title: Comparative genomics reveals convergent evolution between the bamboo-eating giant and red pandas.
abstract: 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.
authors.affiliation: Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Yibo
authors.initials: Y
authors.lastname: Hu
authors.affiliation: Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Wu
authors.affiliation: Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.|University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Shuai
authors.initials: S
authors.lastname: Ma
authors.affiliation: Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.|University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Tianxiao
authors.initials: T
authors.lastname: Ma
authors.affiliation: Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Shan
authors.affiliation: Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.|University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Wang
authors.affiliation: Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Yonggang
authors.initials: Y
authors.lastname: Nie
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.
authors.forename: Zemin
authors.initials: Z
authors.lastname: Ning
authors.affiliation: Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Li
authors.initials: L
authors.lastname: Yan
authors.affiliation: Straits (Fuzhou) Giant Panda Research and Exchange Center, Fuzhou 350001, China.
authors.forename: Yunfang
authors.initials: Y
authors.lastname: Xiu
authors.affiliation: Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; weifw@ioz.ac.cn.|University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Fuwen
authors.initials: F
authors.lastname: Wei
mesh_terms: D000222:Adaptation, Physiological; D053822:Ailuridae / Q000145:classification / Q000235:genetics*; D000818:Animals; D031723:Bambusa / Q000737:chemistry; D005075:Biological Evolution; D004063:Digestion / Q000235:genetics; D005247:Feeding Behavior; D016678:Genome; D060434:Herbivory / Q000235:genetics; D008322:Mammals / Q000145:classification / Q000235:genetics; D010641:Phenotype; D010802:Phylogeny; D011544:Pseudogenes; D043562:Receptors, G-Protein-Coupled / Q000235:genetics; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D013650:Taste Buds; D014034:Toes / Q000033:anatomy & histology / Q000502:physiology; D001503:Ursidae / Q000145:classification / Q000235:genetics*
chemical_list: D043562:Receptors, G-Protein-Coupled
keywords: amino acid convergence; de novo genome; phenotype convergence; positive selection; pseudogenization