Zona pellucida (ZP3) sequence data from 230 Pacific cod (phased)

Genetic differentiation has been observed in marine species even when no
obvious barriers to gene flow exist, and understanding such
differentiation is essential for effective fisheries management. Highly
differentiated outlier loci can provide information on how genetic
variation might contribute to local adaptation but may also be affected by
historical demographic events. A locus which aligned to a predicted zona
pellucida sperm-binding protein 3 gene (ZP3) in Atlantic cod (Gadus
morhua) was previously identified as the highest outlier based on FST in a
RADseq study of Pacific cod (Gadus macrocephalus) across the West Coast of
North America. However, because of the limited length of the RAD sequence
and restricted geographic area of sampling, no conclusion on the
functional significance of the observed variation was possible. In other
marine species, ZP3 is involved in reproductive isolation, local
adaptation, and has neofunctionalized as an antifreeze gene, and so it may
provide important insights in functional population structure of Pacific
cod. Here, we sequenced a 544 bp region of ZP3 in 230 Pacific cod
collected from throughout their geographic range. We observed striking
patterns of spatial structuring of ZP3 haplotypes, with a sharp break near
Kodiak, Alaska, USA where populations within ~200 km of each other are
nearly fixed for different haplotypes, contrasting a pattern of isolation
by distance at other genetic markers in this region (FST = 0.003).
Phylogenetic analysis of ZP3 haplotypes revealed that the more southern
haplotypes appear to be ancestral, with the northern haplotype evolving
more recently, potentially in response to a novel selective pressure as
Pacific cod recolonized northern latitudes after glaciation. The sharp
break in haplotype frequencies suggests strong selective pressures are
operating on small spatial scales and illustrates that selection can
create high divergence even in marine species with ample opportunities for
gene flow.