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Low‐coverage whole‐genome sequencing reveals molecular markers for spawning season and sex identification in Gulf of Maine Atlantic cod (Gadus morhua, Linnaeus 1758)

https://doi.org/10.1002/ece3.7878
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Genome‐enabled prediction through machine learning methods considering different levels of trait complexity
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Modular chromosome rearrangements reveal parallel and nonparallel adaptation in a marine fish
inferredcites →https://doi.org/10.1002/ece3.7878openalex-snapshot
Low‐coverage whole‐genome sequencing reveals molecular markers for spawning season and sex identification in Gulf of Maine Atlantic cod (Gadus morhua, Linnaeus 1758)
inferredcites →https://doi.org/10.1007/978-3-319-24277-4openalex-snapshot
ggplot2
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RAD Sequencing Highlights Polygenic Discrimination of Habitat Ecotypes in the Panmictic American Eel
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Gene selection with guided regularized random forest
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Stock identification and its role in stock assessment and fisheries management: an overview
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An holistic approach to fish stock identification
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Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions
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Fast gapped-read alignment with Bowtie 2
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Characterization of a male specific region containing a candidate sex determining gene in Atlantic cod
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Ectopic expression of a bacterial mercury transporter MerC in root epidermis for efficient mercury accumulation in shoots of Arabidopsis plants
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Three chromosomal rearrangements promote genomic divergence between migratory and stationary ecotypes of Atlantic cod
inferredcites →https://doi.org/10.1038/srep31235openalex-snapshot
Genomic characterization of the Atlantic cod sex-locus
inferredcites →https://doi.org/10.1038/srep34897openalex-snapshot
Correction: Corrigendum: Expression of GhNAC2 from G. herbaceum, improves root growth and imparts tolerance to drought in transgenic cotton and Arabidopsis
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/gbe/evv093openalex-snapshot
Adaptation to Low Salinity Promotes Genomic Divergence in Atlantic Cod ( Gadus morhua L.)
inferredcites →https://doi.org/10.1093/gbe/evw057openalex-snapshot
“Islands of Divergence” in the Atlantic Cod Genome Represent Polymorphic Chromosomal Rearrangements
inferredcites →https://doi.org/10.1093/icesjms/fsq053openalex-snapshot
Simulation modelling as a tool for examining the consequences of spatial structure and connectivity on local and regional population dynamics
inferredcites →https://doi.org/10.1093/icesjms/fsu032openalex-snapshot
Stock identification of Atlantic cod (Gadus morhua) in US waters: an interdisciplinary approach
inferredcites →https://doi.org/10.1093/icesjms/fsu040openalex-snapshot
Fine-scale diel and gender-based patterns in behaviour of Atlantic cod (Gadus morhua) on a spawning ground in the Western Gulf of Maine
inferredcites →https://doi.org/10.1093/icesjms/fsu117openalex-snapshot
Spawning site fidelity by Atlantic cod (Gadus morhua) in the Gulf of Maine: implications for population structure and rebuilding
inferredcites →https://doi.org/10.1093/icesjms/fsz083openalex-snapshot
The relative importance of sub-populations to the Gulf of Maine stock of Atlantic cod
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Genome-wide prediction for complex traits under the presence of dominance effects in simulated populations using GBLUP and machine learning methods
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Effect of dietary medium-chain fatty acids on nursery pig growth performance, fecal microbial composition, and mitigation properties against porcine epidemic diarrhea virus following storage
inferredcites →https://doi.org/10.1098/rspb.2010.0985openalex-snapshot
Parallel adaptive evolution of Atlantic cod on both sides of the Atlantic Ocean in response to temperature
inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
inferredcites →https://doi.org/10.1101/gr.176552.114openalex-snapshot
An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data
inferredcites →https://doi.org/10.1111/1755-0998.12593openalex-snapshot
Practical low‐coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species
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assign POP : An r package for population assignment using genetic, non‐genetic, or integrated data in a machine‐learning framework
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Genomic islands of divergence and their consequences for the resolution of spatial structure in an exploited marine fish
inferredcites →https://doi.org/10.1111/eva.12055openalex-snapshot
Spatiotemporal SNP analysis reveals pronounced biocomplexity at the northern range margin of A tlantic cod G adus morhua
inferredcites →https://doi.org/10.1111/eva.12524openalex-snapshot
Applications of random forest feature selection for fine‐scale genetic population assignment
inferredcites →https://doi.org/10.1111/eva.12861openalex-snapshot
Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole‐genome sequencing
inferredcites →https://doi.org/10.1111/j.1755-0998.2010.02846.xopenalex-snapshot
Assessing the power of informative subsets of loci for population assignment: standard methods are upwardly biased
inferredcites →https://doi.org/10.1111/mec.12284openalex-snapshot
A genomic island linked to ecotype divergence in A tlantic cod
inferredcites →https://doi.org/10.1111/mec.12454openalex-snapshot
Genomic divergence between the migratory and stationary ecotypes of A tlantic cod
inferredcites →https://doi.org/10.1111/mec.13211openalex-snapshot
Integration of Random Forest with population‐based outlier analyses provides insight on the genomic basis and evolution of run timing in Chinook salmon (Oncorhynchus tshawytscha)
inferredcites →https://doi.org/10.1111/mec.13592openalex-snapshot
Two adjacent inversions maintain genomic differentiation between migratory and stationary ecotypes of Atlantic cod
inferredcites →https://doi.org/10.1111/mec.14207openalex-snapshot
Genome architecture enables local adaptation of Atlantic cod despite high connectivity
inferredcites →https://doi.org/10.1111/mec.14442openalex-snapshot
Ancient chromosomal rearrangement associated with local adaptation of a postglacially colonized population of Atlantic Cod in the northwest Atlantic
inferredcites →https://doi.org/10.1126/science.aac9819openalex-snapshot
Slow adaptation in the face of rapid warming leads to collapse of the Gulf of Maine cod fishery
inferredcites →https://doi.org/10.1139/cjfas-2017-0254openalex-snapshot
Genomic tools for management and conservation of Atlantic cod in a coastal marine protected area
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Toolboxes for a standardised and systematic study of glycans
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Identification of three novel OA1 gene mutations identified in three families misdiagnosed with congenital nystagmus and carrier status determination by real-time quantitative PCR assay
inferredcites →https://doi.org/10.1186/1471-2156-4-s1-s64openalex-snapshot
Mapping complex traits using Random Forests
inferredcites →https://doi.org/10.1186/s12711-019-0503-5openalex-snapshot
Strong selection pressures maintain divergence on genomic islands in Atlantic cod (Gadus morhua L.) populations
inferredcites →https://doi.org/10.1186/s12859-014-0356-4openalex-snapshot
ANGSD: Analysis of Next Generation Sequencing Data
inferredcites →https://doi.org/10.1186/s12864-016-3448-xopenalex-snapshot
An improved genome assembly uncovers prolific tandem repeats in Atlantic cod
inferredcites →https://doi.org/10.1186/s12864-017-3660-3openalex-snapshot
Highly localized divergence within supergenes in Atlantic cod (Gadus morhua) within the Gulf of Maine
inferredcites →https://doi.org/10.1186/s12864-017-3806-3openalex-snapshot
Whole genome sequencing reveals within-host genetic changes in paired meningococcal carriage isolates from Ethiopia
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KAML: improving genomic prediction accuracy of complex traits using machine learning determined parameters
inferredcites →https://doi.org/10.1186/s13059-020-1930-xopenalex-snapshot
CUBIC: an atlas of genetic architecture promises directed maize improvement
inferredcites →https://doi.org/10.1371/journal.pone.0106380openalex-snapshot
Long Distance Linkage Disequilibrium and Limited Hybridization Suggest Cryptic Speciation in Atlantic Cod
inferredcites →https://doi.org/10.1371/journal.pone.0216992openalex-snapshot
Adaptive genetic variation underlies biocomplexity of Atlantic Cod in the Gulf of Maine and on Georges Bank
inferredcites →https://doi.org/10.1371/journal.pone.0217841openalex-snapshot
Suicidal ideations among medical students: The role of anhedonia and type D personality
inferredcites →https://doi.org/10.1534/genetics.118.301336openalex-snapshot
Inferring Population Structure and Admixture Proportions in Low-Depth NGS Data
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
inferredcites →https://doi.org/10.3354/meps06983openalex-snapshot
Dispersal modeling of fish early life stages: sensitivity with application to Atlantic cod in the western Gulf of Maine
inferredcites →https://doi.org/10.3354/meps08612openalex-snapshot
Fine-scale spatial and temporal genetic structure of Atlantic cod off the Atlantic coast of the USA
inferredcites →https://doi.org/10.3389/fpls.2020.00388openalex-snapshot
An Updated Checklist of the Sicilian Native Edible Plants: Preserving the Traditional Ecological Knowledge of Century-Old Agro-Pastoral Landscapes
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Genome-Wide Prediction of Complex Traits in Two Outcrossing Plant Species Through Deep Learning and Bayesian Regularized Neural Network
inferredcites →https://doi.org/10.48550/arxiv.1306.0237openalex-snapshot
Guided Random Forest in the RRF Package

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1111/jfb.70070zenodo-depositor-declared
Prematuration differences in male and female Atlantic cod: Investigating sex ratio, length and ecotype disparities in juveniles
inferred← citeshttps://doi.org/10.1111/fme.12655openalex-snapshot
Genetic sex determination improves Canadian Atlantic salmon ( Salmo salar ) population assessments
inferred← citeshttps://doi.org/10.1139/cjfas-2022-0232openalex-snapshot
Quantifying genetic differentiation and population assignment between two contingents of Atlantic mackerel (Scomber scombrus) in the Northwest Atlantic
inferred← citeshttps://doi.org/10.3389/fmars.2023.978694openalex-snapshot
Analysis of reproductive traits reveals complex population dynamics on a small geographical scale in Atlantic herring
inferred← citeshttps://doi.org/10.3390/ani13061089openalex-snapshot
Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations
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