DOI: 10.5061/dryad.msbcc2g5z
title: Data from: Population genomics of endangered lenoks (<em>Brachymystax</em> spp.) in China reveals the presence of cryptic species

description: Lenoks, species within the genus Brachymystax, are freshwater salmonids
 with a scattered distribution in the rivers of Siberia, Northeast China,
 Xinjiang, Hebei, and the Qinling Mountains. Owing to long-term population
 declines, all species assigned to
 Brachymystax are protected by law in China. However, the
 evolutionary history and species-level systematics of this genus remain
 controversial, complicating taxonomic designations and conservation
 efforts. In particular, the geographical separation of populations may
 have resulted in the formation of phenotypically similar cryptic species.
 We built a chromosome-level genome assembly of B.
 tsinlingensis and re-sequenced the genomes of 103 individuals of
 Chinese Brachymystax spp. from
 five geographically isolated
 locations. Population genomic and phylogenomic analyses based on
 nuclear SNPs and mitochondrial genomes revealed six different genetic
 lineages, of which at least one, the Hebei
 lineage, represents a cryptic species. Notably,
 the results suggest that the sympatric species B.
 lenok and B. tumensis are not close relatives,
 but the former is more closely related to the new species
 B. sp. Xinjiang with an estimated divergence time of c. 630
 Ka, indicating that closely-related sympatric species
 may not have evolved via sympatric speciation in areas influenced
 by Pleistocene climate changes. We observed mito-nuclear
 phylogenomic discordance in Brachymystax caused by the strong
 gene flow between B. lenok and B. tumensis. Phylogenetic
 and demographic analyses emphasize the important role of interglacial
 refugia in promoting speciation and underscore the impact of historical
 gene flow. Compared to other lenoks, the Gansu population had the lowest
 genetic diversity, suggesting that particular attention to protect its
 genetic resources may be required. Finally, we suggest that cross-regional
 proliferation and release of lenoks should be banned in the future to
 protect the genetic integrity of these divergent groups.
description: # Lenok_SNP.nexus ``` Description: Neighbor-joining (NJ) phylogenetic tree
 constructed based on genome-wide single nucleotide polymorphisms (SNPs)
 Content: Including all 103 resequenced samples used in this study Format:
 Nexus ``` Lenok_MT.nexus ``` Description: Neighbor-joining (NJ)
 phylogenetic tree constructed based on mitochondrial DNA (mtDNA) sequences
 Content: Including the complete mitochondrial DNA sequences generated from
 the 103 resequenced samples in this study Format: Nexus ``` Lenok.MT.fa
 ``` Description: Mitochondrial sequences generated for 103 resequenced
 samples using the mia software Content: Including 103 mitochondrial DNA
 sequences with sequence IDs consistent with Supplemental Table S1 Format:
 Fasta ``` Lenok.SNP.fa.gz ``` Description: SNP consensus sequences used
 for constructing the phylogenetic tree (Lenok_SNP.nexus), which are core
 analytical sequences filtered from genome-wide SNP loci as described in
 the manuscript Content: Including SNP consensus sequences of 103 samples
 with sequence IDs consistent with Supplemental Table S1, as well as the
 Atlantic salmon sequence (SLM01) as the outgroup Format: Gzip-compressed
 fasta ``` Lenok.BEAST.fa ``` Description: SNP data used for Bayesian
 factor analysis in the BEAST software, generated by random sampling of the
 whole genome and conversion of homozygous/heterozygous loci Content:
 Including data of 103 samples with sequence IDs consistent with
 Supplemental Table S1 Format: Fasta (0 = homozygous for reference allele,
 1 = heterozygous, 2 = homozygous for alternative allele) ```
 Lenok.ILS_TREE.tar.gz ``` Description: Tree files used for quIBL analysis.
 100 bp SNP alignment fragments were randomly extracted for four target
 three-population combinations (HLJL-XIN-HLJT, SNX-HEB-HLJT, SNX-HEB-HLJL,
 SNX-HEB-XIN), and 500,000 tree files were generated for each combination
 through 100 independent quIBL runs Content: Including four folders, each
 containing a single tree file with 500,000 trees Format: Newick ```
 Supplemental_Table_S1.csv ``` Description: Detailed record of the basic
 information of the 103 individuals subjected to genome-wide resequencing
 in this study Format: Sample ID (unique identification number of the
 genome-wide resequenced individual); Population Name (abbreviation of the
 population to which the individual belongs); Breeds (species/lineage to
 which the individual belongs); Province (sampling province of the
 individual); City/Country (sampling city/district/county of the
 individual); Sample Site (specific sampling location of the individual
 (river/basin)); Depth (genome-wide resequencing depth); MSMC2 (whether the
 individual was used for MSMC2 analysis (population historical dynamics
 inference analysis)) ``` Supplemental_Table_S4.csv ``` Description:
 Quality metrics of the raw sequencing data of the 103 individuals
 subjected to genome-wide resequencing in this study Format: Sample ID
 (unique identification number of the genome-wide resequenced individual);
 Population Name (abbreviation of the population to which the individual
 belongs); RawReads (number of raw reads obtained by sequencing); RawBases
 (total amount of raw bases obtained by sequencing); Length (length of
 sequencing reads); Q20 (proportion of bases with a sequencing quality
 value ≥20); Q30 (proportion of bases with a sequencing quality value ≥30);
 GC (GC base content ratio of sequencing sequences) ```
 Supplemental_Table_S5.csv ``` Description: Analysis results of the
 NewHybrids software, used to determine whether hybridization events
 occurred in HLJL and HLJT populations and identify hybrid offspring
 samples Format: Sample (analysis serial number of the sample); IndivName
 (unique identification number of the sample for hybridization analysis,
 consistent with Sample ID); 1.000/0.000/0.000/0.000 (posterior probability
 of the sample belonging to homozygous parent 1 (P1));
 0.000/0.000/0.000/1.000 (posterior probability of the sample belonging to
 homozygous parent 2 (P2)); 0.000/0.500/0.500/0.000 (posterior probability
 of the sample belonging to F1 hybrid (P1×P2 first filial generation));
 0.250/0.250/0.250/0.250 (posterior probability of the sample belonging to
 F2 hybrid (F1×F1 second filial generation)); 0.500/0.250/0.250/0.000
 (posterior probability of the sample belonging to backcross generation 1
 (F1×P1)); 0.000/0.250/0.250/0.500 (posterior probability of the sample
 belonging to backcross generation 1 (F1×P2)) ``` Supplemental_Table_S6.csv
 ``` Description: Optimal likelihood run results of population genetic
 simulation analysis using the Fastsimcoal3 software Format: Including
 ancestral population size (ANCSIZE); population sizes of different
 lineages (L(HLJL), M(HLJT), S(SNX), X(XIN), G(GAN), H(HEB)) (NPOPL, NPOPM,
 NPOPS, NPOPX, NPOPG, NPOPH); population divergence times (e.g., TDIV1,
 TDIV2, TDIV3, TDIV5); population fusion/contact times (e.g., TINT_LM,
 TINT_HM, TINT_HL); lineage divergence completion times
 (TDIVCOMP1~TDIVCOMP4); bidirectional migration rates (e.g., MIGLM,
 MIGML,MIGHM, MIGMH); maximum estimated likelihood value (MaxEstLhood);
 maximum observed likelihood value (MaxObsLhood) ``` Supplemental_File.pdf
 ``` Description: Including Supplemental Table S2, Supplemental Table S3,
 Supplemental Table S7 and Supplemental Figure S1-S10 Table_S2: Short
 summary of BUSCO Table_S3: Summary of repeats Table_S7: BF values of
 different species delimitation models FIGURE S1. Four alternative models
 for Fastsimcoal3 simulation. FIGURE S2. Heatmap of Hi-C analysis for the
 assembled reference genome. Chromosomes were sorted and named by size,
 with blue outlines. FIGURE S3. Circos plot of sequence synteny between
 Brachymystax tsinlingensis and Salmo salar. Chromosomes and their lengths
 are labeled and colored on the outer ring. FIGURE S4. Genomic landscape of
 Brachymystax tsinlingensis. A: Gene density; B: GC content; C: Total
 repeat density; D: SNP density. FIGURE S5. Pattern of SNP numbers across
 different lenok groups. FIGURE S6. Site frequency spectrum of six
 populations. FIGURE S7. Admixture analysis results for K = 2-7 with
 corresponding CV values. FIGURE S8. TreeMix analysis results for other
 different K values. FIGURE S9. OptM output for all TreeMix results. Upper
 panel: Mean and standard deviation (SD) of the composite likelihood L(m)
 and proportion of variance explained across five iterations. Bottom panel:
 Second-order rate of change (Δm) across different values of m. FIGURE S10.
 Distribution of Delta BIC values for the other three triplets
 (SNX-HEB-HLJL, SNX-HEB-HLJT, SNX-HEB-XIN). ```