Article
Multidisciplinary Sciences
Kara J. Andres, David M. Lodge, Jose Andres
Summary: Environmental DNA (eDNA) sampling is a powerful and efficient approach for collecting information about species, and it may also provide information about population-level genetic variability. In this study, the researchers used eDNA sampling to estimate the genetic diversity and structure of an invasive fish species in the Great Lakes region. The study found that the genetic patterns observed from eDNA analysis were consistent with conventional tissue-based estimates. This research highlights the potential for eDNA sampling to reveal detailed population characteristics that can inform monitoring and management plans for difficult-to-sample species.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Genetics & Heredity
Toshifumi Minamoto
Summary: In an era of severe biodiversity loss, biological monitoring is becoming increasingly important. The analysis of environmental DNA (eDNA) has emerged as a new method that can revolutionize the monitoring of aquatic ecosystems. Over the past decade, macro-organismal eDNA analysis has made significant progress and is quickly becoming the preferred method for non-destructive and non-invasive biological monitoring. This review summarizes the development and techniques of macro-organismal eDNA analysis, and discusses the future prospects of combining these methods with advanced analytical techniques in the fields of molecular biology and molecular genetics.
Article
Biodiversity Conservation
M. Laporte, C. S. Berger, E. Garcia-Machado, G. Cote, O. Morissette, L. Bernatchez
Summary: The study found that the use of environmental DNA (eDNA) metabarcoding can accurately assess the composition and spatial distribution of freshwater fish communities. In a transplant experiment in the St. Lawrence River, the eDNA of brown trout was detected at five locations up to 5,000 meters from the cage, but only one sampling location downstream from the cage showed a significant impact on community composition. Cluster analysis confirmed the impact of the brown trout eDNA on community composition, separating this location from others. No evidence of transport effect of brown trout eDNA on fish community composition was observed in other sampling locations.
ECOLOGICAL INDICATORS
(2022)
Article
Agriculture, Dairy & Animal Science
Anne Katrine Norgaard Svenningsen, Cino Pertoldi, Dan Bruhn
Summary: This study evaluated the efficiency of eDNA metabarcoding and conventional survey methods in detecting amphibian species in Danish lakes and ponds. The results showed that eDNA metabarcoding can detect multiple amphibian species and provide important knowledge on their distribution and occurrence. Applying eDNA techniques as a supplement allows for more frequent monitoring.
Article
Biodiversity Conservation
Wenhao Li, Tianjian Song, Xianglei Hou, Mingshuo Qin, Chunxia Xu, Yiming Li
Summary: In this study, eDNA metabarcoding was used to measure anuran diversity at 288 sites in 18 regions of Hainan Island, demonstrating that it can be a rapid and accurate method for large-scale surveys of anuran biodiversity.
Review
Biochemistry & Molecular Biology
Meng Yao, Shan Zhang, Qi Lu, Xiaoyu Chen, Si-Yu Zhang, Yueqiao Kong, Jindong Zhao
Summary: The vast declines in freshwater and marine fish diversity and population abundance have serious implications for ecosystems and human livelihoods. Environmental DNA (eDNA) biomonitoring provides an efficient and cost-effective method for assessing species occurrences and population trends in aquatic environments. This study analyzes 416 fish eDNA studies, highlighting the potential of eDNA technology in improving fish conservation and fisheries management. The study also identifies methodological concerns and provides guidelines for effective sampling in different aquatic habitats.
Article
Biochemistry & Molecular Biology
Rein Brys, Annelies Haegeman, David Halfmaerten, Sabrina Neyrinck, Ariane Staelens, Johan Auwerx, Tom Ruttink
Summary: The study utilized a fine-scale water sampling design combined with eDNA metabarcoding to investigate occupancy patterns and spatial dispersion of eDNA of fish and amphibian species in a lentic system. Results showed high eDNA decay rates and limited spatial eDNA dispersal, with the eDNA sampling method demonstrating high sensitivity in detecting individual presence. This approach allowed for precise monitoring of spatial occupancy patterns of aquatic species in the ecosystem.
Article
Ecology
Ameli Kirse, Sarah J. Bourlat, Kathrin Langen, Vera G. Fonseca
Summary: Metabarcoding is a powerful tool for assessing ecological patterns and diversity in different habitats. This study focuses on using eDNA metabarcoding to assess invertebrate biodiversity in soil samples, comparing different DNA extraction methods and marker genes. The results show that the choice of marker and DNA extraction method significantly impacts species detection rates and community composition, highlighting the importance of methodology in accurate ecological assessments.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Review
Environmental Sciences
Mieke van der Heyde, Michael Bunce, Paul Nevill
Summary: Environmental DNA (eDNA) metabarcoding is a valuable tool for monitoring the restoration of terrestrial ecosystems. Key factors to consider in using eDNA for monitoring include sample substrate selection, sample collection and storage, assay selection, and data interpretation. The majority of eDNA-based restoration studies are conducted in Europe, North America, and Australia, with soil microbial communities being the most targeted taxa and forests being the most studied ecosystem.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Fisheries
Gert-Jan Jeunen, Miles Lamare, Jennifer Devine, Stefano Mariani, Sadie Mills, Jackson Treece, Sara Ferreira, Neil J. Gemmell
Summary: Given the challenges of monitoring the Southern Ocean through visual observations, this study explores the potential of marine sponge eDNA monitoring to assess the fish community in the region. The findings show that eDNA provides a more comprehensive view of the fish community compared to catch records, highlighting its potential for improving our understanding of this understudied ecosystem and aiding conservation efforts.
REVIEWS IN FISH BIOLOGY AND FISHERIES
(2023)
Article
Multidisciplinary Sciences
Zeshu Yu, Shin-ichi Ito, Marty Kwok-Shing Wong, Susumu Yoshizawa, Jun Inoue, Sachihiko Itoh, Ryuji Yukami, Kazuo Ishikawa, Chenying Guo, Minoru Ijichi, Susumu Hyodo
Summary: In this study, the performance of two OceanDNA analysis methods, qPCR and MiFish, were tested to determine the distribution of small pelagic fish in the open ocean. The results showed a positive correlation between the two methods, but the detection rate using qPCR was consistently higher than that of MiFish. It was recommended to use both methods together to monitor the quantitative distribution and fish community structures of small pelagic fish species.
Article
Environmental Sciences
Peter A. U. Staehr, Karsten Dahl, Helle Buur, Cordula Goeke, Rumakanta Sapkota, Anne Winding, Marina Panova, Matthias Obst, Per Sundberg
Summary: This study investigated the use of eDNA metabarcoding as a supplement to traditional diver-based monitoring of marine boulder reef biodiversity within the photic zone. The results showed that eDNA sampling provided a substantial supplement to traditional monitoring, despite a low detection of macroalgae. This suggests that eDNA methods should be added to conventional monitoring programs in the future.
FRONTIERS IN MARINE SCIENCE
(2022)
Review
Environmental Sciences
Miaolian Zhang, Yingtong Zou, Shan Xiao, Jing Hou
Summary: This article introduces the application of environmental DNA metabarcoding technology in aquatic ecosystems and points out some limitations of existing technologies. With the development of big data and artificial intelligence, this technology has further potential for development.
MARINE POLLUTION BULLETIN
(2023)
Article
Biochemistry & Molecular Biology
Wang Cai, Lynsey R. Harper, Erika F. Neave, Peter Shum, Jamie Craggs, Maria Belen Arias, Ana Riesgo, Stefano Mariani
Summary: Large and diverse marine ecosystems present challenges for biodiversity monitoring. Recent studies have shown that sponges can serve as natural samplers for detecting marine vertebrates. However, little is known about the dynamics of eDNA particles in sponge tissue and how effective sponge sampling is compared to water samples. This study found that sponges and water samples have similar detectability for fish, but different sponge species vary in performance. Some sponges are suitable as natural samplers, while others may introduce difficulties in laboratory processing. An initial optimization phase is recommended for future studies using sponges for biodiversity assessment.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemistry & Molecular Biology
Laetitia Mathon, Alice Valentini, Pierre-Edouard Guerin, Eric Normandeau, Cyril Noel, Clement Lionnet, Emilie Boulanger, Wilfried Thuiller, Louis Bernatchez, David Mouillot, Tony Dejean, Stephanie Manel
Summary: This study evaluated the performance of 13 bioinformatic programs and pipelines in analyzing fish eDNA metabarcoding data, finding marked differences among programs during the taxonomic assignment step and varying running times for each step. The choice of algorithm for taxonomic assignment was shown to have a significant impact on diversity estimates.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Genetics & Heredity
Roger Huerlimann, Jeff A. Cowley, Nicholas M. Wade, Yinan Wang, Naga Kasinadhuni, Chon-Kit Kenneth Chan, Jafar Jabbari, Kirby Siemering, Lavinia Gordon, Matthew Tinning, Juan D. Montenegro, Gregory E. Maes, Melony J. Sellars, Greg J. Coman, Sean McWilliam, Kyall R. Zenger, Mehar S. Khatkar, Herman W. Raadsma, Dallas Donovan, Gopala Krishna, Dean R. Jerry
Summary: This study presents the draft genome assembly of an Australian black tiger shrimp, revealing the presence of endogenous viral elements. The discovery of these elements has implications for disease detection and the understanding of shrimp immune mechanisms.
G3-GENES GENOMES GENETICS
(2022)
Article
Fisheries
Jarrod L. Guppy, Adrien F. Marc, Dean R. Jerry
Summary: Breeding programs for barramundi are hindered by lack of control over sexual development. Hormonally-induced precocious female barramundi have shown reproductive ability and can produce sufficient offspring. Further research can enhance the spawning capacity of precocious females.
Editorial Material
Biodiversity Conservation
Sally C. Y. Lau, Jan M. Strugnell
Summary: The Southern Ocean is facing unprecedented environmental risks and consequences from climate change. The response of the benthic fauna, which evolved in isolation, to future changes remains uncertain. Understanding the persistence of benthic fauna through past glacial-interglacial cycles provides valuable insights for future predictions. Currently, preserving genetic diversity and connectivity between populations is crucial for species to adapt.
GLOBAL CHANGE BIOLOGY
(2022)
Correction
Multidisciplinary Sciences
Roger Huerlimann, Nicholas M. Wade, Lavinia Gordon, Juan D. Montenegro, Jake Goodall, Sean McWilliam, Matthew Tinning, Kirby Siemering, Erika Giardina, Dallas Donovan, Melony J. Sellars, Jeff A. Cowley, Kelly Condon, Greg J. Coman, Mehar S. Khatkar, Herman W. Raadsma, Gregory E. Maes, Kyall R. Zenger, Dean R. Jerry
SCIENTIFIC REPORTS
(2022)
Article
Ecology
Alyssa M. Budd, Julie B. Robins, Olivia Whybird, Dean R. Jerry
Summary: The study found that there was no general pattern of increasing female-specific DNA methylation markers with increasing length in barramundi, and female-specific DNA methylation arises rapidly during sex change. Additionally, differences in DNA methylation between males and females of similar lengths suggest that female-specific DNA methylation occurs rapidly during sex change rather than gradually with fish growth. Moreover, region-specific differences in length-at-sex change are accompanied by differences in DNA methylation, which are consistent with variability in sea temperature and salinity.
ECOLOGY AND EVOLUTION
(2022)
Review
Biodiversity Conservation
Jan M. Strugnell, Helen McGregor, Nerida G. Wilson, Karina T. Meredith, Steven L. Chown, Sally C. Y. Lau, Sharon A. Robinson, Krystyna M. Saunders
Summary: Anthropogenic climate change is causing observable changes in Antarctica and the Southern Ocean, impacting local ecosystems and the Earth's climate system. Understanding Antarctica's paleoecosystems and past climate change helps constrain future projections. Biological archives provide valuable information about past ecological change and help constrain current models.
GLOBAL CHANGE BIOLOGY
(2022)
Article
Ecology
Donald T. McKnight, Roger Huerlimann, Deborah S. Bower, Lin Schwarzkopf, Ross A. Alford, Kyall R. Zenger
Summary: The bacterial and fungal microbiomes of four Australian frog species were examined to understand their role in infection dynamics. Both microbial communities were correlated, suggesting mutual influences. There was mixed evidence of associations between richness and the fungal disease, with high richness potentially providing protection.
Article
Biodiversity Conservation
Alyssa M. Budd, Tom Schils, Madalyn K. Cooper, Mitchell B. Lyons, Matthew S. Mills, Mari E. Deinhart, Agnes Le Port, Roger Huerlimann, Jan M. Strugnell
Summary: Evidence-based environmental management is crucial for achieving global conservation commitments. Innovative ecological monitoring techniques, such as environmental DNA surveys, can help fill biodiversity knowledge gaps. These methods offer opportunities to overcome logistical and financial challenges previously associated with traditional monitoring.
BIOLOGICAL CONSERVATION
(2023)
Article
Ecology
Cecilia Villacorta-Rath, Bridget S. Green, Caleb Gardner, Nick P. Murphy, Carla A. Souza, Jan M. Strugnell
Summary: This study investigated the morphological and genetic differences in recently settled southern rock lobster recruits on the east coast of Tasmania, Australia. The findings suggest that the larval dispersal history may play a role in determining the phenotype of settlement recruits.
ECOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Adrien F. Marc, Jarrod L. Guppy, Hayley Marshall, Dean R. Jerry, Donna Rudd, Damien B. B. P. Paris
Summary: Reliable short-term chilled sperm storage is crucial for captive breeding of barramundi. This study optimized the composition of a non-activating medium (NAM) for short-term chilled storage by mimicking the biochemical profile of captive-bred barramundi's seminal and blood plasma. The optimized NAM significantly extended the functional lifespan of spermatozoa during chilled storage.
FISH PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Sally C. Y. Lau, Jan M. Strugnell, Chester J. Sands, Catarina N. S. Silva, Nerida G. Wilson
Summary: Understanding the drivers of evolutionary innovation is crucial for understanding how evolutionary processes unfold. This study examined the Southern Ocean brittle stars and found that the species Ophionotus victoriae and O. hexactis are closely related with interspecific gene flow. Different refugia were identified for each species during the late Pleistocene, and gene flow was observed between different oceanic currents and local oceanographic regimes. A strong association was detected between outlier loci and salinity in O. hexactis, suggesting adaptation related to evolutionary innovations. These findings provide valuable insights into the drivers of innovation in the Southern Ocean fauna.
Article
Marine & Freshwater Biology
Sarah Lok Ting Kwong, Cecilia Villacorta-Rath, Morgan Pratchett, Sven Uthicke
Summary: Population irruptions of crown-of-thorns seastar pose a perennial threat to Indo-Pacific coral reefs. Telomere length can be used to estimate age in CoTS, with adult individuals generally exhibiting shorter telomeres than juveniles. However, there is variation within age groups and no significant relationship has been found between telomere length and external features indicating age. Additionally, sub-optimal diet results in accelerated telomere attrition in CoTS.
Article
Marine & Freshwater Biology
Qiaz Q. H. Hua, Vicki A. Thomson, Jan M. Strugnell, Jasmin C. Martino, Bronwyn M. Gillanders, Zoe A. Doubleday
Summary: This study sampled octopods from commercial fisheries in southeast Australia to identify species, examine phylogeographic relationships, genetic structure within populations, and look for adaptive genetic variation. The study identified two octopus species, 'Octopus berrima' and 'Octopus pallidus', and found genetic and morphological differences among populations of both species. These findings provide important information for conservation and management decisions regarding octopod fisheries in southeast Australia.
Article
Multidisciplinary Sciences
Megan E. E. Cundy, Julia Santana-Garcon, Alexander G. G. McLennan, Marcelle E. E. Ayad, Philipp E. E. Bayer, Madalyn Cooper, Shannon Corrigan, Emily Harrison, Chris Wilcox
Summary: Seafood mislabelling and species substitution pose challenges to sustainable, responsible, and ethical fishing practices. A study in Australia found that 11.8% of tested seafood did not match their label, with sharks, rays, and snappers having the highest mislabelling rate. Furthermore, most seafood labels used vague common names or umbrella terms, concealing the sale of threatened species and products with lower nutritional quality or potential health risks. The study highlights the need for stronger labelling regulations to ensure accurately represented, sustainable seafood and improve consumer confidence.
SCIENTIFIC REPORTS
(2023)
Review
Computer Science, Artificial Intelligence
Alzayat Saleh, Marcus Sheaves, Dean Jerry, Mostafa Rahimi Azghadi
Summary: This paper introduces the application of deep learning in underwater fish habitat monitoring. The tutorial explains the key concepts of DL and provides a step-by-step procedure for developing DL algorithms. Additionally, the paper surveys underwater fish datasets and various DL techniques, and discusses the challenges and opportunities in the field.
EXPERT SYSTEMS WITH APPLICATIONS
(2024)
