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Genome and population evolution and environmental adaptation of Glyptosternon maculatum on the Qinghai-Tibet Plateau

Shi-Jun Xiao Zen-Bo Mou Rui-Bin Yang Ding-Ding Fan Jia-Qi Liu Yu Zou Shi-Lin Zhu Ming Zou Chao-Wei Zhou Hai-Ping Liu

Shi-Jun Xiao, Zen-Bo Mou, Rui-Bin Yang, Ding-Ding Fan, Jia-Qi Liu, Yu Zou, Shi-Lin Zhu, Ming Zou, Chao-Wei Zhou, Hai-Ping Liu. Genome and population evolution and environmental adaptation of Glyptosternon maculatum on the Qinghai-Tibet Plateau. Zoological Research, 2021, 42(4): 502-513. doi: 10.24272/j.issn.2095-8137.2021.096
Citation: Shi-Jun Xiao, Zen-Bo Mou, Rui-Bin Yang, Ding-Ding Fan, Jia-Qi Liu, Yu Zou, Shi-Lin Zhu, Ming Zou, Chao-Wei Zhou, Hai-Ping Liu. Genome and population evolution and environmental adaptation of Glyptosternon maculatum on the Qinghai-Tibet Plateau. Zoological Research, 2021, 42(4): 502-513. doi: 10.24272/j.issn.2095-8137.2021.096

青藏高原黑斑原鮡的基因组与群体进化和环境适应性研究

doi: 10.24272/j.issn.2095-8137.2021.096

Genome and population evolution and environmental adaptation of Glyptosternon maculatum on the Qinghai-Tibet Plateau

Funds: This project was supported by the Key Research and Development Projects in Tibet: Preservation of Characteristic Biological Germplasm Resources and Utilization of Gene Technology in Tibet (XZ202001ZY0016N), National Natural Science Foundation of China (32072980), and Special Finance of Tibet Autonomous Region (XZNKY-2019-C-053)
More Information
  • 摘要: 持续的海拔抬升使得青藏高原成为了研究基因组进化和高原环境适应性理想的“天然实验室”。目前,尚不清楚古地理和古气候是如何影响高原特色鱼类的基因组和群体进化的。黑斑原鮡是一种青藏高原特有的极危鮡科鱼类。该研究发现黑斑原鮡基因组内的主要转座子序列发生了周期性地扩张,扩张的时间与青藏高原形成过程中的主要地理和气候时间高度吻合。更有意思的是,黑斑原鮡基因组内的组蛋白发生了大量扩张,研究发现组蛋白的扩张可能是由于LINE重复序列复制介导的。群体研究表明,黑斑原鮡群体分别在约260万年和1万年前经历了二次大规模的种群衰退,时间上与第四季末次冰期和新仙女木事件时间一致。因此,我们推测青藏高原的古地理和古气候是高原鱼类基因组和群体进化的主要推动力。古地质运动和气候波动都可以破坏和改变原始高原鱼类赖以生存的栖息地和水系,从而导致了黑斑原鮡群体的瓶颈效应并限制了群体之间的基因交流,这有可能就是目前黑斑原鮡群体遗传多样性较低和处于极危状态的原因。
    # Authors contributed equally to this work
  • Figure  1.  Sampling sites (red spot) for fish species on the Qinghai-Tibet Plateau

    Altitude is represented by color bar. Species abbreviations are: Glyptosternon maculatum (GM), Exostoma labiatum (EL), Pareuchiloglanis feae (PF), Pareuchiloglanis kamengensis (PK), Glyptothorax quadriocellatus (GQ), Glyptothorax fukiensis honghensis (GFH), Glyptothorax interspinalum (GI), Glyptothorax cavia (GC), Glyptothorax dorsalis (GD), Glyptothorax zainaensis (GZ), Glyptothorax trilineatus (GT), Glyptothorax minimaculatus (GMN), Glyptothorax laosensis (GL), Bagarius yarrelli (BY), Pseudecheneis sulcatus (PS), and Leiocassis longirostris (LL).

    Figure  2.  Phylogeny among sisorid catfish on Qinghai-Tibet Plateau and repeat content comparison of Glyptosternon maculatum to other teleosts

    A: Phylogeny of QTP sisorid fish collected using transcriptome data and G. maculatum genome. Species highlighted by colors from glyptosternoid and non-glyptosternoid belong to Sisoridae, while other species are not from the family. Speciation divergence periods are labeled at branches with 95% confidence interval in parentheses. Divergence periods with red points were used for time recalibration. B: Repeat content in genomes of species closely related to G. maculatum and detailed repetitive element categories, including LINE (red), LTR (green), DNA transposon (blue), and other (blank).

    Figure  3.  Expansion of LINE/RTE-BovB and LINE/L2 in Glyptosternon maculatum genome with tectonic movements and climate change during Qinghai-Tibet Plateau formation

    A: Episodic bursts of RTE-BovB (red) and L2 (green) around ~30, ~20, and ~5-1 Mya after India-Eurasia collision, corresponding to Gangdese Movement and two uplift accelerations of QTP ~30 Mya (black dashed line). Recent burst is highlighted in red. Gray shows major tectonic movements. B: Global surface temperature (solid black line) and decrease in temperature per million years (dashed line) after plate collision. Data were collected from a previous paleoclimatology study (Zachos et al., 2001).

    Figure  4.  Transposon mediated expansion of histone and folate-related functional genes in Glyptosternon maculatum genome

    A: GO functional enrichment for expanded gene families in G. maculatum genome. B: Number of histones and their positional relationship with transposons in G. maculatum genome, compared with their counterparts in P. fulvidraco and I. punetaus. Color represents repetitive types. C: Distribution of insertion times for all LINE/L2 and those with histone genes. D: Expanded and naturally selected genes in folate metabolism. E: Expansion of mthfd1l gene in G. maculatum genome compared to P. fulvidraco and I. punetaus genomes. F: Synteny of repetitive elements around duplicated mthfd1l gene in G. maculatum genome. LINE RTE-BovB (red) and L2 (green) content is shown around genes.

    Figure  5.  Population structure and history for Glyptosternon maculatum

    A: Geographical representation of GM2900 (red), GM4100 (blue), and GM4500 (green). B: Principal component analysis (PCA) for all samples using whole-genome variants. C: Phylogenetic relationship among samples based on whole-genome variant data. D: Genetic structures of population samples. E: Average altitude of QTP (left Y axis and black sold line), relative Eurasian ice volume (left Y axis and blue dashed line), and effective population size from MSMC (right Y axis and solid red/blue/green line) in last 4 Mya. Effective population size (Ne) profiles were deduced from MSMC. Altitude of QTP and relative Eurasian ice volume were referenced from previous study (Yang et al., 2016). Gray highlights major tectonic movements. F: Demographic scenario for three populations deduced from G-PhoCS. Color scheme for each population is identical to above plot, and width indicates relative effective population size. Branch represents splits among populations. Numbers on arrows show migration rates among populations. Major climate events, including Quaternary glaciation ~2.6 Mya and Younger Dryas ~10 kyr BP, are labeled with red triangles along geological time.

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出版历程
  • 收稿日期:  2021-03-28
  • 录用日期:  2021-07-09
  • 网络出版日期:  2021-07-13
  • 刊出日期:  2021-07-18

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