| 1. |
- Capo, Eric, et al.
(författare)
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Droplet digital PCR applied to environmental DNA, a promising method to estimate fish population abundance from humic-rich aquatic ecosystems
- 2021
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Ingår i: Environmental DNA. - : John Wiley & Sons. - 2637-4943. ; 3:2, s. 343-352
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Tidskriftsartikel (refereegranskat)abstract
- Measures of environmental DNA (eDNA) concentrations in water samples have the potential to be both a cost-efficient and a nondestructive method to estimate fish population abundance. However, the inherent temporal and spatial variability in abiotic and biotic conditions in aquatic systems have been suggested to be a major obstacle to determine relationships between fish eDNA concentrations and fish population abundance. Moreover, once water samples are collected, methodological biases are common, which introduces additional sources of variation to potential relationships between eDNA concentrations and fish population abundance. Here, we evaluate the performance of applying the droplet digital PCR (ddPCR) method to estimate fish population abundance in experimental enclosures. Using large-scale enclosure ecosystems that contain populations of nine-spined stickleback (Pungitius pungitius), we compared the concentrations of fish eDNA (COI mitochondrial region, 134 bp) obtained with the ddPCR method with high precision estimates of fish population abundance (i.e., number of individuals) and biomass. To evaluate the effects of contrasted concentrations of humic substances (potential PCR inhibitors) on the performance of ddPCR assays, we manipulated natural dissolved organic carbon (DOC) concentrations (range 4–11 mg/L) in the enclosures. Additionally, water temperature (+2°C) was manipulated in half of the enclosures. Results showed positive relationships between eDNA concentration and fish abundance and biomass estimates although unexplained variation remained. Still and importantly, fish eDNA estimates from high DOC enclosures were not lowered by potential inhibitory effects with our procedure. Finally, water temperature (although only 2°C difference) was neither detected as a significant factor influencing fish eDNA estimates. Altogether, our work highlights that ddPCR-based eDNA is a promising method for future quantification of fish population abundance in natural systems.
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| 2. |
- Capo, Eric, et al.
(författare)
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Lake sedimentary dna research on past terrestrial and aquatic biodiversity: Overview and recommendations
- 2021
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Ingår i: Quaternary. - : MDPI. - 2571-550X. ; 4:1
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Forskningsöversikt (refereegranskat)abstract
- The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.
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| 3. |
- Englund, Göran, 1957-, et al.
(författare)
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Holocene extinctions of a top predator : effects of time, habitat area and habitat subdivision
- 2020
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Ingår i: Journal of Animal Ecology. - : John Wiley & Sons. - 0021-8790 .- 1365-2656. ; 89:5, s. 1202-1215
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Tidskriftsartikel (refereegranskat)abstract
- Loss of habitat and changes in the spatial configuration of habitats are major drivers of species extinctions, but the responses to these drivers differ between organisms. To advance theory on how extinction risk from different types of habitat alteration relates to species-specific traits, there is a need for studies of the long-term extinction dynamic of individual species. The goal of this study was to quantify how habitat area and the spatial configuration of habitats affect extinction rate of an aquatic top predator, the northern pike Esox lucius L. We recorded the presence/absence of northern pike in 398 isolated habitat fragments, each one consisting of a number of interconnected lakes. Time since isolation of the habitat fragments, caused by cut-off from the main dispersal source in the Baltic Sea, varied between 0 and 10,000 years. Using survival regression, we analysed how pike population survival was affected by time since isolation, habitat size and habitat subdivision. The approach builds on the assumptions that pike colonized all fragments before isolation and that current absences result from extinctions. We verified these assumptions by testing (a) if pike was present in the region throughout the entire time period when the lakes formed and (b) if pike typically colonize lakes that are formed today. We also addressed the likelihood that unrecorded anthropogenic introductions could bias our estimates of extinction rate. Our results supported the interpretation that current patterns of presence/absence in our study system are shaped by extinctions. Further, we found that time since isolation and fragment area had strong effects on pike population survival. In contrast, spatial habitat subdivision (i.e. if a fragment contained few large lakes or many small lakes) and other environmental covariates describing climate and productivity were unrelated to pike survival. Over all, extinction rate was high in young fragments and decreased sharply with increasing fragment age. Our study demonstrates how the link between extinction rate and habitat size and spatial structure can be quantified. More similar studies may help us find generalizations that can guide management of habitat size and connectivity.
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| 4. |
- Kanbar, Hussein Jaafar, et al.
(författare)
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Geochemical identification of potential DNA-hotspots and DNA-infrared fingerprints in lake sediments
- 2020
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Ingår i: Applied Geochemistry. - : Elsevier. - 0883-2927 .- 1872-9134. ; 122
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Tidskriftsartikel (refereegranskat)abstract
- DNA preserved in sedimentary materials can be used to study past ecosystem changes, such as species' colonization and extinction. It is believed that minerals, especially clay minerals, enhance the preservation of DNA. However, the role of minerals, as well as organic matter, on DNA sorption in heterogeneous sediments is still not clear. In this study, we examined the effect of mineral and organic matter on DNA binding in lake sediments. Bulk and size-fractionated sediments (0–4, 4–16, 16–64, and >64 μm), having different mineral and organic composition, were used to test DNA sorption; similar experiments were also run after the removal of sedimentary organic matter. Additionally, diffuse reflectance infrared spectroscopy (DRIFT) was used to determine the chemical changes caused by DNA sorption and subsequently produce a DNA-infrared (IR) fingerprint. Clay minerals were the main minerals to sorb DNA in the different samples. Moreover, mica promoted DNA sorption in all size fractions, while chlorite promoted DNA sorption in size fractions greater than 16 μm; clay-mineral and organo-mineral complexes caused a preference of certain clay minerals over others. Sedimentary organic matter affected DNA sorption by covering as well as by amplifying potential DNA binding sites, yet DNA sorption did not change significantly. DNA sorption showed IR spectral modifications mainly at ~1640, 1416, and 1231 cm−1. Interestingly, the DNA-IR fingerprint in the heterogeneous sediments was evident by those peaks after spectral subtraction. Finally, we proposed a simple model, based on sediment geochemistry, that can be used to determine potential DNA-hotspots in sediments.
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| 5. |
- Kanbar, Hussein Jaafar, et al.
(författare)
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Tracking mineral and geochemical characteristics of Holocene lake sediments : the case of Hotagen, west-central Sweden
- 2021
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Ingår i: Journal of Soils and Sediments. - : Springer. - 1439-0108 .- 1614-7480. ; 21:9, s. 3150-3168
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Intact lake sediments reflect the development of terrestrial ecosystems. This development can be understood by decoding mineral and geochemical information of sedimentary archives. Therefore, we characterized a Holocene lake sediment core and revealed bulk to micro-scale variations via a combination of geochemical techniques and statistical methods.Methods: A 2.3 m sediment core was collected from Hotagen, a lake in west-central Sweden; a sediment sample was collected every 5 cm. A part of each sediment sample was kept untreated (named bulk) and another part was size-fractionated into < 4, 4–16, 16–64, and > 64 µm subsamples. Characterization was then made with respect to grain size distribution (GSD), physico-chemical parameters, geochemical properties, organic composition, and mineralogy. The sediments were investigated at bulk, micro-, and elemental scales using powder X-ray diffraction (XRD), diffuse reflectance infrared Fourier transform spectroscopy (DRIFT), and scanning electron microscopy coupled to energy-dispersive X-ray spectroscopy (SEM–EDX).Results: The deepest sediment was identified as glacial till dating back to the Late Pleistocene. The bulk sediments showed a clear distinction between 0–195 cm (unit 1, U1) and 200–225 cm (unit 2, U2) depths. Quartz and feldspar minerals decreased and organic matter and clay minerals increased from the till towards the lower limit of U1. The development in the sedimentary properties marked the transformation of the terrestrial ecosystem from glacier-covered land to vegetated areas. This development was also well reflected by the appearance of X-ray amorphous materials and the formation of distinct organo-mineral aggregates; chlorite was the predominant clay mineral in these aggregates. The geochemical variation between U2 and U1 sediments was further established by resolving the DRIFT spectral components through multivariate curve resolution alternating least square (MCR-ALS). The U1 sediments settled over a period of ~ 7500 years and showed comparable mineral, geochemical, and organic composition. However, the size-fractionated sediments, mainly < 4 µm, showed diverse mineral and geochemical composition. Indeed, these sediments were distinct by containing relatively higher amounts of X-ray amorphous materials and clay minerals, the latter had variable Na, Mg, and K contents.Conclusion: The combined use of geochemical and statistical approaches used in this study followed the mineral and geochemical development of sediments that had settled during the Late Pleistocene and Early Holocene Epochs. Finally, the U2 sediments marked the terrestrial ecosystem development that occurred during the late glaciation, deglaciation, and post-glaciation periods. Graphical abstract: [Figure not available: see fulltext.]
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| 6. |
- Olajos, Fredrik, et al.
(författare)
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Consistent findings from ddPCR and metabarcoding analyses of piscivorous bird diets
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The diet of apex predators is crucial for addressing fundamental ecological questions. The diets ofpiscivorous birds have traditionally been studied using invasive methods that may be harmful.Consequently, researchers have been compelled to explore alternative options. Molecular toolshave proven effective in discerning dietary preferences of piscivorous birds. In this study, a totalof 151 faecal samples were collected from 6 bird species of lacustrine piscivorous birds occupying36 lakes from 2018 to 2022. Faecal samples were analysed using two molecular methods todetermine the proportion of fish DNA using 1) high-throughput sequencing metabarcoding withthe teleo-2 universal fish primer and 2) a digital droplet PCR array with 7 species-specific newlydesigned primers targeting the most common prey fish species in Scandinavian freshwaterecosystems. The dominant prey species identified by both methods were: whitefish (Coregonuslavaretus), Eurasian perch (Perca fluviatilis) and Eurasian minnow (Phoxinus phoxinus). The twomethods showed a high degree of agreement, suggesting that they both provide accurateassessments of the dietary compositions of bird diets.
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| 7. |
- Olajos, Fredrik, et al.
(författare)
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Estimating species colonization dates using DNA in lake sediment
- 2018
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Ingår i: Methods in Ecology and Evolution. - : British Ecological Society. - 2041-210X. ; 9:3, s. 535-543
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Tidskriftsartikel (refereegranskat)abstract
- Detection of DNA in lake sediments holds promise as a tool to study processes like extinction, colonization, adaptation and evolutionary divergence. However, low concentrations make sediment DNA difficult to detect, leading to high false negative rates. Additionally, contamination could potentially lead to high false positive rates. Careful laboratory procedures can reduce false positive and negative rates, but should not be assumed to completely eliminate them. Therefore, methods are needed that identify potential false positive and negative results, and use this information to judge the plausibility of different interpretations of DNA data from natural archives.We developed a Bayesian algorithm to infer the colonization history of a species using records of DNA from lake-sediment cores, explicitly labelling some observations as false positive or false negative. We illustrate the method by analysing DNA of whitefish (Coregonus lavaretus L.) from sediment cores covering the past 10,000 years from two central Swedish lakes. We provide the algorithm as an R-script, and the data from this study as example input files.In one lake, Stora Lögdasjön, where connectivity with the proto-Baltic Sea and the degree of whitefish ecotype differentiation suggested colonization immediately after deglaciation, DNA was indeed successfully recovered and amplified throughout the post-glacial sediment. For this lake, we found no loss of detection probability over time, but a high false negative rate. In the other lake, Hotagen, where connectivity and ecotype differentiation suggested colonization long after deglaciation, DNA was amplified only in the upper part of the sediment, and colonization was estimated at 2,200 bp based on the assumption that successful amplicons represent whitefish presence. Here the earliest amplification represents a false positive with a posterior probability of 41%, which increases the uncertainty in the estimated time of colonization.Complementing careful laboratory procedures aimed at preventing contamination, our method estimates contamination rates from the data. By combining these results with estimates of false negative rates, our models facilitate unbiased interpretation of data from natural DNA archives.
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| 8. |
- Olajos, Fredrik, et al.
(författare)
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Fish colonization patterns in central Sweden from dropletdigital PCR and shotgun sequencing of sedimentary DNA
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The natural establishment of Scandinavian fish populations took place following the lastdeglaciation 9,000 to 12,000 years ago when the retreating ice exposed new habitats. Accessibilityof lakes from the Proto-Baltic sea and the southern freshwater habitats was influenced by theirelevation relative to the post-glacial coastline, with some lakes being unreachable due to migrationbarriers. Long standing hypotheses regarding colonization routes have been formulated based onmodern distribution patterns, knowledge of historic climate variations, and species’ tolerances toenvironmental conditions. These hypotheses have not been tested with other forms of evidencebecause long-term data on past fish histories are limited. In this study, the colonization history ofseveral fish species was investigated using historical data combined with analyses of sedimentaryDNA from Lake Hotagen in central Sweden which is located above the post-glacial coastline.DNA was analyzed with droplet digital PCR (ddPCR) and metagenomic shotgun sequencingapproaches. The ddPCR array used specific primers of seven species known to have beenhistorically present at the lake, and successfully detected 5/7 species in the top 80 cm (~3000 years)of the sediment core where DNA was best preserved. Metagenomics however detected 6/8expected genera in all sediment samples dating back 7000 years. Based on our findings, we inferthat 1) (dd)PCR based methods had too low sensitivity to allow consistent detection of fish inancient samples and 2) metagenomics, while sufficiently sensitive, require expanded databases toincrease granularity across species, especially those who are currently underrepresented. 3) Mostfish species likely colonized lake Hotagen soon after the last deglaciation despite the presence ofmigration barriers.
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| 9. |
- Olajos, Fredrik, 1987-
(författare)
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Using environmental DNA to unravel aquatic ecosystem dynamics
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Human-induced climate change has led to unprecedented declines in Earth's biodiversity and significant habitat loss. Aquatic ecosystems areespecially at risk, facing pollution, overexploitation, and destruction. Consequently, monitoring biodiversity is critical. Traditional monitoring methods are often low in detection rates, time-consuming, invasive, and harmful to species, which hampers comprehensive biodiversity assessments. Environmental DNA (eDNA) offers a rapid alternative fortaxonomic identification, extracting genetic material from soil, sediments, or water without capturing living organisms, proving useful where traditional methods fall short. However, its integration into aquatic ecology is hampered by unresolved methodological issues.This thesis demonstrates how eDNA can help reconstruct fish colonization histories in lakes post-glacial retreat. I employed species-specific primers with digital droplet PCR and metagenomic shotgun sequencing on ancient DNA from Holocene lake sediments. My findings show the detectability of DNA from ancient fish populations. However, each method exhibited technical limitations that led to varying degrees offalse negatives and false positive results. Additionally, I examined how Northern pike (Esox Lucius) affects ecological speciation in Europeanwhitefish (Coregonus lavaretus), promoting a shift from insectivorous to piscivorous states, enhancing predator biodiversity and biomass. Dietan alyses of piscivorous birds through digital droplet PCR revealed that smaller whitefish support a larger, more diverse bird community. Finally, I compared two molecular techniques for quantifying bird diets from fecal DNA, finding that metabarcoding with a universal fish primer and digital droplet PCR yielded similar results. This research enhances ourunderstanding of the potential and limitations of molecular tools forspecies identification and aids the integration of eDNA into aquatic ecology.
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| 10. |
- Öhlund, Gunnar, et al.
(författare)
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Apex predator induces predator-rich ecosystem state innorthern lakes
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Large predators are disappearing from ecosystems around the world. If predator speciesfacilitate each other’s existence through niche construction, this development could causecascading predator collapses and reduce ecosystem resilience. However, the importance offacilitation for the assembly and function of predator communities remains poorly understood.Here, we show that a large piscivorous fish, the northern pike (Esox lucius), enables theformation of a numerous and diverse predator community by inducing a dwarf ecotype ofEuropean whitefish (Coregonus lavaretus). Pike increases the standing biomass of prey-sized(<200mm) whitefish with a factor of 12.6, allowing small-gaped fish species (Percafluviatilis, Lota lota, Salvelinus alpinus and Salmo trutta) to go from small-growinggeneralists, to large-growing piscivores. Similarly, a guild of piscivorous birds (Gavia arctica,G. stellata, Sterna paradisaea, S. hirundo, Mergus serrator and M. merganser) shift from amixed diet to relying mainly on whitefish prey in presence of pike. Through this regime shift,the functional piscivore biomass in the non-pike fish community increases with a factor of14.2, and the density- and species richness of piscivorous birds increase with factors of 2.08and 2.16, respectively. Our results demonstrate how feedbacks between presence/absence ofimportant predators and the phenotype of prey may keep complex ecosystems in predator-richor predator-depleted states.
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