Polygenic discrimination of migratory phenotypes in an estuarine forage fish

Abstract

Migration is a complex phenotypic trait with some species containing migratory and non-migratory individuals. Such life history variation may be attributed in part to plasticity, epigenetics, or genetics. Although considered semi-anadromous, recent studies using otolith geochemistry have revealed life history variation within the critically endangered Delta Smelt. Broadly categorizable as migratory or freshwater residents, we examined RADseq data to test for a relationship between genetic variation and migratory behaviors. As previously shown, we found no evidence for neutral population genetic structure within Delta Smelt; however, we found significant evidence for associations between genetic variants and life history phenotypes. Furthermore, Discriminant Analysis of Principal Components, hierarchical clustering, and machine learning resulted in accurate assignment of fish into the freshwater resident or migratory classes based on their genotypes. These results suggest the presence of adaptive genetic variants relating to life history variation within a panmictic population. Mechanisms that may lead to this observation are genotype dependent habitat choice and spatially variable selection, both of which could operate each generation and are not exclusive. Given that the population of cultured Delta Smelt are being used as a refugial population for conservation, as a supply for wild population supplementation, and currently represent the majority of all living individuals of this species, we recommend that the hatchery management strategy consider the frequencies of life history-associated alleles and how to maintain this important aspect of Delta Smelt biological variation while under captive propagation.

Population genomics, life‐history tactics, and mixed‐stock subsistence fisheries in the northernmost American Atlantic salmon populations

“…Indeed, since the time window in which temperature allows smolts to enter the sea in Ungava Bay is very short, late migrants are likely to get stuck in the estuary and have no choice but to adopt an estuarine tactic. Additional studies could investigate the potential role of water temperature, spatially variable selection, and genotype‐dependent habitat choices in this system (Campbell et al., 2022; Pavey et al., 2015).…”

Single generation epigenetic change in captivity and reinforcement in subsequent generations in a delta smelt (Hypomesus transpacificus) conservation hatchery

“…Recognition of life history variation in delta smelt is recent and occurred after the creation of refugial delta smelt population in 2008 and its management plans (Hobbs et al., 2019). Delta smelt are a single panmictic population representing both migratory (semi‐anadromous) and non‐migratory (freshwater resident, brackish water resident) life history types, with evidence of a heritable basis (Campbell et al., 2022). While the life history trajectories of broodstock taken into the hatchery are unknown, the semi‐anadromous life history has been predominant in wild fish in recent years (Hobbs et al., 2019) and likely was much more common in broodstock.…”

“…Delta smelt are a single panmictic population representing both migratory (semi-anadromous) and non-migratory (freshwater resident, brackish water resident) life history types, with evidence of a heritable basis (Campbell et al, 2022). While the life history F I G U R E 4 DNA methylation status of the differentially methylated regions (DMRs) in all the individuals.…”

Mitochondrial DNA and Microsatellite Analyses Showed Panmixia between Temporal Samples in Endangered Anguilla japonica in the Pearl River Basin (China)

“…Additionally, the panmictic phenomenon was also verified in Anguilla anguilla and Anguilla bicolor pacifica , indicating that panmixia is a common feature of eel species [ 36 , 37 ]. In addition, other migratory species such as Hilsa shad ( Tenualosa ilisha ), Delta Smelt ( Hypomesus transpacificus ) and Australian yellowfin bream ( Acanthopagrus australis ) also exhibited a panmictic character [ 43 , 44 , 45 ].…”