Population Genomic Analysis of Two Endemic Schizothoracins Reveals Their Genetic Differences and Underlying Selection Associated with Altitude and Temperature

Animals : an Open Access Journal From MDPI
Tianyan YangBaocheng Guo

Abstract

Schizothoracins are a group of cyprinid fishes distributed throughout the Qinghai-Tibet Plateau, which can be classified in three grades: primitive, specialised and highly specialised according to adaptation ability to plateau environments. As the only specialised schizothoracins in Xinjiang, China, Diptychus maculates and Gymnodiptychus dybowskii are ideal materials for adaptive evolution research. Based on single-nucleotide polymorphism (SNP) loci detected by specific-locus amplified fragment (SLAF) technology, the genome-wide genetic diversities of these two species from nine sites in Xinjiang were evaluated. D.maculates in the Muzat River (BM) and G. dybowskii in the Kaidu River (LKG) presented the lowest genetic diversity levels, whereas D. maculates in the Kumarik River (BK) and G.dybowskii in the Kashi River (LK) were just the opposite. Cluster and principal component analysis demonstrated a distant genetic affinity between D. maculates in the Tashkurgan River (BT) and other populations. Outlier SNP loci were discovered both in D. maculates and G. dybowskii. The coalescent Bayenv and latent factor mixed model (LFMM) methods showed that a total of thirteen and eighteen SNPs in D. maculates were associated with altitude an...Continue Reading

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Datasets Mentioned

BETA
PRJNA599030

Methods Mentioned

BETA
genotyping
PCA
gene exchange

Software Mentioned

BayeScan
PGDSpider
Plink
R package
Stacks
ADE4
Vcftools
SAMtools
- Aligner ( BWA
R package ‘ ADE4 ’

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