Teresita Porter 🙋🏻♀️Estimating Organism Abundance Using Within-Sample Haplotype Frequencies of eDNA Data
https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.70104
RDNAnalysis of seawater for DNA of rare and endangered hammerhead sharks has been used to infer their presence or absence at multiple locations throughout their range. No sharks were captured or observed; accuracy of the inferred distributions depends on the presumed degradation of environmental DNA in hours or days.
Summary: https://scitechdaily.com/scientists-find-endangered-hammerhead-sharks-without-seeing-a-single-one/
Original paper: https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2025.1688088/full
#Science #MarineScience #EnvironmentalMonitoring #EnvironmentalDNA #Hammerheads
"A Metadata Checklist and Data Formatting Guidelines to Make eDNA FAIR (Findable, Accessible, Interoperable, and Reusable)"
TLDR - The new FAIR eDNA (FAIRe) Metadata Checklist offers a standardized approach to make eDNA data findable, accessible, interoperable, and reusable
https://onlinelibrary.wiley.com/doi/10.1002/edn3.70100
#EnvironmentalDNA #eDNA #metadata #biodiversity #detection #monitoring #FAIR
"Fate and transport of environmental DNA: mapping the knowns and unknowns"
TLDR - Review of how eDNA moves and is removed in aquatic systems to improve biodiversity monitoring and interpretation. Grab your macro-species goggles--the focus is on larger organisms, with bacteria mainly noted for eDNA removal and no mention of fungi or other microorganisms that live in aquatic systems.
Fate and transport of environmental DNA: mapping the knowns and unknowns
The use of environmental DNA (eDNA) in routine biomonitoring is transforming our ability to detect and quantify aquatic species. However, translating these indirect molecular detections into ecological insight requires understanding how long eDNA persists and how it moves through the environme...
"Large scale eDNA database reveals potential for pseudo biodiversity"
TLDR - warming waters are bringing more tropical fish northward, creating a short-term illusion of higher biodiversity the authors call 'pseudo biodiversity'
https://sciety-labs.elifesciences.org/articles/by?article_doi=10.21203/rs.3.rs-7872521/v1
#preprint #biodiversity #fish #environmentalDNA #eDNA #ANEMONE
Large scale eDNA database reveals potential for pseudo biodiversity
The spatial and temporal patterns of marine diversity are essential for the sustainable use of fishery resources and the effective management and conservation of marine ecosystems. We investigated the latitudinal diversity gradients of fish genera in Japanese waters using an environmental DNA (eDNA) data. A total of 1,765 environmental DNA surveys across Japan were obtained from the All Nippon eDNA Monitoring Network (ANEMONE) database. We found a negative correlation between fish genus richness and latitude, with a particularly pronounced gradient in summer. Seasonal change in the latitudinal gradient may reflect the increased occurrence of vagrant fish from tropical regions, rather than the commonly assumed pattern of seasonal migration (i.e., southwards in winter and northwards in summer). Furthermore, our results suggests that global warming may lead to a temporary increase in biodiversity by promoting the influx of tropical vagrant fish. However, such increases are unlikely sustainable, as these vagrant species may not establish long-term populations. We refer to this phenomenon as “pseudo biodiversity”, which may give the illusion of increase in biodiversity enhancement in short-term monitoring. This concept warrants attention as similar patterns of apparent biodiversity increase may occur under other circumstances as well.
Terri Blue 🇨🇦😷Thirty novel fungal lineages: formal description based
on environmental samples and DNA
https://mycokeys.pensoft.net/article/161674/
#environmentalDNA #novelFungalLineages #darktaxa #uncultivableFungi #DNABasedTaxonDescriptions
Thirty novel fungal lineages: formal description based on environmental samples and DNA
Molecular analyses of soil and water commonly reveal large proportions of fungal taxa that cannot be assigned to any taxonomic or functional groups. Some of these so-called dark taxa have been encoded alphanumerically, while others have remained completely overlooked. Using long-read sequencing that covers much of the ribosomal RNA operon, we shed light on the phylogenetic and ecological distribution of fungal dark taxa and formally describe 30 of the most prominent phylum- to order-level lineages based on their characteristic DNA features. This increases the known large-scale fungal phylogenetic diversity by roughly one-third. Formal names will enhance taxonomic reproducibility, facilitate communication among researchers, and enable the estimation of conservation and quarantine needs for uncultivable species and higher-ranking taxa. The new species in the respective highest-level novel taxonomic groups include Pantelleria saittana (Pantelleriomycetes), Paraspizellomyces parrentiae (Paraspizellomycetales), Aquieurochytrium lacustre (Aquieurochytriomycetes), Edaphochytrium valuojaense (Edaphochytriomycetes), Tibetochytrium taylorii (Tibetochytriomycetes), Tropicochytrium toronegroense (Tropicochytriomycetes), Algovorax scenedesmi (comb. nov.) and Solivorax pantropicus (Algovoracomycetes), Aquamastix sanduskyensis (Aquamastigomycetes), Cantoromastix holarctica (Cantoromastigomycetes), Dobrisimastix vlkii (Dobrisimastigomycetes), Palomastix lacustris (Palomastigomycetes), Sedimentomastix tueriensis (Sedimentomastigomycetes), Terrincola waldropii (Terrincolales), Curlevskia holarctica (Curlevskiomycota), Mycosocceria estonica (Mycosocceriales), Maerjamyces jumpponenii (Maerjamycetes), Ruderalia cosmopolita (Ruderaliomycetes), Bryolpidium mundanum (Bryolpidiomycetes), Chthonolpidium enigmatum (Chthonolpidiomycetes), Savannolpidium raadiense (Savannolpidiomycetes), Gelotisporidium boreale (Gelotisporidiomycetes), Sumavosporidium sylvestre (Sumavosporidiomycetes), Parakickxella borikenica (Parakickxellomycetes), Aldinomyces tarquinii (Aldinomycota), Borikenia urbinae (Borikeniomycota), Mirabilomyces abrukanus (Mirabilomycota), Nematovomyces vermicola (comb. nov.) and N. soinasteënsis (Nematovomycota), Viljandia globalis (Viljandiomycota), Waitukubulimyces cliftonii (Waitukubulimycota), and Tartumyces setoi (Tartumyceta).
"Invasive species monitoring based on eDNA multiplex PCR sequencing"
https://mbmg.pensoft.net/article/159944/
#InvasiveSpeciesMonitoring #eDNA #EnvironmentalDNA #MultiplexPCR #Metabarcoding
Invasive species monitoring based on eDNA multiplex PCR sequencing
Invasive species pose a significant threat to global biodiversity and the stability of ecosystems. Although environmental DNA (eDNA)-based quantitative PCR is considered effective, its limited multiplexing capacity makes it impractical for large-scale monitoring of invasive species. To address this limitation, we developed a novel and efficient approach for invasive species monitoring by combining multiplex PCR amplification with high-throughput sequencing. In this study, we screened 46 aquatic invasive species of major concern in China. We have integrated and designed 91 pairs of primers that can simultaneously amplify these species in a single PCR system. The validated method was applied to field monitoring in the Pearl River Basin to evaluate its practical performance. Multiplex PCR sequencing successfully detected 28 invasive species, with over 90% of environmental samples testing positive for invasive species DNA, demonstrating the method’s high sensitivity and broad applicability. Furthermore, all 11 invasive species identified through metabarcoding were also consistently detected by multiplex PCR sequencing, showing a strong positive correlation and high concordance across all monitoring sites. In conclusion, multiplex PCR sequencing represents a powerful and cost-effective tool for simultaneously detecting multiple aquatic invasive species in the early stages of invasion. It significantly improves detection efficiency, reduces monitoring costs and provides a solid foundation for developing a scientific and scalable monitoring system for aquatic invasive species.
"Sexing From Seawater: Application of Environmental DNA Beyond Species Detection for Cetaceans"
NIOO-KNAWNew publication: Connecting diversity and process: Eukaryotic #phytoplankton community dynamics across the #YangtzeRiver using #environmentalDNA. #biodiversity #eDNA
https://doi.org/10.1016/j.ecolind.2025.114026
https://doi.org/10.1016/j.ecolind.2025.114026
GenomeBiolEvolWiredu-Boakye et al. analysed 432 DNA damage response (DDR) proteins in 68 genomes, showing that DDR proteins are consistently longer than housekeeping proteins, regardless of life history.
🔗 doi.org/10.1093/gbe/evaf089