Tags:
Molecular biology,
DNA,
RNA,
Long read sequencing,
High throughput sequencing,
RAD-seq,
WGS,
Metabarcoding,
Target enrichment,
Museomics
Publications
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Heuvel-Greve, Martine J. van den; Polling, Marcel; Groot, G. Arjen de; Kodde, Linda; Mulder, Ingeborg M. & Verdaat, Hans
[Show all 11 contributors for this article]
(2026).
Tracking biodiversity in changing Arctic waters: insights from eDNA metabarcoding in Svalbard.
Polar Biology.
ISSN 0722-4060.
49.
doi:
10.1007/s00300-026-03488-9.
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Monitoring biodiversity patterns and their changes in Arctic coastal ecosystems is critical under ongoing climate change. However, common current approaches require high effort and expertise and this in turn limits the spatial and temporal scale of these monitoring efforts. Here, we investigated both the fish and the marine invertebrate communities across Svalbard using a multi-marker environmental DNA metabarcoding approach. We collected and analysed marine water, sediment and zooplankton filtered from marine water from sites influenced by the warm West Spitsbergen Current and the cold East Spitsbergen Current. Following metabarcoding amplification using mitochondrial COI, 12S, 16S and nuclear 18S markers and high-throughput sequencing, we retrieved an extensive overview of Svalbard marine biodiversity. Water, sediment and especially zooplankton samples collected across Svalbard revealed spatial differences in community composition, with significantly distinct assemblages in the northwest and southeast of Svalbard. We identified potential bioindicator species for use in rapid assessment of impacts of marine temperature increase and confirmed observed patterns of ongoing shifts in community structure as a response to changes in dominant water masses. Overall, our findings show that species composition depending on fine-scale climate variation of Arctic waters can be effectively studied and monitored using environmental DNA. These insights can help us understand current and evolving climate-driven changes.
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Gross, Megan; Stoeck, Thorsten; Mauvisseau, Quentin; Schrøder-Nielsen, Audun & Dunthorn, Micah
(2025).
Comparing the precision of two digital PCR applications for copy number comparisons in protists.
Scientific Reports.
15(1),
p. 1–12.
doi:
10.1038/s41598-025-13143-8.
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Abstract Microorganisms play key roles in ecosystem functioning, making reliable methods for assessing their dynamics essential. Advances in molecular technologies now enable their quantification in environmental samples based on DNA marker genes. Among these, digital PCR has emerged as a powerful tool for detecting and quantifying organisms based on their gene copies, with numerous platforms that are currently available. However, these platforms differ in their underlying technologies, and comparative studies that evaluate the performance and reproducibility remain limited. Here we compared different platform parameters across the QX200 digital droplet PCR from Bio-Rad and the QIAcuity One nanoplate-based digital PCR from QIAGEN. We used synthetic oligonucleotides and DNA extracted from varying cell numbers of the ciliate Paramecium tetraurelia and additionally tested the impact of two restriction enzymes on gene copy number quantification. Both platforms demonstrated similar detection and quantification limits and yielded high precision across most analyses. We found a general tendency of higher precision using the HaeIII restriction enzyme instead of EcoRI, especially for the QX200 system. Gene copy number estimates from ciliate DNA were reproducible between platforms and showed a linear trend for an increasing number of cells for both platforms. These findings highlight the importance of cross-platform evaluations to ensure robust and reproducible gene copy number analysis in unicellular eukaryotes and support a potential broader application of digital PCR in environmental monitoring studies.
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Anmarkrud, Jarl Andreas; Rosa, Fabricio dos Anjos Santa; Thorbek, Birgitte Lisbeth Graae; Schrøder-Nielsen, Audun; Sviggum, Silvana Melo & Ready, Jonathan Stuart
[Show all 8 contributors for this article]
(2025).
eDNA Replicates, Polymerase and Amplicon Size Impact Inference of Richness Across Habitats.
Environmental DNA.
7(3).
doi:
10.1002/edn3.70095.
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Environmental DNA-based monitoring has been increasingly used in the last decade to monitor biodiversity in aquatic and terrestrial systems. Molecular-based surveys now allow quick and reliable production of baseline knowledge of species community composition on a large scale, allowing a better understanding of ecosystem function and mitigation of stressors linked to anthropogenic activities. Despite this, technical hurdles often remain, and the impact of replicates, PCR polymerases, and amplicon size on the recovered species richness is still poorly understood. Here, we conducted a large controlled experiment, with bulk samples collected from terrestrial, marine, and freshwater environments to assess the impact of natural and technical replicates, PCR polymerases with different degrees of fidelity or proofreading activity, as well as amplicon size on species richness recovery across habitats. In this study, we consistently found variations in sample species richness depending on PCR polymerase choice. We further demonstrate the dissimilar impacts between natural and technical replicates on species richness recovery and the necessity of increasing natural replications in eDNA-based surveys. We highlight the benefits and limitations of replication strategies, polymerase choice, and amplicon size across terrestrial, marine, and freshwater habitats, and provide recommendations to increase the reliability of future eDNA-based metabarcoding studies.
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Mahlangu, Sibusiso; Ewers, Isabelle; Carvalho, Cintia Oliveira; Schrøder-Nielsen, Audun; Dunthorn, Micah & Karlsen, Hans Erik
[Show all 12 contributors for this article]
(2025).
Investigating the dynamics of the aquatic community in Oslofjord through time series analysis of eDNA.
Journal of Fish Biology.
ISSN 0022-1112.
doi:
10.1111/jfb.70105.
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Understanding the temporal dynamics of marine communities is critical for assessing ecosystem health and guiding conservation efforts. Here, we conducted a survey using environmental DNA (eDNA) metabarcoding with two primer sets, MiFish and Elas02, to investigate seasonal and interannual changes in the fish community of Oslofjord (Norway) over two consecutive years. Using the MitoFish reference database through the Global Biodiversity Information Facility querying tool, we identified 63 fish species and found significant changes in the dominant taxa between seasons and years. Clupea harengus (Atlantic herring) consistently peaked in early spring, while Scomber scombrus (Atlantic mackerel) dominated winter months in the second year. The MiFish primer set showed increased species richness in the second year, whereas the Elas02 primer set showed stable richness despite compositional turnover. Non-metric multidimensional scaling revealed distinct community separation between years in presence/absence of data, driven by species turnover rather than abundance read changes. Our findings support the use of eDNA metabarcoding to capture fine-scale (bi-monthly) temporal dynamics and emphasise the importance of multi-year datasets for distinguishing ecological trends from stochastic changes. This strategy improves monitoring practices for marine ecosystems under anthropogenic stressors.
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Carvalho, Cintia Oliveira; Gromstad, William Esbjug; Dunthorn, Micah; Karlsen, Hans Erik; Schrøder-Nielsen, Audun & Ready, Jonathan Stuart
[Show all 10 contributors for this article]
(2024).
Harnessing eDNA metabarcoding to investigate fish community composition and its seasonal changes in the Oslo fjord.
Scientific Reports.
14(1).
doi:
10.1038/s41598-024-60762-8.
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In the face of global ecosystem changes driven by anthropogenic activities, effective biomonitoring strategies are crucial for mitigating impacts on vulnerable aquatic habitats. Time series analysis underscores a great significance in understanding the dynamic nature of marine ecosystems, especially amidst climate change disrupting established seasonal patterns. Focusing on Norway's Oslo fjord, our research utilises eDNA-based monitoring for temporal analysis of aquatic biodiversity during a one year period, with bi-monthly sampling along a transect. To increase the robustness of the study, a taxonomic assignment comparing BLAST+ and SINTAX approaches was done. Utilising MiFish and Elas02 primer sets, our study detected 63 unique fish species, including several commercially important species. Our findings reveal a substantial increase in read abundance during specific migratory cycles, highlighting the efficacy of eDNA metabarcoding for fish composition characterization. Seasonal dynamics for certain species exhibit clear patterns, emphasising the method's utility in unravelling ecological complexities. eDNA metabarcoding emerges as a cost-effective tool with considerable potential for fish community monitoring for conservation purposes in dynamic marine environments like the Oslo fjord, contributing valuable insights for informed management strategies.
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Queiroz, Anna Karolina Oliveira de; Gasalla, Maria A.; Laux, Marcele; Oliveira, Renato Renison Moreira; Rosa, Fabricio dos Anjos Santa & Schrøder-Nielsen, Audun
[Show all 11 contributors for this article]
(2024).
Dietary metabarcoding of keystone sardine species reveals the importance of their ichthyoplankton prey in food webs of the Southern Brazilian Bight fisheries.
Fisheries Oceanography.
ISSN 1054-6006.
doi:
10.1111/fog.12668.
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Clupeiform fishes are ecologically and economically important species contributing to industrial and artisanal fisheries worldwide. They represent key links in food webs, influencing the dynamic between trophic levels. The dietary interactions of these species are poorly studied in many regions, yet essential for fisheries management. To elucidate the role of these species in food webs of the Southern Brazilian Bight pelagic fisheries, we used metabarcoding analysis of fish stomach contents of Clupeiformes and possible predators. Onboard sampling from March to September 2016 allowed for processing of 87 stomach samples representing 31 species (including 12 samples representing three species of Clupeiformes). Links between trophic levels showed the predominance of Sardinella brasiliensis and Engraulis anchoita as important dietary items of a large range of fishes (28 species belonging to 18 families) and representing the majority of the total prey read abundance assigned to clupeiform fishes (~46% and ~32%, respectively). Opisthonema oglinum contributed to the diet of 16 species in 13 families and ~18% of total read abundance of clupeiform fishes as prey. The appearance of multiple clupeiform taxa in the diet of predators that are not commonly associated with pelagic prey indicates that ecosystem-based fisheries management should not be separated between pelagic and demersal fisheries. The diet of Clupeiformes revealed an unexpectedly large diversity of fish species and a low proportion of invertebrates (<5% of clupeiform prey reads). This was likely due to a combination of both a limitation of the metabarcoding method (primer bias and low success of invertebrate taxonomic identification) as well as a contribution of early life stages (ichthyoplankton) to the diet of these fishes. The potential role of clupeiform fish populations as a constraint to the recruitment from the ichthyoplanktonic phase of other ecologically or commercially important fishes should be considered as an important direction for future studies.
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Carvalho, Cintia Oliveira; Pazirgiannidi, Melina; Ravelomanana, Tsilavina; Andriambelomanana, Fetra; Schrøder-Nielsen, Audun & Ready, Jonathan Stuart
[Show all 9 contributors for this article]
(2024).
Multi-method survey rediscovers critically endangered species and strengthens Madagascar's freshwater fish conservation.
Scientific Reports.
14(1).
doi:
10.1038/s41598-024-71398-z.
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Freshwater ecosystems are crucial for global biodiversity through supporting plant and animal species and providing essential resources. These ecosystems are under significant threat, particularly in island environments such as Madagascar. Our study focuses on the Amboaboa River basin, home to the rare and endemic fish species Rheocles derhami, last recorded in 2013. To assess the status of this and other threatened fish species including Ptychochromis insolitus and Paretroplus gymnopreopercularis, and to understand freshwater fish population dynamics in this biodiversity hotspot, we conducted a comprehensive survey using both environmental DNA (eDNA) and traditional fishing methods. While traditional methods effectively captured a diverse range of species, including several invasive aliens and the critically endangered endemic species that were the focus of this study, the eDNA approach detected only a fraction of these introduced species and struggled to identify some critically endangered endemics at the species level. This highlights the value of combining methods to enhance species detection. We also investigated the trade-offs associated with multi-primer assessments in eDNA analysis, focusing on three different primer combinations targeting the 12S mitochondrial gene: MiFish, Tele02, and Riaz. Additionally, we provided 12S reference barcodes for 10 species across 9 genera of fishes from the region to increase the coverage of the public reference databases. Overall, our study elucidates the current state of freshwater biodiversity in the Amboaboa River basin and underscores the value of employing multiple methods for effective conservation strategies.
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Veltman, Margret; Anthoons, Bastien; Schrøder-Nielsen, Audun; Gravendeel, Barbara & Boer, Hugo de
(2024).
Orchidinae-205: A new genome-wide custom bait set for studying the evolution, systematics, and trade of terrestrial orchids.
Molecular Ecology Resources.
ISSN 1755-098X.
doi:
10.1111/1755-0998.13986.
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Terrestrial orchids are a group of genetically understudied, yet culturally and economically important plants. The Orchidinae tribe contains many species that produce edible tubers that are used for the production of traditional delicacies collectively called ‘salep’. Overexploitation of wild orchids in the Eastern Mediterranean and Western Asia threatens to drive many of these species to extinction, but cost-effective tools for monitoring their trade are currently lacking. Here we present a custom bait kit for target enrichment and sequencing of 205 novel genetic markers that are tailored to phylogenomic applications in Orchidinae s.l. A subset of 31 markers capture genes putatively involved in the production of glucomannan, a water-soluble polysaccharide that gives salep its distinctive properties. We tested the kit on 73 taxa native to the area, demonstrating universally high locus recovery irrespective of species identity, that exceeds the total sequence length obtained with alternative kits currently available. Phylogenetic inference with concatenation and coalescent approaches was robust and showed high levels of support for most clades, including some which were previously unresolved. Resolution for hybridizing and recently radiated lineages remains difficult, but could be further improved by analysing multiple haplotypes and the non-exonic sequences captured by our kit, with the promise to shed new light on the evolution of enigmatic taxa with a complex speciation history. Offering a step-up from traditional barcoding and universal markers, the genome-wide custom loci targeted by Orchidinae-205 are a valuable new resource to study the evolution, systematics and trade of terrestrial orchids.
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Leese, Benjamin E.; Johannessen, Lars Erik; Schrøder-Nielsen, Audun; Mlíkovský, Jiří; Gorney, Don & Schreffler, Leon
[Show all 7 contributors for this article]
(2022).
Additions and updates to the list of specimens of Imperial Woodpecker Campephilus imperialis (Gould, 1832), including genetic analysis of a putative clutch of eggs.
Bulletin of the British Ornithologists’ Club.
ISSN 0007-1595.
142(4),
p. 491–508.
doi:
10.25226/bboc.v142i4.2022.a9.
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We present an addendum to the list of known specimens of Imperial
Woodpecker Campephilus imperialis published by Brown & Clark in 2009. The
addendum adds a total of 31 specimens, comprising 15 mounts, ten study skins,
three skeletons, two skulls and one not extant specimen, bringing the total number
to 189 specimens. It also offers clarification of some of the records presented in
Brown & Clark, as well as revisions of several specimens previously registered as
C. imperialis but later found to be of other species. The latter includes a putative
clutch of Imperial Woodpecker eggs, which was found via genetic analysis to
belong to Burrowing Owl Athene cunicularia.
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Raclariu-Manolică, Ancuţa Cristina; Anmarkrud, Jarl Andreas; Kierczak, Marcin; Rafati, Nima; Thorbek, Birgitte Lisbeth Graae & Schrøder-Nielsen, Audun
[Show all 7 contributors for this article]
(2021).
DNA Metabarcoding for Quality Control of Basil, Oregano, and Paprika.
Frontiers in Plant Science.
doi:
10.3389/fpls.2021.665618.
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Herbs and spices are some of the most vulnerable products in terms of fraud and adulteration in the food sector. Although standard analytical methods are accurate for quality control of specific lead or marker compounds, they cannot accurately assess the entire species composition of many marketed products. Complementary analytical approaches are thus often used for comprehensive screening of herbs and spices. In this study we evaluate DNA metabarcoding for the identification and authentication of 62 products, containing basil, oregano, and paprika collected from different retailers and importers in Norway. Our results show varying degrees of discrepancy between the constituent species and those listed on the product labels, despite high product authenticity. We suggest the false positives result from the sensitivity of DNA metabarcoding and filtering thresholds should be integrated into protocols to reduce false positives. Our results highlight how integrating DNA metabarcoding into the toolbox of analytical methods for quality control of fresh and/or processed plant-based food can improve product quality.
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Nowak, Michael; Pedersen, Anne Tiril Myhre; Brysting, Anne Krag; Schrøder-Nielsen, Audun; Elven, Reidar & Bjorå, Charlotte Sletten
(2020).
Testing hypotheses of hybrid origins for two seashore species of Carex section Phacocystis (Cyperaceae).
Botanical journal of the Linnean Society.
ISSN 0024-4074.
194(1),
p. 110–117.
doi:
10.1093/botlinnean/boaa030.
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Abstract Taxonomists have proposed numerous hybrid species in plants, but to gain a better understanding of the role that hybridization may play in plant diversification, such taxonomic hypotheses must be tested using genomic data. In this study, we employ ddRAD sequence data to test taxonomic hypotheses of hybrid origins in Carex salina and C. ramenskii (Carex section Phacocystis). Sequence data from multiple Norwegian and Icelandic populations of the putative hybrid and parental species were generated for hundreds of ddRAD loci. These data were used to estimate geographical structuring of genetic diversity and admixture and to explicitly test for hybrid origins using several analytical approaches. Our results indicate recurrent hybrid origins for the populations of C. salina and C. ramenskii sampled in our study and show that these populations are characterized by high interspecific heterozygosity. Our results support the idea that hybridization may indeed play an important role in the diversification of lineages of Carex and highlight the important role that clonal propagation might play in maintaining hybrid populations. Future studies focusing on a broader geographical sampling would be needed to assess if the genetic structuring in these Nordic populations reflects range-wide patterns in these hybrid lineages.
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Anthoons, Bastien; Karamichali, Ioanna; Schrøder-Nielsen, Audun; Drouzas, Andreas; Boer, Hugo de & Madesis, Panagiotis
(2020).
Metabarcoding reveals low fidelity and presence of toxic species in short chain-of-commercialization of herbal products.
Journal of Food Composition and Analysis.
ISSN 0889-1575.
doi:
10.1016/j.jfca.2020.103767.
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Kistenich, Sonja; Halvorsen, Rune; Schrøder-Nielsen, Audun; Thorbek, Birgitte Lisbeth Graae; Timdal, Einar & Bendiksby, Mika
(2019).
DNA Sequencing Historical Lichen Specimens.
Frontiers in Ecology and Evolution.
7.
doi:
10.3389/fevo.2019.00005.
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Biological specimens in natural history collections worldwide are increasingly being used in biogeographical, environmental, and taxonomic studies. For their meaningful use, correct species identification is crucial. For example, clarifying if a species is new to science requires an overview of what has already been described. This includes comparisons with existing authoritative specimens (types). Most type specimens are rather old and their DNA expected to be degraded to various extents. Comparative DNA sequence analysis is in regular use in taxonomic research of today and is essential for identifying and delimiting species. In this study, we focus on lichenized fungi (lichens), in which many species groups are highly inconspicuous and impossible to identify to species based on morphology alone. Our aim was to test the non-mutually exclusive hypotheses that DNA quality of lichens depends on (1) time since collection, (2) taxonomic affinity, and/or (3) habitat/ecology. We included two species from each of four different lichen genera (i.e., Cladonia, Nephroma, Peltigera, and Ramalina), each species pair with a different autecology. For each species, we included samples from approximately every 25 years from present to about 150 years back in time. We used a two-step PCR-based approach followed by sequencing on an Ion Torrent PGM to produce target sequences (mtSSU) of degraded DNA. We received satisfactory DNA sequence information for 54 of 56 specimens. We recovered full-length sequences for several more than 100-years-old specimens, including a 127-years-old specimen, and retrieved enough sequence information for species identification of a 150-years-old specimen. As expected, sequencing success was negatively correlated with age of the specimens. It also varied with taxonomic affinity. We found no significant correlation between sequencing success and habitat ecology of the investigated specimens. The herein tested Ion Torrent sequencing approach outperformed Sanger sequencing with regard to sequencing success and efficiency. We find the protocol used herein highly suitable for obtaining sequences from both young and old lichen specimens and discuss potential improvements to it.
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Kearns, Anna Marika; Restani, Marco; Szabo, Ildiko; Schrøder-Nielsen, Audun; Kim, Jin Ah & Richardson, Hayley M.
[Show all 10 contributors for this article]
(2018).
Genomic evidence of speciation reversal in ravens.
Nature Communications.
9(1).
doi:
10.1038/s41467-018-03294-w.
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Many species, including humans, have emerged via complex reticulate processes involving hybridisation. Under certain circumstances, hybridisation can cause distinct lineages to collapse into a single lineage with an admixed mosaic genome. Most known cases of such ‘speciation reversal’ or ‘lineage fusion’ involve recently diverged lineages and anthropogenic perturbation. Here, we show that in western North America, Common Ravens (Corvus corax) have admixed mosaic genomes formed by the fusion of non-sister lineages (‘California’ and ‘Holarctic’) that diverged ~1.5 million years ago. Phylogenomic analyses and concordant patterns of geographic structuring in mtDNA, genome-wide SNPs and nuclear introns demonstrate long-term admixture and random interbreeding between the non-sister lineages. In contrast, our genomic data support reproductive isolation between Common Ravens and Chihuahuan Ravens (C. cryptoleucus) despite extensive geographic overlap and a sister relationship between Chihuahuan Ravens and the California lineage. These data suggest that the Common Raven genome was formed by secondary lineage fusion and most likely represents a case of ancient speciation reversal that occurred without anthropogenic causes.
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Mewicha, Berihun Gebremedhin; Flagstad, Øystein; Bekele, Afework; Gelete, Desalegn Chala; Bakkestuen, Vegar & Boessenkool, Sanne
[Show all 13 contributors for this article]
(2016).
DNA metabarcoding reveals diet overlap between the endangered walia ibex and domestic goats - Implications for conservation.
PLOS ONE.
11(7),
p. 1–18.
doi:
10.1371/journal.pone.0159133.
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Human population expansion and associated degradation of the habitat of many wildlife
species cause loss of biodiversity and species extinctions. The small Simen Mountains
National Park in Ethiopia is one of the last strongholds for the preservation of a number of
afro-alpine mammals, plants and birds, and it is home to the rare endemic Walia ibex, Capra
walie. The narrow distribution range of this species as well as potential competition for
resources with livestock, especially with domestic goat, Capra hircus, may compromise its
future survival. Based on a curated afro-alpine taxonomic reference library constructed for
plant taxon identification, we investigated the diet of the Walia ibex and addressed the dietary
overlap with domestic goat using DNA metabarcoding of faecal samples. Faeces of
both species were collected from different localities in the National Park. We show that both
species are browsers, with forbs, shrubs and trees comprising the largest proportion of their
diet, supplemented by grasses. There was a considerable overlap in dietary preferences.
Several of the preferred diet items of the Walia ibex (Alchemilla sp., Hypericum revolutum,
Erica arborea and Rumex sp.) were also among the most preferred diet items of the domestic
goat. These results indicate that there is potential for competition between the two species,
especially during the dry season, when resources are limited. Our findings, in
combination with the expected increase in domestic herbivores, suggest that management
plans should consider the potential threat posed by domestic goats to ensure future survival
of the endangered Walia ibex.
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Soininen, Eeva M; Gauthier, Gilles; Bilodeau, Frederic; Berteaux, Dominique; Gielly, Ludovic & Taberlet, Pierre
[Show all 14 contributors for this article]
(2015).
Highly overlapping winter diet in two sympatric lemming species revealed by DNA metabarcoding.
PLOS ONE.
10(1).
doi:
10.1371/journal.pone.0115335.
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Sympatric species are expected to minimize competition by partitioning resources, especially when these are limited. Herbivores inhabiting the High Arctic in winter are a prime example of a situation where food availability is anticipated to be low, and thus reduced diet overlap is expected. We present here the first assessment of diet overlap of high arctic lemmings during winter based on DNA metabarcoding of feces. In contrast to previous analyses based on microhistology, we found that the diets of both collared (Dicrostonyx groenlandicus) and brown lemmings (Lemmus trimucronatus) on Bylot Island were dominated by Salix while mosses, which were significantly consumed only by the brown lemming, were a relatively minor food item. The most abundant plant taxon, Cassiope tetragona, which alone composes more than 50% of the available plant biomass, was not detected in feces and can thus be considered to be non-food. Most plant taxa that were identified as food items were consumed in proportion to their availability and none were clearly selected for. The resulting high diet overlap, together with a lack of habitat segregation, indicates a high potential for resource competition between the two lemming species. However, Salix is abundant in the winter habitats of lemmings on Bylot Island and the non-Salix portion of the diets differed between the two species. Also, lemming grazing impact on vegetation during winter in the study area is negligible. Hence, it seems likely that the high potential for resource competition predicted between these two species did not translate into actual competition. This illustrates that even in environments with low primary productivity food resources do not necessarily generate strong competition among herbivores.
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Epp, Laura; Gussarova, Galina; Boessenkool, Sanne; Olsen, J.; Haile, J & Schrøder-Nielsen, Audun
[Show all 13 contributors for this article]
(2015).
Lake sediment multi-taxon DNA from North Greenland records early post-glacial appearance of vascular plants and accurately tracks environmental changes.
Quaternary Science Reviews.
ISSN 0277-3791.
117,
p. 152–163.
doi:
10.1016/j.quascirev.2015.03.027.
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High Arctic environments are particularly sensitive to climate changes, but retrieval of paleoecological data is challenging due to low productivity and biomass. At the same time, Arctic soils and sediments have proven exceptional for long-term DNA preservation due to their constantly low temperatures. Lake sediments contain DNA paleorecords of the surrounding ecosystems and can be used to retrieve a variety of organismal groups from a single sample. In this study, we analyzed vascular plant, bryophyte, algal (in particular diatom) and copepod DNA retrieved from a sediment core spanning the Holocene, taken from Bliss Lake on the northernmost coast of Greenland. A previous multi-proxy study including microscopic diatom analyses showed that this lake experienced changes between marine and lacustrine conditions. We inferred the same environmental changes from algal DNA preserved in the sediment core. Our DNA record was stratigraphically coherent, with no indication of leaching between layers, and our cross-taxon comparisons were in accordance with previously inferred local ecosystem changes. Authentic ancient plant DNA was retrieved from nearly all layers, both from the marine and the limnic phases, and distinct temporal changes in plant presence were recovered. The plant DNA was mostly in agreement with expected vegetation history, but very early occurrences of vascular plants, including the woody Empetrum nigrum, document terrestrial vegetation very shortly after glacial retreat. Our study shows that multi-taxon metabarcoding of sedimentary ancient DNA from lake cores is a valuable tool both for terrestrial and aquatic paleoecology, even in low-productivity ecosystems such as the High Arctic.
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Queiroz, Anna Karolina Oliveira de; Gasalla, Maria A.; Laux, Marcele; Oliveira, Renato Renison Moreira; Rosa, Fabricio dos Anjos Santa & Schrøder-Nielsen, Audun
[Show all 10 contributors for this article]
(2024).
Dietary metabarcoding of keystone sardine species reveals the importance of their ichthyoplankton prey in food webs of the Southern Brazilian Bight fisheries.
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Sajid, Uswa; BATISTA-MORALES, Angelica Maria; Rocha, Lilith Lopes; Rosa, Fabricio dos Anjos Santa; Queiroz, Anna Karolina Oliveira de & Ribas, Talita Fernanda Augusto
[Show all 11 contributors for this article]
(2024).
Evaluating the diet diversity of the Whitemouth Croaker: A comparison between traditional methods and DNA metabarcoding.
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Published
Aug. 9, 2013 11:32 AM
- Last modified
Sep. 13, 2022 1:13 PM
