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Cis -regulatory differences in isoform expression associate with life history strategy variation in Atlantic salmon

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What this work says

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

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Reproductive Ecology: A Tale of Two Sexes

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Life history evolution: successes, limitations, and prospects

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From vestigial to vestigial-like: the Drosophila gene that has taken wing

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Drosophila doublesex gene controls somatic sexual differentiation by producing alternatively spliced mRNAs encoding related sex-specific polypeptides

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Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

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Evolving New Skeletal Traits by cis -Regulatory Changes in Bone Morphogenetic Proteins

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Tick-Bacteria Mutualism Depends on B Vitamin Synthesis Pathways

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Antagonistic regulation of spermatogonial differentiation in zebrafish (Danio rerio) by Igf3 and Amh

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Spermatogenesis in fish

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The role of Amh signaling in teleost fish – Multiple functions not restricted to the gonads

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Evolutionary changes in cis and trans gene regulation

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Morphological evolution caused by many subtle-effect substitutions in regulatory DNA

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Life history trade-offs at a single locus maintain sexually selected genetic variation

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A promoter-level mammalian expression atlas

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Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche

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Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon

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The Atlantic salmon genome provides insights into rediploidization

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Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

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Rapid sex-specific evolution of age at maturity is shaped by genetic architecture in Atlantic salmon

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Sex-dependent dominance maintains migration supergene in rainbow trout

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Vgll3 and the Hippo pathway are regulated in Sertoli cells upon entry and during puberty in Atlantic salmon testis

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Bayesian inference in threshold models using Gibbs sampling

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Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean

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clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

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SIRE EVALUATION AND GENETIC TRENDS

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STAR: ultrafast universal RNA-seq aligner

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fastp: an ultra-fast all-in-one FASTQ preprocessor

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Genome-wide association and longitudinal analyses reveal genetic loci linking pubertal height growth, pubertal timing and childhood adiposity

inferredcites →https://doi.org/10.1093/nar/gkx1165openalex-snapshot

Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues

inferredcites →https://doi.org/10.1098/rspb.2015.3064openalex-snapshot

Genetic basis of adult migration timing in anadromous steelhead discovered through multivariate association testing

inferredcites →https://doi.org/10.1098/rspb.2018.0935openalex-snapshot

Genomic variation underlying complex life-history traits revealed by genome sequencing in Chinook salmon

inferredcites →https://doi.org/10.1101/780437openalex-snapshot

Large single-locus effects for maturation timing are mediated via body condition in Atlantic salmon

inferredcites →https://doi.org/10.1101/gad.274027.115openalex-snapshot

Mechanisms of Hippo pathway regulation

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Analysis of the floral transcriptome uncovers new regulators of organ determination and gene families related to flower organ differentiation in Gerbera hybrida (Asteraceae)

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Comparing parent–offspring regression with frequentist and Bayesian animal models to estimate heritability in wild populations: a simulation study for Gaussian and binary traits

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Increasing the efficiency of MCMC for hierarchical phylogenetic models of categorical traits using reduced mixed models

inferredcites →https://doi.org/10.1111/j.1439-0426.2011.01851.xopenalex-snapshot

Restoring migratory salmonid populations in regulated rivers in the northernmost Baltic Sea area, Northern Finland - biological, technical and social challenges

inferredcites →https://doi.org/10.1111/j.1558-5646.1991.tb04354.xopenalex-snapshot

ON THE LOW HERITABILITY OF LIFE-HISTORY TRAITS

inferredcites →https://doi.org/10.1111/j.1558-5646.2008.00450.xopenalex-snapshot

THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?

inferredcites →https://doi.org/10.1111/jfb.13149openalex-snapshot

From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome‐wide approaches in Atlantic salmon Salmo salar

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Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

inferredcites →https://doi.org/10.1126/science.1230612openalex-snapshot

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Selective trade-offs maintain alleles underpinning complex trait variation in plants

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Pattern and variability in the breeding system of Atlantic salmon (Salmo salar), with comparisons to other salmonids

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The RNA Polymerase II Core Promoter

inferredcites →https://doi.org/10.1186/s12864-017-4205-5openalex-snapshot

Integrative testis transcriptome analysis reveals differentially expressed miRNAs and their mRNA targets during early puberty in Atlantic salmon

inferredcites →https://doi.org/10.1186/s12942-015-0017-5openalex-snapshot

Diet-related chronic disease in the northeastern United States: a model-based clustering approach

inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

inferredcites →https://doi.org/10.1186/s13059-018-1536-8openalex-snapshot

Clust: automatic extraction of optimal co-expressed gene clusters from gene expression data

inferredcites →https://doi.org/10.1194/jlr.m032755openalex-snapshot

Vestigial-like 3 is an inhibitor of adipocyte differentiation

inferredcites →https://doi.org/10.1242/jcs.225946openalex-snapshot

VGLL3 operates via TEAD1, TEAD3 and TEAD4 to influence myogenesis in skeletal muscle

inferredcites →https://doi.org/10.1371/journal.pcbi.1006360openalex-snapshot

ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization

inferredcites →https://doi.org/10.1371/journal.pgen.1005628openalex-snapshot

The vgll3 Locus Controls Age at Maturity in Wild and Domesticated Atlantic Salmon (Salmo salar L.) Males

inferredcites →https://doi.org/10.1371/journal.pgen.1008152openalex-snapshot

Two modes of transvection at the eyes absent gene of Drosophila demonstrate plasticity in transcriptional regulatory interactions in cis and in trans

inferredcites →https://doi.org/10.15252/msb.20145970openalex-snapshot

Predominant contribution of cis‐regulatory divergence in the evolution of mouse alternative splicing

inferredcites →https://doi.org/10.15252/msb.20166941openalex-snapshot

Pervasive isoform‐specific translational regulation via alternative transcription start sites in mammals

inferredcites →https://doi.org/10.1534/g3.119.400882openalex-snapshot

Transcription Profiles of Age-at-Maturity-Associated Genes Suggest Cell Fate Commitment Regulation as a Key Factor in the Atlantic Salmon Maturation Process

inferredcites →https://doi.org/10.1534/genetics.109.104984openalex-snapshot

Cis-regulatory Changes atFLOWERING LOCUS TMediate Natural Variation in Flowering Responses ofArabidopsis thaliana

inferredcites →https://doi.org/10.1534/genetics.112.140954openalex-snapshot

Comparing Enhancer Action in Cis and in Trans

inferredcites →https://doi.org/10.18637/jss.v033.i02openalex-snapshot

MCMC Methods for Multi-Response Generalized Linear Mixed Models: The MCMCglmm R Package

inferredcites →https://doi.org/10.7554/elife.05290openalex-snapshot

A recurrent regulatory change underlying altered expression and Wnt response of the stickleback armor plates gene EDA

What points at this work

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

inferred← citeshttps://doi.org/10.1098/rspb.2020.0867openalex-snapshot

Genetic growth potential, rather than phenotypic size, predicts migration phenotype in Atlantic salmon

inferred← citeshttps://doi.org/10.1111/mec.15822openalex-snapshot

Heterogeneous genetic basis of age at maturity in salmonid fishes

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