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Genomic islands of divergence infer a phenotypic landscape in Pacific lamprey
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  • Jon HessOrcid,
  • Jeramiah Smith,
  • Nataliya Timoshevskaya,
  • Cyndi Baker,
  • Christopher Caudill,
  • David Graves,
  • Matthew Keefer,
  • Andrew KinzigerOrcid,
  • Mary Moser,
  • Laurie Porter,
  • Greg Silver,
  • Steven Whitlock,
  • Shawn Narum
Jon Hess
Orcid
Columbia River Inter-Tribal Fish Commission
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Jeramiah Smith
University of Kentucky
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Nataliya Timoshevskaya
University of Kentucky
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Cyndi Baker
Oregon Department of Fish and Wildlife
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Christopher Caudill
University of Idaho
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David Graves
The Columbia River InterTribal Fish Commission
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Matthew Keefer
University of Idaho
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Andrew Kinziger
Orcid
Humboldt State University
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Mary Moser
Northwest Fisheries Science Center, NOAA Fisheries
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Laurie Porter
Columbia River Inter-Tribal Fish Commission
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Greg Silver
Columbia River Inter-Tribal Fish Commission
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Steven Whitlock
University of Washington
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Shawn Narum
Columbia River Inter-Tribal Fish Commission
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Peer review status:IN REVISION

01 Apr 2020Submitted to Molecular Ecology
02 Apr 2020Submission Checks Completed
02 Apr 2020Assigned to Editor
07 Apr 2020Reviewer(s) Assigned
03 Jun 2020Review(s) Completed, Editorial Evaluation Pending
09 Jun 2020Editorial Decision: Revise Minor
16 Jul 2020Review(s) Completed, Editorial Evaluation Pending
16 Jul 20201st Revision Received
20 Jul 2020Editorial Decision: Revise Minor
26 Jul 2020Review(s) Completed, Editorial Evaluation Pending
26 Jul 20202nd Revision Received

Abstract

Pacific lamprey (Entosphenus tridentatus) is a culturally important and imperiled anadromous fish with a parasitic ocean phase. Biological uncertainties challenge restoration efforts and life-history research is needed to explain observed trait variation and inform management actions. Using two new whole genome assemblies and genotypes from 7,716 single nucleotide polymorphism (SNP) loci in 518 individuals from across the species range, we identified four large regions of high genomic divergence (on chromosomes 01, 02, 04, and 22). We genotyped a subset of 302 broadly distributed SNPs in 2,145 individuals for genotype-by-phenotype trait associations for adult body size, sexual maturity, migration distance and timing, adult swimming ability, and larval growth. Body size traits were strongly associated with SNPs on chromosomes 02 and 04. Moderate associations also implicated SNPs on chromosome 01 as being associated with variation in female maturity. Using genotypic frequencies of candidate SNPs for female maturity and body size, we extrapolated a heterogeneous spatiotemporal distribution of these traits based on independent datasets of larval and adult collections. These maturity and body size results guide future studies to validate these predicted phenotypic distributions across the geographic range and elucidate factors driving regional optimization of these traits for fitness.