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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

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Published on: June 23, 2012

Genomic differentiation in Pacific cod using Pool-Seq.

Ingrid Spies¹, Carolyn Tarpey², Trond Kristiansen³

¹Resource Ecology and Fisheries Management Division Alaska Fisheries Science Center Seattle Washington USA.

Evolutionary Applications

|November 25, 2022

Summary

Genomic islands reveal adaptive differentiation in Pacific cod populations. Despite gene flow, distinct genetic patterns suggest adaptation in vision genes between Bering Sea and Aleutian Island cod.

Keywords:

Pacific cod Pool‐Seq genomic differentiation genomics local adaptation selection selection–migration balance

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Area of Science:

Genomics
Population Genetics
Marine Biology

Background:

Genetic differentiation patterns offer insights into adaptation.
Pacific cod (Gadus macrocephalus) populations exhibit varying degrees of divergence.

Purpose of the Study:

To evaluate genomic differentiation patterns in Pacific cod.
To investigate mechanisms driving divergence among proximate and distant populations.
To identify genomic regions associated with adaptation.

Main Methods:

Pooled whole genome sequencing and gene annotation.
Analysis of environmental covariates.
Calculation of relative divergence (FST) and absolute divergence (dXY).

Main Results:

Eleven genomic islands of differentiation were identified between Aleutian Islands and Bering Sea populations.
Elevated absolute divergence and evidence for selection were found in some genomic islands.
Islands of differentiation were associated with vision system genes.

Conclusions:

Pacific cod populations show evidence of adaptive differentiation despite gene flow.
Genomic islands highlight localized adaptation in response to environmental pressures.
Vision system genes may play a role in adaptive divergence.