Genome-wide analysis reveals regional patterns of drift, structure, and gene flow in longfin smelt (Spirinchus thaleichthys) in the northeastern Pacific

İsmail K Sağlam,Amanda J Finger,Randall Baxter,James Hobbs,Levi S Lewis,Alyssa Benjamin

doi:10.1139/cjfas-2021-0005

Abstract

The southernmost stock of longfin smelt (Spirinchus thaleichthys) is approaching extirpation in the San Francisco Estuary (SFE); however, patterns of genetic structure, diversity and gene flow which are vital for management are poorly understood in this species. Here, we use genome-wide data to evaluate population structure of longfin smelt across a broad latitudinal scale across estuaries ranging from the SFE to Yakutat Bay and Lake Washington, and fine scale within the Fraser River and the SFE. Results indicate high genetic structure between major estuaries, fine-scale structure within the Fraser River, and low levels of structure within the SFE. Genetic structure was more pronounced between northern estuaries whereas southern estuaries showed shared ancestry and ongoing gene flow, most notably unidirectional northward migration out of the SFE. Furthermore, we detected signatures of local adaptation within the Fraser River and the Skeena River estuaries. Taken together, our results identify broad patterns of genetic diversity in longfin smelt shaped by co-ancestry, unidirectional migration and local adaptation. Results also suggest that the SFE population is genetically distinct from northernmost populations and an important source for maintaining nearby populations.

Highlights

Small pelagic forage fishes form an energy conduit from primary producers to top predators and are a critical link in coastal food webs (Lenfest Forage Fish Task Force 2012; Pikitch et al 2014)
Genetic structure and differentiation Genetic structure for longfin smelt throughout their range was high as sampling locations along the northeastern Pacific coast were clearly separated from one another along the four significant PC axes (Fig. 2)
We did not capture any separations among the four San Francisco Estuary (SFE) locations (ALVS, Chipps Island (CHPI), Petaluma River (PETA) and Suisun Bay (SUIB)), between the Fraser locations, nor between COLR and Humboldt Bay (HUMB) along any of the significant PC axes (Fig. 2)

Summary

Introduction

Small pelagic forage fishes form an energy conduit from primary producers to top predators and are a critical link in coastal food webs (Lenfest Forage Fish Task Force 2012; Pikitch et al 2014). Eulachon (Thaleichthys pacificus) was once abundant in many estuaries from San Francisco Bay to the southeastern Bering Sea, but for the past two decades has declined in the southern portion of its range. In Puget Sound, surf smelt (Hypomesus pretiosus), a common, recreationally harvested forage fish has precipitously declined (Greene et al 2015), and in the San Francisco Estuary (SFE), the delta smelt (Hypomesus transpacificus) and the longfin smelt (Spirinchus thaleichthys) are possibly approaching extinction and extirpation, respectively, in the near future (Hobbs et al 2017)

Methods

Results

Discussion

Conclusion