Data from: Investigating the extent of parallelism in morphological and genomic divergence among lake trout ecotypes in Lake Superior

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Description:
Understanding the emergence of species through the process of ecological speciation is a central question in evolutionary biology which also has implications for conservation and management. Lake Trout (Salvelinus namaycush) is renowned for the occurrence of different ecotypes linked to resource and habitat use throughout North America. We aimed to unravel the fine genetic structure of the four Lake Trout ecotypes in Lake Superior. A total of 486 individuals from four sites were genotyped at 6822 filtered SNPs using RADseq technology. Our results revealed different extent of morphological and genetic differentiation within the different sites. Overall, genetic differentiation was weak but significant and was on average three times higher between sites (Mean FST = 0.016) than between ecotypes within sites (Mean FST = 0.005) indicating higher level of gene flow or a more recent shared ancestor between ecotypes within each site than between populations of the same ecotype. Evidence of divergent selection was also found between ecotypes and/or in association with morphological variation. Outlier loci found in genes related to lipid metabolism and visual acuity were of particular interest in this context of ecotypic divergence. However, we did not find clear indication of parallelism at the genomic level, despite the presence of phenotypic parallelism among some ecotypes from different sampling sites. Overall, the occurrence of different levels of both genomic and phenotypic differentiation between ecotypes within each site with several differentiated loci linked to relevant biological functions support the presence of a continuum of divergence in Lake Trout.

Usage Notes:

Geometric morphometric data for body shape for Big Reef

Landmarks and semi-landmarks for body shape for Big Reef fish
Big_Reef_104indv_body.TPS

Genotype data in .vcf format

Filtered SNPs in .vcf format from 486 individuals genotyped at 6822 SNPS
data_6822filtered_snp_486indv_4pop.vcf

Geometric morphometric data for head shape for Big Reef

Landmarks and semi-landmarks for head shape for Big Reef
Big_Reef_104indv_head.TPS

Geometric morphometric data for body shape for Isle Royale

Landmarks and semi-landmarks for body shape for Isle Royale in .tps format
Isle_Royale_144indv_body.TPS

Geometric morphometric data for head shape for Isle Royale

Landmarks and semi-landmarks for head shape for Isle Royale in .tps format
Isle_Royale_144indv_head.TPS

Geometric morphometric data for body shape for Stannard Rock

Landmarks and semi-landmarks for body shape for Stannard Rock in .tps format
Stannard_Rock_128indv_body.TPS

Geometric morphometric data for head shape for Stannard Rock

Landmarks and semi-landmarks for head shape for Stannard Rock in .tps format
Stannard_Rock_128indv_head.TPS

Geometric morphometric data for body shape for Superior Shoals

Landmarks and semi-landmarks for body shape for Superior Shoals in .tps format
Superior_Shoals_125indv_body.TPS

Geometric morphometric data for head shape for Superior Shoals

Landmarks and semi-landmarks for head shape for Superior Shoals in .tps format
Superior_Shoals_125indv_head.TPS

sample_information

Information for each genotyped individuals
Author(s):
Perreault-Payette, Alysse

Perreault-Payette, Alysse

Université Laval
, Muir, Andrew M.

Muir, Andrew M.

Michigan State University
, Goetz, Frederick

Goetz, Frederick

Northwest Fisheries Science Center
, Perrier, Charles

Perrier, Charles

Université Laval
, Normandeau, Eric

Normandeau, Eric

Université Laval
0000-0003-2841-9391
, Sirois, Pascal

Sirois, Pascal

Université Laval
, and Bernatchez, Louis

Bernatchez, Louis

Université Laval
0000-0002-8085-9709
Source Repository:
Dryad
Publisher(s):
Dryad
Access:
Public
URL:
http://datadryad.org/stash/dataset/doi:10.5061/dryad.k713n
Publication date:
2017-01-17
Identifier:
https://doi.org/10.5061/dryad.k713n

Geospatial information

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Citation

APA Citation:
Perreault-Payette, A., Muir, A. M., Goetz, F., Perrier, C., Normandeau, E., Sirois, P., & Bernatchez, L. (2017). Data from: Investigating the extent of parallelism in morphological and genomic divergence among lake trout ecotypes in Lake Superior [Data set]. Dryad. http://datadryad.org/stash/dataset/doi:10.5061/dryad.k713n
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