10.5061/DRYAD.ND853
Hess, Jon E.
Columbia River Inter-Tribal Fish Commission
Campbell, Nathan R.
Columbia River Inter-Tribal Fish Commission
Close, David A.
University of British Columbia
Docker, Margaret F.
University of Manitoba
Narum, Shawn R.
Columbia River Inter-Tribal Fish Commission
Data from: Population genomics of Pacific lamprey: adaptive variation in a
highly dispersive species
Dryad
dataset
2012
Genomics/Proteomics
Life History Evolution
Entosphenus tridentatus
Holocene
2012-10-31T16:03:30Z
2012-10-31T16:03:30Z
en
https://doi.org/10.1111/mec.12150
11552408 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Unlike most anadromous fishes that have evolved strict homing behaviour,
Pacific lamprey (Entosphenus tridentatus) seem to lack philopatry as
evidenced by minimal population structure across the species range. Yet
unexplained findings of within-region population genetic heterogeneity
coupled with the morphological and behavioural diversity described for the
species suggest that adaptive genetic variation underlying fitness traits
may be responsible. We employed restriction site–associated DNA sequencing
to genotype 4439 quality filtered single nucleotide polymorphism (SNP)
loci for 518 individuals collected across a broad geographical area
including British Columbia, Washington, Oregon and California. A subset of
putatively neutral markers (N = 4068) identified a significant amount of
variation among three broad populations: northern British Columbia,
Columbia River/southern coast and ‘dwarf’ adults (FCT = 0.02, P ≪ 0.001).
Additionally, 162 SNPs were identified as adaptive through outlier tests,
and inclusion of these markers revealed a signal of adaptive variation
related to geography and life history. The majority of the 162 adaptive
SNPs were not independent and formed four groups of linked loci. Analyses
with matsam software found that 42 of these outlier SNPs were
significantly associated with geography, run timing and dwarf life
history, and 27 of these 42 SNPs aligned with known genes or highly
conserved genomic regions using the genome browser available for sea
lamprey. This study provides both neutral and adaptive context for
observed genetic divergence among collections and thus reconciles previous
findings of population genetic heterogeneity within a species that
displays extensive gene flow.
Quality filtered genotypes of Pacific lamprey in GENEPOP formatGENEPOP
file: 518 Pacific lamprey individuals from 21 collections, genotyped with
a set of 4,439 quality filtered SNPs from a larger dataset of 8,772 unique
SNP loci identified using methods described by Hess et al. 2013.
"POP" headings delineate collections of individuals and include
collections names listed in Table 1, Hess et al.
2013.Lamprey_4439Loci518IndGP_DRYAD.txt
Oregon
British Columbia
California
Washington