Hierarchical genetic structure and implications for conservation of the world\u2019s largest salmonid, Hucho taimen

Lanie M Galland,Zeb Hogan,Agusto R Luzuriaga-Neira,Olaf P Jensen,Thomas L Parchman,Matthew R Sloat,Joshua P Jahner,James B Simmons,Sudeep Chandra

doi:10.1038/s41598-021-99530-3

Lanie M Galland, Zeb Hogan + Show 7 more

Open Access

https://doi.org/10.1038/s41598-021-99530-3

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Abstract

Population genetic analyses can evaluate how evolutionary processes shape diversity and inform conservation and management of imperiled species. Taimen (Hucho taimen), the world’s largest freshwater salmonid, is threatened, endangered, or extirpated across much of its range due to anthropogenic activity including overfishing and habitat degradation. We generated genetic data using high throughput sequencing of reduced representation libraries for taimen from multiple drainages in Mongolia and Russia. Nucleotide diversity estimates were within the range documented in other salmonids, suggesting moderate diversity despite widespread population declines. Similar to other recent studies, our analyses revealed pronounced differentiation among the Arctic (Selenge) and Pacific (Amur and Tugur) drainages, suggesting historical isolation among these systems. However, we found evidence for finer-scale structure within the Pacific drainages, including unexpected differentiation between tributaries and the mainstem of the Tugur River. Differentiation across the Amur and Tugur basins together with coalescent-based demographic modeling suggests the ancestors of Tugur tributary taimen likely diverged in the eastern Amur basin, prior to eventual colonization of the Tugur basin. Our results suggest the potential for differentiation of taimen at different geographic scales, and suggest more thorough geographic and genomic sampling may be needed to inform conservation and management of this iconic salmonid.

Highlights

Population genetic data is relevant for shaping conservation, restoration, and management activities, and for understanding the response of populations to environmental change
We used catch and release fly fishing to obtain samples from 174 taimen using single, barbless hooks, from five sites across northern Mongolia and four sites in southeastern Russia (Fig. 1, Table 1). These sites are distributed across river systems that drain to the Arctic (Eg, Uur, Delgermörön) and those that drain to the Pacific (Amur basin: Upper and Lower Onon; Tugur basin: Konin, Munikan, Konin/Assyni Junction, and Tugur mainstem)
Using high throughput sequencing of reduced representation libraries, we documented hierarchical patterns of genetic differentiation among taimen sampled across multiple drainages

Summary

Introduction

Population genetic data is relevant for shaping conservation, restoration, and management activities, and for understanding the response of populations to environmental change. Modern high throughput sequencing technologies have enabled genome-wide perspectives and improved our ability to quantify genetic variation across populations, including those of conservation concern[1,2] Reduced representation approaches such as restriction site-associated DNA sequencing (RADseq) and genotyping-by-sequencing (GBS)[3] have facilitated genomewide population genetic analyses in organisms without genomic resources, and have often recovered patterns of fine-scale genetic structure and resolved patterns of recent diversification that were not evident with traditional molecular marker s ystems[4,5]. The apparent monogamous nature of taimen spawning behavior, as well as the timing of pair bond formation, could potentially promote spatial genetic differentiation at some scales despite large movements

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