Living in each other’s pockets: Nucleotide variation inside a genomic island harboring Pan I and its neighbors in Atlantic cod
Author and article information
Abstract
The Pan I locus in Atlantic cod lies in a genomic island of divergence extending over a large genomic region. The locus has two divergent alleles, defined by a single DraI restriction site, that have been related to behavioral differences of habitat selection by depth and temperature. The Pan I locus is known to be under an unusual mix of balancing selection and selective sweeps within the functional types. Here we study nucleotide variation in a 12.5 kb region inside the genomic island harboring Pan I and neighboring loci for sortilin 1 (Sort1) and ataxin 7-like 2 (Atxn7l2) which we partially covered. Variation of the 31 gene copies throughout the region falls into two divergent haplogroups that correlate with the 25 copies of A and six copies of B alleles of Pan I. The unfolded site frequency spectrum for the part with Pacific cod used as the outgroup is trimodal with a mode at singletons and two high frequency modes at 6/31 and 25/31 representing the two genealogical lineages. The folded site frequency spectrum for the entire region similarly has a high frequency mode of mutations that have accumulated on the two lineages. The high frequency of singletons is accounted for by multiple merger coalescent models. Parameter estimates using these models indicate sweepstakes reproduction. The high frequency modes of the spectrum is evidence for balancing selection. Analysis of non-synonymous changes shows that Pan I is at least one focus of selection within the genomic island. There may be multiple sites of selection and epistatic interactions. There is extensive linkage disequilibrium throughout the region. We suggest that the genomic island of divergence is a supergene of co-adapted complexes possibly locked together by structural variation.
Cite this as
2015. Living in each other’s pockets: Nucleotide variation inside a genomic island harboring Pan I and its neighbors in Atlantic cod. PeerJ PrePrints 3:e956v1 https://doi.org/10.7287/peerj.preprints.956v1Author comment
This is a submission to PeerJ.
Sections
Supplemental Information
Supplement to: Living in each other’s pockets: Nucleotide variation inside a genomic island harboring Pan I and its neighbors in Atlantic cod
Gene order of the Pan I locus and its neighboring genes and its orthologs and paralogs across different species
The Pan I locus is the reference gene in the middle, flanked by the Sort1 and Atxn7l2 loci. Orthologs in other species are shown in matching colors. The blues structure at the left is a phylogenetic tree for the Pan I locus. The image is a Phyloview diagram computed by Genomicus (Louis et al., 2013; Muffato et al., 2010) with version 70.01 and search name ENSGMOG00000001154. Phylogenetic tree computed by Ensembl v.70 Flicek et al. (2014)
Additional Information
Competing Interests
The authors declare they have no competing interests.
Author Contributions
Ubaldo Benitez Hernandez conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper, prepared sequences for genebank.
Einar Árnason conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper, prepared sequences for genebank.
Animal Ethics
The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):
The Icelandic Committee for Welfare of Experimental Animals, Chief Veterinary Office at the Ministry of Agriculture, Reykjavik, Iceland has determined that the research conducted here is not subject to the laws concerning the Welfare of Experimental Animals (The Icelandic Law on Animal Protection, Law 15/1994, last updated with Law 157/2012). DNA was isolated from tissue taken from dead fish on board research vessels. Fish were collected during the yearly surveys of the Icelandic Marine Research Institute. All research plans and sampling of fish, including the ones for the current project, have been evaluated and approved by the Marine Research Institute Board of Directors. Samples were also obtained from dead fish from marine research institutes in Norway, the Netherlands, Canada and the US that were similarly approved by the respective ethics boards. The samples from the US used in this study have been described in Cunningham et al. (2009) and the samples from Norway in Árnason and Pálsson (1996a). The samples from Canada consisted of DNA isolated from the samples described in Pogson (2001). The samples
from the Netherlands were obtained from the Beam-Trawl-Survey
(http://www.wageningenur.nl/en/Expertise-Services/Research-Institutes/imares/Weblogs/Beam-Trawl-Survey.htm) of the Institute for Marine Resources & Ecosystem Studies (IMARES), Wageningen University, the Netherlands, which is approved by the IMARES Animal Care Committee and IMARES Board of Directors.
DNA Deposition
The following information was supplied regarding the deposition of DNA sequences:
GenBank accession numbers for sequences reported in this paper are KR011783–KR011814
Funding
Funding was provided by Icelandic Science Foundation grant of excellence (nr. 40303011), a University of Iceland Research Fund grant, a Svala Arnadóttir private foundation grant to Einar Árnason and a doctoral grant (nr. 100590001) from the Icelandic Research Fund for Graduate Students to Ubaldo Benitez Hernandez. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
