Biology subjects

Thomson, L.

Publications and source records attributed to Thomson, L..

9 recordsLinked to original sources

bioRxiv2025

Foraging ecology drives viral community structure in New Zealand's aquatic birds

Wild migratory birds play a major role in the global spread of viruses, yet the diversity, host range and transmission patterns of viruses harboured by migratory species in Aotearoa/New Zealand remain largely unknown. This knowledge gap is critical given New Zealands position along major migratory flyways spanning Oceania, Antarctica and east Asia, where understanding viral diversity is key to assessing the risk of viral introductions such as highly pathogenic avian influenza virus and viral dispersal across these regions. To address this, we conducted the first large-scale metatranscriptomic survey of wild birds from New Zealand and its subantarctic islands, collecting 1,348 samples from 31 host species spanning four avian orders. We identified 118 avian viruses from 17 families, including 107 novel species, greatly expanding our knowledge of avian viral diversity. Viral communities differed significantly by host order and foraging behaviour, with scavenger birds harbouring more diverse viromes than non-scavengers. Although no HPAI subtypes were detected, we recovered a low-pathogenic avian influenza A/H1N9 virus from red knots (Calidris canutus) and a divergent tobanivirus from Auckland Island teal (Anas aucklandica), the first putative avian member of the Tobaniviridae. Notably, we detected 12 mammalian-associated viruses, primarily in scavenger birds, including Hedgehog hepatovirus, Rabbit haemorrhagic disease virus 2, and sea lion astroviruses, with mammalian host reads confirming their dietary origin. This study establishes the first virome baseline for New Zealands migratory birds, highlighting the ecological role of foraging in shaping viral communities and improving regional preparedness for HPAI and other emerging avian pathogens.

microbiology↗

bioRxiv2025

Population genomics of yellow-eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome

Yellow-eyed penguins (hoiho/takaraka, Megadyptes antipodes) are among the worlds rarest penguins and are regarded as a taonga (treasured) species in Aotearoa New Zealand. Since 2019, chicks on the New Zealand mainland have been affected by a deadly neonatal disease called respiratory distress syndrome (RDS), contributing to a decline to fewer than 143 breeding pairs. To investigate the putative genetic basis of this disease, we generated high-quality whole-genome data from 249 individuals spanning the species range, including from the New Zealand mainland (Northern range) and subantarctic Enderby and Campbell Islands (Southern). Population genomic analyses unexpectedly revealed three deeply divergent lineages with negligible gene flow, consistent with recognition of three distinct subspecies. Phylogenetic divergence dating suggests that these splits predate human arrival by several millennia, with the Northern lineage diverging from the Southern populations 5-16 ka. Genome scans for local adaptation revealed regions of strong differentiation, and genome-wide association analyses identified candidate immune and respiratory genes linked to RDS. In partnership with Ng[a]i Tahu, who hold indigenous guardianship over yellow-eyed penguins, we recommend recognition of three subspecies, urgent conservation action for the critically small and rapidly declining Northern subspecies, and the need for immediate population size and trend assessments for Auckland and Campbell Island populations.

genomics↗

bioRxiv2023

Directional predictions of HIV transmission with optimised genomics in cohorts of serodiscordant couples

Viral genetic information from people living with HIV can deepen our understanding of the infections epidemiology at many scales. To better understand the potentials and limits of tools that utilise such information, we show the performance of two representative tools (HIV-TRACE and phyloscanner) in describing HIV transmission dynamics, with different types of genetic data, and compare with previous findings. The samples were collected from three cohort studies in Sub-Saharan Africa and were deep sequenced to produce both short Illumina reads and long PacBio reads. By comparing phyloscanners performance with short and long reads, we show that long reads provide improved phylogenetic resolution for the classic transmission topology in joint within-host trees. Our pipeline accurately predicted the direction of transmission 88%-92% of the time. We also show that the timing of sample collection plays an important role in the reconstruction of directionality using deep sequencing data. Consensus sequences were also generated and used as HIV-TRACE input to show different patterns of clustering sensitivity and specificity for data from different genomic regions or the entire genome. Finally, we discuss adjusting expectations about sensitivity and specificity of different types of sequence data, considering rapid pathogen evolution, and highlight the potentials of high within-host phylogenetic resolution in HIV. In conclusion, viral genetic data collected and presented differently could greatly influence our ability to describe the underlying dynamics. Methods for source attribution analysis have reached levels of superior accuracy. However, residual uncertainty emphasizes sequence analysis alone cannot conclusively prove linkage at the individual level. ImportanceUnderstanding HIV transmission dynamics is key to designing effective HIV testing and prevention strategies. By using different sequencing techniques on well-characterised cohorts, we were able to evaluate the effect of genetic data resolution on the accuracy of identifying likely transmission pairs and the direction of transmission within pairs. We find that the longer reads generated by PacBio sequencing are more suitable for transmission analyses.

genomics↗

bioRxiv2023

Early acting inbreeding depression can evolve as an inbreeding avoidance mechanism

Despite the potential for mechanical, developmental and/or chemical mechanisms to prevent self-fertilization, incidental self-fertilization is inevitable in many predominantly outcrossing species. In such cases, inbreeding can compromise individual fitness. Unquestionably, much of this inbreeding depression is maladaptive. However, we show that when reproductive compensation allows for the replacement of inviable embryos lost early in development, selection can favor deleterious recessive variants that induce "self-sacrificial" death of inbred embryos. Our theoretical results provide numerous testable predictions which could challenge the assumption that inbreeding depression is always maladaptive. Our work is applicable any species that cannot fully avoid inbreeding, exhibits substantial inbreeding depression, and has the potential to compensate embryos lost early in development. In addition to its general applicability our theory suggests that self-sacrificial variants might be responsible for the remarkably low realized selfing rates of gymnosperms with high primary selfing rates, as gymnosperms exhibit strong inbreeding depression, have effective reproductive compensation mechanisms, and cannot evolve chemical self-incompatibility.

evolutionary biology↗

bioRxiv2022

Viral burdens are associated with age and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection related sampling bias.

In this study, we evaluated the impact of viral variant, in addition to other variables, on within-host viral burdens, by analysing cycle threshold (Ct) values derived from nose and throat swabs, collected as part of the UK COVID-19 Infection Survey. Because viral burden distributions determined from community survey data can be biased due to the impact of variant epidemiology on the time-since-infection of samples, we developed a method to explicitly adjust observed Ct value distributions to account for the expected bias. Analysing the adjusted Ct values using partial least squares regression, we found that among unvaccinated individuals with no known prior infection, the average Ct value was 0.94 lower among Alpha variant infections, compared those with the predecessor strain, B.1.177. However, among vaccinated individuals, it was 0.34 lower among Delta variant infections, compared to those with the Alpha variant. In addition, the average Ct value decreased by 0.20 for every 10 year age increment of the infected individual. In summary, within-host viral burdens are associated with age, in addition to the interplay of vaccination status and viral variant.

genetics↗

bioRxiv2022

Linked selection and the evolution of altruism in a family-structured population

Much research on the evolution of altruism via kin selection, group selection, and reciprocity focuses on the role of a single locus or quantitative trait. Very few studies have explored how linked selection, or selection at loci neighboring an altruism locus, impacts the evolution of altruism. While linked selection can decrease the efficacy of selection at neighboring loci, it might have other effects including promoting selection for altruism by increasing relatedness in regions of low recombination. Here, we used population genetic simulations to study how negative selection at linked loci, or background selection, affects the evolution of altruism. When altruism occurs between full siblings, we found that background selection interfered with selection on the altruistic allele, increasing its fixation probability when the altruistic allele was disfavored and reducing its fixation when the allele was favored. In other words, background selection has the same effect on altruistic genes in family-structured populations as it does on other, nonsocial, genes. This contrasts with prior research showing that linked selective sweeps can favor the evolution of cooperation, and we discuss possibilities for resolving these contrasting results.

evolutionary biology↗

bioRxiv2021

The zebrafish presomitic mesoderm elongates through compression-extension

In vertebrate embryos the presomitic mesoderm become progressively segmented into somites at the anterior end while extending along the anterior-posterior axis. A commonly adopted model to explain how this tissue elongates is that of posterior growth, driven in part by the addition of new cells from uncommitted progenitor populations in the tailbud. However, in zebrafish, much of somitogenesis is associated with an absence of overall volume increase and posterior progenitors do not contribute new cells until the final stages of somitogenesis. Here, we perform a comprehensive 3D morphometric analysis of the paraxial mesoderm and reveal that extension is linked to a volumetric decrease, compression in both dorsal-ventral and medio-lateral axes, and an increase in cell density. We also find that individual cells decrease in their cell volume over successive somite stages. Live cell tracking confirms that much of this tissue deformation occurs within the presomitic mesoderm progenitor zone and is associated with non-directional rearrangement. Furthermore, unlike the trunk somites that are laid down during gastrulation, tail somites develop from a tissue that can continue to elongate in the absence of functional PCP signalling. Taken together, we propose a compression-extension mechanism of tissue elongation that highlights the need to better understand the role of tissue intrinsic and extrinsic forces play in regulating morphogenesis.

developmental biology↗

bioRxiv2021

Morphogenetic coupling leads to pattern emergence in the pre somitic mesoderm

As tissues elongate, cell rearrangement alters positional information in manner that must be accounted for to generate gene expression pattern. How this is achieved during paraxial mesoderm elongation is unknown. By reverse-engineering gene regulatory networks that predict single cell expression trajectories across the tissue, we find a network capable of recapitulating the full range of dynamic differentiation profiles observed both in vivo and in vitro. Simulating gene expression profiles on in toto cell tracking data sets reveal that temporal exposure to Wnt and FGF is generated by cell movement. The absence of reversal in gene expression towards a more premature gene expression state predicts the generation of aberrant tbx6 expression in the posterior progenitor zone that we then confirm by quantitative single cell imaging. Taken together, these results demonstrate cell rearrangement tunes the dynamics of mesoderm progenitor differentiation to generate pattern emergence as a function of temporal Wnt and FGF exposure.

developmental biology↗

bioRxiv2018

Feasibility of automated insulin delivery guided by continuous glucose monitoring in extremely preterm infants

One Sentence SummaryClosed loop systems based on subcutaneous glucose measurements could provide an efficacious and safe means of optimizing glucose control in preterm infants while reducing resources required including time of bedside personnel.\n\nAbstractClosed loop systems have been used to optimise insulin delivery in children with diabetes, but they have not been tested in neonatal intensive care. Extremely preterm infants are prone to life-threating hyperglycaemia and hypoglycaemia; both of which have been associated with adverse outcomes. Insulin delivery is notoriously variable in these babies and time-consuming, with management requiring frequent changes of dextrose-containing fluids and careful monitoring. We aimed to evaluate the feasibility of closed loop management of glucose control in preterm infants in a single centre feasibility study with a randomised parallel design. Eligibility criteria included birth weight <1200g and <48hours of age. All infants had subcutaneous continuous glucose monitoring for the first week of life, with those in the intervention group receiving closed loop insulin delivery between 48 and 72hours of age. The primary outcome was percentage of time in target (sensor glucose 4-8mmol/l). The mean (SD) gestational age and birth weight of intervention and control study arms were 27.0(2.4) weeks, 962(164) g and 27.5(2.8) weeks, 823(282) g respectively. The time in target was dramatically increased from median (IQR) 26%(6,64) with paper guidance to 91%(78, 99) during closed loop (p<0.001), without increasing hypoglycaemia. There were no serious adverse events and no difference in total insulin infused. Closed loop glucose control based on subcutaneous glucose measurements is feasible and appears to provide an efficacious means of optimising glucose control in extremely preterm infants.

bioinformatics↗