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Comparative genomics reveals the genetic mechanisms underlying phenotype convergence between the giant and red pandas

Date: 2017-01-18 

Convergent evolution, i.e., parallel evolution of identical or similar traits in distantly related species under similar selective pressures, is a research hotspot in evolutionary biology. Although there are many examples of convergent evolution in nature, the genetic insights into convergent evolution are far less clear. Traditional candidate genes method has limited abilities to uncover the genetic mechanisms of convergent evolution; in contrast, genome-scale analysis provides faster and more comprehensive insights.

The giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens), two species that diverged over 40 million years ago, have distinct phylogenetic positions in the order Carnivora. The giant panda belongs to the family Ursidae, whereas the red panda belongs to the family Ailuridae within the superfamily Musteloidea. However, both pandas have evolved specialized bamboo diet (>90%) and adaptive pseudothumbs that facilitate bamboo grasping, representing a classic example of adaptive evolution and convergent evolution. Especially, the popular 1980 book, “The Panda’s Thumb”, written by Stephen J. Gould, discussed the evolution of the giant panda’s pseudothumb, attracting many public interests. However, until recently, the genetic mechanisms underlying the morphological and physiological convergences in both pandas remain unclear.

Recently, a research team led by Professor Fuwen Wei from the Institute of Zoology, Chinese Academy of Sciences, used comparative genomics to reveal the molecular mechanisms of convergent evolution in both pandas. They de novo sequenced and assembled the red panda whole genome, and re-assembled the giant panda whole genome with added sequencing data. Phylogenomic analysis supported the molecular-based phylogenetic conclusions: the giant panda belongs to the Ursidae and the red panda belongs to the Musteloidea, with the divergence time of 47.5 million years ago estimated.

Genome-scale analysis of adaptive convergence identified 70 adaptively convergent genes in both pandas, some of which were significantly functional enriched in cilium assembly, appendage and limb development, protein digestion and absorption, and retinol metabolism terms or pathways. Two limb development genes, DYNC2H1 and PCNT, are important candidate genes responsible for pseudothumb development. Their mutations are known to produce polydactyly in humans and mice through affecting cilia structure and sonic hedge-hog pathway. Adaptive convergence has also occurred in genes involved in the digestion and utilization of bamboo nutrients such as essential amino acids, essential fatty acids, and vitamins, which may enhance the absorption and utilization of these essential nutrients in both pandas to cope with low-nutrition bamboo diet. Additionally, genome-wide pseudogenization analysis identified 10 common pseudogenes in giant and red pandas, including the umami taste receptor gene TAS1R1. As an interesting genetic convergence scenario, convergent pseudogenization of TAS1R1 may be an evolutionary response to the dietary shift from carnivory and omnivory to herbivory. These findings demonstrate that genetic convergence occurred at multiple levels spanning metabolic pathways, amino acid convergence, and pseudogenization, providing rich insights into both pandas’ morphological and physiological convergences and also offering a fascinating example for genome-scale convergent evolution analysis of dietary shift and specialization.

This study entitled “Comparative genomics reveals convergent evolution between the bamboo-eating giant and red pandas” will be published online in PNAS.

This study was supported by grants from the National Natural Science Foundation of China, Ministry of Science and Technology, and Chinese Academy of Sciences.

Reference: Hu YB, Wu Q, Ma S, Ma TX,…, Wei FW#. (2017) Comparative genomics reveals convergent evolution between the bamboo-eating giant and red pandas. PNAS, doi: www.pnas.org/cgi/doi/10.1073/pnas.1613870114.

Contact: Prof. Fuwen Wei, weifw@ioz.ac.cn 

Institute of Zoology, Chinese Academy of Sciences

Genome-wide phylogenetic tree of giant panda and red panda, and their convergent pseudothumbs