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The Fraser River once supported massive salmon returns. However, over the last century, the largest returns have consistently been less than half of the recorded historical maximum. There is substantial interest from surrounding communities and governments to increase salmon returns for both human use and functional ecosystems. To generate resources for this endeavor, we resequenced genomes of Chinook (Oncorhynchus tshawytscha), coho (Oncorhynchus kisutch), and sockeye salmon (Oncorhynchus nerka) from the Fraser River at moderate coverage (∼16×). A total of 954 resequenced genomes were analyzed, with 681 collected specifically for this study from tissues sampled between 1997 and 2021. An additional 273 were collected from previous studies. At the species level, Chinook salmon appeared to have 1.6-2.1× more SNPs than coho or sockeye salmon, respectively. This difference may be attributable to large historical declines of coho and sockeye salmon. At the population level, 3 Fraser River genetic groups were identified for each species using principal component and admixture analyses. These were consistent with previous research and supports the continued use of these groups in conservation and management efforts. Environmental factors and a migration barrier were identified as major factors influencing the boundaries of these genetic groups. Additionally, 20 potentially adaptive loci were identified among the genetic groups. This information may be valuable in new management and conservation efforts. Furthermore, the resequenced genomes are an important resource for contemporary genomics research on Fraser River salmon and have been made publicly available.
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http://dx.doi.org/10.1093/g3journal/jkae169 | DOI Listing |
Ecology
December 2024
Wildlife Research and Monitoring Section, Ministry of Natural Resources and Forestry, Peterborough, Ontario, Canada.
Animals within social groups respond to costs and benefits of sociality by adjusting the proportion of time they spend in close proximity to other individuals in the group (cohesion). Variation in cohesion between individuals, in turn, shapes important group-level processes such as subgroup formation and fission-fusion dynamics. Although critical to animal sociality, a comprehensive understanding of the factors influencing cohesion remains a gap in our knowledge of cooperative behavior in animals.
View Article and Find Full Text PDFAAPS J
December 2024
Regeneron Pharmaceuticals, Bioanalytical Sciences, 777 Old Saw Mill River Road, Tarrytown, New York, 10591, USA.
The ADA testing strategy for protein therapeutics was established almost two decades ago when assay methodologies were rudimentary, and serious immunogenicity-related safety issues had recently been observed with some biotherapeutics. The current testing paradigm employs multiple tiers and stringent cut points to minimize false negatives, reflecting a conservative stance towards ADA analysis. The development of highly sensitive ADA assay platforms and technologies such as humanized or fully human monoclonal antibody (mAb) drugs has put the traditional, resource-intensive 3-tiered testing approach under scrutiny.
View Article and Find Full Text PDFJ Forensic Sci
December 2024
Centre for Forensic Research, School of Criminology, Simon Fraser University, Burnaby, British Columbia, Canada.
Early detection of submerged bodies is essential to increase the possibility of recovery. Different water bodies present different challenges, particularly rivers and the ocean, where chances of detection are vastly reduced. Modern recreational fish finders incorporate multiple sonar technologies, including Sidescan sonar, at high-frequency resolutions, similar to commercial units.
View Article and Find Full Text PDFNucleic Acids Res
December 2024
Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015.
View Article and Find Full Text PDFOrthop J Sports Med
November 2024
Luminis Health Orthopedics, Pasadena, Maryland, USA.
Background: As machine learning becomes increasingly utilized in orthopaedic clinical research, the application of machine learning methodology to cohort data from the Multicenter ACL Revision Study (MARS) presents a valuable opportunity to translate data into patient-specific insights.
Purpose: To apply novel machine learning methodology to MARS cohort data to determine a predictive model of revision anterior cruciate ligament reconstruction (rACLR) graft failure and features most predictive of failure.
Study Design: Cohort study; Level of evidence, 3.
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