Biology subjects

Baxter, S. W.

Publications and source records attributed to Baxter, S. W..

7 recordsLinked to original sources

bioRxiv2024

The genetic basis of the black pupae phenotype in tephritid fruit flies

The remarkable diversity of insect pigmentation offers a captivating avenue for exploring evolution and genetics. In tephritid fruit flies, decoding the molecular pathways underlying pigmentation traits also plays a central role in applied entomology. Mutant phenotypes like the black pupae (bp) have long been used as a component of genetic sexing strains, allowing male-only release in tephritid sterile insect technique applications. However, the genetic basis of bp remains largely unknown. Here, we present independent evidence from classical and modern genetics showing that the bp phenotype in the GUA10 strain of the Mexican fruit fly, Anastrepha ludens, is caused by a large deletion at the ebony locus resulting in the removal of the entire protein-coding region of the gene. Targeted knockout of ebony induced analogous bp phenotypes across six tephritid species spanning over 50 million years of divergent evolution. This functionally validated our findings and allowed for a deeper investigation into the role of Ebony in pigmentation and development in these species. Our study offers fundamental knowledge for developing new sexing strains based on the bp marker and for future evolutionary developmental biology studies in tephritid fruit flies.

genomics↗

bioRxiv2023

Acetylcholine esterase of Drosophila melanogaster: a laboratory model to explore applications of insecticide susceptibility gene drives

BACKGROUNDOne of the proposed applications of gene drives has been to revert pesticide resistant mutations back to the ancestral susceptible state. Insecticides that have become ineffective because of the rise of resistance could have reinvigorated utility and be used to suppress pest populations again, perhaps at lower application doses. RESULTSWe have created a laboratory model for susceptibility gene drives that replaces field-selected resistant variants of the acetylcholine esterase (Ace) locus of Drosophila melanogaster with ancestral susceptible variants. We constructed a CRISPR/Cas9 homing drive and found that homing occurred in many genetic backgrounds with varying efficiencies. While the drive itself could not be homozygosed, it converted resistant alleles into susceptible ones and produced recessive lethal alleles that could suppress populations. Our studies provided evidence for two distinct classes of Gene Drive Resistance (GDR): rather than being mediated by the conventional Non-Homologous End-joining (NHEJ) pathway, one seemed to involve short homologous repair and the other was defined by genetic background. Additionally, we used simulations to explore a distinct application of susceptibility drives; the use of chemicals to prevent the spread of synthetic gene drives into protected areas. CONCLUSIONSInsecticide susceptibility gene drives could be useful tools to control pest insects however problems associated with particularities of the target loci and GDR will need to be overcome for them to be effective. Furthermore, realistic patterns of pest dispersal and high insecticide exposure rates would be required if susceptibility were to be useful as a safety-switch to prevent the unwanted spread of gene drives.

genetics↗

bioRxiv2020

Genomic evolutionary analysis in R with geaR.

The analysis and interpretation of datasets generated through sequencing large numbers of individual genomes is becoming commonplace in population and evolutionary genetic studies. Here we introduce geaR, a modular R package for evolutionary analysis of genome-wide genotype data. The package leverages the Genomic Data Structure (GDS) format, which enables memory and time efficient querying of genotype datasets compared to standard VCF genotype files. geaR utilizes GRange object classes to partition an analysis based on features from GFF annotation files, select codons based on position or degeneracy, and construct both positional and coordinate genomic windows. Tests of genetic diversity (eg. dXY,{pi} , FST) and admixture [Formula] along with tree building and sequence output, can be carried out on partitions using a single function regardless of sample ploidy or number of observed alleles. The package and associated documentation are available on GitHub at https://github.com/CMWbio/geaR.

genomics↗

bioRxiv2020

White pupae genes in the Tephritids Ceratitis capitata, Bactrocera dorsalis and Zeugodacus cucurbitae: a story of parallel mutations

Mass releases of sterilized male insects, in the frame of sterile insect technique programs, have helped suppress insect pest populations since the 1950s. In the major horticultural pests Bactrocera dorsalis, Ceratitis capitata, and Zeugodacus cucurbitae, a key phenotype white pupae (wp) has been used for decades to selectively remove females before releases, yet the gene responsible remained unknown. Here we use classical and modern genetic approaches to identify and functionally characterize causal wp− mutations in these distantly related fruit fly species. We find that the wp phenotype is produced by parallel mutations in a single, conserved gene. CRISPR/Cas9-mediated knockout of the wp gene leads to the rapid generation of novel white pupae strains in C. capitata and B. tryoni. The conserved phenotype and independent nature of the wp− mutations suggest that this technique can provide a generic approach to produce sexing strains in other major medical and agricultural insect pests.Competing Interest StatementThe authors have declared no competing interest.View Full Text

genetics↗

bioRxiv2018

Assessing genomic admixture between cryptic Plutella moth species following secondary contact

Cryptic species are genetically distinct taxa without obvious variation in morphology and are occasionally discovered using molecular or sequence datasets of populations previously thought to be a single species. The world-wide Brassica pest, Plutella xylostella (diamondback moth), has been a problematic insect in Australia since 1882, yet a morphologically cryptic species with apparent endemism (P. australiana) was only recognized in 2013. Plutella xylostella and P. australiana are able to hybridize under laboratory conditions, and it was unknown whether introgression of adaptive traits could occur in the field to improve fitness and potentially increase pressure on agriculture. Phylogenetic reconstruction of 29 nuclear genomes confirmed P. xylostella and P. australiana are divergent, and molecular dating with 13 mitochondrial genes estimated a common Plutella ancestor 1.96{+/-}0.175 MYA. Sympatric Australian populations and allopatric Hawaiian P. xylostella populations were used to test whether neutral or adaptive introgression had occurred between the two Australian species. We used three approaches to test for genomic admixture in empirical and simulated datasets including i) the f3 statistic at the level of the population, ii) pairwise comparisons of Neis absolute genetic divergence (dXY) between populations and iii) changes in phylogenetic branch lengths between individuals across 50 kb genomic windows. These complementary approaches all supported reproductive isolation of the Plutella species in Australia, despite their ability to hybridize. Finally, we highlight the most divergent genomic regions between the two cryptic Plutella species and find they contain genes involved with processes including digestion, detoxification and DNA binding.

evolutionary biology↗

bioRxiv2017

A global Brassica pest and a sympatric cryptic ally, Plutella australiana (Lepidoptera: Plutellidae), show strong divergence despite the capacity to hybridize

The diamondback moth, Plutella xylostella, has been intensively studied due to its ability to evolve insecticide resistance and status as the worlds most destructive pest of brassicaceous crops. The surprise discovery of a cryptic ally, Plutella australiana Landry & Hebert, with apparent endemism to Australia, immediately raised questions regarding the extent of ecological and genetic diversity between these two species, whether gene flow could occur, and ultimately if specific management was required. Here, we show that despite sympatric distributions and the capacity to hybridize in controlled laboratory experiments, striking differences in genetic and phenotypic traits exist that are consistent with contrasting colonization histories and reproductive isolation after secondary contact. Almost 1500 Plutella individuals were collected from wild and cultivated brassicaceous plants at 75 locations throughout Australia. Plutella australiana was commonly found on all Brassica host types sampled except commercial vegetables, which are routinely sprayed with insecticide. Bioassays using four commonly-used insecticides found that P. australiana was 19-306 fold more susceptible than P. xylostella. Genome-wide SNPs derived from RADseq revealed substantially higher levels of genetic diversity across P. australiana compared with P. xylostella nuclear genomes, yet both species showed limited variation in mtDNA. Infection with a single Wolbachia subgroup B strain was fixed in P. australiana, suggesting that a selective sweep contributed to low mtDNA diversity, while a subgroup A strain infected just 1.5 % of P. xylostella. Although P. australiana is a potential pest of brassica crops, it is of secondary importance to P. xylostella.

genetics↗

bioRxiv2017

Genome-Wide SNP Discovery In Field And Laboratory Colonies Of Australian Plutella Species

Understanding dispersal and gene flow is an important focus of evolutionary biology, conservation biology and pest management. The diamondback moth, Plutella xylostella, is a worldwide pest of Brassica vegetable and oilseed cropping systems. This insect has high dispersal ability, which has important consequences for population dynamics and the potential spread of insecticide resistance genes. Population genetic studies of the diamondback moth have found little evidence of population structure, suggesting that frequent intermixing occurs within regions, however the patterns of local and regional dispersal remain to be identified. For this and many other pest species, understanding dispersal is crucial for developing integrated management tactics such as forecasting systems and insecticide resistance management plans. In recent years, next generation sequencing (NGS) methods have provided previously unparalleled resolution for population genetic studies in a wide range of species. Here, we assessed the potential of NGS-derived molecular markers to provide new insights about population structure in the diamondback moth. We use restriction-site-associated DNA sequencing (RAD-Seq) to discover hundreds to thousands of single nucleotide polymorphism (SNP) markers in nine field and laboratory-reared populations collected from Australia. Genotypic data from RAD-Seq markers identified a cryptic species, P. australiana, among individuals collected from a wild host, Diplotaxis sp., indicating strong divergence in the nuclear genomes of two Australian Plutella lineages. Significant genetic differentiation was detected among populations of P. xylostella used in our study, however this could be explained by reduced heterozogosity and genetic drift in laboratory-reared populations founded by relatively few individuals. This study demonstrates that RAD-Seq is a powerful method for generating SNP markers for population genetic studies in this species.

ecology↗