Biology subjects

Berg, N.

Publications and source records attributed to Berg, N..

4 recordsLinked to original sources

bioRxiv2026

Seasonal patterns of environmental DNA detection for freshwater unionid mussels

Environmental DNA (eDNA) provides a powerful non-invasive tool for monitoring freshwater mussel assemblages, yet detection probabilities can be influenced by reproductive behaviors, seasonal vertical migration, and hydrological conditions. This study assessed eDNA detection from April through October across two diverse mussel beds in Ohio, encompassing species with both tachytictic (short-term brooders) and bradytictic (long-term brooders) reproductive strategies. Mussel DNA was consistently detected across seasons, with detection patterns generally aligning with species observed through a visual tactile survey. Overall, the eDNA sequence abundance was positively correlated with tactile mussel counts, however congruence between the two surveys was strongest during low discharge and when the surveys occurred in close temporal proximity to one another. This study finds that eDNA sampling for freshwater mussels performs adequately within the currently prescribed survey window for visual surveys. However, seasonal factors such as endobenthic burial behavior and high discharge events may have reduced detection efficiency, particularly in Killbuck Creek, where species richness was lowest during periods of high flow in early spring. Therefore, decisions made regarding the timing of eDNA surveys should consider local environmental conditions (e.g., temperature and flow) to achieve optimal results.

ecology↗

bioRxiv2026

Assessment of Environmental DNA Surveys for the Cryptic Salamander Mussel (Simpsonaias ambigua)

Simpsonaias ambigua (Salamander Mussel), is a small and thin shelled freshwater mussel often found in difficult to survey habitats, such as beneath slab stones, in the crevices of rock walls, or buried within roots of emergent vegetation and in undercuts of banks. The use of environmental DNA (eDNA - genetic material released from urine, waste, mucus, or sloughed cells) sampling may improve detection and assessment of presence / absence for this rare mussel in comparison to visual tactile techniques. This study completed side by side comparisons of traditional mussel searches and eDNA for a direct assessment of mussel detection efficiencies. Surveying was conducted in several waterbodies of different habitat characteristics with varying abundances of S. ambigua. Additionally, a broad assessment of S. ambigua presence was conducted throughout the proposed critical habitat reach of the Blanchard River in northwest Ohio, to assess if the species remained extant. All eDNA samples were also assessed for the presence of Necturus maculosus (Mudpuppy), the obligate host species for S. ambigua. The eDNA sampling successfully detected S. ambigua from multiple sites and watersheds where it was found with visual surveys. In some cases, eDNA detections occurred in locations where over 16 hours of search yielded only a single individual or fresh dead shells, supporting the sensitivity of eDNA for detection of rare species. Furthermore, probability of detection analysis suggests eDNA sampling can provide high detection efficiency with relatively low effort in comparison to visual searches. The development and validation of an eDNA protocol for the simultaneous detection of S. ambigua and its host salamander increases survey efficiency, reduces field costs, and can support future conservation efforts for listing drainages of extant populations and monitoring conservation goals.

ecology↗

bioRxiv2023

Influenza A Virus Infections Sense Host Membrane Tension to Dynamically Tune Assembly

Enveloped viruses often exhibit a pleomorphic morphology, ranging in size from 100nm spheres to tens-of-micron long filaments. For influenza A virus (IAV), spheres enable rapid replication and minimize metabolic cost, while filaments resist effects of antibodies or other cell-entry pressures. The current paradigm is that virion shape changes require genetic adaptation; however, a virus evolved to alter its shape phenotypically would outperform one that relies on genetic selection. Using a novel quantitative flow virometry assay to characterize virion shape dynamics we find that IAV rapidly tunes its shape distribution to favor spheres under optimal, and filaments under attenuating conditions including the presence of antibodies. We identify membrane tension as a key cue sensed by IAV determining shape distributions. This phenotypic shift outpaces genetic change and serves to enable additional life cycles under pressure. Our work expands knowledge of the complex host-virus interplay to include viral responses to the local environment by optimizing its structure to maximize replication and ultimately host-host transmission.

microbiology↗

bioRxiv2023

Influenza A genomic diversity during human infections underscores the strength of genetic drift and the existence of tight transmission bottlenecks

Influenza infections result in considerable public health and economic impacts each year. One of the contributing factors to the high annual incidence of human influenza is the viruss ability to evade acquired immunity through continual antigenic evolution. Understanding the evolutionary forces that act within and between hosts is therefore critical to interpreting past trends in influenza virus evolution and in predicting future ones. Several studies have analyzed the longitudinal patterns of influenza A virus genetic diversity in natural human infections to assess the relative contributions of selection and genetic drift on within-host evolution. However, in these natural infections, within-host viral populations harbor very few single nucleotide variants, limiting our resolution in understanding the forces acting on these populations in vivo. Further, low levels of within host viral genetic diversity limit the ability to infer the extent of drift across transmission events. Here, we propose to use influenza virus genomic diversity as an alternative signal to better understand within and between host patterns of viral evolution. Specifically, we focus on the dynamics of defective viral genomes (DVGs) which harbor large internal deletions in one or more of influenza viruss eight gene segments. Our longitudinal analyses of DVGs show that influenza A virus populations are highly dynamic within hosts, corroborating previous findings based on viral genetic diversity that point towards the importance of genetic drift in driving within-host viral evolution. Further, our analysis of DVG populations across transmission pairs indicate that DVGs rarely appeared to be shared, consistent with previous findings indicating the presence of tight transmission bottlenecks. Our analyses demonstrate that viral genomic diversity can be used to complement analyses based on viral genetic diversity to reveal processes that drive viral evolution within and between hosts. Author summaryDuring viral replication within infected individuals, different types of mutation can occur. Point mutations introduce genetic diversity, with some sites in the viral genome becoming polymorphic at the viral population level. Structural mutations that result in deletions in the viral genome can also occur, contributing to genomic diversity in the viral population. Defective viral genomes (DVGs) are a particular type of this genomic diversity that are incapable of establishing productive infection on their own, but persist during infection through cellular coinfection with infectious virus. Here, we first identify DVGs in deep sequencing data from natural infections of influenza A virus subtype H3N2 and then use these DVGs to inform our understanding of within-host viral evolution and transmission dynamics. By analyzing DVG populations over time within infected individuals and between transmission pairs, we find that influenza A virus populations are shaped by genetic drift and tight transmission bottlenecks. Our results add to our understanding of influenza genomic diversity within-and between-hosts and demonstrate the possibility of considering the full suite of viral diversity to understand drivers of viral evolution.

evolutionary biology↗