Monitoring terrestrial wildlife by combining hybridization capture and metabarcoding data from waterhole environmental DNA

Li, Juan; Seeber, Peter A.; Axtner, Jan; Crouthers, Rachel; Groenenberg, Milou; Koehncke, Arnulf; Courtiol, Alexandre; Pin, Chanratana; Greenwood, Alex D.

doi:10.1016/j.biocon.2023.110168

Cited by 6 publications

(1 citation statement)

References 63 publications

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“…Enrichment probes were designed from mitogenomes of 17 herbivorous mammal species that currently or previously occurred in the Arctic (Appendix 1-table 2) and few lichen sequences (Appendix 1-table 3). Genomic libraries were produced according to Li et al, 2013 with some modifications (Seeber et al, 2019;Seeber et al, 2023;Li et al, 2023; Supplement section 2). Filtered reads were mapped to mammalian mitogenomes, followed by BLASTn alignment against the complete NCBI nucleotide database and subsequent metagenomic analyses using MEGAN (Huson et al, 2016).…”

Section: Field Sites Dna Isolation and Hybridization Capture Enrichmentmentioning

confidence: 99%

Mitochondrial genomes of Pleistocene megafauna retrieved from recent sediment layers of two Siberian lakes

Seeber,

Batke,

Dvornikov

et al. 2023

Preprint

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Ancient environmental DNA (aeDNA) from lake sediments has yielded remarkable insights for the reconstruction of past ecosystems, including suggestions of late survival of extinct species. However, translocation and lateral inflow of DNA in sediments can potentially distort the stratigraphic signal of the DNA. Using three different approaches on two short lake sediment cores of the Yamal peninsula, West Siberia, with ages spanning only the past hundreds of years, we detect DNA and assembled mitochondrial genomes of multiple mammoth and woolly rhinoceros individuals—both species that have been extinct for thousands of years on the mainland. The occurrence of clearly identifiable aeDNA of extinct Pleistocene megafauna (e.g., > 400K reads in one core) throughout these two short subsurface cores, along with specificities of sedimentology and dating, confirm that processes acting on regional scales, such as extensive permafrost thawing, can influence the aeDNA record and should be accounted for in aeDNA paleoecology.

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Section: Field Sites Dna Isolation and Hybridization Capture Enrichmentmentioning

confidence: 99%

Mitochondrial genomes of Pleistocene megafauna retrieved from recent sediment layers of two Siberian lakes

Seeber,

Batke,

Dvornikov

et al. 2023

Preprint

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A quantitative analysis of vertebrate environmental DNA degradation in soil in response to time, UV light, and temperature

Guthrie,

Cooper,

Bateman

et al. 2024

Environmental DNA

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Environmental DNA (eDNA) degradation influences the effectiveness of eDNA‐based biodiversity monitoring, but the factors that determine the rate of decay of eDNA in terrestrial environments are poorly understood. We assessed the persistence of vertebrate eDNA from a mock vertebrate community created with soil from zoo enclosures holding 10 target species from different taxonomic classes (reptiles, birds, and mammals) and of different biomass (little penguin and giraffe). We examined species detection rates resulting from eDNA metabarcoding, as well as relative eDNA concentrations via qPCR, from soil samples over eight time points (0–12 weeks), during exposure to three ambient temperatures (10, 25, and 40°C) and three levels of ultraviolet B (UV‐B) radiation (0%, 50%, and 100% intensity). We recorded considerable variation in detectability between species, independent of temperature, and UV‐B effects. Quantitative polymerase chain reaction (PCR) indicated degradation of eDNA over time for all temperature and UV treatments, although it was still possible to detect eDNA from some species after 12 weeks. Degradation rates were lowest for high UV‐B treatments, presumably due to UV‐B reducing bacterial metabolism. The temperatures investigated did not influence eDNA decay. Our results indicate that eDNA in soil can persist under a range of temperatures and high UV radiation for longer than expected. Sheltered sites with minimal UV‐B radiation, which have previously been considered ideal sites for terrestrial eDNA collection, may not be optimal for eDNA persistence in some cases due to microbial decay. A better understanding of eDNA degradation in terrestrial environments is needed to enhance the accuracy of eDNA metabarcoding for surveying terrestrial vertebrate communities.

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Estimation of Species Abundance Based on the Number of Segregating Sites using Environmental DNA (eDNA)

Ai,

Yuan,

Wang

et al. 2024

Preprint

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The advance of environmental DNA (eDNA) has enabled rapid and non-invasive species detection in aquatic environments. Although most studies focus on assessing the absence or presence of species, some recent studies explored the potential of using eDNA concentration of targeted genes to quantify species abundance. However, eDNA concentration could be easily perturbed by various biotic or abiotic factors, obscuring the concentration-species abundance relationship. Here, we propose using the number of segregating sites as a proxy for estimating species abundance. We examined the relationship between the number of segregating sites and species abundance in silico, in vitro, and in situ (mesocosm experiments) using two brackish goby species, Acanthogobius hasta and Tridentiger bifasciatus. Analyses of the simulated data and in vitro data with DNA mixed from a known number of individuals showed a strong correlation between the number of segregating sites and species abundance (R2 > 0.9; P < 0.01). Results from the mesocosm experiment further validated the correlation (R2 = 0.70, P < 0.01). Such correlation was not affected by biotic factors, including body size and feeding behavior of the fish (P > 0.05). Results of the cross-validation test also showed that the number of segregating sites predicted species abundance more accurately and robustly than the eDNA concentration did. Overall, the number of segregating sites is a more accurate and robust indicator of species abundance than eDNA concentration. This advancement can significantly enhance the quantitative capabilities of eDNA technology.

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Monitoring terrestrial wildlife by combining hybridization capture and metabarcoding data from waterhole environmental DNA

Cited by 6 publications

References 63 publications

Mitochondrial genomes of Pleistocene megafauna retrieved from recent sediment layers of two Siberian lakes

Mitochondrial genomes of Pleistocene megafauna retrieved from recent sediment layers of two Siberian lakes

A quantitative analysis of vertebrate environmental DNA degradation in soil in response to time, UV light, and temperature

Estimation of Species Abundance Based on the Number of Segregating Sites using Environmental DNA (eDNA)

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