Biology subjects

O'Brien, E. K.

Publications and source records attributed to O'Brien, E. K..

6 recordsLinked to original sources

bioRxiv2026

A Disease-Agnostic Nasal Microbiome Wellness Index for Standardized Assessment of Upper-Airway Respiratory Health

BackgroundUpper-airway and respiratory conditions impose a large and growing global burden, yet there is no standardized way to assess whether a nasal microbiome is "healthy". Currently, monitoring remains reactive, beginning only after symptoms manifest. The nasal cavity is well suited to proactive monitoring: it shapes respiratory health and pathogen colonization resistance, and can be sampled non-invasively and repeatedly. To address this gap, we introduce the Nasal Microbiome Wellness Index (NMWI), a disease-agnostic, continuous score of nasal microbiome health derived from LASSO-penalized logistic regression. Rather than counting taxa, it learns which taxa (and in what balance) characterize a healthy nose and returns the predicted log-odds that a profile resembles a healthy state. The index was trained on 1654 nasal 16S rRNA gene amplicon sequencing samples (589 healthy, 1065 non-healthy) pooled from 27 publicly available studies, uniformly reprocessed through a single computational pipeline. ResultsThe NMWI comprises an interpretable signature of 24 taxa whose combined relative abundances determine the health-associated log-odds. Health-associated genera such as Corynebacterium and Cutibacterium raised the score, while dysbiosis-associated genera such as Pseudomonas and Escherichia-Shigella lowered it. The NMWI substantially outperformed the Shannon, Simpson, and Chao1 diversity indices, which showed negligible, directionally inconsistent separation between healthy and non-healthy samples (|Cliffs{delta} | = 0.01-0.20), whereas the NMWI produced large, consistent separation ({delta} = 0.65). It achieved a balanced accuracy of 74.37% on the training data (resubstitution estimate), and 73.43% under repeated 10-times 10-fold cross-validation. Performance remained stable at mean balanced accuracy of 73.82% under a leave-one-study-out framework, reflecting cross-study generalizability. In independent external cohorts, the balanced accuracy was 71.49%, and leave-one-disease-out analysis (in which each disease condition was withheld from training) showed a mean balanced accuracy of 63.92% across unseen conditions, consistent with a disease-agnostic design. The index also generalized across heterogeneous datasets spanning multiple 16S rRNA gene hypervariable regions--to our knowledge the first demonstration of such cross-study, cross-region transferability for the nasal cavity. ConclusionsThe NMWI distills a complex nasal microbial profile into a single interpretable score computed directly from the 16S rRNA gene data that dominate existing nasal research, making it immediately applicable to published and future datasets without re-sequencing. By replacing descriptive, diversity-based comparison with a quantitative standard, it offers a reproducible, open-source foundation for cross-study benchmarking, individual-level phenotyping, and longitudinal respiratory wellness monitoring.

bioinformatics↗

bioRxiv2021

Predicted responses to selection across the climatic range of a rainforest Drosophila without local adaptation: environmental variation limits trait divergence along ecological gradients

Evolutionary responses to environmental change require heritable variation in traits under selection. Both heritability and selection vary with the environment, and may also covary, so environmental variation can affect evolutionary rates. However, simultaneous estimates of heritability and selection across environmental gradients in the field are rare. We estimated environmental variation in selection on three traits (cold tolerance, heat tolerance, and wing size) of the rainforest fruitfly Drosophila birchii. We transplanted flies in cages along two elevational gradients in north-east Queensland, Australia, and calculated the genetic covariance of trait values with fitness (productivity in cages) at each site. For wing size, we estimated heritability at each site from the correlation between field-reared offspring and their laboratory-reared relatives. We used estimates of selection and heritability to predict selection responses along the elevation gradients, and compared these with trait variation observed in flies sourced from populations at elevational extremes. We found evidence for divergent selection on cold tolerance across elevation at one gradient. Heritability of wing size was highest at gradient ends, and the size of the predicted response to selection on this trait increased with elevation. However, the direction of selection varied, even among adjacent sites, making such selection unlikely to cause divergence of this trait with elevation. None of the traits differed between populations from elevational extremes at either gradient. Variation in the strength and direction of selection over small spatial scales, as well as in time, may explain why predicted responses to selection are often not seen in natural populations.

evolutionary biology↗

bioRxiv2021

The predictive potential of key adaptation parameters and proxy fitness traits between benign and stressful thermal environments

Understanding the adaptive potential of a species is key when predicting whether a species can contend with climate change. Adaptive capacity depends on the amount of genetic variation within a population for relevant traits. However, genetic variation changes in different environments, making it difficult to predict whether a trait will respond to selection when not measured directly in that environment. Here, we investigated how genetic variances, and phenotypic and genetic covariances, between a fitness trait and morphological traits changed between thermal environments in two closely-related Drosophila. If morphological traits strongly correlate with fitness, they may provide an easy-to-measure proxy of fitness to aid in understanding adaptation potential. We used a parent-offspring quantitative genetic design to test the effect of a benign (23{degrees}C) and stressful (28{degrees}C) thermal environment on genetic variances of fecundity and wing size and shape, and their phenotypic and genetic covariances. We found genetic variances were higher within the stressful environment for fecundity but lower within the stressful environment for wing size. We did not find evidence for significant phenotypic correlations. Phenotypic and genetic correlations did not reveal a consistent pattern between thermal environments or within or between species. This corroborates previous research and reiterates that conclusions drawn in one environment about the adaptive potential of a trait, and the relationship of that trait with fitness, cannot be extrapolated to other environments or within or between closely-related species. This confirms that researchers should use caution when generalising findings across environments in terms of genetic variation and adaptive potential.

evolutionary biology↗

bioRxiv2020

Molecular analyses reveal consistent food web structure with elevation in rainforest Drosophila - parasitoid communities

The analysis of interaction networks across spatial environmental gradients is a powerful approach to investigate the responses of communities to global change. Using a combination of DNA metabarcoding and traditional molecular methods we built bipartite Drosophila-parasitoid food webs from six Australian rainforest sites across gradients spanning 850 m in elevation and 5{degrees} Celsius in mean temperature. Our cost-effective hierarchical approach to network reconstruction separated the determination of host frequencies from the detection and quantification of interactions. The food webs comprised 5-9 host and 5-11 parasitoid species at each site, and showed a lower incidence of parasitism at high elevation. Despite considerable turnover in the relative abundance of host Drosophila species, and contrary to some previous results, we did not detect significant changes to fundamental metrics of network structure including nestedness and specialisation with elevation. Advances in community ecology depend on data from a combination of methodological approaches. It is therefore especially valuable to develop model study systems for sets of closely-interacting species that are diverse enough to be representative, yet still amenable to field and laboratory experiments.

ecology↗

bioRxiv2018

Low but genetically variable male mating ability in a tropical Drosophila despite fitness benefits of remating

Mating success is the main source of fitness variation in males, meaning that males should capitalise on all opportunities for mating. Strong selection on male mating success should also reduce genetic variation in male mating traits relative to other traits. We quantified mating latency, mating duration and productivity in males of the tropical fruitfly, Drosophila birchii, from 30 isofemale lines collected from across two elevational gradients, when they were given opportunities to mate with up to four females consecutively. Male remating rates were low compared to other Drosophila (only 14 - 27% of males achieved a fourth mating), with mean mating durations approximately doubling across successive copulations. However, although successive remating produced progressively fewer offspring, it consistently increased overall male reproductive success, with males that mated four times more than doubling offspring number compared to males mating only once. We also found no reduction in the productivity of sons emerging from later matings, indicating a sustained cumulative fitness benefit to remating. Heritable variation was observed for most traits (H2 = 0.035 - 0.292) except mating latency, but there was no divergence in trait means with elevation. The observed restricted remating ability of male D. birchii, despite the clear benefits of remating, may be due to a low encounter rate with females in the field, leading to high investment per gamete (or ejaculate). However, it remains unclear why genetic variation in these traits is high, given we observe no variation in these traits across elevational gradients known to affect local population density.

evolutionary biology↗

bioRxiv2018

Interacting effects of the abiotic and biotic environment on fitness of rainforest Drosophila

Competition within and between species can have large effects on fitness and may therefore drive local adaptation. However, these effects are rarely tested systematically, or considered when predicting species responses to environmental change. We used a field transplant experiment to test the effects of intra and interspecific competition on fitness across the ecological niches of two rainforest Drosophila species that replace each other along an elevation gradient. For the species with the broader elevational range, we also tested for adaptation to the local abiotic and biotic environment. In both species, intraspecific competition reduced productivity more than interspecific competition at the centre of its elevational range, while interspecific competition had a stronger effect at the range edge, where the competing species is more abundant. Local adaptation was detected in the centre of the range of the more widespread species, but only in the presence of intraspecific competition. This study is the first to demonstrate that fitness effects of inter-specific competition increase at ecological margins, while intra-specific competition has more pervasive effects at range centres. This is a key assumption of "tangled bank" models of community evolution and has important implications for predicting the resilience of ecological networks to global change.

evolutionary biology↗