Katrín Halldórsdóttir and Einar Árnason. 2019.  Extensive structural variation between ecotypes of Atlantic cod, Gadus morhua, revealed with linked-read sequencing and optical mapping.

Poster presented at Speciation: Gordon Research Conference, Ventura, California, USA. March 10--15, 2019.

Several “stocks” are recognized for fisheries management among Atlantic cod. The stocks are populations
that differ from each other in various biological traits, life history, habitat selection, and productivity, but their
evolutionary status and connectivity are debated. To what extent, if any, are they reproductively isolated?
In Norway, the migratory Northeast-Arctic cod and the stationary Norway coastal cod, which differ in otolith
shape and some phenotypes were considered cryptic sibling species (Møller, 1968) based on hemoglobin
and other protein variation, whereas Williams (1975) argued for panmixia and that strong natural selection in
every generation recreates the observed differentiation. These two forms are now referred to as the shallow-
water stationary or coastal and deep-water migratory or frontal behavioral ecotypes among Atlantic cod as
defined by storage tag data (Pampoulie et al., 2007). Chromosomal rearrangements on linkage group LG01
(Kirubakaran et al., 2016) and on linkage groups LG02, LG07, and LG12 (Berg et al., 2016) promote diver-
gence between the ecotypes. The reference genome sequence of Atlantic cod, Gadmor2 (Tørresen et al.,
2016), was based on DNA from the migratory frontal behavioral ecotype. Here, we study structural variation
using single molecule sequencing of DNA from a coastal ecotype specimen from Iceland and compare it to
the reference genome.

The large chromosomal rearrangements, primarily inversion, on linkage groups LG01, LG02, LG07, and LG12
have been interpreted as a case of genomic islands of divergence, associated with ecological divergence, un-
der high levels of gene flow between the two ecotypes (Hemmer-Hansen et al., 2013). Here we show, using
whole genome sequencing of single molecules and optical mapping, that the structural variation is much
more widespread over the genome than previously described. We found signs of large chromosomal structural variation in almost all Linkage groups, to a different extent. The results of the linked-read sequencing showed147 large structural variants calls (that are >= 30kb). These results show the importance of look-
ing at phased data when investigating structural variation. The observed chromosomal structural variation
likely suppresses recombination in heterozygotes thus affecting gene flow and local adaptation and promoting
reproductive isolation and speciation among ecotypes.