12 research outputs found
Comparative genomics and signatures of selection in North Atlantic eels
No full textComparative genomic approaches can identify putative private and shared signatures of selection. We performed a comparative genomic study of North Atlantic eels, European eel (Anguilla Anguilla) and American eel (A. rostrata). The two sister species are nearly undistinguishable at the phenotypic level and despite a wide non-overlapping continental distribution, they spawn in partial sympatry in the Sargasso Sea. Taking advantage of the newly assembled and annotated genome, we used genome wide RAD sequencing data of 359 individuals retrieved from Sequence Nucleotide Archive and state-of-the-art statistic tests to identify putative genomic signatures of selection in North Atlantic eels. First, using the FST and XP-EHH methods, we detected apparent islands of divergence on a total of 7 chromosomes, particularly on chromosomes 6 and 10. Gene ontology analyses suggested candidate genes mainly related to energy production, development and regulation, which could reflect strong selection on traits related to eel migration and larval duration time. Gene effect prediction using SNPeff showed a high number of SNPs in noncoding regions, pointing to a possible regulatory role. Second, using the iHS method we detected shared regions under selection on a total of 11 chromosomes. Several hypotheses might account for the detection of shared islands of selection in North Atlantic eels, including parallel evolution due to adaptation to similar environments and introgression. Future comparative genomic studies will be needed to further clarify the causes and consequences of introgression, including the directionality of these introgression events
Kortlægning af udbredelsen af krebs og krebsepest i danske ferske vande
No full textDenne rapport beskriver resultaterne af en landsdækkende kortlægning af udbredelsen af krebs og krebsepest i Danmarks ferske vande. Projektet er udført i perioden 1. maj 2020 til 1. december 2021.Den primære undersøgelsesmetode, der er anvendt, er indsamling af vandprøver, som er blevet filtrerede og konserverede på stedet. Filtratet er efterfølgende anvendt til analyse for forekomst af DNA – såkaldt miljø-DNA eller eDNA – fra krebs og krebsepest. Der er indsamlet vandprøver fra vandløb og de dertil knyttede søer i hele landet inkl. otte større øer, hvor der findes væsentlige vandløb: Mors, Als, Ærø, Langeland, Lolland, Falster, Møn og Bornholm. Gennem analyse af disse indsamlede prøver, er udbredelsen af krebs og krebsepest på landsplan beskrevet. Herudover er der udført en mere detaljeret indsamling af vandprøver fra både vandløb og store samt små søer på fem udvalgte øer: Samsø, Als, Ærø, Langeland og Møn, for dels at beskrive omfanget af forekomst af krebs i Danmarks mange småsøer og dels at vurdere om en eller flere af de undersøgte øer egner sig som såkaldt safesite eller ”reservat” for flodkrebs (Astacus astacus). Ud af Danmarks ca. 900 selvstændige vandløb, blev det valgt at undersøge alle de vandløb, der har et hovedløb på mindst 10 km længde, for dem der er længere end 20 km med én prøve pr. 10 km. For kortere vandløb blev 50 % af dem, der har en længde mellem 5 og 10 km undersøgt samt 20 % af vandløbene med længde mellem 2 og 5 km. Vandløb < 2 km blev ikke undersøgt. Den anvendte teststrategi for de indsamlede prøver er følgende: alle de indsamlede prøver er blevet testet for forekomst af tre arter af ferskvandskrebs: flodkrebs, signalkrebs (Pacifastacus leniusculus) og galizisk sumpkrebs (Astacus leptodactylus). Alle prøver, der blev fundet positive for krebs, er efterfølgende blevet testet for forekomsten af krebsepest (Aphanomyces astaci), idet krebsepest er en obligat parasit, der ikke kan forventes at forekomme i vandområder uden en bestand af krebs, der kan være vært for parasitten. Endelig er en række udvalgte prøver fra vandløb blevet testet for forekomst af marmorkrebs (Procambarus virginalis) og Louisiana flodkrebs (Procambarus clarkii). I alt blev 838 stationer besøgt, heraf 635 beliggende i vandløb og 203 beliggende i søer. Det resulterede i indsamling af 768 prøver, hvor mellem 0,5 og 5 l vand blev filtreret. På en del stationer var mængden af partikler i vandet så stor, at filteret stoppede til inden målet på 5 l var nået. På 70 stationer var det slet ikke muligt at indsamle vandprøve, enten grundet udtørring eller fordi intensiv algevækst umuliggjorde filtrering fuldstændigt. I nogle tilfælde kunne der vælges et alternativ til udtørrede søer, mens det ikke var tilfældet for vandløb, idet de udtørrede vandløb primært var beliggende på Møn og Bornholm, hvor samtlige vandløb blev undersøgt. Analyse af de indsamlede vandprøver resulterede i sikker detektion af flodkrebs på 57 stationer beliggende i 35 vandsystemer, heraf 2 beliggende i søer, begge på Møn. Signalkrebs blev fundet på 106 stationer beliggende i 49 vandsystemer, heraf 3 beliggende i søer på Als. Galizisk sumpkrebs blev kun fundet på 6 stationer i 5 vandsystemer, 4 beliggende på Sjælland og én på Lolland. Krebsepest blev konstateret på 54 stationer beliggende i 21 vandsystemer. Der blev ikke konstateret forekomst af hverken marmorkrebs eller Louisiana flodkrebs i de 192 prøver, der blev analyseret for disse to arter.Generelt har det været muligt at påvise forekomst af krebs på lokaliteter, hvor der i forvejen var kendt forekomst af en af de tre fundne arter. Det kan derfor konkluderes, at eDNA er en velegnet metode til kortlægning af udbredelse af krebs og krebsepest i ferske vande. Kortlægningen har vist, at signalkrebs findes udbredt over hele landet og i dag må betegnes som den mest udbredte art af ferskvandskrebs i Danmark. Flodkrebs findes også i alle landsdele, men en del bestande er under pres fra signalkrebs og/eller krebsepest. For den galiziske sumpkrebs vedkommende, er udbredelsen primært afgrænset til Sjælland. Krebsepest findes udbredt over hele landet, primært i forbindelse med forekomst af signalkrebs
Den sjældne, danske fisk med den markante snude er en gammel, ganske særlig fisk. Det konkluderer et nyt studie, som DTU Aqua har deltaget i, trykt i tidsskriftet Molecular Ecology.
No full textSnæblen er en helt unik fisk i den danske natur – den sidste naturlige bestand, der er tilbage i Danmark, findes i Vidå i Sønderjylland, og så er snæblen nu ekstra særlig, idet spritny forskning slår fast, at den sølvblanke, slanke fisk af laksetypen, som man indtil nu har ment delte gener med fisken helt indtil for ca. 2.000 år siden, i virkeligheden udviklede sin egen genetiske linje for helt op til 7.500 år siden
WINDNA:eDNA based solutions for biodiversity monitoring at offshore wind farms
No full textThe transition towards renewable energy may have substantial impact on marine ecosystems in the near future. Wind energy is planned to expand by a factor 10 in the North Sea region alone by 2050. The ambitious political objectives seek to shift from a "no net loss" (NNL) to a "marine net gain" (MNG) approach when licensing projects. Hence, there is a pressing need to document the impact of offshore wind on marine biodiversity. However, traditional methods are costly, labor-intensive, and lack both taxonomic and spatio-temporal resolution. The "WINDNA" project will evaluate the potential of environmental DNA (eDNA) and aim to provide new cost-effective and comprehensive marine biodiversity data. Key aspects involve examining the spatial and temporal scales of marine biodiversity using traditional water sampling by boat as well as an offshore-deployed automated environmental sample processor and an autonomous underwater vehicle (ESP2 and ESP3). Furthermore, "WINDNA" focuses on monitoring biodiversity changes during the early stages of artificial reef succession. The "WINDNA" project provides a pragmatic approach, aligning with environmental and political goals contributing to the sustainable growth of renewable energy while prioritizing positive biodiversity impact. The presentation will include preliminary data
Using eDNA to estimate biomass of bycatch in pelagic fisheries
No full textAbstract In recent years, the analysis of environmental DNA (eDNA) has significantly improved, allowing for high‐resolution species identification and possible biomass quantification from water samples. Fisheries management typically requires monitoring of catches, including precise information about bycatch quantities to make sound assessments of exploitation rates. Bycatch assessment is particularly challenging in large catches (>500 T), and the current practice of visual assessment of subsampled catches is time‐consuming, requires extensive labor, and often has low precision. We explored the feasibility for applying eDNA‐based methods for studying catch composition using the pelagic North Sea herring fishery with bycatch of mackerel as a case. First, we experimentally simulate a series of catches using a range of herring and mackerel weight proportions to establish relationships under real fisheries scenarios. The relationship is subsequently used to estimate the biomass of mackerel bycatch from eDNA from three herring catches, by sampling and comparing processing water both onboard ships and at the processing factory. All samples are analyzed using species‐specific quantitative PCR (qPCR). The experiments reveled a strong correlation between DNA and weight fractions characterized by a constant overrepresentation of mackerel DNA compared to expected mackerel weight. We found that eDNA‐based and visual methods applied to the same landing reflect the within catch variability in species composition alike, however, the methods can show disparity in total estimates of mackerel biomass. Accounting for haul mixing within total landed catches increases the precision of the factory and ship eDNA‐based estimates for the same catch. We show that eDNA‐based bycatch estimates provide coherent quantitative data, and likely improve quality and reduce costs of collecting fisheries‐dependent data and thereby contribute to securing sustainable fisheries
eDNA based bycatch assessment in pelagic fish catches
No full textAbstract Pelagic fish like herring, sardines, and mackerel constitute an essential and nutritious human food source globally. Their sustainable harvest is promoted by the application of precise, accurate, and cost-effective methods for estimating bycatch. Here, we experimentally test the new concept of using eDNA for quantitative bycatch assessment on the illustrative example of the Baltic Sea sprat fisheries with herring bycatch. We investigate the full pipeline from sampling of production water on vessels and in processing factories to the estimation of species weight fractions. Using a series of controlled mixture experiments, we demonstrate that the eDNA signal from production water shows a strong, seasonally consistent linear relationship with herring weight fractions, however, the relationship is influenced by the molecular method used (qPCR or metabarcoding). In four large sprat landings analyzed, despite examples of remarkable consistency between eDNA and visual reporting, estimates of herring bycatch biomass varied between the methods applied, with the eDNA-based estimates having the highest precision for all landings analyzed. The eDNA-based bycatch assessment method has the potential to improve the quality and cost effectiveness of bycatch assessment in large pelagic fisheries catches and in the long run lead to more sustainable management of pelagic fish as a precious marine resource
Nanopore environmental DNA sequencing of catch water for estimating species composition in demersal bottom trawl fisheries
No full textBycatch and discards, representing unwanted catches, undermine sustainable fisheries and hinder the conservation of vulnerable and endangered species. To effectively monitor bycatch and enhance the effectiveness of management measures while promoting sustainable fishing practices, reliable data is essential. Here, we explore the use of Nanopore metabarcoding to analyze the catch composition in demersal bottom fisheries. We collected eDNA samples directly from an onboard catch holding tank (catch water) for 10 fishing hauls from a fishing vessel operating in the Skagerrak (North-East Atlantic). The approach involved sequencing a combination of long (~2 kb) and short (~170–313 bp) mitochondrial amplicons and was validated by analyzing a fishery-related mock community sample and fishing haul replicates. Overall, the detection rate accuracy was 95\% for landed species, and replicates obtained from the same fishing haul showed consistent results, validating the robustness of this approach. The detection rate accuracy for all caught species observed on board (including the non-landed fraction) was 81\%. Undetected species were always limited to species in low abundance, but may also be attributed to problems with identifying closely related species due to the impact of sequencing errors and limited diagnostic variation in the genetic regions used. In the future, such biases may be reduced by using additional markers to increase species discrimination power and applying newly available technological advantages in flow cell chemistry to improve sequencing accuracy. In conclusion, this study demonstrates the effectiveness of Nanopore eDNA sequencing of catch water for estimating species composition in demersal bottom trawl fisheries, including catches of non-commercial and threatened and vulnerable species, without disrupting fishing activities. Incorporating eDNA analysis of catch water may therefore help facilitate effective monitoring, leading to better-informed fisheries management, biodiversity conservation efforts, and the implementation of relevant legislation such as the EU landing obligation.JRC.D.2 - Ocean and Wate
Nanopore environmental DNA sequencing of catch water for estimating species composition in demersal bottom trawl fisheries
No full textBycatch and discards, representing unwanted catches, undermine sustainable fisheries and hinder the conservation of vulnerable and endangered species. To effectively monitor bycatch and enhance the effectiveness of management measures while promoting sustainable fishing practices, reliable data is essential. Here, we explore the use of Nanopore metabarcoding to analyze the catch composition in demersal bottom fisheries. We collected eDNA samples directly from an onboard catch holding tank (catch water) for 10 fishing hauls from a fishing vessel operating in the Skagerrak (North-East Atlantic). The approach involved sequencing a combination of long (~2 kb) and short (~170–313 bp) mitochondrial amplicons and was validated by analyzing a fishery-related mock community sample and fishing haul replicates. Overall, the detection rate accuracy was 95% for landed species, and replicates obtained from the same fishing haul showed consistent results, validating the robustness of this approach. The detection rate accuracy for all caught species observed on board (including the non-landed fraction) was 81%. Undetected species were always limited to species in low abundance, but may also be attributed to problems with identifying closely related species due to the impact of sequencing errors and limited diagnostic variation in the genetic regions used. In the future, such biases may be reduced by using additional markers to increase species discrimination power and applying newly available technological advantages in flow cell chemistry to improve sequencing accuracy. In conclusion, this study demonstrates the effectiveness of Nanopore eDNA sequencing of catch water for estimating species composition in demersal bottom trawl fisheries, including catches of non-commercial and threatened and vulnerable species, without disrupting fishing activities. Incorporating eDNA analysis of catch water may therefore help facilitate effective monitoring, leading to better-informed fisheries management, biodiversity conservation efforts, and the implementation of relevant legislation such as the EU landing obligation
Monitoring of environmental DNA from nonindigenous species of algae, dinoflagellates and animals in the North East Atlantic
No full textMonitoring the distribution of marine non-indigenous species is a challenging task. To support this monitoring, we developed and validated the specificity of 12 primer-probe assays for detection of environmental DNA (eDNA) from marine species all non-indigenous to Europe. The species include sturgeons, a Pacific red algae, oyster thief, a freshwater hydroid from the Black Sea, Chinese mitten crab, Pacific oyster, warty comb jelly, sand gaper, round goby, pink salmon, rainbow trout and North American mud crab. We tested all assays in the laboratory, on DNA extracted from both the target and non-target species to ensure that they only amplified DNA from the intended species. Subsequently, all assays were used to analyse water samples collected at 16 different harbours across two different seasons during 2017. We also included six previously published assays targeting eDNA from goldfish, European carp, two species of dinoflagellates of the genera Karenia and Prorocentrum, two species of the heterokont flagellate genus Pseudochattonella. Conventional monitoring was carried out alongside eDNA sampling but with only one sampling event over the one year. Because eDNA was relatively fast and easy to collect compared to conventional sampling, we sampled eDNA twice during 2017, which showed seasonal changes in the distribution of non-indigenous species. Comparing eDNA levels with salinity gradients did not show any correlation. A significant correlation was observed between number of species detected with conventional monitoring methods and number of species found using eDNA at each location. This supports the use of eDNA for surveillance of the distribution of marine non-indigenous species, where the speed and relative easy sampling in the field combined with fast molecular analysis may provide advantages compared to conventional monitoring methods. Prior validation of assays increases taxonomic precision, and laboratorial setup facilitates analysis of multiple samples simultaneously. The specific eDNA assays presented here can be implemented directly in monitoring programmes across Europe and potentially worldwide to infer a more precise picture of the dynamics in the distribution of marine non-indigenous species
