Article
Biochemistry & Molecular Biology
Sara Kurland, Atal Saha, Naomi Keehnen, Maria de la Paz Celorio-Mancera, David Diez-del-Molino, Nils Ryman, Linda Laikre
Summary: This study assesses the temporal trends in genetic diversity in Swedish wild brown trout populations using whole genome sequencing and newly adopted indicators. The results show declines in diversity in some lakes and high levels of inbreeding. The study also identifies genes related to skin pigmentation, reproduction, and immunity that may be undergoing adaptive selection.
Article
Multidisciplinary Sciences
Sarah L. Chang, Hillary G. M. Ward, Michael A. Russello
Summary: Differentiating life history variants is crucial for fisheries management, especially in mixed-stock fisheries where traditional survey methods may not be accurate. A study developed a GT-seq panel with 288 targeted SNPs to accurately identify kokanee stock in British Columbia, Canada, achieving high self-assignment accuracy and perfect assignment to geographic basin, migratory form, and reproductive ecotype. The GT-seq panel was successfully applied to Wood Lake, demonstrating high concordance with previous assignments and scalability for future applications.
Article
Chemistry, Analytical
Ethan Stancliffe, Michaela Schwaiger-Haber, Miriam Sindelar, Matthew J. Murphy, Mette Soerensen, Gary J. Patti
Summary: The success of precision medicine relies on collecting large-scale data from populations. This study presents an untargeted metabolomics workflow for large-scale projects and uses a reference sample and computational approaches for data processing, resulting in distinct features associated with geographic location.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Ethan Stancliffe, Michaela Schwaiger-Haber, Miriam Sindelar, Matthew J. Murphy, Mette Soerensen, Gary J. Patti
Summary: This paper presents an untargeted metabolomics workflow designed for large-scale projects, which includes evaluating a reference sample and using specific computational methods for data processing and analysis. The study identifies distinct features associated with the geographic location of participants.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Simon Blanchet, Laura Fargeot, Allan Raffard
Summary: This paper proposes using candidate genes phylogenetically-conserved across species as an inclusive biodiversity unit that transcends the intra- and interspecific boundaries, deepening our understanding of how evolution has shaped biodiversity and how biodiversity alters ecological dynamics. The framework combines knowledge from functional genomics and functional ecology, providing guidelines and examples for identifying phylogenetically-conserved candidate genes (PCCGs) within communities and measuring biodiversity from PCCGs. This framework also links biodiversity measured at PCCGs to ecosystem functions and highlights the eco-evolutionary processes shaping PCCG diversity patterns.
Article
Biochemistry & Molecular Biology
Dominic G. G. Swift, Shannon J. J. O'Leary, R. Dean Grubbs, Bryan S. S. Frazier, Andrew T. T. Fields, Jayne M. M. Gardiner, J. Marcus Drymon, Dana M. M. Bethea, Tonya R. R. Wiley, David S. S. Portnoy
Summary: Understanding microevolutionary forces and population structure is crucial for effective management of exploited species. This study investigated the genetic structure of blacktip sharks using mitochondrial sequences and SNP-containing loci. The results revealed three genetically distinct units, suggesting regional philopatry and local adaptation. The findings highlight the importance of conserving essential habitats to maintain adaptive variation and enhance species resilience against environmental change.
Article
Biochemistry & Molecular Biology
Matthew J. Christmas, Julia C. Jones, Anna Olsson, Ola Wallerman, Ignas Bunikis, Marcin Kierczak, Valentina Peona, Kaitlyn M. Whitley, Tuuli Larva, Alexander Suh, Nicole E. Miller-Struttmann, Jennifer C. Geib, Matthew T. Webster
Summary: Evidence suggests that gene flow commonly occurs between recently diverged species, despite barriers to gene flow. Genetic barriers to gene flow often accumulate in regions of low recombination and near centromeres.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biodiversity Conservation
Phoebe A. Burns, Kevin C. Rowe, Marissa L. Parrott, Emily Roycroft
Summary: Modern sequencing approaches, especially museum genomics, have allowed for the reconstruction of population decline and extinction by integrating genomic data from collections across decades. Understanding species declines is crucial for conservation and genetic management, particularly in Australia where European invasion has led to the highest rate of mammal extinction. Using historical museum specimens and tissue collections, researchers generated genomic data from extinct and surviving populations of the endangered Australian Pookila. The study revealed significant loss of genetic diversity and highlighted the vulnerability of small remnant populations to extinction.
BIOLOGICAL CONSERVATION
(2023)
Article
Biodiversity Conservation
Michael H. H. Price, Jonathan W. Moore, Brendan M. Connors, Kyle L. Wilson, John D. Reynolds
Summary: The study revealed that wild sockeye salmon populations in the Skeena River watershed have declined over the past century, but the artificial enhancement of one population has offset these declines to maintain aggregate levels similar to historical ones. Population diversity has decreased by 70%, with a shift in life-history diversity. Despite stability in total returns, a reduction in spatial extent may impact local fisheries and ecosystems.
JOURNAL OF APPLIED ECOLOGY
(2021)
Article
Ecology
Emily Roycroft, Craig Moritz, Kevin C. Rowe, Adnan Moussalli, Mark D. B. Eldridge, Roberto Portela Miguez, Maxine P. Piggott, Sally Potter
Summary: The application of high-throughput, short-read sequencing to degraded DNA has increased the feasibility of generating genomic data from historical museum specimens. However, the success and quality of sequence data can vary greatly. This study found that DNA sequence libraries prepared from toe pad or bone subsamples performed significantly better than those taken from the skin for historical rodent specimens. The choice of mapping approach also influenced the final data quality and population genomic inference. Accurate and reliable sequence data from historical specimens has important outcomes for evolutionary studies.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Carl R. Hutter, Kerry A. Cobb, Daniel M. Portik, Scott L. Travers, Perry L. Wood, Rafe M. Brown
Summary: Researchers introduced a genomic resource suite called FrogCap, consisting of approximately 15,000 markers for evolutionary studies in frogs. The modular design of FrogCap allows for selection of different types of markers and SNPs based on the desired phylogenetic scale. The study demonstrated the effectiveness of FrogCap for deep phylogenetic relationships and shallow population genetics studies.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biodiversity Conservation
Orly Razgour, Cecilia Montauban, Francesca Festa, Daniel Whitby, Javier Juste, Carlos Ibanez, Hugo Rebelo, Sandra Afonso, Michael Bekaert, Gareth Jones, Carol Williams, Katherine Boughey
Summary: Anthropogenically driven environmental changes have led to severe declines of wildlife populations, with little empirical evidence to understand historical population trends. This study develops molecular approaches to provide evidence of historic population changes and identifies drivers of these changes, showing significant declines in bat populations and their relationship to colonial shipbuilding and loss of large oak trees. Genomic approaches can inform conservation management and species recovery interventions, bridging the gap between genomic research and direct conservation applications. Collaborative studies for other priority species are urgently needed.
JOURNAL OF APPLIED ECOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Fatima Sanchez-Barreiro, Shyam Gopalakrishnan, Jazmin Ramos-Madrigal, Michael Westbury, Marc de Manuel, Ashot Margaryan, Marta M. Ciucani, Filipe G. Vieira, Yannis Patramanis, Daniela C. Kalthoff, Zena Timmons, Thomas Sicheritz-Ponten, Love Dalen, Oliver A. Ryder, Guojie Zhang, Tomas Marques-Bonet, Yoshan Moodley, M. Thomas P. Gilbert
Summary: Large vertebrates, such as the white rhinoceros, have experienced significant decline in populations due to human activities. Genetic data from resequenced white rhinoceros genomes show a decrease in genomic diversity and increase in inbreeding coefficients, especially in the northern white rhinoceros (NWR) and the southern white rhinoceros (SWR). Despite the genetic impacts, the surviving SWR does not show a significant accumulation of genetic load compared to its historical counterpart. These findings have implications for informing conservation efforts for white rhinoceros populations.
Article
Genetics & Heredity
Eric B. Rondeau, Kris A. Christensen, David R. Minkley, Jong S. Leong, Michelle T. T. Chan, Cody A. Despins, Anita Mueller, Dionne Sakhrani, Carlo A. Biagi, Quentin Rougemont, Eric Normandeau, Steven J. M. Jones, Robert H. Devlin, Ruth E. Withler, Terry D. Beacham, Kerry A. Naish, Jose M. Yanez, Roberto Neira, Louis Bernatchez, William S. Davidson, Ben F. Koop
Summary: The coho salmon populations in North America have significantly declined, and analysis of genomic data suggests bottleneck events after glacial retreat as a possible cause. A chromosome-level genome assembly and genome resequencing of 83 coho salmon were performed to aid in stock management and conservation efforts.
G3-GENES GENOMES GENETICS
(2023)
Article
Fisheries
Terry D. Beacham, Colin Wallace, Kim Jonsen, Ben J. G. Sutherland, Carrie Gummer, Eric B. Rondeau
Summary: This study utilized genetic analysis to accurately determine population structure and stock identification of Pacific Chinook salmon, providing important references for fishery management and offering new conservation strategies for Canadian Chinook salmon.
CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES
(2021)
Article
Multidisciplinary Sciences
Atal Saha, Matthew Kent, Lorenz Hauser, Daniel P. Drinan, Einar E. Nielsen, Jon-Ivar Westgaard, Sigbjorn Lien, Torild Johansen
Summary: This study reveals significant genetic differentiation among different ecotypes of Sebastes mentella, indicating potential local adaptation. The research also identifies additional sub-structuring within the 'shallow' and 'deep' pelagic ecotypes. The findings provide novel genomic tools for future investigations and management of S. mentella.
Article
Fisheries
Martin Lindegren, Mikael van Deurs, Aurore Maureaud, James T. Thorson, Dorte Bekkevold
Summary: Many marine fish species have wide distribution, but failing to acknowledge distinct populations within these species may lead to overestimation of stock's harvest potential. This study developed a statistical approach to identify population boundaries for European sprat, revealing regional differences in abundance patterns and confirming genetic studies showing reproductive isolation between different regions. The statistical approach can complement genetic methods and guide spatial management efforts for sustainable exploitation under changing climate conditions.
ICES JOURNAL OF MARINE SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Johanna Sunde, Yeserin Yildirim, Petter Tibblin, Dorte Bekkevold, Christian Skov, Oscar Nordahl, Per Larsson, Anders Forsman
Summary: Understanding the relative effects of isolation by distance, environment, and resistance on neutral and adaptive genetic diversity is crucial for biodiversity protection. Studies show that different modes of isolation interactively shape genetic variation patterns, with neutral variation influenced by all three modes and adaptive variation mainly influenced by environmental conditions.
Article
Biochemistry & Molecular Biology
Belen Jimenez-Mena, Hugo Flavio, Romina Henriques, Alice Manuzzi, Miguel Ramos, Dorte Meldrup, Janette Edson, Snaebjorn Palsson, Gudbjorg Asta Olafsdottir, Jennifer R. Ovenden, Einar Eg Nielsen
Summary: This research presents specific guidelines and considerations for designing capture sequencing experiments for population genetics, focusing on neutral genomic regions and regions subject to selection. The bait design process for three fish species was described, and the performance of the approach was evaluated across historical and modern samples. The supeRbaits R-package, which implements the workflow used for designing the bait sets, is user-friendly and versatile.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biodiversity Conservation
Konstantinos Gkagkavouzis, Spiros Papakostas, Francesco Maroso, Nikoleta Karaiskou, Adrian Carr, Einar Eg Nielsen, Luca Bargelloni, Alexandros Triantafyllidis
Summary: This study investigates aquaculture-induced evolution in gilthead seabream using a panel of 1159 genome-wide SNPs, identifying candidate SNPs and associated genes related to stress tolerance, disease resistance, and sexual maturation. The findings suggest evidence of aquaculture-induced evolution in the species, despite its suggested early stage of domestication, and call for further research with higher density SNP panels to elucidate the genomic architecture of domestication in gilthead seabream.
Article
Fisheries
Sunnvor Kongsstovu, Svein-Ole Mikalsen, Eydna Homrum, Jan Arge Jacobsen, Thomas D. D. Als, Hannes Gislason, Paul Flicek, Einar Eg Nielsen, Hans Atli Dahl
Summary: The study investigated the genetic population structure of herring in the Faroese and surrounding waters, developing genetic markers to distinguish between different herring management units. Results showed all four stocks appeared to be genetically differentiated populations, with lower levels of differentiation observed between two of the populations.
FISHERIES RESEARCH
(2022)
Article
Fisheries
Helle Torp Christensen, Frank Riget, Anja Retzel, Erik Haar Nielsen, Einar Eg Nielsen, Rasmus Berg Hedeholm
Summary: Mixed-stock fisheries pose challenges for management, and this study demonstrates the practical application of high-resolution genetic stock monitoring in managing mixed Atlantic cod stocks in western Greenland.
ICES JOURNAL OF MARINE SCIENCE
(2022)
Article
Environmental Sciences
Steen Wilhelm Knudsen, Martin Hesselsoe, Jens Thaulow, Sune Agersnap, Brian Klitgaard Hansen, Magnus Wulff Jacobsen, Dorte Bekkevold, Soren K. S. Jensen, Peter Rask Moller, Jesper H. Andersen
Summary: Researchers have developed and validated eDNA assays for marine nonindigenous species. The results show that eDNA sampling is faster and easier compared to conventional monitoring methods, and the use of eDNA can provide more accurate information on the distribution of species.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Multidisciplinary Sciences
Alice Manuzzi, Belen Jimenez-Mena, Romina Henriques, Bonnie J. Holmes, Julian Pepperell, Janette Edson, Mike B. Bennett, Charlie Huveneers, Jennifer R. Ovenden, Einar E. Nielsen
Summary: Over the last century, shark populations have declined due to overexploitation and the use of shark control programs. A study in eastern Australia found a significant change in the genetic composition of tiger sharks born between 1939 and 2015, suggesting a shift in the relative contribution of two cryptic populations.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Edward D. D. Farrell, Leif Andersson, Dorte Bekkevold, Neil Campbell, Jens Carlsson, Maurice W. W. Clarke, Afra Egan, Arild Folkvord, Michael Gras, Susan Maersk Lusseau, Steven Mackinson, Cormac Nolan, Steven O'Connell, Michael O'Malley, Martin Pastoors, Mats E. E. Pettersson, Emma White
Summary: This study utilized genetic sequencing to analyze Atlantic herring, revealing temporal and spatial differences between populations and developing a highly accurate genetic assignment model to determine the population origin of herring caught.
ROYAL SOCIETY OPEN SCIENCE
(2022)
Article
Fisheries
Dorte Bekkevold, Florian Berg, Patrick Polte, Valerio Bartolino, Henn Ojaveer, Henrik Mosegaard, Edward D. Farrell, Jelena Fedotova, Jakob Hemmer-Hansen, Bastian Huwer, Vanessa Trijoulet, Christoffer Moesgaard Albertsen, Angela P. Fuentes-Pardo, Tomas Groehsler, Mats Pettersson, Teunis Jansen, Arild Folkvord, Leif Andersson
Summary: We developed and validated a mixed-stock analysis (MSA) method to assign individuals to populations in mixed-stock samples of Atlantic herring. The method showed unprecedented accuracy in monitoring spatio-temporal dynamics with complex stock mixing. The analysis revealed potential overestimation of certain stocks and the importance of re-evaluating stock definitions.
ICES JOURNAL OF MARINE SCIENCE
(2023)
Article
Fisheries
P. Urban, D. Bekkevold, H. Degel, B. K. Hansen, M. W. Jacobsen, A. Nielsen, E. E. Nielsen
Summary: Environmental DNA (eDNA) is useful for species identification and quantification in fisheries, especially in estimating bycatch proportions. In this study, we used experimental set-ups to simulate fishery catches and tested the suitability of different types of water for species quantification. By using species-specific quantitative PCR, we found a strong correlation between species-to-species weight fractions and eDNA fractions in mixtures. Accounting for size-based differences in DNA abundance improved the accuracy of bycatch assessment, thus enhancing the quality of fisheries-dependent data.
ICES JOURNAL OF MARINE SCIENCE
(2023)
Article
Multidisciplinary Sciences
Eeva Jansson, Ellika Faust, Dorte Bekkevold, Maria Quintela, Caroline Durif, Kim Tallaksen Halvorsen, Geir Dahle, Christophe Pampoulie, James Kennedy, Benjamin Whittaker, Laila A. Unneland, Soren Post, Carl Andre, Kevin A. Glover
Summary: Using two approaches, researchers investigated the population genetic structure of the lumpfish in the North Atlantic and found extensive population structuring, including a major split between the East and West Atlantic and a distinct Baltic Sea population. The study suggests that despite its potential for dispersal and gene-flow, the lumpfish exhibits natal homing behavior and local populations with adaptive differences.
Article
Multidisciplinary Sciences
Guobjoerg Asta Olafsdottir, Shaun Turnbull, Ingibjoerg G. Jonsdottir, Anja Nickel, Hjalti Karlsson, Theresa Henke, Einar Eg Nielsen, Snaebjoern Palsson
Summary: Atlantic cod, an economically important fish in the North Atlantic, shows population variation and life-history changes. A study in NW-Iceland found distinct segregation of juvenile cod by depth. Understanding the physiological mechanism behind this segregation is important for marine spatial planning and conservation tools.