4.7 Article

Estimating the extended and hidden species diversity from environmental DNA in hyper-diverse regions

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biology

Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding

Laetitia Mathon et al.

Summary: Using environmental DNA metabarcoding, researchers have found that coral reefs have higher fish biodiversity than previously thought. This method also revealed hidden patterns and provided a fresh perspective on the assembly rules of fish communities on reefs.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2022)

Article Ecology

The Effect of Activity, Energy Use, and Species Identity on Environmental DNA Shedding of Freshwater Fish

Bettina Thalinger et al.

Summary: The study reveals the importance of fish physiology and behavior in the interpretation of eDNA quantities, with differences found between species. Through experiments, it was demonstrated that fish activity levels and energy use are positively correlated with target eDNA quantities, highlighting the need to incorporate species-specific traits into eDNA monitoring and conservation efforts.

FRONTIERS IN ECOLOGY AND EVOLUTION (2021)

Article Biodiversity Conservation

GAPeDNA: Assessing and mapping global species gaps in genetic databases for eDNA metabarcoding

Virginie Marques et al.

Summary: GAPeDNA is a user-friendly web interface that provides a global overview of genetic database completeness for a given taxon, guiding future sequencing efforts and supporting larger-scale eDNA inventories. The global fish case study shows gaps increase towards the tropics, highlighting priority areas for fish sequencing and future research directions.

DIVERSITY AND DISTRIBUTIONS (2021)

Article Biology

Environmental DNA metabarcoding reveals and unpacks a biodiversity conservation paradox in Mediterranean marine reserves

Emilie Boulanger et al.

Summary: The study surveyed fish assemblages in six Mediterranean no-take reserves and adjacent fishing grounds using environmental DNA, finding that there were fewer fish species in marine reserves compared to nearby fished areas, with a marked change in fish species composition under different managements. This paradoxical gradient in species richness is mainly driven by species often overlooked by classical visual surveys but detected with eDNA.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2021)

Article Multidisciplinary Sciences

At-risk marine biodiversity faces extensive, expanding, and intensifying human impacts

Casey C. O'Hara et al.

Summary: The study reveals that marine species worldwide are sensitive to human activities and climate change, with impacts expanding and intensifying over time. Fishing activities dominate impacts in national waters, while climate stressors are driving the expansion and intensification of impacts.

SCIENCE (2021)

Article Biodiversity Conservation

Use of environmental DNA in assessment of fish functional and phylogenetic diversity

Virginie Marques et al.

Summary: This study compared the performance of eDNA metabarcoding and long-term remote video in assessing phylogenetic and functional diversity of marine fishes. It found that eDNA detected more molecular operational taxonomic units and functional entities than video, indicating the potential of eDNA metabarcoding in accurately census biodiversity factors in marine systems.

CONSERVATION BIOLOGY (2021)

Article Marine & Freshwater Biology

Highly diverse mesophotic reef fish communities in Raja Ampat, West Papua

Dominic A. Andradi-Brown et al.

Summary: Research on mesophotic coral ecosystems in the Raja Ampat archipelago revealed exceptionally diverse fish communities with depth-driven structures. While higher human population density was associated with lower abundance of key fisheries families, there was no evidence of depth refuge from fishing in these ecosystems. Additionally, fish abundance declined further from major regional markets, likely due to historical fisheries pressure.

CORAL REEFS (2021)

Article Biodiversity Conservation

Fishing restrictions and remoteness deliver conservation outcomes for Indonesia's coral reef fisheries

Stuart J. Campbell et al.

CONSERVATION LETTERS (2020)

Article Multidisciplinary Sciences

Conservation prioritization can resolve the flagship species conundrum

Jennifer McGowan et al.

NATURE COMMUNICATIONS (2020)

Article Biodiversity Conservation

Fishing for mammals: Landscape-level monitoring of terrestrial and semi-aquatic communities using eDNA from riverine systems

Naiara Guimaraes Sales et al.

JOURNAL OF APPLIED ECOLOGY (2020)

Article Biology

Accumulation curves of environmental DNA sequences predict coastal fish diversity in the coral triangle

Jean-Baptiste Juhel et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2020)

Article Ecology

A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish

Shan Zhang et al.

METHODS IN ECOLOGY AND EVOLUTION (2020)

Article Biodiversity Conservation

Reef Life Survey: Establishing the ecological basis for conservation of shallow marine life

Graham J. Edgar et al.

BIOLOGICAL CONSERVATION (2020)

Article Biodiversity Conservation

Combined use of eDNA metabarcoding and video surveillance for the assessment of fish biodiversity

Michael Stat et al.

CONSERVATION BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Pelagic Subsidies Underpin Fish Productivity on a Degraded Coral Reef

Renato A. Morais et al.

CURRENT BIOLOGY (2019)

Review Biotechnology & Applied Microbiology

A review on the applications and recent advances in environmental DNA (eDNA) metagenomics

Deviram Garlapati et al.

REVIEWS IN ENVIRONMENTAL SCIENCE AND BIO-TECHNOLOGY (2019)

Article Ecology

Non-specific amplification compromises environmental DNA metabarcoding with COI

Rupert A. Collins et al.

METHODS IN ECOLOGY AND EVOLUTION (2019)

Article Multidisciplinary Sciences

Unexpected fish diversity gradients in the Amazon basin

Thierry Oberdorff et al.

SCIENCE ADVANCES (2019)

Review Biology

Predicting the fate of eDNA in the environment and implications for studying biodiversity

Jori B. Harrison et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2019)

Article Biology

The hidden half: ecology and evolution of cryptobenthic fishes on coral reefs

Simon J. Brandl et al.

BIOLOGICAL REVIEWS (2018)

Article Multidisciplinary Sciences

Environmental DNA illuminates the dark diversity of sharks

Germain Boussarie et al.

SCIENCE ADVANCES (2018)

Review Multidisciplinary Sciences

The future of hyperdiverse tropical ecosystems

Jos Barlow et al.

NATURE (2018)

Article Multidisciplinary Sciences

Mapping knowledge gaps in marine diversity reveals a latitudinal gradient of missing species richness

Andre Menegotto et al.

NATURE COMMUNICATIONS (2018)

Article Biodiversity Conservation

Using dark diversity and plant characteristics to guide conservation and restoration

Jesper Erenskjold Moeslund et al.

JOURNAL OF APPLIED ECOLOGY (2017)

Article Biochemistry & Molecular Biology

OBITOOLS: a UNIX-inspired software package for DNA metabarcoding

Frederic Boyer et al.

MOLECULAR ECOLOGY RESOURCES (2016)

Article Biochemistry & Molecular Biology

Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

Alice Valentini et al.

MOLECULAR ECOLOGY (2016)

Article Multidisciplinary Sciences

Bright spots among the world's coral reefs

Joshua E. Cinner et al.

NATURE (2016)

Article Multidisciplinary Sciences

Swarm: robust and fast clustering method for amplicon-based studies

Frederic Mahe et al.

Article Multidisciplinary Sciences

A Global Estimate of the Number of Coral Reef Fishers

Louise S. L. Teh et al.

PLOS ONE (2013)

Article Multidisciplinary Sciences

Global Biogeography of Reef Fishes: A Hierarchical Quantitative Delineation of Regions

Michel Kulbicki et al.

PLOS ONE (2013)

Review Environmental Sciences

Papuan Bird's Head Seascape: Emerging threats and challenges in the global center of marine biodiversity

Sangeeta Mangubhai et al.

MARINE POLLUTION BULLETIN (2012)

Article Ecology

Dark diversity: shedding light on absent species

Meelis Paertel et al.

TRENDS IN ECOLOGY & EVOLUTION (2011)

Article Biotechnology & Applied Microbiology

An In silico approach for the evaluation of DNA barcodes

Gentile Francesco Ficetola et al.

BMC GENOMICS (2010)

Article Environmental Studies

Illegal, unreported and unregulated fisheries catch in Raja Ampat Regency, Eastern Indonesia

Divya A. Varkey et al.

MARINE POLICY (2010)

Article Biology

A Nonparametric Lower Bound for the Number of Species Shared by Multiple Communities

H. -Y Pan et al.

JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS (2009)

Article Biology

The completeness of taxonomic inventories for describing the global diversity and distribution of marine fishes

Camilo Mora et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2008)

Article Biochemistry & Molecular Biology

The EMBL Nucleotide Sequence Database

W Baker et al.

NUCLEIC ACIDS RESEARCH (2000)