Article
Genetics & Heredity
J. A. M. Erven, C. Cakirlar, D. G. Bradley, D. C. M. Raemaekers, O. Madsen
Summary: This study evaluated the imputation of ancient Sus scrofa genomes and found that the accuracy of imputation is affected by factors such as genetic architecture and divergence in the reference panel. Despite achieving high genotype concordance, the imputed genotypes did not fully capture the diversity present in the original genomes, leading to biases in downstream analyses.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Emily Dziedzic, Brian Sidlauskas, Richard Cronn, James Anthony, Trevan Cornwell, Thomas A. Friesen, Peter Konstantinidis, Brooke E. Penaluna, Staci Stein, Taal Levi
Summary: The use of eDNA for species detection is changing the way global biodiversity is monitored. However, the lack of regional, vouchered, genomic sequence information, especially including intraspecific variation, hinders management agencies from fully utilizing eDNA to monitor taxa and implement eDNA analyses. This study created a database of complete mitogenomic sequences for all of Oregon's fishes, providing valuable insights into the taxonomic value and limits of complete mitogenomic sequences and informing the development of future eDNA assays and environmental genomics methods.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Multidisciplinary Sciences
Maxime Borry, Alexander Huebner, Adam B. Rohrlach, Christina Warinner
Summary: DNA de novo assembly can reconstruct longer DNA fragments from short reads, allowing investigation of ancient microbiome diversity. However, ancient samples often contain environmental contamination, requiring reliable methods to distinguish ancient from modern DNA, PyDamage is a robust automated approach for estimating and authenticating ancient DNA.
Article
Multidisciplinary Sciences
Diyendo Massilani, Mike W. Morley, Susan M. Mentzer, Vera Aldeias, Benjamin Vernot, Christopher Miller, Mareike Stahlschmidt, Maxim B. Kozlikin, Michael Shunkov, Anatoly P. Derevianko, Nicholas J. Conard, Sarah Wurz, Christopher S. Henshilwood, Javi Vasquez, Elena Essel, Sarah Nagel, Julia Richter, Birgit Nickel, Richard G. Roberts, Svante Paeaebo, Viviane Slon, Paul Goldberg, Matthias Meyer
Summary: DNA preserved in ancient sediments can provide valuable genetic information about past hominin and environmental diversity. This study demonstrates that resin-impregnated archaeological sediment blocks can effectively preserve DNA from hominins and other mammals. Microsampling analysis of sediment blocks from Denisova Cave reveals significant variation in the taxonomic composition of mammalian DNA at a millimeter-scale, with DNA concentrated in small particles such as bone and feces fragments. The study also successfully extracts Neanderthal DNA from a sediment block, closely related to a previously recovered Neanderthal toe bone.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Andrew Dopheide, Talia Brav-Cubitt, Anastasija Podolyan, Richard A. B. Leschen, Darren Ward, Thomas R. Buckley, Manpreet K. Dhami
Summary: The lack of locally relevant DNA reference databases limits the potential for DNA-based biodiversity monitoring. This study demonstrates a sensitive and efficient method for generating DNA barcodes from invertebrate specimens, providing a foundation for DNA-based assessments and monitoring of biodiversity.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemistry & Molecular Biology
Rui Martiniano, Bianca De Sanctis, Pille Hallast, Richard Durbin
Summary: This study presents a new likelihood-based workflow, pathPhynder, for joint analysis of ancient DNA and modern phylogenies. By utilizing all polymorphic sites in the target sequence, this method effectively determines the most likely placement of ancient samples in the phylogeny and assigns them to haplogroups.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Xenia Keighley, Maiken Hemme Bro-Jorgensen, Hans Ahlgren, Paul Szpak, Marta Maria Ciucani, Fatima Sanchez Barreiro, Lesley Howse, Anne Birgitte Gotfredsen, Aikaterini Glykou, Peter Jordan, Kerstin Liden, Morten Tange Olsen
Summary: The study investigated the factors influencing the preservation of ancient pinniped DNA, finding that the geographic origin of samples, skeletal element types, collagen content, and collection year significantly impact endogenous content and DNA damage. It was discovered that skeletal elements and sample context were the most influential factors in DNA preservation.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Multidisciplinary Sciences
Pavel Tarlykov, Sabina Atavliyeva, Dana Auganova, Ilyas Akhmetollayev, Tatyana Loshakova, Victor Varfolomeev, Yerlan Ramankulov
Summary: By studying the genetic diversity of ancient domestic sheep from two settlements in Kazakhstan, researchers found that the specimens from both sites had similar distribution patterns of mitochondrial DNA haplogroups, indicating early sheep introduction into the region. These results are important for understanding sheep migrations in the Eurasian steppe and emphasize the significance of genomic analysis of earlier local lineages.
Article
Genetics & Heredity
Luis Neto, Nadia Pinto, Alberto Proenca, Antonio Amorim, Eduardo Conde-Sousa
Summary: Forensic genetics relies on DNA-based taxonomy, with tools like BOLD or GenBank being crucial for taxonomic assignment. Software tools like 4SpecID can help audit and annotate reference libraries for forensic applications. It is important to validate data from independent sources to ensure accuracy and reliability.
Article
Biodiversity Conservation
Niko Kasalo, Josip Skejo, Martin Husemann
Summary: The COI gene is commonly used as a DNA barcode for species identification. This study summarizes the metadata of COI sequences and conducts phylogenetic analysis on photographically vouchered sequences using Maximum Likelihood and Bayesian analysis. The results show that the dataset is skewed towards the subfamily Tetriginae, with most records identified only at the family level and undersampling in most regions. Furthermore, most sequences lack photographic vouchers and the taxonomic backbone of BOLD is outdated. The phylogenetic analysis reveals that COI barcodes generally cluster corresponding to species, but some clusters remain ambiguous, and deeper nodes lack strong support, indicating a weak phylogenetic signal beyond the specific level.
Article
Biochemistry & Molecular Biology
Emese Meglecz
Summary: The COInr database is a freely available and comprehensive database of COI reference sequences extracted from BOLD and NCBI nucleotide databases. It allows users to customize the database according to their needs and is suitable for creating custom databases.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Fisheries
Rupert A. Collins, Giulia Trauzzi, Katherine M. Maltby, Thomas I. Gibson, Frances C. Ratcliffe, Jane Hallam, Sophie Rainbird, James Maclaine, Peter A. Henderson, David W. Sims, Stefano Mariani, Martin J. Genner
Summary: The accuracy and reliability of DNA metabarcoding analyses rely on the quality and breadth of reference libraries supporting them, but obtaining and managing large volumes of sequence data on public repositories remains a challenge. This study introduces a pipeline for downloading, cleaning, and annotating mitochondrial DNA sequences for specific fish species, with features including support for multiple metabarcode markers, quality control, and coverage reports. This pipeline aims to facilitate the scaling up of fish metabarcoding across wide spatial gradients.
JOURNAL OF FISH BIOLOGY
(2021)
Article
Virology
Axel A. Guzman-Solis, Miguel Alejandro Navarro, Maria C. Avila-Arcos, Daniel Blanco-Melo
Summary: The study of ancient viruses through analysis of ancient human remains' nucleic acids has provided valuable information about past epidemics and the evolution of viral families. It has also revealed the significance and key roles of ancient viruses in human evolution and history.
ANNUAL REVIEW OF VIROLOGY
(2023)
Article
Parasitology
Iracy Maiany Nunes Soares, Julio Cesar Polonio, Joao Antonio Cyrino Zequi, Halison Correia Golias
Summary: This study reviews the taxonomic proposals and molecular methods available for identifying the genus Aedes from 2010 to 2021. The current keys for morphological identification are not sufficient to differentiate certain species. Various molecular techniques, such as Multiplex PCR and DNA barcoding, have been used to identify Aedes species. However, catalogued data is limited to medically important taxa. The integrative taxonomy approach may improve species delimitation.
Article
Biochemistry & Molecular Biology
Zachary Gold, Emily E. Curd, Kelly D. Goodwin, Emma S. Choi, Benjamin W. Frable, Andrew R. Thompson, Harold J. Walker, Ronald S. Burton, Dovi Kacev, Lucas D. Martz, Paul H. Barber
Summary: This study evaluates the performance of DNA metabarcoding in classifying fish species in the California Current Large Marine Ecosystem. It shows that a regional database provides higher accuracy than a global one, and highlights the tradeoff between accuracy and misclassification when setting taxonomic cutoff scores. Additionally, adding new reference sequences improves the identification of native species in environmental DNA samples, emphasizing the importance of curated reference databases for effective metabarcoding.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Biochemistry & Molecular Biology
Ulla von Ammon, Xavier Pochon, Paula Casanovas, Branwen Trochel, Martin Zirngibl, Austen Thomas, Jan Witting, Paul Joyce, Anastasija Zaiko
Summary: This study aimed to optimize environmental DNA (eDNA) sampling by comparing two different sampling methods and filters, and assessing their impact on biodiversity through metabarcoding analysis. The results showed that bucket sampling combined with self-preserving filters had the highest amplicon sequence variant (ASV) richness, while net sampling combined with 5μm pore size filters captured more metazoan taxa. These findings are important for optimizing eDNA sampling protocols in marine biodiversity research and surveillance.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Gert-Jan Jeunen, Jasmine S. Cane, Sara Ferreira, Francesca Strano, Ulla von Ammon, Hugh Cross, Robert Day, Sean Hesseltine, Kaleb Ellis, Lara Urban, Niall Pearson, Pamela Olmedo-Rojas, Anya Kardailsky, Neil J. Gemmell, Miles Lamare
Summary: Aquatic environmental DNA (eDNA) surveys are revolutionizing marine ecosystem monitoring, but the time-consuming active filtration step remains a bottleneck. This study investigated the similarities and differences between eDNA signals obtained from various sources, including water, filter-feeding organisms, and sponge material. The results showed that vertebrate eDNA signals from water and sponge samples were highly concordant, highlighting the potential of using marine sponges as an additional tool for eDNA-based biodiversity surveys. Caution should be taken to minimize the impact on marine communities during eDNA sampling.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Fisheries
S. Muncaster, A. Goikoetxea, P. M. Lokman, C. E. Moraes, E. L. Damsteegt, J. Edgecombe, N. J. Gemmell, E. V. Todd
Summary: Socially induced sex change is regulated by a combination of genes and epigenetic factors that control sex differentiation and cell fate. The molecular basis for this transformation is still largely unknown. Recent research suggests that both epigenetic effects and genes involved in cell fate are important drivers of sex change.
REVIEWS IN FISH BIOLOGY AND FISHERIES
(2023)
Article
Fisheries
Clare I. M. Adams, Gert-Jan Jeunen, Hugh Cross, Helen R. Taylor, Antoine Bagnaro, Kim Currie, Chris Hepburn, Neil J. Gemmell, Lara Urban, Federico Baltar, Michael Stat, Michael Bunce, Michael Knapp
Summary: In response to climate change, efficient monitoring methods are needed for rapidly shifting biodiversity patterns in the oceans. Environmental DNA (eDNA) metabarcoding has emerged as a cost-effective solution. Using eDNA, we detected four community types across a transect in the Southern Hemisphere and found that diversity patterns were mainly driven by planktonic organisms. This technique lays the foundations for multi-trophic environmental monitoring efforts.
ICES JOURNAL OF MARINE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Allison K. Miller, Cara L. Brosnahan, Anjali Pande, Cindy F. Baker, Jemma L. Geoghegan, Jane Kitson, Neil J. Gemmell, Edwina J. Dowle
Summary: Infectious diseases have a significant impact on various organisms, and understanding the interactions between hosts and pathogens is crucial for their conservation and management. The use of genomic approaches has made it easier to obtain this knowledge quickly, however, many species still face challenges in accessing appropriate samples and data. Archival materials, such as formalin-fixed paraffin-embedded tissue samples, may provide a valuable resource for studying pathogen emergence and host responses over long periods of time.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Zoology
Kaj Kamstra, Chloe van der Burg, Haylee M. Quertermous, Simon Muncaster, Erica V. Todd, Christine L. Jasoni, Culum Brown, Neil J. Gemmell
Summary: For most vertebrates, sexual fate is genetically determined and remains fixed throughout life. However, for some teleost fishes sex is more plastic. Significant progress has been made in characterising the cellular and molecular processes that underpin gonadal sex change. The brain-mediated mechanisms that underlie and initiate this transformation, however, remain poorly understood.
NEW ZEALAND JOURNAL OF ZOOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Andrew T. M. Bagshaw, Neil J. Gemmell
Summary: In recent years, scientists have shifted their focus from studying the relationships between adjacent nucleotides to exploring the larger scale structure of DNA. A little-known technique called non-denaturing bisulfite modification of genomic DNA in conjunction with high-throughput sequencing has provided valuable insights. This technique has revealed a gradient in reactivity that increases towards the 5' end of poly-dC:dG mononucleotide repeats, suggesting the presence of positive-roll bending not predicted by existing models. Furthermore, these repeats are enriched at positions relative to the nucleosome dyad that bend towards the major groove, providing important information about DNA packaging.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Nataliya Timoshevskaya, Kaan Eskut, Vladimir A. Timoshevskiy, Sofia M. C. Robb, Carson Holt, Jon E. Hess, Hugo J. Parker, Cindy F. Baker, Allison K. Miller, Cody Saraceno, Mark Yandell, Robb Krumlauf, Shawn R. Narum, Ralph T. Lampman, Neil J. Gemmell, Jacquelyn Mountcastle, Bettina Haase, Jennifer R. Balacco, Giulio Formenti, Sarah Pelan, Ying Sims, Kerstin Howe, Olivier Fedrigo, Erich D. Jarvis, Jeramiah J. Smith
Summary: Programmed DNA loss is a gene silencing mechanism found in various vertebrate and nonvertebrate lineages. The evolution of somatically eliminated sequences in these species has been difficult to reconstruct due to repetitive and duplicated sequences. However, an improved assembly of the sea lamprey genome has enabled analysis that sheds light on the recruitment of genes to the germline-specific fraction and reveals the roles of segmental duplication and positive selection in the long-term evolution of germline-specific chromosomes.
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)
Meeting Abstract
Zoology
K. A. Morrissey, J. Samson, M. Rivera, L. Bu, V. L. Hansen, N. J. Gemmell, M. G. Gardner, T. Bertozzi, R. D. Miller
INTEGRATIVE AND COMPARATIVE BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Anna C. Clark, Rey Edison, Kevin Esvelt, Sebastian Kamau, Ludovic Dutoit, Jackson Champer, Samuel E. Champer, Philipp W. Messer, Alana Alexander, Neil J. Gemmell
Summary: This manuscript introduces a framework for identifying and evaluating target genes based on biological gene function, gene expression, and results from mouse knockout models. The framework identifies 16 genes essential for male fertility and 12 genes important for female fertility that may be feasible targets for mammalian gene drives and other genetic pest control technologies.
MOLECULAR ECOLOGY RESOURCES
(2023)
