Biology subjects

Obbard, D.

Publications and source records attributed to Obbard, D..

6 recordsLinked to original sources

bioRxiv2025

Predictors of protein evolution in the drosophilid immune system

The evolutionary dynamics of immune genes are shaped by diverse selective pressures, yet the relative roles of gene-level traits, functional specialization, and pathway context remain poorly understood. Here, we applied a meta-analytic mixed model approach to quantify how immune-pathway genes differ from other genes in their rates of protein sequence divergence (dN/dS), evidence for positive selection, and gene turnover rate ({lambda}), while simultaneously accounting for gene length, expression level, genetic and protein-protein interactions, and structural features such as relative solvent accessibility (RSA). In general, rates of sequence evolution were strongly and positively associated with RSA, and negatively with gene length, expression, and genetic/protein-protein interactions, while gene turnover rate was largely unaffected by these factors. We find immune genes evolved significantly faster at the protein sequence level than non-immune genes, but contrary to our expectation exhibited lower gene turnover rates. Functional and pathway-level analyses revealed accelerated evolution in effectors, receptors, and antiviral genes, with cGAS-STING and Toll pathways showing the highest dN/dS. Gene turnover rate was elevated only in effectors, whereas cellular defence genes were particularly conserved. We also found evidence for elevated proportion of sites under episodic positive selection in immune genes, particularly in effectors, indicating ongoing adaptive diversification. These findings highlight how immune diversification in Drosophilidae arises from multiple, partly independent evolutionary axes, shaped jointly by structural constraints, functional roles, and lineage-specific pathogen pressures.

molecular biology↗

bioRxiv2025

Transcriptomic analysis of non-model Drosophilidae reveals novel AMP candidates

BackgroundDrosophila melanogaster has been a valuable model for dissecting the molecular architecture of innate immunity. However, the family Drosophilidae encompasses over 4000 species, spanning deep evolutionary divergences and diverse ecologies. Here, we use immune challenge with the gram-negative pathogen Providencia rettgeri to investigate the conservation and evolution of immune responses in three non-model drosophilid species that diverged from D. melanogaster over 45 million years ago--Hirtodrosophila cameraria, H. confusa, and Scaptodrosophila deflexa. ResultsWe find that all three species retain a core set of immune signaling and recognition genes, but exhibit substantial variation in effector gene content and inducibility. In particular, Scaptodrosophila deflexa lacks orthologs of multiple antimicrobial peptides (AMPs) known from D. melanogaster, including DptA, AttA, and AttC, and shows little transcriptional response to bacterial-challenge with Providencia rettgeri. In contrast, both of the Hirtodrosophila species exhibit substantial transcriptional responses, including strong induction of canonical Imd pathway genes. Microbiome profiling of our samples revealed higher Providencia abundance in H. cameraria, and high levels of the defensive symbiont Spiroplasma in S. deflexa--potentially explaining differences in infection outcome. Our combined annotation and expression analysis of these species also allowed us to identify 20 novel AMP-like candidates, many with structural features like known AMPs. ConclusionsOur study demonstrates the feasibility of functional immune analyses in non-model Drosophila species and reveals striking lineage-specific differences in immune gene repertoire and expression. These findings highlight the importance of non-model, wild-derived taxa for uncovering novel immune effectors and understanding evolutionary forces shaping insect immunity.

evolutionary biology↗

bioRxiv2025

Comparative gene annotation of 304 species of Drosophilidae

High-quality genome annotations are essential if we are to address central questions in comparative genomics, such as the origin of new genes, the drivers of genome size variation, and the evolutionary forces shaping gene content and structure. Here, we present protein-coding gene annotations for 301 species of the family Drosophilidae, generated using the Comparative Annotation Toolkit (CAT) and BRAKER3, and incorporating available RNA-seq and protein evidence. We take a comparative phylogenetic approach to annotation, with the aim of improving consistency and accuracy, and to generate a robust set of gene annotations and orthology assignments. We analyze our annotations using a phylogenetic mixed-model approach and find that gene number and CDS length exhibit moderate phylogenetic heritability (40% and 9.7%, respectively). For comparison, we also present analyses using a subset of the 215 highest quality genomes, although the findings were not markedly different. Our work suggests that while evolutionary history contributes to variation in these traits, species-specific factors--including assembly error--play a substantial role in shaping observed differences. To illustrate the utility of our annotations for comparative analyses, we investigate codon usage bias and amino acid composition across Drosophilidae. We find that codon usage is correlated with overall GC content and evolves slowly, but that it is also strongly shaped by selection--such that, in general, species with the strongest selection on synonymous codon usage show the lowest GC bias in third codon positions. This comparative annotation dataset forms part of an on-going collaborative project to sequence and annotate all species of Drosophilidae, with data and annotations being made rapidly and freely available on an on-going basis. We hope that this effort will serve as a foundation for studies in evolutionary and functional genomics and comparative biology across Drosophilidae.

genomics↗

bioRxiv2023

Viruses in laboratory Drosophila and their impact on host gene expression

Drosophila melanogaster has one of the best characterized antiviral immune responses among invertebrates. However, relatively few easily-transmitted natural virus isolates are available, and so many Drosophila experiments have been performed using artificial infection routes and artificial host-virus combinations. These may not reflect natural infections, especially for subtle phenotypes such as gene expression. Here, to explore the laboratory virus community and to better understand how natural virus infections induce changes in gene expression, we analyse seven publicly available D. melanogaster transcriptomic sequencing libraries that were originally sequenced for projects unrelated to virus infection. We find ten known viruses--including five that have not been experimentally isolated--but no previously unknown viruses. Our analysis of host gene expression found numerous genes were differentially expressed in flies that were naturally infected with a virus. For example, flies infected with nora virus showed patterns of gene expression consistent with intestinal vacuolization and host attempted repair via the upd3 JAK/STAT pathway. We also found marked sex-differences in virus-induced differential gene expression. Our results show that natural virus infection in laboratory Drosophila does indeed induce detectable changes in gene expression, suggesting that this may form an important background condition for experimental studies in the laboratory.

evolutionary biology↗

bioRxiv2018

Widespread gene duplication and adaptive evolution in the RNA interference pathways of the Drosophila obscura group

BackgroundRNA interference (RNAi) related pathways provide defense against viruses and transposable elements, and have been implicated in the suppression of meiotic drive elements. Genes in these pathways often exhibit high levels of adaptive substitution, and over longer timescales show frequent gene duplication and loss-- most likely as a consequence of their role in mediating conflict with these parasites. This is particularly striking for Argonaute 2 (Ago2), which is ancestrally the key effector of antiviral RNAi in insects, but has repeatedly formed new testis-specific duplicates in the recent history of the Drosophila obscura group.\n\nResultsHere we take advantage of publicly available genomic and transcriptomic data to identify six further RNAi-pathway genes that have duplicated in this clade of Drosophila, and examine their evolutionary history. As seen for Ago2, we observe high levels of adaptive amino-acid substitution and changes in sex-biased expression in many of the paralogs. However, our phylogenetic analysis suggests that co-duplications of the RNAi machinery were not synchronous, and our expression analysis fails to identify consistent male-specific expression.\n\nConclusionsThese results confirm that RNAi genes, including genes of the antiviral and piRNA pathways, undergo frequent independent duplications and that their history has been particularly labile within the Drosophila obscura group. However, they also suggest that the selective pressures driving these changes have not been consistent, implying that more than one selective agent may be responsible.

evolutionary biology↗

bioRxiv2018

Genomic analysis of European Drosophila melanogaster populations on a dense spatial scale reveals longitudinal population structure and continent-wide selection

Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatio-temporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterise variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.

evolutionary biology↗