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

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.

The life aquatic: advances in marine vertebrate genomics

“…For example, the most enriched gene ontology categories for inferred regulatory elements that originated in tetrapods after their divergence from the coelacanth lineage were those associ ated with the sense of airborne smells 13,19 . By contrast, the gene family involved in olfactory receptor activity was the most decreased gene orthologue cluster in the genome of the Yangtze River dolphin, Lipotes vexillifer (known as the Baiji) 9 , and olfactory and taste receptors were under-represented in the genome of the minke whale, …”

“…Comparative genomic studies between sister marine and terrestrial species have provided insights into candidate functional genomic changes underpinning adaptation to the locomotory, sensory, thermal, osmoregulatory and pathogenic challenges associated with life in the sea [6][7][8][9] . At the population level, novel genomic approaches are emerging that can tease apart the complexity of the confounding effects of population structuring, large effective population size and high connectivity on population-level genetic inference 10 .…”

Molecular Footprints of Aquatic Adaptation Including Bone Mass Changes in Cetaceans

“…Recent sequencing efforts of several whales and dolphins have provided many insights into the potential evolutionary adaptations to aquatic lifestyle and physiology (Lindblad-Toh et al. 2011; Zhou et al. 2013, 2015; Yim et al.…”

The Role of Genomics in Conservation and Reproductive Sciences

“…Conservation genetics has historically focused on observed differences (or levels of genetic divergence) among individuals and populations, subspecies, or breeds of domestic animals as might be quantifi ed by (1) estimating mean observed and expected heterozygosity averaged over the typed loci, (2) the average number of alleles, or (3) allelic richness (Luikart and Cornuet 1998 ). When groups of individuals do not have a large number of fi xed differences (for example populations that are recently isolated or relatively inbred), molecular differentiation is estimated by differences in allele frequencies among populations as specifi c differences will be rare Zhou et al ( 2013 ) and most common alleles will be shared across groups (e.g. MacHugh et al 1998 ;Balloux and Lugon-Moulin 2002 ;Laval et al 2002 ).…”

“…This was done for the giant panda by Zhou et al ( 2013 ), who sequenced 34 pandas at ~4.7-fold coverage from the three main areas where this species is found in western China. Although only two subspecies of giant panda have been recognized, analyses of genetic structure resolved giant pandas into three genetic clusters, with the isolated population in the Qinling Mountains, being the most distinct and estimated to have diverged about 300,000 years ago.…”