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.

taimen_allSamples.vcf.gz

vcf file after stringent filtering steps for the dataset in which all samples from all basins were analyzed together. File compressed using gzip.

taimen_pacificSubset.vcf.gz

vcf file after stringent filtering steps for the dataset in which the Pacific subset of samples from Amur and Tugur basins were analyzed. File compressed using gzip.

taimen_fastqs.tar.gz

Directory including all fastq files for each individual included in this study. Compressed as a tar archive. 

fastq_IDs_withPops.csv

csv file matching individual fastq IDs with populations.

barcodes.pl

Custon Perl script for correcting one or two bp sequencing errors in barcode sequences, remove barcodes and cut-site associated bases, and match sequences with individual sample names. ****We have become aware that some of the MIDs we used are 1 bp Levenshtein edit distance from one another and that therefore, different MID sets should be used in the future. This was not an issue with the MIDs used for this study, but for a larger collection.