eProbe: a capture probe design toolkit for genetic diversity reconstructions from ancient environmental DNA DOI Creative Commons
Zihao Huang, Zhengquan Gu, Yuanyang Cai

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 3, 2024

Abstract Ancient environmental DNA (aeDNA) is now commonly used in paleoecology and evolutionary ecology, yet due to difficulties gaining sufficient genome coverage on individual species from metagenome data, its genetic perspectives remain largely uninvestigated. Hybridization capture has proven as an effective approach for enriching the of target species, thus increasing sequencing data enabling population genetics analysis. However, date there no tool available designing probe sets tailored aeDNA based genetics. Here we present eProbe , efficient, flexible easy-to-use program toolkit that provides a complete workflow design, assessment validation. By benchmarking set foxtail millet, annual grass, made by workflow, demonstrate remarkable increase capturing efficiency, with taxa recovery rate improved 577-fold, achieved soil capture-sequencing even higher than directly shotgun sequenced plant tissues. Probes underwent our filtering panels show notably efficiency. The enabled accurate analysis, effectively inferring fine-scale structures patterns, well genotypes functional genes.

Language: Английский

Sediment DNA can revolutionize archaeology—if it is used the right way DOI Creative Commons
Vera Aldeias, Mareike C. Stahlschmidt

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(26)

Published: June 20, 2024

This study unravels a concerning capability in Large Language Models (LLMs): the ability to understand and induce deception strategies. As LLMs like GPT-4 intertwine with human communication, aligning them values becomes paramount. ...Large language models (LLMs) are currently at forefront of intertwining AI systems communication everyday life. Thus, is great importance. However, given steady increase reasoning abilities, ...

Language: Английский

Citations

7
Tibetan terrestrial and aquatic ecosystems collapsed with cryosphere loss inferred from sedimentary ancient metagenomics DOI Creative Commons
Sisi Liu, Kathleen R. Stoof‐Leichsenring, Lars Harms

et al.

Science Advances, Journal Year: 2024, Volume and Issue: 10(21)

Published: May 23, 2024

Glacier and permafrost shrinkage land-use intensification threaten mountain wildlife affect nature conservation strategies. Here, we present paleometagenomic records of terrestrial aquatic taxa from the southeastern Tibetan Plateau covering last 18,000 years to help understand complex alpine ecosystem dynamics. We infer that steppe-meadow became woodland at 14 ka (cal BP) controlled by cryosphere loss, further driving a herbivore change wild yak deer. These findings weaken hypothesis top-down control large herbivores in ecosystem. find turnover communities ka, transitioning glacier-related (blue-green) algae abundant nonglacier-preferring picocyanobacteria, macrophytes, fish, otters. There is no evidence for substantial effects livestock herding either Using network analysis, assess stress-gradient reveal root hemiparasitic cushion plants are keystone taxa. With ongoing protection their habitats likely be benefit on Plateau.

Language: Английский

Citations

4
Reconciling the role of mineral surfaces for bacterial evolution: Importance of minerals in the dissemination of antibiotic resistance DOI

Saghar Hendiani,

Carlota Carbajo,

Pablo Nicolas Arellano Caicedo

et al.

The Science of The Total Environment, Journal Year: 2025, Volume and Issue: 962, P. 178301 - 178301

Published: Jan. 1, 2025

Language: Английский

Citations

0
Neolithic pastoralism and plant community interactions at high altitudes of the Pyrenees, southern Europe DOI Creative Commons
Irene Julián-Posada, Graciela Gil‐Romera, Sandra Garcés‐Pastor

et al.

Communications Earth & Environment, Journal Year: 2025, Volume and Issue: 6(1)

Published: Jan. 24, 2025

Language: Английский

Citations

0
The Impact of Flow Velocity on Environmental DNA Detectability for the Application in River Systems DOI Creative Commons

Jelle A. Dercksen,

Jan Willem Foppen, Astrid Blom

et al.

Environmental DNA, Journal Year: 2025, Volume and Issue: 7(3)

Published: May 1, 2025

ABSTRACT Organisms perpetually release genetic material in their surroundings, referred to as environmental DNA (eDNA), which can be captured and subsequently analyzed detect biodiversity across the tree of life. In lotic, dynamic environments, little is known about specific factors that affect concentration eDNA between by host its dissemination into environment. This gap knowledge introduces significant uncertainty when applying a monitoring tool. Our objective provide insight on concentrations ecosystems representative rivers streams. To this end, we conducted series laboratory experiments rotating circular (annular) flume, allows for extended degradation under conditions flow. Here, show flow velocity impacts observed over time. results suggest flow‐induced transport keeps suspension, reducing removal from water column, increased eDNA. We temporary increase early phase flume experiment with highest velocity. seems due combination low rates high shear stress, fragment homogenize particles column. The our study importance better understanding assessing detection probability eDNA, both controlled larger‐scale conditions.

Language: Английский

Citations

0
The potential of lacustrine sedimentary ancient DNA for revealing human postglacial recolonization patterns in northern Sweden – a review DOI Creative Commons
Ernst Johnson, Carl Regnéll, Peter D. Heintzman

et al.

Boreas, Journal Year: 2024, Volume and Issue: 53(3), P. 347 - 359

Published: May 26, 2024

The postglacial recolonization of Fennoscandian flora and fauna was initiated when the land became accessible as last ice sheet retreated. In northern Sweden, plants are represented in pollen macrofossil records, but there is no genetic evidence from first plants, animals or humans region, mainly owing to an absence osteological finds. questions who peoples, pioneers, were where they came therefore remain unanswered. Previous palaeogenomic analyses remains adjacent regions have suggested that two main routes into Sweden could been taken by one SW through modern‐day Denmark Norway, east via Finland. However, direct pioneers exists. Modern technology has provided ancient DNA field with updated toolbox allow for novel approaches revealing origin profiles Scandinavians, which sedimentary (sedaDNA) well placed. Lake sediments now a routine source sedaDNA used record environmental changes detect species lived surrounding lake catchment. This review will provide context background, summary ground‐breaking studies within lacustrine sedaDNA, relevant methodology address scientific at hand. We conclude mature enough insight origins arrival times migrated Sweden.

Language: Английский

Citations

2
SedaDNA reveals mid-to late Holocene aquatic plant and algae changes in Luanhaizi Lake on the Tibetan Plateau DOI
Hanqiu Xu,

Lian‐Fang Feng,

Naimeng Zhang

et al.

Palaeogeography Palaeoclimatology Palaeoecology, Journal Year: 2024, Volume and Issue: 650, P. 112344 - 112344

Published: June 22, 2024

Language: Английский

Citations

2
Sample Preservation Solution Increases Nucleic Acid Yield and Environmental RNA Quality in Sediments Across an Estuarine Salinity Gradient DOI Creative Commons
Christopher Keneally, Virginie Gaget, Stephen P. Kidd

et al.

Environmental DNA, Journal Year: 2024, Volume and Issue: 6(5)

Published: Sept. 1, 2024

ABSTRACT Environmental nucleic acid‐based assessments are powerful tools for understanding microbial ecology, and environmental degradation in aquatic environments. This approach is particularly useful guiding restoration estuaries, some of the most degraded ecosystems world. The recent popularity this has been accompanied by a parallel increase diversity applied methods. A range best practice methods exist across field that can be employed selected based on considerations such as physicochemical gradients, maximizing yield, quality acids sampled sites within study area. consistent to intra‐study acid sampling also ensures accurate comparison between those sites. evaluates (eNA) salinity gradients ecosystems, focusing impact preservation techniques DNA (eDNA) yield RNA (eRNA) quality. Fieldwork was conducted at three Coorong estuary system South Australia, representing low salinity, marine, hypersaline conditions. Snap freezing LifeGuard solution treatments were situ compare their effects yields eRNA integrity. enhanced eDNA sediments but negatively impacted integrity marine Conversely, treatment with consistently improved both recovery all levels, which makes good candidate preserving eNA molecules gradients. underscores necessity tailoring sample specific conditions eNA‐based community coastal ecosystems. These findings contribute development robust protocols benthic communities under varying

Language: Английский

Citations

2
The sedaDNA revolution and archaeology: Progress, challenges, and a research agenda DOI Creative Commons
Antony G. Brown,

M. I. Lucas,

Inger Greve Alsos

et al.

Journal of Archaeological Science, Journal Year: 2024, Volume and Issue: 174, P. 106132 - 106132

Published: Dec. 18, 2024

Language: Английский

Citations

1
eProbe: a capture probe design toolkit for genetic diversity reconstructions from ancient environmental DNA DOI Creative Commons
Zihao Huang, Zhengquan Gu, Yuanyang Cai

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 3, 2024

Abstract Ancient environmental DNA (aeDNA) is now commonly used in paleoecology and evolutionary ecology, yet due to difficulties gaining sufficient genome coverage on individual species from metagenome data, its genetic perspectives remain largely uninvestigated. Hybridization capture has proven as an effective approach for enriching the of target species, thus increasing sequencing data enabling population genetics analysis. However, date there no tool available designing probe sets tailored aeDNA based genetics. Here we present eProbe , efficient, flexible easy-to-use program toolkit that provides a complete workflow design, assessment validation. By benchmarking set foxtail millet, annual grass, made by workflow, demonstrate remarkable increase capturing efficiency, with taxa recovery rate improved 577-fold, achieved soil capture-sequencing even higher than directly shotgun sequenced plant tissues. Probes underwent our filtering panels show notably efficiency. The enabled accurate analysis, effectively inferring fine-scale structures patterns, well genotypes functional genes.

Language: Английский

Citations

0