Search

Resistance to pesticides is typically identified via laboratory bioassays after field control failures are observed, but the results of such assays are rarely validated through experiments under field conditions. Such validation is particularly important when only a low-to-moderate level of resistance is detected in the laboratory. Here we undertake such a validation for organophosphate resistance in the agricultural pest mite Halotydeus destructor, in which low-to-moderate levels of resistance to organophosphorus pesticides have evolved in Australia. Using data from laboratory bioassays, we show that resistance to the organophosphate chlorpyrifos is higher (around 100-fold) than resistance to another organophosphate, omethoate (around 7-fold). In field trials, both these chemicals were found to effectively control pesticide-susceptible populations of H. destructor. However, when applied to a resistant mite population in the field, the effectiveness of chlorpyrifos was substantially decreased. In contrast, omethoate remained effective when tested alone or as a mixture with chlorpyrifos. We also show that two novel (non-pesticide) treatments, molasses and wood vinegar, are ineffective in controlling H. destructor when sprayed to pasture fields at rates of 4 L/ha. These findings suggest a close link between levels of resistance quantified through laboratory bioassays and the field effectiveness of pesticides; however, in the case of H. destructor, this does not necessarily mean all field populations possessing organophosphate resistance will respond similarly given the potentially complex nature of the underlying resistance mechanism(s).

Chemical resistance in pest organisms threatens global food security and human health, yet resistance issues are mostly dealt with reactively. Predictive models of resistance risk provide an avenue for field practitioners to implement proactive pest management but require knowledge of factors that drive resistance evolution. Despite the importance of chemical selection pressure on resistance evolution, poor availability of chemical usage data has limited the use of a general multi-species measure of selection pressure in predictive models. We demonstrate the use of pesticide product registrations as a predictor of resistance status and potential proxy of chemical selection pressure. Pesticide product registrations were obtained for 427 USA and 209 Australian agricultural arthropod pests, for 42 and 39 chemical Mode of Action (MoA) groups, respectively. We constructed Bayesian logistic regressions of resistance status as a function of the number of pesticide product registrations and two ecological traits, phagy and voltinism. Our models were well-supported with demonstrated power to discriminate between resistant and susceptible observations in both USA and Australian species sets using cross-validation. Importantly, we observed strong support for a positive association between pesticide products and resistance status. Our work expands the horizon for proactive management by quantitatively linking a proxy for selection pressure on pest species to different chemical MoAs. This proxy for selection pressure can be combined with ecological information to predict the resistance risk in agricultural pests. Because pesticide product registrations can typically be derived from publicly available data, we believe there is broad applicability to other agricultural pests such as weeds and fungi, and to other geographical regions beyond the USA and Australia.

In this issue of Molecular Ecology, Tepolt et al. (2021) illustrate how the genetic architecture of adaptation and life history influence invasive success. A marvel of many invasive species is that they are incredibly successful despite evolutionary expectations that they will have low adaptive potential and suffer inbreeding depression due to initially small founding population sizes. Determining the combinations of ecoevolutionary factors that permit this apparent "genetic paradox of invasions" is an ongoing endeavour of invasive species research. Tepolt et al. (2021) study the European green crab in its invasive range on the North American west coast. Following a single introduction into California, this crab quickly spread across a wide latitude gradient, despite low diversity in the original founding population. Adaptation of this crab to clinal variation in temperature appeared largely driven by an inferred chromosomal inversion. This inversion exists as a balanced polymorphism in the European home range of green crabs and is associated with thermal tolerance. Tepolt et al. (2021) therefore demonstrate that adaptive evolution post introduction need not be impeded by bottlenecks if variation at key parts of the genome is available and can be maintained in introduced populations. Moreover, Tepolt et al. (2021) show how chromosomal inversions acting as large-effect loci might facilitate rapid responses to selection in introduced populations.

The redlegged earth mite, Halotydeus destructor (Tucker, 1925: Trombidiformes, Eupodoidea, Penthaleidae), is an invasive mite species. In Australia, this mite has become a pest of winter pastures and grain crops. We report the complete mitogenome for H. destructor, the first to represent the family Penthaleidae, superfamily Eupodoidea. The mitogenome of H. destructor is 14,691 bp in size, and has a GC content of 27.87%, 13 protein‐coding genes, two rRNA genes, and 22 tRNA genes. We explored evolutionary relationships of H. destructor with other members of the Trombidiformes using phylogenetic analyses of nucleotide sequences and the order of protein‐coding and rRNA genes. We found strong, consistent support for the superfamily Tydeoidea being the sister taxon to the superfamily Eupodoidea based on nucleotide sequences and gene arrangements. Moreover, the gene arrangements of Eupodoidea and Tydeoidea are not only identical to each other but also identical to that of the hypothesized arthropod ancestor, showing a high level of conservatism in the mitogenomic structure of these mite superfamilies. Our study illustrates the utility of gene arrangements for providing complementary information to nucleotide sequences with respect to inferring the evolutionary relationships of species within the order Trombidiformes. The mitogenome of H. destructor provides a valuable resource for further population genetic studies of this important agricultural pest. Given the co‐occurrence of closely related, morphologically similar Penthaleidae mites with H. destructor in the field, a complete mitogenome provides new opportunities to develop metabarcoding tools to study mite diversity in agro‐ecosystems. Moreover, the H. destructor mitogenome fills an important taxonomic gap that will facilitate further study of trombidiform mite evolution., We report the complete mitogenome sequence of the redlegged earth mite, Halotydeus destructor (Tucker). We used Bayesian phylogenetic analyses to contextualize the relationship of H. destructor with other trombidiform mites. Phylogenies were inferred from protein‐coding and rRNA genes using nucleotide sequences and a novel characterization of gene order arrangements.

Genomic data provide valuable insights into pest management issues such as resistance evolution, historical patterns of pest invasions and ongoing population dynamics. We assembled the first reference genome for the redlegged earth mite,Halotydeus destructor(Tucker, 1925), to investigate adaptation to pesticide pressures and demography in its invasive Australian range using whole-genome pool-seq data from regionally distributed populations. Our reference genome comprises 132 autosomal contigs, with a total length of 48.90 Mb. We observed a large complex ofacegenes, which has presumably evolved from a long history of organophosphate selection inH. destructorand may contribute toward organophosphate resistance through copy number variation, target-site mutations, and structural variants. In the putative ancestralH. destructor acegene, we identified three target-site mutations (G119S, A201S, and F331Y) segregating in organophosphate resistant populations. Additionally, we identified two newparasodium channel gene mutations (L925I and F1020Y) that may contribute to pyrethroid resistance. Regional structuring observed in population genomic analyses indicates that gene flow inH. destructordoes not homogenise populations across large geographic distances. However, our demographic analyses were equivocal on the magnitude of gene flow; the short invasion history ofH. destructormakes it difficult to distinguish scenarios of complete isolation vs. ongoing migration. Nonetheless, we identified clear signatures of reduced genetic diversity and smaller inferred effective population sizes in eastern vs. western populations, which is consistent with the stepping-stone invasion pathway of this pest in Australia. These new insights will inform development of diagnostic genetic markers of resistance, further investigation into the multifaceted organophosphate resistance mechanism, and predictive modelling of resistance evolution and spread.

Aim: Globally distributed pelagic fishes are typified by very low to negligible genetic differentiation at oceanic scales arising from high gene flow and (or) large population sizes. However, genomic approaches employing thousands of loci to characterise genetic variation can illuminate subtle patterns of genetic structure and facilitate demographic inference, such that effects arising from gene flow and population size can be partially decoupled. We used a population genomics approach to identify putative stocks in a circumtropical pelagic fish, wahoo, and to assess global connectivity in this species. Location: Indo-Pacific and Atlantic Oceans. Taxon: Wahoo, Acanthocybium solandri (Cuvier, 1832). Methods: Globally distributed wahoo samples from 11 locations (representing a total of 296 individuals) were sequenced using a pool-seq ezRAD approach to obtain 1289–9825 genome-wide SNP loci per population pair for analyses of genetic structure at a minor allele frequency (MAF) >0.05. Demographic inference using a diffusion approximation method (∂a∂i) was performed using 11,495–12,812 SNPs per population pair at a MAF >0.02. Results: Genetic structure, measured as F , was overall low, suggesting very little heterogeneity amongst sample pairs (pairwise F ≤ 0.021). However, there was a clear signal of regional genetic structuring between ocean basins. A principal coordinate analysis separated samples from the Indo-Pacific with those from the Atlantic and an analysis of molecular variance suggested that ~77% of variation in genetic structure was amongst regions. Our demographic analyses found greater support for models including migration over simple models of isolation. Main conclusions: Our study provides the most thorough genetic investigation of wahoo to date. We provide evidence for global connectivity of wahoo populations over their evolutionary history, but we also provide the first indication of subtle regional structure between the Indo-Pacific and Atlantic Oceans, which occurs against a background of high gene flow. The identification of regional stocks will inform new management strategies and guide future investigations in wahoo, an increasingly important species in global fisheries. ST ST

Quantifying how chemical tolerance of pest arthropods varies with temperature is important for understanding the outcomes of chemical control, for measuring and monitoring resistance, and for predicting how pesticide resistance will evolve under future climate change. We studied the redlegged earth mite, Halotydeus destructor (Tucker), a winter-active invasive agricultural pest in Australia. Using a replicated block experiment, we tested the effect of different thermal conditions on the expression of chemical tolerance to a pyrethroid and two organophosphates. Our chemical bioassays were conducted on two redlegged earth mite populations: one possessed organophosphate resistance, whilst the other was susceptible to pesticides. Mites were first acclimated at cool (4 °C) and warm (14 °C) conditions and then exposed to pesticides in both cool (11 °C) and warm (18 °C) test conditions.Warm test conditions generally reduced chemical tolerance to all pesticides relative to cool test conditions. Median lethal dose (LDOur data provides context for prior theoretical work demonstrating climatically constrained pesticide resistances in Australian redlegged earth mites. Estimates of temperature dependent toxicity measured in this study may be useful in parameterizing models of redlegged earth mite control under an increasingly warm and more variable climate. © 2022 The Authors. Pest Management Science published by John WileySons Ltd on behalf of Society of Chemical Industry.

The Scaptodrosophila genus represents a large group of drosophilids with a worldwide distribution and a predominance of species in Australia, but there is little information on the presence and impacts of Wolbachia endosymbionts in this group. Here we describe the first Wolbachia infection from this group, wClay isolated from Scaptodrosophila claytoni (van Klinken), a species from the east coast of Australia. The infection is polymorphic in natural populations, occurring at a frequency of around 6%-10%. wClay causes male killing, producing female-biased lines; most lines showed 100% male killing, though in 1 line it was80%. The lines need to be maintained through the introduction of males unless the infection is removed by tetracycline treatment. wClay is transmitted at a high fidelity (98.6%) through the maternal lineage and has been stable in 2 laboratory lines across 24 generations, suggesting it is likely to persist in populations. The infection has not been previously described but is closely related to the male-killing Wolbachia recently described from Drosophila pandora based on multilocus sequence typing and the wsp gene. Male-killing Wolbachia are likely to be common in drosophilids but remain difficult to detect because the infections can often be at a low frequency.

Koala retrovirus (KoRV) is a recently endogenized retrovirus associated with neoplasia and immunosuppression in koala populations. The virus is known to display sequence variability and to be present at varying prevalence in different populations, with animals in southern Australia displaying lower prevalence and viral loads than northern animals. This study used a PCR and next-generation sequencing strategy to examine the diversity of the KoRV env gene in both proviral DNA and viral RNA forms in two distinct populations representative of the ‘northern’ and ‘southern’ koala genotypes. The current study demonstrated that the full range of KoRV subtypes is present across both populations, and in both healthy and sick animals. KoRV-A was the predominant proviral subtype in both populations, but there was marked diversity of DNA and RNA subtypes within individuals. Many of the northern animals displayed a higher RNA viral diversity than evident in their proviral DNA, indicating relatively higher replication efficiency of non-KoRV-A subtypes. The southern animals displayed a lower absolute copy number of KoRV than the northern animals as reported previously and a higher preponderance of KoRV-A in individual animals. These discrepancies in viral replication and diversity remain unexplained but may indicate relative protection of the southern population from KoRV replication due to either viral or host factors and may represent an important protective effect for the host in KoRV’s ongoing entry into the koala genome.

In this study, we sequenced the full mitochondrial genome of Bathygobius cocosensis, an abundant intertidal fish species, which may provide insights into the evolutionary genetics of chaotic genetic patchiness and range expansion in marine systems. The mitochondrial genome is 16,692 bp, and contains 13 protein-coding genes along with 22 tRNA and 2 rRNA genes and a D-loop region, arranged similarly to other Gobiidae species. A Bayesian phylogeny of Gobiidae species indicates close relationships to the genus Glossogobius. The B. cocosensis mitochondrial genome is now available through GenBank (Accession = MG704838).

Interactions among selection, gene flow, and drift affect the trajectory of adaptive evolution. In natural populations, the direction and magnitude of these processes can be variable across different spatial, temporal, or ontogenetic scales. Consequently, variability in evolutionary processes affects the predictability or stochasticity of microevolutionary outcomes. We studied an intertidal fish, Bathygobius cocosensis (Bleeker, 1854), to understand how space, time, and life stage structure genetic and phenotypic variation in a species with potentially extensive dispersal and a complex life cycle (larval dispersal preceding benthic recruitment). We sampled juvenile and adult life stages, at three sites, over three years. Genome-wide SNPs uncovered a pattern of chaotic genetic patchiness, that is, weak-but-significant patchy spatial genetic structure that was variable through time and between life stages. Outlier locus analyses suggested that targets of spatially divergent selection were mostly temporally variable, though a significant number of spatial outlier loci were shared between life stages. Head shape, a putatively ecologically responsive (adaptive) phenotype in B. cocosensis also exhibited high temporal variability within sites. However, consistent spatial relationships between sites indicated that environmental similarities among sites may generate predictable phenotype distributions across space. Our study highlights the complex microevolutionary dynamics of marine systems, where consideration of multiple ecological dimensions can reveal both predictable and stochastic patterns in the distributions of genetic and phenotypic variation. Such considerations probably apply to species that possess short, complex life cycles, have large dispersal potential and fecundities, and that inhabit heterogeneous environments.

Complex life cycles may evolve to dissociate distinct developmental phases in an organism's lifetime. However, genetic or environmental factors may restrict trait independence across life stages, constraining ontogenetic trajectories. Quantifying covariance across life stages and their temporal variability is fundamental in understanding life-history phenotypes and potential distributions and consequences for selection. We studied developmental constraints in an intertidal fish (Bathygobius cocosensis: Gobiidae) with a discrete pelagic larval phase and benthic juvenile phase. We tested whether traits occurring earlier in life affected those expressed later, and whether larval traits were decoupled from postsettlement juvenile traits. Sampling distinct cohorts from three annual breeding seasons afforded tests of temporally variability in trait covariance. From otoliths (fish ear stones), we measured hatch size, larval duration, pelagic growth (larval traits) and early postsettlement growth (juvenile trait) in 124 juvenile B. cocoensis. We used path analyses to model trait relationships with respect to their chronological expression, comparing models among seasons. We also modelled the effect of season and hatch date on each individual trait to quantify their inherent variability. Our path analyses demonstrated a decoupling of larval traits on juvenile growth. Within the larval phase, longer larval durations resulted in greater pelagic growth, and larger size-at-settlement. There was also evidence that larger hatch size might reduce larval durations, but this effect was only marginally significant. Although pelagic and postsettlement growth were decoupled, pelagic growth had postsettlement consequences: individuals with high pelagic growth were among the largest fish at settlement, and remained among the largest early postsettlement. We observed no evidence that trait relationships varied among breeding seasons, but larval duration differed among breeding seasons, and was shorter for larvae hatching later within each season. Overall, we demonstrate mixed support for the expectation that traits in different life stages are independent. While postsettlement growth was decoupled from larval traits, pelagic development had consequences for the size of newly settled juveniles. Temporal consistency in trait covariances implies that genetic and/or environmental factors influencing them were stable over our three-year study. Our work highlights the importance of individual developmental experiences and temporal variability in understanding population distributions of life-history traits.

Related plants are often hypothesized to interact with similar sets of pollinators and herbivores, but this idea has only mixed empirical support. This may be because plant families vary in their tendency to share interaction partners. We quantify overlap of interaction partners for all pairs of plants in 59 pollination and 11 herbivory networks based on the numbers of shared and unshared interaction partners (thereby capturing both proportional and absolute overlap). We test for relationships between phylogenetic distance and partner overlap within each network; whether these relationships varied with the composition of the plant community; and whether well-represented plant families showed different relationships. Across all networks, more closely related plants tended to have greater overlap. The strength of this relationship within a network was unrelated to the composition of the network's plant component, but, when considered separately, different plant families showed different relationships between phylogenetic distance and overlap of interaction partners. The variety of relationships between phylogenetic distance and partner overlap in different plant families probably reflects a comparable variety of ecological and evolutionary processes. Considering factors affecting particular species-rich groups within a community could be the key to understanding the distribution of interactions at the network level.

The montane forests of south-eastern Nigeria are of immense conservation value due to their high levels of biodiversity and endemism. Yet despite increasing anthropogenic disturbance and forest fragmentation, little is known about the genetics of resident tree populations. We used a set of conserved chloroplast simple sequence repeat (SSR) primers to quantify and directly compare genetic diversity in three tree species: Cordia millenii, West African Cordia; Entandrophragma angolense, tiama mahogany; and Lovoa trichilioides, African walnut, within a single montane forest. Additionally, we assessed the diversity of West African Cordia between forests at a local and regional scale. Results indicate that for our focal loci, in all three species, there is a general lack of chloroplast genetic diversity. Our study is particularly relevant because it considers genetic diversity among multiple tree species simultaneously. This work represents the first study of its kind in the region, and will pioneer the way for future conservation genetic studies in montane Nigeria.

The interaction between granivorous scatterhoarding mammals and plants is a conditional mutualism: scatterhoarders consume seeds (acting as predators), but the movement of seed by scatterhoarders may contribute to dispersal (acting as mutualists). Understanding the ecological factors that shape this relationship is highly relevant in anthropogenically disturbed tropical forests where large-bodied frugivores are extirpated. In such forests, large-seeded trees that once depended on these frugivores for dispersal may now only have scatterhoarders as prospective dispersers. We studied Carapa oreophila (Meliaceae) in an Afromontane forest, to test the hypotheses that the proportion of seeds immediately consumed or hoarded (dispersed) would vary over a disturbance gradient. Temporal replication also afforded exploration of how habitat effects might vary with food availability. Using a Bayesian framework, we demonstrate that seeds were more likely to be hoarded in less disturbed forest, irrespective of temporal variation in food abundance. In contrast, forest disturbance only appeared to increase seed predation in temporal replicates that coincided with sustained food availability. These results highlight the potential variability in the dynamics between plants and scatterhoarders over fine temporal scales, elucidating possible ecological scenarios where scatterhoarders might act as mutualists (contributing positively to plant recruitment). Our study also fills important knowledge gaps about the importance of scatterhoarders as dispersers in tropical forests depleted of large-bodied frugivores, particularly in Africa where scatterhoarding mutualisms have not been extensively studied.

Seed dispersal may be essential to: i) escape parent-proximity mortality, ii) colonize new areas, or iii) reach favorable microsites (Schupp, 1993). Sensitivity of large-bodied animals to anthropogenic disturbance puts dependent large-seeded tree species at high risk of dispersal limitation (Cardoso da Silva & Tabarelli, 2000; Babweteera

Mitochondrial cytochrome oxidase I (COI) gene sequencing (DNA barcoding) of Ciona specimens from New Zealand (NZ) led to the first record of the solitary ascidian Ciona savignyi in the Southern Hemisphere. We sought to quantify C. savignyi COI genetic diversity around the NZ archipelago and to compare this with diversity within C. savignyi’s native range in the north-west Pacific. Ciona savignyi specimens were collected from two NZ sites and from three sites around Japan. COI sequences (595 bp) were amplified and measures of genetic diversity were calculated. Based on differences between their COI sequences we developed a PCR-based assay to distinguish C. savignyi from the morphologically similar C. intestinalis. A total of 12 C. savignyi COI haplotypes were recovered from the 76 samples. Of the four haplotypes observed in NZ, two were unique. From the 10 haplotypes observed in the Japan samples, eight were unique. The C. savignyi populations in Japan were found to contain higher haplotype diversity when compared with those in NZ. The NZ samples contained only a small subset of the haplotype variation of the Japan samples, however, NZ samples did harbor two haplotypes not observed in the Japan samples. A PCR-based assay developed from the COI sequences was able to reliably discriminate the two Ciona species. The low COI genetic diversity within the two NZ C. savignyi populations sampled is consistent with a founder effect associated loss of genetic diversity. The robust PCR-based assay for distinguishing C. savignyi and C. intestinalis may find application in ecological and taxonomic studies and can be applied to both archival materials and live animals.