Chapter 22 - Red panda genomics and the evidence for two species

Abstract

This chapter introduces the latest research advances of red panda genomics. Using next-generation sequencing technology, the genome of Chinese red panda has been de novo sequenced and assembled, providing an important genetic resource for red panda study and conservation. Comparative genomics reveals the genetic mechanisms of morphological (pseudo-thumb) and physiological (specialized bamboo diet) convergences between giant and red pandas. Population genomics found that the red pandas could be classified into two phylogenetic species, Himalayan red panda (A. fulgens) and Chinese red panda (A. styani), based on the evidence from whole-genome SNPs, mitochondrial genomes and Y-chromosome SNPs. The Yalu Zangbu River, rather than the Nujiang River, is most likely the boundary of two species. Furthermore, the two species have obviously different evolutionary histories. The southern Tibet-Gaoligong population of Chinese red panda may be the glacial refugia, with the highest genetic diversity and more gene flow output. The Himalayan red panda has much lower genetic diversity, higher linkage disequilibrium and higher genetic load, which could be explained by its continuously decreasing demographic history. These findings have important implications for wild red panda conservation and captive red panda genetic management.