Biology subjects

Jeffery, N. W.

Publications and source records attributed to Jeffery, N. W..

3 recordsLinked to original sources

bioRxiv2025

Automated eDNA and eRNA Profiling for Biodiversity Monitoring in Marine and Freshwater Ecosystems

Automated sampling enables the collection and analysis of eDNA from regions that are limited by site access, sampling times, and operator safety. eDNA sampling devices must be rigorously tested against existing technologies to demonstrate fitness across different operational settings and sample quality. The Dartmouth Ocean Technologies, Inc. (DOT) automated eDNA sampler preserves samples and can be deployed at a range of temperatures and depths. The DOT sampler has previously been tested in marine environments for up to three months, with validation against manual protocols. In this study we tested the DOT sampler in four water bodies in Nova Scotia, Canada, with an expanded set of genetic analyses. We successfully profiled prokaryotes, eukaryotes, and fish using the 16S, 18S, and 12S ribosomal RNA genes respectively, in a brackish pond, a freshwater lake, and two marine harbours. eDNA samples collected by the DOT sampler were statistically concordant with manual Niskin-bottle samples in a range of aqueous habitats. We detected taxonomic groups consistent with the salinity level of each sampled habitat, including invasive species such as smallmouth bass and chain pickerel in the freshwater lake. One marine harbour was sampled at pre-defined time intervals in the days following a significant rainfall event during which site access was limited. We detected ten times as many probable fecal-associated bacteria by proportion at this site relative to the other marine harbour. Onboard preservation of samples in RNAlater allowed the identification of groups with different levels of metabolic activity, and shotgun metagenomic analysis identified key metabolic pathways and a small number of sequences with homology to known antimicrobial-resistance genes.

ecology↗

bioRxiv2024

Diving into broad-scale and high-resolution population genomics to decipher drivers of structure and climatic vulnerability in a marine invertebrate

Species with widespread distributions play a crucial role in our understanding of climate change impacts on population structure. In marine species, population structure is often governed by both high connectivity potential and selection across strong environmental gradients. Despite the complexity of factors influencing marine populations, studying species with broad distribution can provide valuable insights into the relative importance of these factors and the consequences of climate-induced alterations across environmental gradients. We used the northern shrimp Pandalus borealis and its wide latitudinal distribution to identify current drivers of population structure and predict the species vulnerability to climate change. Individuals sampled across 24{degrees} latitude were genotyped at high geographic-(54 stations) and genetic-(14,331 SNPs) resolutions to assess genetic variation and environmental correlations. Four populations were identified in addition to finer substructure associated to local adaptation. Geographic patterns of neutral population structure reflected predominant oceanographic currents, while a significant proportion of the genetic variation was associated with gradients in salinity and temperature. Adaptive landscapes generated using climate projections suggest a larger genomic offset in the southern extent of the P. borealis range, where shrimp had the largest adaptive standing genetic variation. Our genomic results combined with recent observations point to the non-recovery in southern regions and an impending vulnerable status in the regions at higher latitude for P. borealis. They also provide rare insights into the drivers of population structure and climatic vulnerability of a widespread meroplanktonic species, which is crucial to understand future challenges associated with invertebrates essential to ecosystem functioning.

genomics↗

bioRxiv2017

The genome sizes of ostracod crustaceans correlate with body size and phylogeny

Within animals a positive correlation between genome size and body size has been detected in several taxa but not in others, such that it remains unknown how pervasive this pattern may be. Here we provide another example of a positive relationship, in a group of crustaceans whose genome sizes have not previously been investigated. We analyze genome size estimates for 46 species across Class Ostracoda, including 29 new estimates made using Feulgen image analysis densitometry and flow cytometry. Genome sizes in this group range ~80-fold, a level of variability that is otherwise not seen in crustaceans with the exception of some malacostracan orders. We find a strong positive correlation between genome size and body size across all species, including after phylogenetic correction. We additionally detect evidence of XX/XO sex determination in all three species of myodocopids where male and female genome sizes were estimated. On average, genome sizes are larger but less variable in myodocopids than in podocopids, and marine ostracods have larger genomes than freshwater species, but this appears to be explained by phylogenetic inertia. The relationship between phylogeny, genome size, body size, and habitat is complex in this system, and will benefit from additional data collection across various habitats and ostracod taxa.

evolutionary biology↗