A complex phenotype in salmon controlled by a simple change in migratory timing

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Science  30 Oct 2020:
Vol. 370, Issue 6516, pp. 609-613
DOI: 10.1126/science.aba9059

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Unexpectedly simple

Chinook salmon are known to return to spawn at two distinct times of the year: spring and fall. Individuals that return during these times have generally been referred to as parts of distinct groups, or ecotypes, with traits specific to their timing and presumed divergence being caused by the lack of interbreeding. By looking at genomes across fish from both runs, Thompson et al. found that a single genomic region of interest was nearly perfectly associated with run timing but not with other traits such as maturity and fat reserves (see the Perspective by McKinney). Further, they conclude that the region operates as a Mendelian trait, with assortment dictating run timing and associated phenotypes being caused by the migration environment rather than genetics.

Science, this issue p. 609; see also p. 526


Differentiation between ecotypes is usually presumed to be complex and polygenic. Seasonal patterns of life history in salmon are used to categorize them into ecotypes, which are often considered “distinct” animals. Using whole-genome sequencing and tribal fishery sampling of Chinook salmon, we show that a single, small genomic region is nearly perfectly associated with spawning migration timing but not with adiposity or sexual maturity, traits long perceived as central to salmon ecotypes. Distinct migration timing does not prevent interbreeding between ecotypes, which are the result of a simple, ancient polymorphism segregating within a diverse population. Our finding that a complex migratory phenotype results from a single gene region will facilitate conservation and restoration of this iconic fish.

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