doi: 10.1038/ncomms3708.
Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations
Xuming Zhou 1, Fengming Sun, Shixia Xu, Guangyi Fan, Kangli Zhu, Xin Liu, Yuan Chen, Chengcheng Shi, Yunxia Yang, Zhiyong Huang, Jing Chen, Haolong Hou, Xuejiang Guo, Wenbin Chen, Yuefeng Chen, Xiaohong Wang, Tian Lv, Dan Yang, Jiajian Zhou, Bangqing Huang, Zhengfei Wang, Wei Zhao, Ran Tian, Zhiqiang Xiong, Junxiao Xu, Xinming Liang, Bingyao Chen, Weiqing Liu, Junyi Wang, Shengkai Pan, Xiaodong Fang, Ming Li, Fuwen Wei, Xun Xu, Kaiya Zhou, Jun Wang, Guang Yang
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- PMID:24169659
- PMCID: PMC3826649
- DOI: 10.1038/ncomms3708
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Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations
Xuming Zhou et al. Nat Commun.2013.
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Abstract
The baiji, or Yangtze River dolphin (Lipotes vexillifer), is a flagship species for the conservation of aquatic animals and ecosystems in the Yangtze River of China; however, this species has now been recognized as functionally extinct. Here we report a high-quality draft genome and three re-sequenced genomes of L. vexillifer using Illumina short-read sequencing technology. Comparative genomic analyses reveal that cetaceans have a slow molecular clock and molecular adaptations to their aquatic lifestyle. We also find a significantly lower number of heterozygous single nucleotide polymorphisms in the baiji compared to all other mammalian genomes reported thus far. A reconstruction of the demographic history of the baiji indicates that a bottleneck occurred near the end of the last deglaciation, a time coinciding with a rapid decrease in temperature and the rise of eustatic sea level.
Figures
(a) Venn diagram showing unique and overlapping gene families in the baiji, common bottlenose dolphin, dog, human, and mouse. (b andc) Phylogenetic tree and divergence times estimated for the baiji and other mammals. Numbers associated with each terminal branch in light blue are mean rates of synonymous substitution values (rS). Numbers associated with each branch designate the number of gene families that have expanded (green) and contracted (red) since the split from the common ancestor. Triangle arrows and the numbers under them denote the most recent common ancestor (TMCRA), and the scale units are million years ago. The standard error range for each age is represented by the dashed line. The red solid circles on the branch nodes denote the node as an ‘age constraint’ used in the estimation of the time of divergence.
Smoothed curves on the top represent global climate, sea surface temperature (SST) of South China Sea, and global sea-level fluctuations. Horizontal dashed line marks present SST for modern times. The age units for all graphs are years.
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