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Hu Y, Hu Y, Zhou W, Wei F. Conservation Genomics and Metagenomics of Giant and Red Pandas in the Wild. Annu Rev Anim Biosci 2024; 12:69-89. [PMID: 37863091 DOI: 10.1146/annurev-animal-021022-054730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
Giant pandas and red pandas are endangered species with similar specialized bamboo diet and partial sympatric distribution in China. Over the last two decades, the rapid development of genomics and metagenomics research on these species has enriched our knowledge of their biology, ecology, physiology, genetics, and evolution, which is crucial and useful for their conservation. We describe the evolutionary history, endangerment processes, genetic diversity, and population structure of wild giant pandas and two species of red pandas (Chinese and Himalayan red pandas). In addition, we explore how genomics and metagenomics studies have provided insight into the convergent adaptation of pandas to the specialized bamboo diet. Finally, we discuss how these findings are applied to effective conservation management of giant and red pandas in the wild and in captivity to promote the long-term persistence of these species.
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Affiliation(s)
- Yisi Hu
- College of Forestry, Jiangxi Agricultural University, Nanchang, China;
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wenliang Zhou
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Fuwen Wei
- College of Forestry, Jiangxi Agricultural University, Nanchang, China;
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Feng P, Liang X, Yu H, Dong X, Liang Q, Dai C. The evolution of bitter taste receptor gene in primates: Gene duplication and selection. Ecol Evol 2023; 13:e10610. [PMID: 37841228 PMCID: PMC10571502 DOI: 10.1002/ece3.10610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 09/08/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023] Open
Abstract
Bitter taste perception plays an important role in preventing animals from digesting poisonous and harmful substances. In primates, especially the Cercopithecidae species, most species feed on plants; thus, it is reasonable to speculate that most of the bitter taste receptor genes (T2Rs) of primates are under purifying selection to maintain the functional stability of bitter taste perception. Gene duplication has happened in T2Rs frequently, and what will be the fate of T2Rs copies is another question we are concerned about. To answer these questions, we selected the T2Rs of primates reported in another study and conducted corresponding selective pressure analyses to determine what kind of selective pressure was acting on them. Further, we carried out selective pressure analyses on gene copies and their corresponding ancestors by considering several possible situations. The results showed that among the 25 gene groups examined here, 15 groups are subject to purifying selection and others are under relaxed selection, with many positively selected sites detected. Gene copies existed in several groups, but only some groups (clade1_a1-b2, clade1_c-c2, clade1_d1-d3, clade1_f1-f2, T2R10, T2R13, and T2R42) have positively selected sites, inferring that they may have some relation to functional divergence. Taken together, T2Rs in primates are under diverse selective pressures, and most gene copies are subject to the same selective pressures. In such cases, the copies may be just to keep the function conservative, and more copies can increase the quantity of the bitter taste receptor, raise the efficiency of bitter substance recognition, and finally enhance the fitness of feeding during the evolutionary course of primates. This study can improve our understanding of T2Rs evolution in primates.
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Affiliation(s)
- Ping Feng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People's Republic of ChinaGuangxi Normal UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinGuangxiChina
| | - Xinyue Liang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People's Republic of ChinaGuangxi Normal UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinGuangxiChina
| | - Hongling Yu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People's Republic of ChinaGuangxi Normal UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinGuangxiChina
| | - Xiaoyan Dong
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People's Republic of ChinaGuangxi Normal UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinGuangxiChina
| | - Qiufang Liang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People's Republic of ChinaGuangxi Normal UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinGuangxiChina
| | - Chuanyin Dai
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People's Republic of ChinaGuangxi Normal UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinGuangxiChina
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Jiao H, Wang Q, Wang BJ, Li K, Lövy M, Nevo E, Li Q, Su W, Jiang P, Zhao H. Local adaptation of bitter taste and ecological speciation in a wild mammal. Mol Biol Evol 2021; 38:4562-4572. [PMID: 34240186 PMCID: PMC8476172 DOI: 10.1093/molbev/msab205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sensory systems are attractive evolutionary models to address how organisms adapt to local environments that can cause ecological speciation. However, tests of these evolutionary models have focused on visual, auditory, and olfactory senses. Here, we show local adaptation of bitter taste receptor genes in two neighboring populations of a wild mammal—the blind mole rat Spalax galili—that show ecological speciation in divergent soil environments. We found that basalt-type bitter receptors showed higher response intensity and sensitivity compared with chalk-type ones using both genetic and cell-based functional analyses. Such functional changes could help animals adapted to basalt soil select plants with less bitterness from diverse local foods, whereas a weaker reception to bitter taste may allow consumption of a greater range of plants for animals inhabiting chalk soil with a scarcity of food supply. Our study shows divergent selection on food resources through local adaptation of bitter receptors, and suggests that taste plays an important yet underappreciated role in speciation.
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Affiliation(s)
- Hengwu Jiao
- Department of Ecology, Tibetan Centre for Ecology and Conservation at Wuhan University-Tibet University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Qian Wang
- Department of Ecology, Tibetan Centre for Ecology and Conservation at Wuhan University-Tibet University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Bing-Jun Wang
- Department of Ecology, Tibetan Centre for Ecology and Conservation at Wuhan University-Tibet University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Kexin Li
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa, 3498838, Israel.,State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Matěj Lövy
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, 37005, Czech Republic
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa, 3498838, Israel
| | - Qiyang Li
- Department of Ecology, Tibetan Centre for Ecology and Conservation at Wuhan University-Tibet University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wenchuan Su
- Department of Ecology, Tibetan Centre for Ecology and Conservation at Wuhan University-Tibet University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Peihua Jiang
- Monell Chemical Senses Center, Philadelphia, Pennsylvania, 19104, USA
| | - Huabin Zhao
- Department of Ecology, Tibetan Centre for Ecology and Conservation at Wuhan University-Tibet University, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.,Research Center for Ecology, College of Science, Tibet University, Lhasa, 850000, China
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Itoigawa A, Fierro F, Chaney ME, Lauterbur ME, Hayakawa T, Tosi AJ, Niv MY, Imai H. Lowered sensitivity of bitter taste receptors to β-glucosides in bamboo lemurs: an instance of parallel and adaptive functional decline in TAS2R16? Proc Biol Sci 2021; 288:20210346. [PMID: 33849315 PMCID: PMC8059561 DOI: 10.1098/rspb.2021.0346] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Bitter taste facilitates the detection of potentially harmful substances and is perceived via bitter taste receptors (TAS2Rs) expressed on the tongue and oral cavity in vertebrates. In primates, TAS2R16 specifically recognizes β-glucosides, which are important in cyanogenic plants' use of cyanide as a feeding deterrent. In this study, we performed cell-based functional assays for investigating the sensitivity of TAS2R16 to β-glucosides in three species of bamboo lemurs (Prolemur simus, Hapalemur aureus and H. griseus), which primarily consume high-cyanide bamboo. TAS2R16 receptors from bamboo lemurs had lower sensitivity to β-glucosides, including cyanogenic glucosides, than that of the closely related ring-tailed lemur (Lemur catta). Ancestral reconstructions of TAS2R16 for the bamboo-lemur last common ancestor (LCA) and that of the Hapalemur LCA showed an intermediate sensitivity to β-glucosides between that of the ring-tailed lemurs and bamboo lemurs. Mutagenetic analyses revealed that P. simus and H. griseus had separate species-specific substitutions that led to reduced sensitivity. These results indicate that low sensitivity to β-glucosides at the cellular level—a potentially adaptive trait for feeding on cyanogenic bamboo—evolved independently after the Prolemur–Hapalemur split in each species.
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Affiliation(s)
- Akihiro Itoigawa
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, 41-2 Kanrin, Inuyama, Aichi 484-8506, Japan.,Japan Society for the Promotion of Science, Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Fabrizio Fierro
- The Institute of Biochemistry, Food Science and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
| | - Morgan E Chaney
- Department of Anthropology, Kent State University, Kent, OH 44242, USA
| | - M Elise Lauterbur
- Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ 85721, USA
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, N10W5, Kita-ku, Sapporo, Hokkaido 060-0810, Japan.,Japan Monkey Centre, 26 Inuyamakanrin, Inuyama, Aichi 484-0081, Japan
| | - Anthony J Tosi
- Department of Anthropology, Kent State University, Kent, OH 44242, USA
| | - Masha Y Niv
- The Institute of Biochemistry, Food Science and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
| | - Hiroo Imai
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, 41-2 Kanrin, Inuyama, Aichi 484-8506, Japan
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