Biology subjects

Brown, A. G.

Publications and source records attributed to Brown, A. G..

5 recordsLinked to original sources

bioRxiv2026

Sedimentary ancient DNA analysis from the Iron Age courtyard and cooking pit site of Rodskjaer in Troms, Northern Norway

Courtyard sites, which are Iron Age structures unique to Norway, are often associated with cooking pit fields suggesting feasting practices, but little is known about the main purpose of these sites. To address this, a framework for sedimentary ancient DNA (sedaDNA) metabarcoding sampling was undertaken at the site of Rodskjaer, northern Norway. Of the 63 sediment samples from cooking pits, fire pits, a hearth, a fireplace, the natural shell-sand and topsoil, 52 successfully detected plant and animal sedaDNA. The plant diversity was high with 41-100 taxa. SedaDNA identified archaeologically significant taxa that were not detected by other methods, including Avena (oats), Quercus (oak), Equus (horse), and Salmo salar (salmon). Additionally, from inter-sample comparison, and with reference to worm sedaDNA we identified the archaeological contexts that were affected by partial bioturbation and root penetration that restricted interpretation of spatial or temporal differences in use of these features. This pioneering study shows the importance of taking many samples from modern and natural sediments as well as using multi-proxy analysis when conducting sedaDNA metabarcoding studies at open-air archaeological sites. If these factors are taken into consideration, sedaDNA from cooking pits can be a valuable resource for investigating uses of courtyard and cooking pit field sites.

genetics↗

bioRxiv2025

Capture probe, metabarcoding, or shotgun sequencing: which best reflects local vegetation?

O_LIMetabarcoding is the most widely applied method for studying plant communities using environmental DNA, with shotgun sequencing and capture probes being alternative methods. Any methods ability to detect and correctly identify plant taxa may vary with DNA preservation, DNA reference library and the size of the local flora, making it difficult to compare results from different environments. C_LIO_LIHere we compare these methods using lake surface-sediments from Northern Fennoscandia with the PhyloNorway genome skim reference library (1500 taxa) that includes almost all species of the regional flora. We also undertook vegetation surveys from around the lakes to estimate the true positive detection rate, identify false positive detections, and provide optimal filtering cut-off thresholds for the three methods. C_LIO_LIOptimal filter cutoffs were one PCR replicate and 3 reads for metabarcoding, and 3.2x10e-6 and 5.6x10e-6 of queried reads, respectively, for the shotgun and capture probe data. Applying these thresholds, the rate of false positives was too high for reliable identification at species level based on shotgun (49%) and capture probes (62%), whereas it was low for metabarcoding (5-12%). All methods were reliable at genus and family levels after applying the optimal filtering thresholds (<4% false positives). Our results show that metabarcoding on average detects 2.1 times as many true positive taxa as shotgun sequencing, and 6.4 times as many taxa as capture probes. Proportions of filtered metabarcoding and shotgun reads were significantly related to abundance categories from vegetation surveys, but this was not the case for capture probe data. C_LIO_LIWe expect the false positive rate of shotgun sequencing to decrease with increasing genome completeness in the reference libraries, and be advantageous for highly degraded DNA with fragments too short for metabarcoding. At present, metabarcoding provides the highest detectability and taxonomic resolution for correct identification of vascular plants. C_LI

ecology↗

bioRxiv2025

Maximizing vegetation representation of the catchment in sedimentary DNA with targeted cores in small lakes

Sedimentary DNA is becoming an invaluable tool for biodiversity assessments across spatial and temporal scales. Accurate interpretation, however, requires a clear understanding of its origin and taphonomy, from transport to preservation processes within lake systems. Insights into these processes are crucial for developing efficient sampling methods for precise ecological monitoring. Our analysis of 42 adjacent surface sediment sample replicates shows that deeper, central samples, with reduced influence from aquatic taxa, exhibit greater taxonomic richness compared to near-shore samples. By comparing these results to systematic vegetation surveys, we demonstrate that central cores are optimal as they capture the main taxonomic richness in the catchment, while marginal samples near inflows are essential for detecting rarer, spatially restricted taxa. This study highlights the potential of central-core sampling to effectively capture vegetation profiles in small, bathymetrically simple lakes, while enhancing the understanding of DNA transport mechanisms in catchments with similar topographic or hydrological characteristics.

ecology↗

bioRxiv2023

Environmental DNA of aquatic macrophytes: the potential for reconstructing past and present vegetation and environments

Environmental DNA is increasingly being used to reconstruct past and present biodiversity including from freshwater ecosystems. Here, we first review and compare studies that use metagenomics, targeted capture, and various barcoding and metabarcoding markers, in order to explore how each of these methods can be used to capture aquatic vegetation diversity and change. We then investigate the extent to which such a record can be leveraged for reconstructing local environmental conditions, using a case study based on macrophyte ecological niches. We find that, with state-of-the-art DNA barcode reference libraries, using metabarcoding to target the P6 loop region of the chloroplast trnL (UAA) intron is optimal to maximise taxonomic resolution and the diversity of past macrophyte communities. Shotgun sequencing also retrieves a high proportion of aquatic macrophyte diversity, but has the lowest taxonomic resolution, and targeted capture needs to be more widely applied before comparisons can be made. From our case study, we infer past aquatic habitats from sedimentary ancient DNA records of macrophyte taxa. We reconstructed Holocene thermal range, continentality, water pH, trophic status, and light conditions in northern Fennoscandia. We show an overall stability since 9,000 years ago, even though individual lakes display different trends and variation in local climatic and physico-chemical conditions. Combined with the availability of near-exhaustive barcode and traits databases, metabarcoding data can support wider ecological reconstructions that are not limited to aquatic plant taxonomic inventories but can also be used to infer past changes in water conditions and their environmental drivers. Sedimentary DNA is also a powerful tool to measure present diversity, as well as to reconstruct past lacustrine and fluvial communities of aquatic macrophytes.

ecology↗

bioRxiv2020

Holocene plant diversity revealed by ancient DNA from 10 lakes in northern Fennoscandia

The effects of climate change on species richness is debated but can be informed by the past. Here, we assess the impact of Holocene climate changes and nutrients on terrestrial plant richness across multiple sites from northern Fennoscandia using new sedimentary ancient DNA (sedaDNA) data quality control methods. We find that richness increased steeply during the rapidly warming Early Holocene. In contrast to findings from most pollen studies, we show that richness continued to increase through the Middle to Late Holocene even though temperature decreased, with the regional species pool only stabilizing during the last two millennia. Furthermore, overall increase in richness was greater in catchments with higher soil nutrient availability. We suggest that richness will rapidly increase with ongoing warming, especially at localities with high nutrient availability and even in the absence of increased human activity in the region, although delays of millennia may be expected.

ecology↗