Biology subjects

Thia, J. A.

Publications and source records attributed to Thia, J. A..

11 recordsLinked to original sources

bioRxiv2026

A new Serratia taxon found in a trombidiform mite shows genomic evidence of host adaptation but is phylogenetically distinct from Serratia symbiotica

Abstract 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.

evolutionary biology↗

bioRxiv2025

New genomic resources for an invasive mite pest help guide the development of KASP markers for pesticide resistance screening

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 four 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.

genomics↗

bioRxiv2025

High-throughput chemical toxicity testing for beneficial insects: The value of coated vials

Non-target effects of insecticides used in agriculture can impact the ecosystem services provided by beneficial insects. Understanding the broader effects of chemical usage requires multi-species 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 Hippodamia variegata ladybird beetle, and the parasitoid wasp, Diaeretiella rapae. These natural enemies were exposed to multiple doses of 3 insecticides that are registered for aphid control in Australian agriculture: alpha-cypermethrin (pyrethroid), dimethoate (organophosphate), and sulfoxaflor (sulfoximine). Modelled dose-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.

zoology↗

bioRxiv2024

Spread of a single superclone drives insecticide resistance in Acyrthosiphon kondoi across an invasive range

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 in other aphid pests that are linked to resistance. 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.

evolutionary biology↗

bioRxiv2024

A novel framework for assessing the robustness of genomic animal models applied to a wild marine fish

In highly dispersive taxa, gene flow can homogenise genetic variation over broad spatial and temporal scales. However, phenotypic differentiation can still arise when heritable genetic variation is available to selection and (or) when organisms exhibit plasticity. Disentangling heritable versus non-heritable components of variation is possible using genomic animal models, but this approach has been underused in wild organisms. We investigated head shape variation in the marine cryptobenthic fish Bathygobius cocosensis, a highly dispersive species occupying heterogeneous environments. Head shape, a diet-related trait, is spatially structured in Australian populations. We curated a unique dataset comprising genotypic, phenotypic, and environmental variation to: (1) contrast the scales over which genetic and phenotypic variation are structured; and (2) quantify heritable versus non-heritable contributions to head shape variation using genomic animal models and comparisons between FST, PST, and QST. At macrogeographic scales (hundreds of kilometres) and over time (2 years), phenotypic differentiation (0.0001 [≤] PST [≤] 0.47) exceeded both genomic and additive genetic differentiation (0.001 [≤] FST[≤] 0.004 and 0.00001 [≤] QST [≤] 0.004, respectively). This suggests head shape variation may primarily reflect (non-heritable) plastic responses, rather than (heritable) adaptive genetic changes in mean head shape. At microgeographic scales, associations between head shape and tide pool variables were temporally variable, indicating that local environmental conditions may structure phenotypes within populations. Overall, this study highlights the value of genomic animal models for disentangling heritable and non-heritable components of phenotypic variation in dispersive marine taxa. It provides an integrative analysis linking genetic, phenotypic, and environmental variation in a cryptobenthic fish, highlighting how phenotypic divergence can emerge without strong genetic differentiation, and challenging the common assumption that phenotypic divergence necessarily implies adaptation.

genomics↗

bioRxiv2023

'Drifting' Buchnera genomes track the microevolutionary trajectories of their aphid hosts

Evolution of Buchnera-aphid host symbioses is often studied among species at macroevolutionary scales. Investigations within species offer a different perspective about how eco-evolutionary processes shape patterns of genetic variation at microevolutionary scales. Our study leverages new and publicly available whole-genome sequencing data to study Buchnera-aphid host evolution in Myzus persicae, the peach potato aphid, a globally invasive and polyphagous pest. Across 43 different asexual, clonally reproducing isofemale strains, we examined patterns of genomic covariation between Buchnera and their aphid host and considered the distribution of mutations in protein-coding regions of the Buchnera genome. We found Buchnera polymorphisms within aphid strains, suggesting the presence of genetically different Buchnera strains within the same clonal lineage. Genetic distance between pairs of Buchnera samples was positively correlated to genetic distance between their aphid hosts, indicating shared evolutionary histories. However, there was no segregation in the genetic variation of both M. persicae and Buchnera with plant host (Brassicaceae and non-tobacco Solanaceae) and no associations between genetic and geographic distance at global or regional spatial scales. Abundance patterns of non-synonymous mutations were similar to synonymous mutations in the Buchnera genome, and both mutation classes had similar site frequency spectra. We hypothesize that a predominance of neutral processes results in the Buchnera of M. persicae to simply drift with the evolutionary trajectory of their aphid hosts. Our study presents a unique microevolutionary characterisation of Buchnera-aphid host genomic covariation across multiple aphid clones. This provides a new perspective on the eco-evolutionary processes generating and maintaining polymorphisms in a major pest aphid species and its obligate primary endosymbiont.

evolutionary biology↗

bioRxiv2022

Evolution of an acetylcholinesterase gene complex and its contribution to organophosphate insensitivity in an invasive mite pest

BACKGROUNDInvasive Australian populations of redlegged earth mite, Halotydeus destructor (Tucker), are evolving increasing organophosphate resistance. In addition to the canonical ace gene, the target gene of organophosphates, the H. destructor genome contains many radiated ace-like genes that vary in copy number and amino acid sequence. In this work, we characterise copy number and target-site mutation variation at the canonical ace and ace-like genes and test for potential associations with organophosphate insensitivity. This was achieved through comparisons of whole-genome pool-seq data from alive and dead mites following organophosphate exposure. RESULTSA combination of increased copy number and target-site mutations at the canonical ace was associated with organophosphate insensitivity in H. destructor. Resistant populations were segregating for G119S, A201S, F331Y at the canonical ace. A subset of populations also had copy numbers of canonical ace >2, which potentially helps over-express proteins carrying these target-site mutations. Haplotypes possessing different copy numbers and target-site mutations of the canonical ace gene may be under selection across H. destructor populations. We also detected some evidence that increases in copy number of radiated ace-like genes are associated with organophosphate insensitivity, which might suggest potential roles in sequestration or breakdown of organophosphates. CONCLUSIONDifferent combinations of target-site mutations and (or) copy number variation in the canonical ace and ace-like genes may provide non-convergent ways for H. destructor to respond to organophosphate selection. However, these changes may only play a partial role in organophosphate insensitivity, which appears to have a polygenic architecture.

evolutionary biology↗

bioRxiv2022

The redlegged earth mite draft genome provides new insights into pesticide resistance evolution and demography in its invasive Australian range

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 of ace genes, which has presumably evolved from a long history of organophosphate selection in H. destructor and may contribute toward organophosphate resistance through copy number variation, target-site mutations, and structural variants. In the putative ancestral H. destructor ace gene, we identified three target-site mutations (G119S, A201S, and F331Y) segregating in organophosphate resistant populations. Additionally, we identified two new para sodium channel gene mutations (L925I and F1020Y) that may contribute to pyrethroid resistance. Regional structuring observed in population genomic analyses indicates that gene flow in H. destructor does not homogenise populations across large geographic distances. However, our demographic analyses were equivocal on the magnitude of gene flow; the short invasion history of H. destructor makes 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.

genomics↗

bioRxiv2022

Incorporating selection pressures into risk predictions of chemical resistance evolution in pest organisms

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.

evolutionary biology↗

bioRxiv2022

DAPC of genotype data only requires the first k - 1 PC axes for k populations

Discriminant analysis of principal components (DAPC) has become a popular method for visualising population structure due to its simplicity, computational speed, and freedom from demographic assumptions. Despite the popularity of DAPC, there has been little discussion on best practise. In this work, I provide guidelines for standardising the use of DAPC in studies of population genetic structure. An often-overlooked fact is that DAPC generates a model describing the genetic differences among a set of populations defined by a researcher. I demonstrate that appropriate parameterisation of this model is critical for obtaining biologically meaningful results. I show that the number of leading PC axes used as predictors of among population differences, paxes, should not exceed the k - 1 biologically informative PC axes that are expected for k effective populations in a genotype dataset. This k - 1 criterion for paxes selection is more appropriate compared to the widely used proportional variance criterion, which often results in a choice of paxes >> k - 1. DAPC parameterised with no more than the leading k - 1 PC axes is: (1) more parsimonious; (2) captures maximal among-population variation on biologically relevant predictors; (3) less sensitive to unintended interpretations of population structure; and (4) more generally applicable to independent sample sets. Assessing model fit should be routine practise and can aid interpretation of population structure when implementing DAPC. Additionally, it is imperative that researchers clearly articulate their study goals, that is, testing a priori expectations versus studying de novo inferred populations. Distinguishing between these goals is important because it dictates whether a researchers results can be treated as a test of the hypothesis that significant genetic differences exist among populations. Defining populations a priori (before observing the genotype data) constitutes a true hypothesis test, but populations defined de novo (after observing the genotype data) cannot be used to test this hypothesis due to issues with circularity. The discussion and practical recommendations provided in this work provide the molecular ecology community a roadmap for applying DAPC to their genotype datasets.

genetics↗

bioRxiv2019

genomalicious: serving up a smorgasbord of R functions for population genomic analyses

Turning SNP data into biologically meaningful results requires considerable computational acrobatics, including importing, exporting, and manipulating data among different analytical packages and programming environments, and finding ways to visualise results for data exploration and presentation. I present GENOMALICIOUS, an R package designed to provide a selection of functions for population genomicists to simply, intuitively, and flexibly, guide SNP data through their analytical pipelines, within and outside R. At the core of the original GENOMALICIOUS workflow is the conversion of genomic variant data into a data.table object. This provides a useful way of storing large amounts of data in an intuitive format that can be easily manipulated using methods unique to this object class. Over time, GENOMALICIOUS has grown to cater to a range of analyses in population structure and demography, adaptive evolution, quantitative traits, and phylogenetics. Researchers using pooled allele frequencies, or individually sequenced genotypes, are sure to find functions that accommodate their tastes in GENOMALICIOUS. The simplicity and accessibility of pipelines in GENOMALICIOUS may also serve as a useful tool for teaching basic population genetics and genomics in an R environment. The source code and a series of tutorials for this package are freely available on GitHub

bioinformatics↗