Biology subjects

Rijal, D. P.

Publications and source records attributed to Rijal, D. P..

6 recordsLinked to original sources

bioRxiv2025

Enhanced reconstruction of Holocene bryophytes from sedimentary ancient DNA using bryophyte-specific primers

The Arctic is warming rapidly, yet long-term data on how this affects bryophytes, key components of Arctic vegetation, remain limited. Sedimentary ancient DNA (sedaDNA) provides high-resolution taxonomic insights that can reveal vegetational responses to past environmental change, including functional responses via trait associations, but effective genomic tools for bryophyte sedaDNA are lacking. We applied bryophyte-specific primers targeting p6 loop in plastid DNA and compared their performance with bryophyte bycatch from vascular plant-specific primers. Using data from bryophyte-specific primers, we analyzed richness patterns across environmental gradients and assessed their potential for environmental reconstruction. The primers resolved nearly 60% of taxa to species level and over 80% to genus level, recovering 2.63 times more taxa with 1.48 times higher species-level resolution than vascular plant-specific primers. Taxonomic richness increased nonlinearly over time and along precipitation gradients, while exhibiting unimodal relationship with temperature and glacial activity. High-resolution data also enabled trait assignments for most bryophyte taxa, allowing temporal analyses of community development and functional dynamics. Overall, our results demonstrate that bryophyte-specific primers substantially improve bryophyte recovery from sedaDNA and, when combined with trait information, provide a powerful approach for reconstructing past bryophyte ecosystems and investigating functional ecological dynamics under long-term environmental change.

ecology↗

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↗

bioRxiv2019

Forest canopy resists plant invasions: a case study of Chromolaena odorata in sub-tropical Sal (Shorea robusta) forests of Nepal

Invasive Alien Species cause tremendous ecological and economic damage in agriculture, forestry, aquatic ecosystems, and pastoral resources. They are one of the major threats to biodiversity conservation. Understanding the spatial pattern of invasive species and disentangling the biophysical drivers of invasion at forest stand level is essential for managing invasive species in forest ecosystems and the wider landscape. However, forest-level and species-specific information on invasive species abundance and area of extent is largely lacking. In this context, we analysed the cover of one of the worlds worst invasive plant species Chromolaena odorata in Sal (Shorea robusta Gaertn.) forest in central Nepal. Vegetation was sampled in four community-managed forests using 0.01 ha square quadrats, covering forest edge to the interior. Chromolaena cover, floral richness, tree density, forest canopy cover, shrub cover, and tree basal area were measured in each plot. We also estimated the level of disturbance in plots, and calculated distance from the plot to the nearest road. We also explored forest and invasive species management practices in community forests.\n\nChromolaena cover was found to be negatively correlated with forest canopy cover, distance to the nearest road, angle of slope and shrub cover. Canopy cover had the greatest effect on the Chromolaena cover. Chromolaena cover did not show any pattern along native species richness gradients. In conclusion, forest canopy cover is the overriding biotic covariate affecting Chromolaena cover in Sal forests. The practical application of our results in managing Chromolaena in forest ecosystems is discussed.

ecology↗