Jens Carlsson
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View article: Basking sharks (Cetorhinus maximus) in the Northeast Atlantic show high occurrence of parasitism by sea lamprey (Petromyzon marinus)
Basking sharks (Cetorhinus maximus) in the Northeast Atlantic show high occurrence of parasitism by sea lamprey (Petromyzon marinus) Open
Sea lamprey ( Petromyzon marinus ) are anadromous fish that spend one to two years as haematophagous ectoparasites in marine environments. This study provides the first quantitative insight into their feeding phase, which remains poorly un…
View article: Comparing Genome Sequencing Methods to Reconstruct the Spread of Piscine Myocarditis Virus in Ireland
Comparing Genome Sequencing Methods to Reconstruct the Spread of Piscine Myocarditis Virus in Ireland Open
Piscine myocarditis virus (PMCV), a double‐stranded RNA virus, is the causative agent of cardiomyopathy syndrome (CMS) in Atlantic salmon Salmo salar , which was first reported in Ireland in 2012. PMCV continues to be a disease threat to A…
View article: Ancient sedimentary DNA reveals a more biodiverse ancient Ireland.
Ancient sedimentary DNA reveals a more biodiverse ancient Ireland. Open
The island of Ireland has been highlighted as one of the most nature depleted areas on Earth1, however it has significant potential for largescale nature restoration2. However, there remains uncertainty around which species naturally colon…
View article: Rise of the Cybercrabs: how digital cloning in an integrated taxonomic framework can support deep-sea exploration
Rise of the Cybercrabs: how digital cloning in an integrated taxonomic framework can support deep-sea exploration Open
Taxonomy has been a labour-intensive field of expertise based on hours of manual work and lengthy comments that are mainly bound to books and publications on a two-dimensional world. But every species described is a three-dimensional organ…
View article: Potential origins of fish toti-like viruses in invertebrates
Potential origins of fish toti-like viruses in invertebrates Open
The virus family Totiviridae had originally been considered to include only viruses which infected fungal and protist hosts, but since 2006 a growing number of viruses found in invertebrates and fish have been shown to cluster phylogenetic…
View article: The bacterial hitchhiker’s guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind
The bacterial hitchhiker’s guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind Open
Environmental DNA (eDNA) metabarcoding from water samples has, in recent years, shown great promise for biodiversity monitoring. However, universal primers targeting the cytochrome oxidase I ( COI ) marker gene popular in metazoan studies …
View article: A baseline for the genetic stock identification of Atlantic herring, <i>Clupea harengus</i>, in ICES Divisions 6.a, 7.b–c
A baseline for the genetic stock identification of Atlantic herring, <i>Clupea harengus</i>, in ICES Divisions 6.a, 7.b–c Open
Atlantic herring in ICES Divisions 6.a, 7.b-c comprises at least three populations, distinguished by temporal and spatial differences in spawning, which have until recently been managed as two stocks defined by geographic delineators. Outs…
View article: Farrell_et_al_6a_herring_baseline_ESM_tables_figures from A baseline for the genetic stock identification of Atlantic herring, <i>Clupea harengus</i>, in International Council for Exploration of the Sea Divisions 6.a, 7.b–c
Farrell_et_al_6a_herring_baseline_ESM_tables_figures from A baseline for the genetic stock identification of Atlantic herring, <i>Clupea harengus</i>, in International Council for Exploration of the Sea Divisions 6.a, 7.b–c Open
ESM Tables and Figures
View article: Farrell_et_al_6a_herring_baseline_ESM_tables_figures from A baseline for the genetic stock identification of Atlantic herring, <i>Clupea harengus</i>, in ICES Divisions 6.a, 7.b–c
Farrell_et_al_6a_herring_baseline_ESM_tables_figures from A baseline for the genetic stock identification of Atlantic herring, <i>Clupea harengus</i>, in ICES Divisions 6.a, 7.b–c Open
ESM Tables and Figures
View article: The bacterial hitchhiker’s guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind
The bacterial hitchhiker’s guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind Open
Environmental DNA (eDNA) metabarcoding from water samples has, in recent years, shown great promise for biodiversity monitoring. However, universal primers targeting the cytochrome oxidase I (COI) marker gene popular in metazoan studies ha…
View article: Supplementary material 1 from: Zafeiropoulos H, Gargan L, Hintikka S, Pavloudi C, Carlsson J (2021) The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data. Metabarcoding and Metagenomics 5: e69657. https://doi.org/10.3897/mbmg.5.69657
Supplementary material 1 from: Zafeiropoulos H, Gargan L, Hintikka S, Pavloudi C, Carlsson J (2021) The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data. Metabarcoding and Metagenomics 5: e69657. https://doi.org/10.3897/mbmg.5.69657 Open
The mitochondrial cytochrome C oxidase subunit I gene (COI) is commonly used in environmental DNA (eDNA) metabarcoding studies, especially for assessing metazoan diversity. Yet, a great number of COI operational taxonomic units (OTUs) or/a…
View article: Supplementary material 4 from: Zafeiropoulos H, Gargan L, Hintikka S, Pavloudi C, Carlsson J (2021) The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data. Metabarcoding and Metagenomics 5: e69657. https://doi.org/10.3897/mbmg.5.69657
Supplementary material 4 from: Zafeiropoulos H, Gargan L, Hintikka S, Pavloudi C, Carlsson J (2021) The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data. Metabarcoding and Metagenomics 5: e69657. https://doi.org/10.3897/mbmg.5.69657 Open
Figure S2
View article: Supplementary material 2 from: Zafeiropoulos H, Gargan L, Hintikka S, Pavloudi C, Carlsson J (2021) The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data. Metabarcoding and Metagenomics 5: e69657. https://doi.org/10.3897/mbmg.5.69657
Supplementary material 2 from: Zafeiropoulos H, Gargan L, Hintikka S, Pavloudi C, Carlsson J (2021) The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data. Metabarcoding and Metagenomics 5: e69657. https://doi.org/10.3897/mbmg.5.69657 Open
The mitochondrial cytochrome C oxidase subunit I gene (COI) is commonly used in environmental DNA (eDNA) metabarcoding studies, especially for assessing metazoan diversity. Yet, a great number of COI operational taxonomic units (OTUs) or/a…
View article: Supplementary material 3 from: Zafeiropoulos H, Gargan L, Hintikka S, Pavloudi C, Carlsson J (2021) The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data. Metabarcoding and Metagenomics 5: e69657. https://doi.org/10.3897/mbmg.5.69657
Supplementary material 3 from: Zafeiropoulos H, Gargan L, Hintikka S, Pavloudi C, Carlsson J (2021) The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data. Metabarcoding and Metagenomics 5: e69657. https://doi.org/10.3897/mbmg.5.69657 Open
Figure S1
View article: The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data
The Dark mAtteR iNvestigator (DARN) tool: getting to know the known unknowns in COI amplicon data Open
The mitochondrial cytochrome C oxidase subunit I gene (COI) is commonly used in environmental DNA (eDNA) metabarcoding studies, especially for assessing metazoan diversity. Yet, a great number of COI operational taxonomic units (OTUs) or/a…
View article: Development of an environmental DNA assay and field validation for the detection of invasive pink salmon <i>Oncorhynchus gorbuscha</i>
Development of an environmental DNA assay and field validation for the detection of invasive pink salmon <i>Oncorhynchus gorbuscha</i> Open
Pink salmon Oncorhynchus gorbuscha was introduced from its native range in the Pacific to Northwest Russia several times since the 1950s. While this species has been regularly observed in rivers in northern Norway since then, there has bee…
View article: Comparative analysis of single nucleotide polymorphisms and microsatellite markers for parentage verification and discovery within the equine Thoroughbred breed
Comparative analysis of single nucleotide polymorphisms and microsatellite markers for parentage verification and discovery within the equine Thoroughbred breed Open
Short tandem repeat (STR), also known as microsatellite markers are currently used for genetic parentage verification within equine. Transitioning from STR to single nucleotide polymorphism (SNP) markers to perform equine parentage verific…
View article: Bacteria are everywhere, even in your COI marker gene data!
Bacteria are everywhere, even in your COI marker gene data! Open
The mitochondrial cytochrome C oxidase subunit I gene (COI) is commonly used in eDNA metabarcoding studies, especially for assessing metazoan diversity. Yet, a great number of COI operational taxonomic units or/and amplicon sequence varian…
View article: Bacteria are everywhere, even in your COI data: Τhe art of getting to know the unknown unknowns and shine light on the dark matter!
Bacteria are everywhere, even in your COI data: Τhe art of getting to know the unknown unknowns and shine light on the dark matter! Open
Environmental DNA (eDNA) metabarcoding has been commonly used in recent years (Jeunen et al. 2019) for the identification of the species composition of environmental samples. By making use of genetic markers anchored in conserved gene regi…
View article: Investigation of the Transcriptomic Response of Atlantic Salmon (Salmo Salar) Exposed to Paramoeba Perurans Using Next Generation Sequencing
Investigation of the Transcriptomic Response of Atlantic Salmon (Salmo Salar) Exposed to Paramoeba Perurans Using Next Generation Sequencing Open
Amoebic Gill Disease (AGD), caused by the protozoan extracellular parasite Paramoeba perurans , is a disease affecting Atlantic salmon ( Salmo salar ) aquaculture. Many studies to date have investigated the pathogenesis of ADG focusing on …
View article: Nanopore whole genome sequencing and partitioned phylogenetic analysis supports a new salmonid alphavirus genotype (SAV7)
Nanopore whole genome sequencing and partitioned phylogenetic analysis supports a new salmonid alphavirus genotype (SAV7) Open
Salmon pancreas disease virus , more commonly known as salmonid alphavirus (SAV), is a single-stranded positive sense RNA virus and the causative agent of pancreas disease and sleeping disease in salmonids. In this study, a unique strain o…
View article: Investigating the impact of low-head dams on sediment transport dynamics in gravel-cobble streams
Investigating the impact of low-head dams on sediment transport dynamics in gravel-cobble streams Open
<p>Sediment connectivity, though typically viewed as subsidiary to concerns surrounding fish passage, serves an important role in a functioning riverine ecosystem, with both substrate stability and particle size distribution acting a…
View article: Investigating a simplified method for noninvasive genetic sampling in East African mammals using silica dried scat swabs
Investigating a simplified method for noninvasive genetic sampling in East African mammals using silica dried scat swabs Open
Swabbing scat has proved to be an effective noninvasive method to collect DNA from mammals in the field. Previously, this method has relied on preservative liquids or freezing to preserve the DNA collected on swabs. In this study, we deter…
View article: The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean
The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean Open
View article: Detection of haplosporidian protistan parasites supports an increase to their known diversity, geographic range and bivalve host specificity
Detection of haplosporidian protistan parasites supports an increase to their known diversity, geographic range and bivalve host specificity Open
Haplosporidian protist parasites are a major concern for aquatic animal health, as they have been responsible for some of the most significant marine epizootics on record. Despite their impact on food security, aquaculture and ecosystem he…
View article: The application of CRISPR‐Cas for single species identification from environmental DNA
The application of CRISPR‐Cas for single species identification from environmental DNA Open
We report the first application of CRISPR‐Cas technology to single species detection from environmental DNA (eDNA). Organisms shed and excrete DNA into their environment such as in skin cells and faeces, referred to as environmental DNA (e…
View article: Environmental (e)DNA detection of the invasive pink salmon <i>Oncorhynchus gorbuscha</i> during the 2017 Norwegian invasion
Environmental (e)DNA detection of the invasive pink salmon <i>Oncorhynchus gorbuscha</i> during the 2017 Norwegian invasion Open
The pink salmon Oncorhynchus gorbuscha was introduced from its native range in the Pacific to Northwest Russia several times since the 1950’s. While this species has been regularly observed in rivers in Northern Norway since that time, the…
View article: New insights into Siboglinidae microbiota - external tube contributes to an increment of the total microbial biomass
New insights into Siboglinidae microbiota - external tube contributes to an increment of the total microbial biomass Open
Siboglinid worms were sampled from four mud volcanoes in the Gulf of Cádiz (El Cid MV, Bonjardim MV, Al Gacel MV and Anastasya MV). These invertebrates are characteristic to cold seeps and are known to host chemosynthetic endosymbionts in …
View article: New insights into Siboglinidae microbiota - external tube contributes to an increment of the total microbial biomass
New insights into Siboglinidae microbiota - external tube contributes to an increment of the total microbial biomass Open
Siboglinid worms were sampled from four mud volcanoes in the Gulf of Cádiz (El Cid MV, Bonjardim MV, Al Gacel MV and Anastasya MV). These invertebrates are characteristic to cold seeps and are known to host chemosynthetic endosymbionts in …
View article: The Arrival of Steppe and Iranian Related Ancestry in the Islands of the Western Mediterranean
The Arrival of Steppe and Iranian Related Ancestry in the Islands of the Western Mediterranean Open
A series of studies have documented how Steppe pastoralist-related ancestry reached central Europe by at least 2500 BCE, while Iranian farmer-related ancestry was present in Aegean Europe by at least 1900 BCE. However, the spread of these …