for the general use of Rickettsiella as a biological control agent, which could be released into natural populations as part of area-wide strategies to establish infections and suppress pest populations.

Genomic resources provide tools for understanding the evolution of resistance and monitoring resistance as it develops, which can assist the adoption of pesticide resistance management strategies. The invasive redlegged earth mite, Halotydeus destructor , is a major pest of grain and pasture crops in Australia and is increasingly developing resistance to broad-spectrum pesticides. Here, we assembled a chromosomal-level genome of H. destructor , which comprises eight chromosomes totalling 46 Mb. We also compiled a rich genomic dataset of 190 H. destructor populations (whole-genome pooled sequencing) collected across its invasive Australian range (thousands of kilometers), in four years (2018, 2021, 2022, and 2023), and generated resistance phenotypes to multiple pesticide compounds widely used to manage this pest. These genomic resources were used to provide the most detailed characterisation of genetic structure in Australia to date, highlighting complex patterns of regional structuring and isolation-by-distance. We then screened this population genomic dataset to identify target-site mutations in the ace (acetylcholinesterase) and para (voltage-gated sodium channel) genes, which are the targets of organophosphate and pyrethroid pesticides, respectively. Genotype–phenotype associations suggest that the ace G119S mutation has a strong contribution to chlorpyrifos resistance, but not omethoate resistance. Association tests also suggest that para L1024F mutation has a strong, but weakening, contribution to pyrethroid resistance. We then developed and validated a Kompetitive allele-specific PCR (KASP) assay for the ace G1195S and para L1024F mutations linked to chlorpyrifos and bifenthrin resistance, respectively, and demonstrate how these assays can be applied to quantify allele frequencies in pooled DNA extractions. The KASP markers that we have developed will be valuable in facilitating rapid spatiotemporal screening of key resistance mutations in target genes. Our work also suggests a non-target gene basis for omethoate resistance, and a potential shift to other non-target gene mechanisms for pyrethroid resistance. To that end, our new chromosome-level assembly will be important for characterising the genetic architecture of those resistances.

Populations under similar selection pressures may adapt via parallel evolution or dispersal of advantageous alleles. Here, we investigated insecticide resistance in the invasive blue-green aphid, Acyrthosiphon kondoi, which reproduces clonally in Australia and has rapidly developed resistance across geographic locations. Using genomic, transcriptomic, and experimental approaches, we explored the evolutionary origins and molecular mechanisms of resistance. We developed the first nuclear genome assembly for A. kondoi (443.8 Mb, 28,405 annotated genes, BUSCO score 97.5%) and a partial mitochondrial assembly (11,598 bp). All resistant strains shared a common ancestor, supporting the spread of a resistant “superclone” lineage that is distinct from susceptible strains. Resistance was associated with over-expression of an esterase gene that was homologous to E4/FE4 esterases that are linked to resistance in other aphid pests. Functional experiments in Drosophila melanogaster confirmed a causal role of this E4-like esterase in resistance to organophosphates, carbamates, and pyrethroids. These findings highlight how clonal dispersal and insecticide overuse can transform local adaptation into a widespread pest management issue. Our results suggest a parallel macroevolutionary response to insecticide selection in A. kondoi and other aphid species at the gene family level, but with a distinct regulatory mechanism in A. kondoi. Given the rapid spread of the resistant superclone, alternative management strategies, including expanded chemical control options and enhanced biological control, are urgently needed to mitigate this growing pest problem.

The genetic basis of pesticide resistance has been widely studied, but the exact nature of this evolutionary process in the field is often unclear, particularly when a limited number of populations is considered and when there is a lag between the evolutionary event and its investigation. We showed that an unprecedented number of recurrently evolved mutations in an arthropod pest, the two-spotted spider mite Tetranychus urticae, drive the rapid evolution of resistance to a recently commercialized acaricide, cyetpyrafen. We first observed high levels of resistance that appeared and became widespread within three years. Genome scans revealed genetic heterogeneity of resistance among populations and identified 15 target mutations, including six mutations on five amino acid residues of subunit sdhB, and nine mutations on three amino acid residues of subunit sdhD of the pesticide target succinate dehydrogenase, with as many as five substitutions on one residue. No mutations were present in 2,317 screened historical specimens, suggesting that mutations arose rapidly through de novo substitutions or from very rare segregating mutations. Identical mutations recurrently appeared in different genetic backgrounds, increasing the likelihood of resistance evolution. The high number of mutational options available for the evolution of target site resistance in this pest challenges resistance management practices.

Nontarget effects of insecticides used in agriculture can impact the ecosystem services provided by beneficial insects. Understanding the broader effects of chemical usage requires multispecies investigations on the impact of different insecticide active ingredients. In this work, we tested the utility of coated vials as a quick, cheap, and efficient dried residue chemical toxicity assay. This method was compared against dishes sprayed with a Potter tower, which is an industry standard instrument used to apply precise insecticide doses. Our study focused on 2 natural enemies of aphids, larval and adult stages of the Hippodamia variegata (Goeze 1777) ladybird beetle, and the parasitoid wasp, Diaeretiella rapae (McIntosh 1855). These natural enemies were exposed to multiple concentrations of 3 insecticides registered for aphid control in Australian agriculture: alpha-cypermethrin (pyrethroid), dimethoate (organophosphate), and sulfoxaflor (sulfoximine). Modelled concentration–response relationships showed evidence of general differences in the intercepts between methods, but not in slope (rate of mortality with concentration). However, these subtle statistically significant effects did not translate into marked differences in LC50-values, which were comparable across assay methods for all natural enemies and insecticides tested. Coated vials therefore produced estimates of chemical toxicity that were consistent with those derived from Potter tower sprays. This underscores the validity of coated vials as a method for performing high-throughput chemical toxicity experiments, as required when examining different populations of multiple taxa across a range of insecticide active ingredients.