Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations

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

Distribution of the p.V37I Variation in the Patient and Control Groups.

<p>Distribution of the p.V37I Variation in the Patient and Control Groups.</p

Hearing Levels in the Patient Groups with the Homozygous and Compound p.V37I Variant.

<p>The Friedman rank-sum test (M-test) was used to identify significant differences in hearing level among the groups, and H = 0.4375, P>0.25.</p><p>Hearing Levels in the Patient Groups with the Homozygous and Compound p.V37I Variant.</p

Hearing levels of patients with the p.V37I/c.235delC compound heterozygous variation.

<p>Hearing levels of patients with the p.V37I/c.235delC compound heterozygous variation.</p

The Relationship between the p.V37I Mutation in <i>GJB2</i> and Hearing Phenotypes in Chinese Individuals

<div><p>The most common cause of nonsyndromic autosomal recessive hearing loss is mutations in <i>GJB2</i>. The mutation spectrum and prevalence of mutations vary significantly among ethnic groups, and the relationship between p.V37I mutation in <i>GJB2</i> and the hearing phenotype is controversial. Among the 3,864 patients in this study, 106 (2.74%) had a homozygous p.V37I variation or a compound p.V37I plus other <i>GJB2</i> pathogenic mutation, a frequency that was significantly higher than that in the control group (600 individuals, 0%). The hearing loss phenotype ranged from mild to profound in all patients with the homozygous p.V37I variation or compound p.V37I plus other <i>GJB2</i> pathogenic mutation. There was no difference in the distribution of the hearing level in the group with the homozygous p.V37I variation and the group with the compound p.V37I variation plus pathogenic mutation. Most patients (66.04%) with the V37I-homozygous variation or p.V37I plus other pathogenic mutation had a mild or moderate hearing level. This study found a definite relationship between p.V37I and deafness, and most patients who carried the pathogenic combination with p.V37I mutation had mild or moderate hearing loss. Therefore, otolaryngologists should consider that the milder phenotype might be caused by the <i>GJB2</i> p.V37I mutation.</p></div