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Comparative genomics reveals convergent evolution between the bamboo-eating giant and red pandas

Significance The giant panda and red panda are obligate bamboo-feeders that independently evolved from meat-eating ancestors and possess adaptive pseudothumbs, making them ideal models for studying convergent evolution. In this study, we identified genomic signatures of convergent evolution associated with bamboo eating. Comparative genomic analyses revealed adaptively convergent genes potentially involved with pseudothumb development and essential bamboo nutrient utilization. We also found that the umami taste receptor gene TAS1R1 has been pseudogenized in both pandas. These findings provide insights into genetic mechanisms underlying phenotypic convergence and adaptation to a specialized bamboo diet in both pandas and offer an example of genome-scale analyses for detecting convergent evolution. Phenotypic convergence between distantly related taxa often mirrors adaptation to similar selective pressures and may be driven by genetic convergence. The giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens) belong to different families in the order Carnivora, but both have evolved a specialized bamboo diet and adaptive pseudothumb, representing a classic model of convergent evolution. However, the genetic bases of these morphological and physiological convergences remain unknown. Through de novo sequencing the red panda genome and improving the giant panda genome assembly with added data, we identified genomic signatures of convergent evolution. Limb development genes DYNC2H1 and PCNT have undergone adaptive convergence and may be important candidate genes for pseudothumb development. As evolutionary responses to a bamboo diet, adaptive convergence has occurred in genes involved in the digestion and utilization of bamboo nutrients such as essential amino acids, fatty acids, and vitamins. Similarly, the umami taste receptor gene TAS1R1 has been pseudogenized in both pandas. These findings offer insights into genetic convergence mechanisms underlying phenotypic convergence and adaptation to a specialized bamboo diet.