Biology subjects

Allen, M. J.

Publications and source records attributed to Allen, M. J..

6 recordsLinked to original sources

bioRxiv2026

MillionTrees: A global benchmark for tree detection across geography, sensor, and annotation geometry

Airborne tree monitoring using remotely sensed data, combined with the growth of computer vision models for object detection and segmentation, can facilitate broad scale assessment of tree health, ecology and ecosystem function. However, datasets for airborne tree detection have been largely limited to a single geography, resolution, or annotation approach, making it difficult to develop general models and benchmark their utility for broad applications. We compile existing and newly published annotation datasets to create a comprehensive dataset for training and evaluating airborne tree detection in RGB imagery. The MillionTrees dataset has over a million individual trees from a broad range of forest types, tree species, and geographic locations. In addition, it has six million weakly supervised annotations from a range of sources including airborne LiDAR and photogrammetry, arborist surveys, and simulated landscapes. An evaluation standard is provided to facilitate rapid model development. We benchmark several existing tree detection algorithms and demonstrate that while current open-source models do not generalize across the diverse datasets in the benchmark, training on MillionTrees improves both within-domain and out-of-domain performance. Held-out validation datasets using ground truth derived from terrestrial LiDAR paired with overhead RGB show that overfitting to test data is common and hyperparameter tuning is an underappreciated challenge towards a global zero shot tree detection method. We discuss the limitations of the currently available data for airborne RGB tree detection, how to create more robust evaluation data and the need for better understanding of the uncertainty and utility of tree detection from airborne remote sensing.

ecology↗

bioRxiv2026

IRF7 deficiency increases disease severity independently of TLR7 recognition in Influenza A infection in mice

Influenza A virus (IAV) remains a major cause of respiratory morbidity and mortality, yet the role of Toll-like receptor 7 (TLR7), an RNA sensor, and its downstream signaling events, such as interferon regulatory factor 7 (IRF7), in IAV infection remain unclear. To address this question, we used single-cell RNA sequencing, genetic mouse models, and immunological analysis. Single -cell transcriptomic profiling of the infected lungs revealed robust upregulation of Tlr7 and genes associated with interferon pathways in dendritic cells and B cells, alongside widespread induction of Irf7 across immune and non-immune compartments. Tlr7-deficient mice exhibited normal viral control, lung pathology, and survival following IAV challenge. In contrast, Irf7 deficiency resulted in significantly increased disease severity, impaired early interferon responses, exacerbated bronchial epithelial hyperplasia, and defective early humoral priming. In assessing adaptive immunity, both Irf7-deficient andTlr7-deficient mice had reduced antihemagglutinin antibody production. Mechanistically, IRF7 protein expression and downstream signaling were largely preserved in TLR7-deficient mice, indicating that IRF7 activation during IAV infection occurs independently of TLR7. Collectively, these findings identify IRF7 as a non-redundant determinant of innate immunity and disease outcomes during IAV infection, while positioning TLR7 as a modulatory factor primarily influencing adaptive immune maturation. Our study refines current models of antiviral sensing by uncoupling receptor induction from functional necessity and highlights IRF7 as a critical downstream regulator dictating host defense against acute influenza A infection. ImportanceInfluenza A virus is a respiratory pathogen that remains a major threat to global health as a seasonal disease and a source of periodic pandemics. The outcomes of the infection can range from mild illness to severe pneumonia and death, particularly in vulnerable populations, yet the reasons why some individuals develop more severe disease are not fully understood. Early immune defenses in the lungs are critical for controlling the virus, but they can also contribute to harmful inflammation if not properly regulated. In particular, key sensors that detect viral genetic material and the signaling pathways that activate antiviral responses play an essential role in shaping these outcomes. The significance of our study lies in defining how these early immune mechanisms influence the course of influenza A infection, providing insight that may guide the development of improved therapies for influenza and related respiratory viruses.

immunology↗

bioRxiv2022

Long-read powered viral metagenomics in the oligotrophic Sargasso Sea

In the summer months, the waters of the Sargasso Sea are nutrient-limited and strongly stratified, serving as a model system for the predicted warmer and nutrient-limited oceans of the Anthropocene. The dominant microorganisms of surface waters are key drivers of the global carbon cycle. However, the viruses of the Sargasso Sea that shape these host communities and influence host biogeochemical function are not well understood. Here, we apply a hybrid sequencing approach that combines short- and long reads to survey Sargasso Sea phage communities via metagenomics at the viral maximum (80m) and mesopelagic (200m) depths. Taxonomically, we identified 2,301 Sargasso Sea phage populations (~species-level taxonomy) across 186 genera. Over half of the phage populations lacked representation in other global ocean viral metagenomes, whilst 177 phage genera lacked representation in phage isolate databases. Viral fraction and cell-associated viral communities captured in short-read data were distinct and decoupled at both depths, possibly indicating low active lytic viral replication in the Sargasso Sea, with viral turnover occurring across periods longer than the sampling period of three days. Inclusion of long read data was critical for (1) the identification of 79 ecologically important and common viral genomes; (2) capturing the extent of viral genome microdiversity; and (3) enabling the recovery of hypervariable regions in viral genomes predicted to encode proteins involved in host recognition, DNA synthesis and DNA packaging. Host prediction was only possible for ~4% of viral populations. Genomes of phages known to infect Prochlorococcus and Pelagibacter were poorly represented in our data, supporting recent evidence of low infection levels in the dominant bacterial taxa of oligotrophic regions. SubjectsBioinformatics, Genomics, Marine Biology, Microbiology, Virology Sequence data accession numbersPRJNA767318

microbiology↗

bioRxiv2022

Pelagibacter phage Skadi - An abundant polar specialist that exemplifies ecotypic niche specificity among the most abundant viruses on Earth

Bacteria in the SAR11 clade are the most abundant members of surface marine bacterioplankton and are a critical component of global biogeochemical cycles. Similarly, pelagiphages that predate SAR11 are both ubiquitous and highly abundant in the oceans. These viruses are predicted to shape SAR11 community structures and increase carbon turnover throughout the oceans. Yet, ecological drivers of host and niche specificity of pelagiphage populations are poorly understood. Here we report the global distribution of a novel pelagiphage called Skadi isolated from the Western English Channel using a cold-water ecotype of SAR11 (HTCC1062) as bait. Skadi is closely related to the globally dominant pelagiphage HTVC010P. We show that, along with other HTVC010P-type viruses, Skadi belongs to a distinct viral family within the order Caudovirales for which we propose the name Ubiqueviridae. Metagenomic read recruitment identifies Skadi as one of the most abundant pelagiphages on Earth. Skadi is a polar specialist, replacing HTVC010P at high latitudes. Experimental evaluation of Skadi host-range against cold- and warm-water SAR11 ecotypes supported cold-water specialism. Read mapping from the Global Ocean Viromes project (GOV2) showed that relative abundance of Skadi correlated negatively with temperature, and positively with nutrients, available oxygen and chlorophyll concentrations. In contrast, relative abundance of HTVC010P correlated negatively with oxygen and positively with salinity, with no significant correlation to temperature. The majority of other pelagiphages were scarce in most marine provinces, with a few representatives constrained to discrete ecological niches. Our results suggest that pelagiphage populations persist within a global viral seed-bank, with environmental parameters and host availability selecting for a few ecotypes that dominate ocean viromes.

microbiology↗

bioRxiv2020

Efficient Dilution-to-Extinction isolation of novel virus-host model systems for fastidious heterotrophic bacteria

Microbes and their associated viruses are key drivers of biogeochemical processes in marine and soil biomes. While viruses of phototrophic cyanobacteria are well-represented in model systems, challenges of isolating marine microbial heterotrophs and their viruses have hampered experimental approaches to quantify the importance of viruses in nutrient recycling. A resurgence in cultivation efforts has improved the availability of fastidious bacteria for hypothesis testing, but this has not been matched by similar efforts to cultivate their associated bacteriophages. Here, we describe a high-throughput method for isolating important virus-host systems for fastidious heterotrophic bacteria that couples advances in culturing of hosts with sequential enrichment and isolation of associated phages. Applied to six monthly samples from the Western English Channel, we first isolated one new member of the globally dominant bacterial SAR11 clade and three new members of the methylotrophic bacterial clade OM43. We used these as bait to isolate 117 new phages including the first known siphophage infecting SAR11, and the first isolated phage for OM43. Genomic analyses of 13 novel viruses revealed representatives of three new viral genera, and infection assays showed that the viruses infecting SAR11 have ecotype-specific host-ranges. Similar to the abundant human-associated phage {Phi}CrAss001, infection dynamics within the majority of isolates suggested either prevalent lysogeny or chronic infection, despite a lack of associated genes; or host phenotypic bistability with lysis putatively maintained within a susceptible subpopulation. Broader representation of important virus-host systems in culture collections and genomic databases will improve both our understanding of virus-host interactions, and accuracy of computational approaches to evaluate ecological patterns from metagenomic data.

microbiology↗

bioRxiv2018

Long-read metagenomics reveals cryptic and abundant marine viruses

Marine viruses impact global biogeochemical cycles via their influence on host community structure and function, yet our understanding of viral ecology is constrained by limitations in culturing of important hosts and the lack of a universal gene to facilitate community surveys. Short-read viral metagenomic studies have provided clues to viral function and first estimates of global viral gene abundance and distribution. However, short-read assemblies are confounded by populations with high levels of strain evenness and nucleotide diversity (microdiversity), limiting assembly of some of the most abundant viruses on Earth. Assembly across genomic islands which likely contain niche-defining genes that drive ecological speciation is also challenging. While such populations and features are successfully captured by single-virus genomics and fosmid-based approaches, both techniques require considerable cost and technical expertise. Here we established a low-cost, low-input, high throughput alternative method for improving assembly of viral metagenomics using long read technology. Named VirION (Viral, long-read metagenomics via MinION sequencing), our sequencing approach and complementary bioinformatics pipeline (i) increased number and completeness of assembled viral genomes compared to short-read sequencing methods; (ii) captured populations of abundant viruses with high microdiversity missed by short-read methods and (iii) captured more and longer genomic islands than short-read methods. Thus, VirION provides a high throughput and cost-effective alternative to fosmid and single-virus genomic approaches to more comprehensively explore viral communities in nature.

genomics↗