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O'Connor, T.

Publications and source records attributed to O'Connor, T..

9 recordsLinked to original sources
bioRxiv2026

Interspecies variation of 45S ribosomal DNA in vertebrates

Ribosomal DNA (rDNA) remains one of the least resolved components of complex genomes despite its central role in cellular function and evolutionary inference. Using chromosome-scale assemblies from the Vertebrate Genomes Project, we present a comparative analysis of the 45S rDNA locus across vertebrates. rDNA organization varies widely among clades, with lineage-specific differences in chromosomal distribution, copy number, and positional bias. Mammals and birds typically restrict rDNA to few, often terminal loci, whereas amphibians and several fish lineages exhibit highly dispersed architectures, including extreme cases spanning dozens of chromosomes. Copy number varies by more than an order of magnitude and does not scale simply with repeat-unit size or predicted functional demand, consistent with rDNA functioning as a flexible genomic reservoir rather than a direct proxy for ribosome production. At the sequence level, the 45S unit resolves into distinct evolutionary regimes. Genes encoding rRNAs (18S, 5.8S, 28S) remain highly conserved and retain strong phylogenetic signal, whereas internal transcribed spacers show rapid divergence, lineage-specific expansion, and pronounced asymmetry between intergenic spacers ITS1 and ITS2. Sequence-structure analyses reveal a gradient of constraint across the locus, from tightly coupled evolution in rRNA-encoding regions to increasingly permissive regimes in spacers. Structure-informed phylogenetic inference yields modest but consistent improvements under high divergence, highlighting its value when sequence signal degrades. Together, these results establish the 45S rDNA locus as a multi-layered evolutionary system integrating deep conservation with structural plasticity across vertebrates.

genomics↗
bioRxiv2025

Unifying population structure and relatedness analysis through a coalescent approach

Standard methods in genome-wide association studies (GWAS) partition genetic similarity into recent familial relationship, modeled by a genetic relationship matrix (GRM), and distant relatedness, adjusted for using principal components (PCs). This practice relies on an implicit causal model that conflates population structure with confounding. Here, we challenge this approach by developing a unified framework grounded in coalescent theory. We introduce the Coefficient of Genealogical Similarity (GeSi), a statistic derived from a model of shared derived alleles that captures the full continuum of shared ancestry and can be estimated directly from genotype data. This leads to a new classification of GRMs into "full" matrices, which capture the complete genealogy, and "shallow" matrices, which measure only recent relatedness. Systematic benchmarking demonstrates that full GRMs are sufficient to model the genetic covariance from population structure, rendering PC adjustment for this purpose redundant. This finding clarifies that the justifiable role for PCs in such a model is to correct for true environmental or complex genetic confounders. Our analyses of empirical data confirm that including PCs can improve model fit, providing evidence that such confounding is present and correlated with axes of genetic variation. This work establishes a new theoretical framework that disentangles the modeling of genealogical relatedness from the correction of confounding, reframing the role of PCs as proxies for the latter and challenging the rationale for including the top PCs merely to capture maximal genetic variance.

genetics↗
bioRxiv2024

Adult expression of the cell adhesion protein Fasciclin 3 is required for the maintenance of adult olfactory interneurons

The proper functioning of the nervous system is dependent on the establishment and maintenance of intricate networks of neurons that form functional neural circuits. Once neural circuits are assembled during development, a distinct set of molecular programs is likely required to maintain their connectivity throughout the lifetime of the organism. Here, we demonstrate that Fasciclin 3 (Fas3), an axon guidance cell adhesion protein, is necessary for the maintenance of the olfactory circuit in adult Drosophila. We utilized the TARGET system to spatiotemporally knockdown Fas3 in selected populations of adult neurons. Our findings show that Fas3 knockdown results in the death of olfactory circuit neurons and reduced survival of adults. We also demonstrated that Fas3 knockdown activates caspase-3 mediated cell death in olfactory local interneurons, which can be rescued by overexpressing p35, an anti-apoptotic protein. This work adds to the growing set of evidence indicating a critical role for axon guidance proteins in the maintenance of neuronal circuits in adults. SUMMARY STATEMENTLittle is known about the maintenance of adult neural circuits. We show that the continuous expression of Fasciclin 3, a cell adhesion protein involved in axon guidance, is required for neuronal survival in the adult olfactory circuit.

neuroscience↗
bioRxiv2021

Age and infectious dose significantly affect disease progression after RHDV2 infection in naive domestic rabbits

Rabbit haemorrhagic disease virus 2 (RHDV2 or GI.2, referring to any virus with lagovirus GI.2 structural genes) is a recently emerged calicivirus that causes generalised hepatic necrosis and disseminated intravascular coagulation leading to death in susceptible lagomorphs (rabbits and hares). Previous studies investigating the virulence of RHDV2 have reported conflicting results, with case fatality rates ranging from 0% to 100% even within a single study. Lagoviruses are of particular importance in Australia and New Zealand where they are used as biocontrol agents to manage wild rabbit populations; wild rabbits threaten over 300 native species and result in economic impacts in excess of $200 million AUD to Australian agricultural industries. It is critically important that any pest control method is both highly effective (i.e., virulent, in the context of viral biocontrols) and has minimal animal welfare impacts. To determine whether RHDV2 might be a suitable candidate biocontrol agent, we investigated the virulence and disease progression of a naturally occurring Australian recombinant RHDV2 in both 5-week-old and 11-week-old New Zealand White laboratory rabbits after either high or low dose oral infection. Objective measures of disease progression were recorded through continuous body temperature monitoring collars, continuous activity monitors, and twice daily observations. We observed a 100% case fatality rate in both infected kittens and adult rabbits after either high dose or low dose infection. Clinical signs of disease, such as pyrexia, weight loss, and reduced activity, were evident in the late stages of infection. Clinical disease, i.e., welfare impacts, were limited to the period after the onset of pyrexia, lasting on average 12 hours and increasing in severity as disease progressed. These findings confirm the high virulence of this RHDV2 variant in naive rabbits. While age and infectious dose significantly affected disease progression, the case fatality rate was consistently 100% under all conditions tested.

microbiology↗
bioRxiv2021

Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history

The distribution of the black rat (Rattus rattus) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population history of European black rats, we generated a de novo genome assembly of the black rat, 67 ancient black rat mitogenomes and 36 ancient nuclear genomes from sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of mitochondrial DNA confirm that black rats were introduced into the Mediterranean and Europe from Southwest Asia. Genomic analyses of the ancient rats reveal a population turnover in temperate Europe between the 6th and 10th centuries CE, coincident with an archaeologically attested decline in the black rat population. The near disappearance and re-emergence of black rats in Europe may have been the result of the breakdown of the Roman Empire, the First Plague Pandemic, and/or post-Roman climatic cooling.

evolutionary biology↗
bioRxiv2020

Population sequencing data reveal a compendium of mutational processes in human germline

Mechanistic processes underlying human germline mutations remain largely unknown. Variation in mutation rate and spectra along the genome is informative about the biological mechanisms. We statistically decompose this variation into separate processes using a blind source separation technique. The analysis of a large-scale whole genome sequencing dataset (TOPMed) reveals nine processes that explain the variation in mutation properties between loci. Seven of these processes lend themselves to a biological interpretation. One process is driven by bulky DNA lesions that resolve asymmetrically with respect to transcription and replication. Two processes independently track direction of replication fork and replication timing. We identify a mutagenic effect of active demethylation primarily acting in regulatory regions. We also demonstrate that a recently discovered mutagenic process specific to oocytes can be localized solely from population sequencing data. This process is spread across all chromosomes and is highly asymmetric with respect to the direction of transcription, suggesting a major role of DNA damage.

genetics↗
bioRxiv2019

T-Gene: Improved target gene prediction

MotivationIdentifying the genes regulated by a given transcription factor (its \"target genes\") is a key step in developing a comprehensive understanding of gene regulation. Previously we developed a method for predicting the target genes of a transcription factor (TF) based solely on the correlation between a histone modification at the TFs binding site and the expression of the gene across a set of tissues. That approach is limited to organisms for which extensive histone and expression data is available, and does not explicitly incorporate the genomic distance between the TF and the gene.\n\nResultsWe present the T-Gene algorithm, which overcomes these limitations. T-Gene can be used to predict which genes are most likely to be regulated by a TF, and which of the TFs binding sites are most likely involved in regulating particular genes. T-Gene calculates a novel score that combines distance and histone/expression correlation, and we show that this score accurately predicts when a regulatory element bound by a TF is in contact with a genes promoter, achieving median positive predictive value (PPV) above 50%. T-Gene is easy to use via its web server or as a command-line tool, and can also make accurate predictions (median PPV above 40%) based on distance alone when extensive histone/expression data is not available for the organism. T-Gene provides an estimate of the statistical significance of each of its predictions.\n\nAvailabilityThe T-Gene web server, source code, histone/expression data and genome annotation files are provided at http://meme-suite.org.\n\nContacttimothybailey@unr.edu

bioinformatics↗
bioRxiv2017

Evolution of Hominin Polyunsaturated Fatty Acid Metabolism: From Africa to the New World

BackgroundThe metabolic conversion of dietary omega-3 and omega-6 18 carbon (18C) to long chain (> 20 carbon) polyunsaturated fatty acids (LC-PUFAs) is vital for human life. Fatty acid desaturase (FADS) 1 and 2 catalyze the rate-limiting steps in the biosynthesis of LC-PUFAs. The FADS region contains two haplotypes; ancestral and derived, where the derived haplotypes are associated with more efficient LC-PUFA biosynthesis and is nearly fixed in Africa. In addition, Native American populations appear to be nearly fixed for the lesser efficient ancestral haplotype, which could be a public health problem due to associated low LC-PUFA levels, while Eurasia is polymorphic. This haplotype frequency distribution is suggestive of archaic re-introduction of the ancestral haplotype to non-African populations or ancient polymorphism with differential selection patterns across the globe. Therefore, we tested the FADS region for archaic introgression or ancient polymorphism. We specifically addressed the genetic architecture of the FADS region in Native American populations to better understand this potential public health impact.\n\nResultsWe confirmed Native American ancestry is nearly fixed for the ancestral haplotype and is under positive selection. The ancestral haplotype frequency is also correlated to Siberian populations geographic location further suggesting the ancestral haplotype s role in cold weather adaptation and leading to the high haplotype frequency within Native American populations. We also find that the Neanderthal is more closely related to the derived haplotypes while the Denisovan clusters closer to the ancestral haplotypes. In addition, the derived haplotypes have a time to the most recent common ancestor of 688,474 years ago which is within the range of the modern-archaic hominin divergence.\n\nConclusionsThese results support an ancient polymorphism forming in the FADS gene region with differential selection pressures acting on the derived and ancestral haplotypes due to the old age of the derived haplotypes and the ancestral haplotype being under positive selection in Native American ancestry populations. Further, the near fixation of the less efficient ancestral haplotype in Native American ancestry suggests the need for future studies to explore the potential health risk of associated low LC-PUFA levels in Native American ancestry populations.

evolutionary biology↗