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Poirier AC, Melin AD. Smell throughout the life course. Evol Anthropol 2024:e22030. [PMID: 38704704 DOI: 10.1002/evan.22030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 04/12/2024] [Accepted: 04/18/2024] [Indexed: 05/07/2024]
Abstract
The sense of smell is an important mediator of health and sociality at all stages of life, yet it has received limited attention in our lineage. Olfaction starts in utero and participates in the establishment of social bonds in children, and of romantic and sexual relationships after puberty. Smell further plays a key role in food assessment and danger avoidance; in modern societies, it also guides our consumer behavior. Sensory abilities typically decrease with age and can be impacted by diseases, with repercussions on health and well-being. Here, we critically review our current understanding of human olfactory communication to refute outdated notions that our sense of smell is of low importance. We provide a summary of the biology of olfaction, give a prospective overview of the importance of the sense of smell throughout the life course, and conclude with an outline of the limitations and future directions in this field.
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Affiliation(s)
- Alice C Poirier
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
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2
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Simon M, Widdig A, Weiß BM. Sniffing behavior of semi free-ranging Barbary macaques (Macaca sylvanus). Am J Primatol 2024; 86:e23611. [PMID: 38409866 DOI: 10.1002/ajp.23611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 02/05/2024] [Accepted: 02/10/2024] [Indexed: 02/28/2024]
Abstract
Olfaction is one of the evolutionarily oldest senses and plays a fundamental role in foraging and social interactions across mammals. In primates, the role of olfaction is now well recognized, but better investigated in strepsirrhine and platyrrhine primates than in catarrhines. We observed the sniffing behavior of semi-free ranging Barbary macaques, Macaca sylvanus, at Affenberg Salem, Germany, to assess how frequently macaques sniff and in which contexts, and how sniffing is affected by sex and age. Focal observations of 24 males and 24 females aged 1-25 years showed that Barbary macaques sniffed, on average, 5.24 times per hour, with more than 80% of sniffs directed at food. Irrespective of the context, younger individuals sniffed more often than older ones. Females' sniffs were more often directed at food than male sniffs, while males sniffed more often than females in a social context. Sniffs at conspecifics occurred primarily in a sexual context, with 70% of social sniffs directed at female anogenital swellings performed by males. Of the observed 176 anogenital inspections, 51 involved sniffing of the swelling. Olfactory inspections were followed by copulation significantly less often than merely visual inspections, suggesting that anogenital odors may play a role in male mating decisions, but the role of olfaction in sexual interactions warrants further investigations. In sum, results show that Barbary macaques routinely use olfaction during feeding, but also in a socio-sexual context, corroborating the relevance of the olfactory sense in the lives of catarrhine primates.
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Affiliation(s)
- Miriam Simon
- Behavioral Ecology Research Group, Institute of Biology, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
- Division of Anthropology, Institute of Organismic and Molecular Evolution, Gutenberg University, Mainz, Germany
| | - Anja Widdig
- Behavioral Ecology Research Group, Institute of Biology, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
- Department of Human Behavior, Research Group Primate Behavioural Ecology, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Brigitte M Weiß
- Behavioral Ecology Research Group, Institute of Biology, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
- Department of Human Behavior, Research Group Primate Behavioural Ecology, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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3
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Niimura Y, Biswa BB, Kishida T, Toyoda A, Fujiwara K, Ito M, Touhara K, Inoue-Murayama M, Jenkins SH, Adenyo C, Kayang BB, Koide T. Synchronized Expansion and Contraction of Olfactory, Vomeronasal, and Taste Receptor Gene Families in Hystricomorph Rodents. Mol Biol Evol 2024; 41:msae071. [PMID: 38649162 PMCID: PMC11035023 DOI: 10.1093/molbev/msae071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/02/2024] [Accepted: 03/03/2024] [Indexed: 04/25/2024] Open
Abstract
Chemical senses, including olfaction, pheromones, and taste, are crucial for the survival of most animals. There has long been a debate about whether different types of senses might influence each other. For instance, primates with a strong sense of vision are thought to have weakened olfactory abilities, although the oversimplified trade-off theory is now being questioned. It is uncertain whether such interactions between different chemical senses occur during evolution. To address this question, we examined four receptor gene families related to olfaction, pheromones, and taste: olfactory receptor (OR), vomeronasal receptor type 1 and type 2 (V1R and V2R), and bitter taste receptor (T2R) genes in Hystricomorpha, which is morphologically and ecologically the most diverse group of rodents. We also sequenced and assembled the genome of the grasscutter, Thryonomys swinderianus. By examining 16 available genome assemblies alongside the grasscutter genome, we identified orthologous gene groups among hystricomorph rodents for these gene families to separate the gene gain and loss events in each phylogenetic branch of the Hystricomorpha evolutionary tree. Our analysis revealed that the expansion or contraction of the four gene families occurred synchronously, indicating that when one chemical sense develops or deteriorates, the others follow suit. The results also showed that V1R/V2R genes underwent the fastest evolution, followed by OR genes, and T2R genes were the most evolutionarily stable. This variation likely reflects the difference in ligands of V1R/V2Rs, ORs, and T2Rs: species-specific pheromones, environment-based scents, and toxic substances common to many animals, respectively.
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Affiliation(s)
- Yoshihito Niimura
- Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Bhim B Biswa
- Mouse Genomics Resource Laboratory, National Institute of Genetics, Mishima, Japan
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Shizuoka, Japan
| | - Takushi Kishida
- Curatorial Division, Museum of Natural and Environmental History, Shizuoka, Japan
- Present address: College of Bioresource Sciences, Nihon University, Fujisawa, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Kazumichi Fujiwara
- Mouse Genomics Resource Laboratory, National Institute of Genetics, Mishima, Japan
| | - Masato Ito
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazushige Touhara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Scott H Jenkins
- Wildlife Research Center, Kyoto University, Kyoto, Japan
- Present address: Biosphere Informatics Laboratory, Department of Social Informatics, Graduate School of Informatics, Kyoto, Japan
| | - Christopher Adenyo
- Livestock and Poultry Research Centre, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Boniface B Kayang
- Department of Animal Science, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Tsuyoshi Koide
- Mouse Genomics Resource Laboratory, National Institute of Genetics, Mishima, Japan
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Shizuoka, Japan
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4
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Shao Y, Zhou L, Li F, Zhao L, Zhang BL, Shao F, Chen JW, Chen CY, Bi X, Zhuang XL, Zhu HL, Hu J, Sun Z, Li X, Wang D, Rivas-González I, Wang S, Wang YM, Chen W, Li G, Lu HM, Liu Y, Kuderna LFK, Farh KKH, Fan PF, Yu L, Li M, Liu ZJ, Tiley GP, Yoder AD, Roos C, Hayakawa T, Marques-Bonet T, Rogers J, Stenson PD, Cooper DN, Schierup MH, Yao YG, Zhang YP, Wang W, Qi XG, Zhang G, Wu DD. Phylogenomic analyses provide insights into primate evolution. Science 2023; 380:913-924. [PMID: 37262173 DOI: 10.1126/science.abn6919] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/26/2023] [Indexed: 06/03/2023]
Abstract
Comparative analysis of primate genomes within a phylogenetic context is essential for understanding the evolution of human genetic architecture and primate diversity. We present such a study of 50 primate species spanning 38 genera and 14 families, including 27 genomes first reported here, with many from previously less well represented groups, the New World monkeys and the Strepsirrhini. Our analyses reveal heterogeneous rates of genomic rearrangement and gene evolution across primate lineages. Thousands of genes under positive selection in different lineages play roles in the nervous, skeletal, and digestive systems and may have contributed to primate innovations and adaptations. Our study reveals that many key genomic innovations occurred in the Simiiformes ancestral node and may have had an impact on the adaptive radiation of the Simiiformes and human evolution.
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Affiliation(s)
- Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Long Zhou
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Fang Li
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Institute of Animal Sex and Development, ZhejiangWanli University, Ningbo 315100, China
| | - Lan Zhao
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China
| | | | - Chun-Yan Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xupeng Bi
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiao-Lin Zhuang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650204, China
| | | | - Jiang Hu
- Grandomics Biosciences, Beijing 102206, China
| | - Zongyi Sun
- Grandomics Biosciences, Beijing 102206, China
| | - Xin Li
- Grandomics Biosciences, Beijing 102206, China
| | - Depeng Wang
- Grandomics Biosciences, Beijing 102206, China
| | | | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Yun-Mei Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
| | - Wu Chen
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou 510070, China
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Hui-Meng Lu
- School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Lukas F K Kuderna
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA 92122, USA
| | - Kyle Kai-How Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA 92122, USA
| | - Peng-Fei Fan
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhi-Jin Liu
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - George P Tiley
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
- Japan Monkey Centre, Inuyama, Aichi 484-0081, Japan
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | | | - Yong-Gang Yao
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650204, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiao-Guang Qi
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650204, China
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5
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Han W, Wu Y, Zeng L, Zhao S. Building the Chordata Olfactory Receptor Database using more than 400,000 receptors annotated by Genome2OR. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2539-2551. [PMID: 35696018 DOI: 10.1007/s11427-021-2081-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 01/20/2022] [Indexed: 06/15/2023]
Abstract
Olfactory receptors are poorly annotated for most genome-sequenced chordates. To address this deficiency, we developed a nhmmer-based olfactory receptor annotation tool Genome2OR ( https://github.com/ToHanwei/Genome2OR.git ), and used it to process 1,695 sequenced chordate genomes in the NCBI Assembly database as of January, 2021. In total, 765,248 olfactory receptor genes were annotated, with 404,426 functional genes and 360,822 pseudogenes, which represents a four-fold increase in the number of annotated olfactory receptors. Based on the annotation data, we built a database called Chordata Olfactory Receptor Database (CORD, https://cord.ihuman.shanghaitech.edu.cn ) for archiving, analysing and disseminating the data. Beyond the primary data, we offer derivative information, including pictures of species, cross references to public databases, structural models, sequence similarity networks and sequence profiles in the CORD. Furthermore, we did brief analyses on these receptors, including building a huge protein sequence similarity network covering all receptors in the database, and clustering them into 20 communities, classifying the 20 communities into three categories based on their presences/absences in ray-finned fish and/or lobe-finned fish. We infer that olfactory receptors should have unique activation and desensitization mechanisms by analysing their sequences and structural models. We believe the CORD can benefit the researchers and the general public who are interested in olfaction.
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Affiliation(s)
- Wei Han
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Liting Zeng
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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6
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Yasunaga M, Takai E, Hattori S, Tatematsu K, Kuroda S. Effects of 3-octen-2-one on human olfactory receptor responses to vanilla flavor. Biosci Biotechnol Biochem 2022; 86:1562-1569. [PMID: 36073350 DOI: 10.1093/bbb/zbac147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022]
Abstract
Most of the odors that humans perceive daily are complex odors. It is believed that the modulation, enhancement, and suppression of overall complex odors are caused by interactions between odor molecules. In this study, to understand the interaction between odor molecules at the level of human olfactory receptor responses, the effects of 3-octen-2-one, which has been shown to modulate vanilla flavors, were analyzed using a human olfactory receptor sensor that uses all human olfactory receptors (388 types) as sensing molecules. As a result, the response intensity of 1 common receptor (OR1D2) was synergistically enhanced in vanilla flavor with 3-octen-2-one compared with vanilla flavor, and the response of 1 receptor (OR5K1) to vanilla flavor was completely suppressed. These results strongly suggested that the response of human olfactory receptors to complex odors is enhanced or suppressed by relatively few other odor molecules.
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Affiliation(s)
- Motoki Yasunaga
- Analytical Research Department, Soda Aromatic Co., Ltd., 1573-4 Funakata, Noda, Chiba 270-0233Japan
| | - Eiji Takai
- Analytical Research Department, Soda Aromatic Co., Ltd., 1573-4 Funakata, Noda, Chiba 270-0233Japan
| | - Shoji Hattori
- Analytical Research Department, Soda Aromatic Co., Ltd., 1573-4 Funakata, Noda, Chiba 270-0233Japan
| | - Kenji Tatematsu
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047Japan.,R&D Center, Komi Hakko Co., Technoalliance C Bldg. 3F, Osaka University, 2-8 Yamadaoka, Suita, Osaka 565-0871Japan
| | - Shun'ichi Kuroda
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047Japan.,R&D Center, Komi Hakko Co., Technoalliance C Bldg. 3F, Osaka University, 2-8 Yamadaoka, Suita, Osaka 565-0871Japan
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7
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Non-visual senses in fruit selection by the mantled howler monkey (Alouatta palliata). Primates 2022; 63:293-303. [PMID: 35289382 DOI: 10.1007/s10329-022-00984-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 02/22/2022] [Indexed: 10/18/2022]
Abstract
There is extensive knowledge about the visual system and the implications of the evolution of trichromatic color vision in howler monkeys (genus Alouatta) related to food selection; however, information about the other sensory systems is limited. In this study we assessed the use of touch, sniffing, and taste in fruit evaluation by 20 adult mantled howler monkeys (Alouatta palliata) on Agaltepec Island, Mexico. During 9 months of observation, we recorded the frequency that each monkey used touch, sniffing, and taste in evaluating cryptic fruits (that remain green during their ripening process) and conspicuous fruits (with red, yellow, or orange colorations when they are ripe). Sucrose content and hardness measurements were made to establish the degree of ripeness of the fruits. We found that mantled howler monkeys used long behavioral sequences during conspicuous fruit investigations. Sniffing was used infrequently, but significantly more often in the evaluation of conspicuous-ripe and unripe fruits compared to cryptic-ripe and unripe fruits. During the evaluation of cryptic-ripe fruits, mantled howler monkeys increased the use of touch compared to evaluating cryptic-unripe fruits. We did not find significant differences in the use of taste in the evaluation of cryptic and conspicuous fruits (both ripe and unripe). Our results suggest that the non-visual senses play an essential role in fruit selection by howler monkeys, with differences in the behavioral strategy according to the fruit's conspicuity. The multimodal signals of ripe and unripe fruits allow the howler monkeys to assess their palatability before being consumed.
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8
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Li B, Kamarck ML, Peng Q, Lim FL, Keller A, Smeets MAM, Mainland JD, Wang S. From musk to body odor: Decoding olfaction through genetic variation. PLoS Genet 2022; 18:e1009564. [PMID: 35113854 PMCID: PMC8812863 DOI: 10.1371/journal.pgen.1009564] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 12/01/2021] [Indexed: 12/30/2022] Open
Abstract
The olfactory system combines input from multiple receptor types to represent odor information, but there are few explicit examples relating olfactory receptor (OR) activity patterns to odor perception. To uncover these relationships, we performed genome-wide scans on odor-perception phenotypes for ten odors in 1000 Han Chinese and validated results for six of these odors in an ethnically diverse population (n = 364). In both populations, consistent with previous studies, we replicated three previously reported associations (β-ionone/OR5A1, androstenone/OR7D4, cis-3-hexen-1-ol/OR2J3 LD-band), but not for odors containing aldehydes, suggesting that olfactory phenotype/genotype studies are robust across populations. Two novel associations between an OR and odor perception contribute to our understanding of olfactory coding. First, we found a SNP in OR51B2 that associated with trans-3-methyl-2-hexenoic acid, a key component of human underarm odor. Second, we found two linked SNPs associated with the musk Galaxolide in a novel musk receptor, OR4D6, which is also the first human OR shown to drive specific anosmia to a musk compound. We noticed that SNPs detected for odor intensity were enriched with amino acid substitutions, implying functional changes of odor receptors. Furthermore, we also found that the derived alleles of the SNPs tend to be associated with reduced odor intensity, supporting the hypothesis that the primate olfactory gene repertoire has degenerated over time. This study provides information about coding for human body odor, and gives us insight into broader mechanisms of olfactory coding, such as how differential OR activation can converge on a similar percept.
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Affiliation(s)
- Bingjie Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Skin and Cosmetics Research, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Marissa L. Kamarck
- Monell Chemical Senses Center, Philadelphia, Pennsylvania, United States of America
- Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Qianqian Peng
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fei-Ling Lim
- Unilever Research & Development, Colworth, United Kingdom
| | - Andreas Keller
- Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, New York State, United States of America
| | | | - Joel D. Mainland
- Monell Chemical Senses Center, Philadelphia, Pennsylvania, United States of America
- Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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9
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de Sousa AA, Todorov OS, Proulx MJ. A natural history of vertebrate vision loss: Insight from mammalian vision for human visual function. Neurosci Biobehav Rev 2022; 134:104550. [PMID: 35074313 DOI: 10.1016/j.neubiorev.2022.104550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 10/08/2021] [Accepted: 01/20/2022] [Indexed: 11/28/2022]
Abstract
Research on the origin of vision and vision loss in naturally "blind" animal species can reveal the tasks that vision fulfills and the brain's role in visual experience. Models that incorporate evolutionary history, natural variation in visual ability, and experimental manipulations can help disentangle visual ability at a superficial level from behaviors linked to vision but not solely reliant upon it, and could assist the translation of ophthalmological research in animal models to human treatments. To unravel the similarities between blind individuals and blind species, we review concepts of 'blindness' and its behavioral correlates across a range of species. We explore the ancestral emergence of vision in vertebrates, and the loss of vision in blind species with reference to an evolution-based classification scheme. We applied phylogenetic comparative methods to a mammalian tree to explore the evolution of visual acuity using ancestral state estimations. Future research into the natural history of vision loss could help elucidate the function of vision and inspire innovations in how to address vision loss in humans.
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Affiliation(s)
- Alexandra A de Sousa
- Centre for Health and Cognition, Bath Spa University, Bath, United Kingdom; UKRI Centre for Accessible, Responsible & Transparent Artificial Intelligence (ART:AI), University of Bath, United Kingdom.
| | - Orlin S Todorov
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Michael J Proulx
- UKRI Centre for Accessible, Responsible & Transparent Artificial Intelligence (ART:AI), University of Bath, United Kingdom; Department of Psychology, REVEAL Research Centre, University of Bath, Bath, United Kingdom
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10
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Sin SYW, Cloutier A, Nevitt G, Edwards SV. Olfactory receptor subgenome and expression in a highly olfactory procellariiform seabird. Genetics 2021; 220:6458329. [PMID: 34888634 DOI: 10.1093/genetics/iyab210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
Procellariiform seabirds rely on their sense of smell for foraging and homing. Both genomes and transcriptomes yield important clues about how olfactory receptor (OR) subgenomes are shaped by natural and sexual selection, yet no transcriptomes have been made of any olfactory epithelium of any bird species thus far. Here we assembled a high-quality genome and nasal epithelium transcriptome of the Leach's storm-petrel (Oceanodroma leucorhoa) to extensively characterize their OR repertoire. Using a depth-of-coverage-assisted counting method, we estimated over 160 intact OR genes (∼500 including OR fragments). This method reveals the highest number of intact OR genes and the lowest proportion of pseudogenes compared to other waterbirds studied, and suggests that rates of OR gene duplication vary between major clades of birds, with particularly high rates in passerines. OR expression patterns reveal two OR genes (OR6-6 and OR5-11) highly expressed in adults, and four OR genes (OR14-14, OR14-12, OR10-2, and OR14-9) differentially expressed between age classes of storm-petrels. All four genes differentially expressed between age classes were more highly expressed in chicks compared to adults, suggesting that ORs genes may exhibit ontogenetic specializations. Three highly differentially expressed OR genes also had high copy number ratios, suggesting that expression variation may be linked to copy number in the genome. We provide better estimates of OR gene number by using a copy number-assisted counting method, and document ontogenetic changes in OR gene expression that may be linked to olfactory specialization. These results provide valuable insight into the expression, development, and macroevolution of olfaction in seabirds.
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Affiliation(s)
- Simon Yung Wa Sin
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.,School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Alison Cloutier
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Gabrielle Nevitt
- Department of Neurobiology, Physiology and Behavior and the Graduate Group in Ecology, University of California, Davis, CA 95616, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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11
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AlMatrouk A, Lemons K, Ogura T, Lin W. Modification of the Peripheral Olfactory System by Electronic Cigarettes. Compr Physiol 2021; 11:2621-2644. [PMID: 34661289 DOI: 10.1002/cphy.c210007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Electronic cigarettes (e-cigs) are used by millions of adolescents and adults worldwide. Commercial e-liquids typically contain flavorants, propylene glycol, and vegetable glycerin with or without nicotine. These chemical constituents are detected and evaluated by chemosensory systems to guide and modulate vaping behavior and product choices of e-cig users. The flavorants in e-liquids are marketing tools. They evoke sensory percepts of appealing flavors through activation of chemical sensory systems to promote the initiation and sustained use of e-cigs. The vast majority of flavorants in e-liquids are volatile odorants, and as such, the olfactory system plays a dominant role in perceiving these molecules that enter the nasal cavity either orthonasally or retronasally during vaping. In addition to flavorants, e-cig aerosol contains a variety of by-products generated through heating the e-liquids, including odorous irritants, toxicants, and heavy metals. These harmful substances can directly and adversely impact the main olfactory epithelium (MOE). In this article, we first discuss the olfactory contribution to e-cig flavor perception. We then provide information on MOE cell types and their major functions in olfaction and epithelial maintenance. Olfactory detection of flavorants, nicotine, and odorous irritants and toxicants are also discussed. Finally, we discuss the cumulated data on modification of the MOE by flavorant exposure and toxicological impacts of formaldehyde, acrolein, and heavy metals. Together, the information presented in this overview may provide insight into how e-cig exposure may modify the olfactory system and adversely impact human health through the alteration of the chemosensory factor driving e-cig use behavior and product selections. © 2021 American Physiological Society. Compr Physiol 11:2621-2644, 2021.
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Affiliation(s)
- Abdullah AlMatrouk
- General Department of Criminal Evidence, Forensic Laboratories, Ministry of Interior, Farwaniyah, Kuwait.,Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Kayla Lemons
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, North Carolina, USA.,Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Tatsuya Ogura
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Weihong Lin
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, Maryland, USA
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12
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Marcinek P, Haag F, Geithe C, Krautwurst D. An evolutionary conserved olfactory receptor for foodborne and semiochemical alkylpyrazines. FASEB J 2021; 35:e21638. [PMID: 34047404 DOI: 10.1096/fj.202100224r] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 12/11/2022]
Abstract
Molecular recognition is a fundamental principle in biological systems. The olfactory detection of both food and predators via ecological relevant odorant cues are abilities of eminent evolutionary significance for many species. Pyrazines are such volatile cues, some of which act as both human-centered key food odorants (KFOs) and semiochemicals. A pyrazine-selective odorant receptor has been elusive. Here we screened 2,3,5-trimethylpyrazine, a KFO and semiochemical, and 2,5-dihydro-2,4,5-trimethylthiazoline, an innate fear-associated non-KFO, against 616 human odorant receptor variants, in a cell-based luminescence assay. OR5K1 emerged as sole responding receptor. Tested against a comprehensive collection of 178 KFOs, we newly identified 18 pyrazines and (2R/2S)-4-methoxy-2,5-dimethylfuran-3(2H)-one as agonists. Notably, OR5K1 orthologs in mouse and domesticated species displayed a human-like, potency-ranked activation pattern of pyrazines, suggesting a domestication-led co-evolution of OR5K1 and its orthologs. In summary, OR5K1 is a specialized olfactory receptor across mammals for the detection of pyrazine-based key food odors and semiochemicals.
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Affiliation(s)
- Patrick Marcinek
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany.,Hamilton Germany GmbH, Gräfelfing, Germany
| | - Franziska Haag
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Christiane Geithe
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany.,Brandenburg University of Technology Cottbus - Senftenberg, Senftenberg, Germany
| | - Dietmar Krautwurst
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
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13
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Gaudel F, Guiraudie-Capraz G, Féron F. Limbic Expression of mRNA Coding for Chemoreceptors in Human Brain-Lessons from Brain Atlases. Int J Mol Sci 2021; 22:ijms22136858. [PMID: 34202385 PMCID: PMC8267617 DOI: 10.3390/ijms22136858] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/15/2021] [Accepted: 06/22/2021] [Indexed: 12/21/2022] Open
Abstract
Animals strongly rely on chemical senses to uncover the outside world and adjust their behaviour. Chemical signals are perceived by facial sensitive chemosensors that can be clustered into three families, namely the gustatory (TASR), olfactory (OR, TAAR) and pheromonal (VNR, FPR) receptors. Over recent decades, chemoreceptors were identified in non-facial parts of the body, including the brain. In order to map chemoreceptors within the encephalon, we performed a study based on four brain atlases. The transcript expression of selected members of the three chemoreceptor families and their canonical partners was analysed in major areas of healthy and demented human brains. Genes encoding all studied chemoreceptors are transcribed in the central nervous system, particularly in the limbic system. RNA of their canonical transduction partners (G proteins, ion channels) are also observed in all studied brain areas, reinforcing the suggestion that cerebral chemoreceptors are functional. In addition, we noticed that: (i) bitterness-associated receptors display an enriched expression, (ii) the brain is equipped to sense trace amines and pheromonal cues and (iii) chemoreceptor RNA expression varies with age, but not dementia or brain trauma. Extensive studies are now required to further understand how the brain makes sense of endogenous chemicals.
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14
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Tsuchiya S, Terada Y, Matsuyama M, Yamazaki-Ito T, Ito K. A new screening method for identifying chemosensory receptors responding to agonist. Biosci Biotechnol Biochem 2021; 85:1521-1525. [PMID: 33693463 DOI: 10.1093/bbb/zbab035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/01/2021] [Indexed: 11/12/2022]
Abstract
Humans sense taste and smell of various chemical substances through approximately 430 chemosensory receptors. The overall picture of ligand-chemosensory receptor interactions has been partially clarified because of numerous interactions. This study presents a new method that enables a rapid and simple screening of chemosensory receptors. It would be useful for identifying chemosensory receptors activated by taste and odor substances.
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Affiliation(s)
- Sakura Tsuchiya
- Department of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Suruga-ku, Shizuoka, Japan
| | - Yuko Terada
- Department of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Suruga-ku, Shizuoka, Japan
| | - Minami Matsuyama
- Department of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Suruga-ku, Shizuoka, Japan
| | - Toyomi Yamazaki-Ito
- Department of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Suruga-ku, Shizuoka, Japan
| | - Keisuke Ito
- Department of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Suruga-ku, Shizuoka, Japan
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15
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Liu H, Chen C, Lv M, Liu N, Hu Y, Zhang H, Enbody ED, Gao Z, Andersson L, Wang W. A chromosome-level assembly of blunt snout bream (Megalobrama amblycephala) reveals an expansion of olfactory receptor genes in freshwater fish. Mol Biol Evol 2021; 38:4238-4251. [PMID: 34003267 PMCID: PMC8476165 DOI: 10.1093/molbev/msab152] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The number of olfactory receptor genes (ORs), which are responsible for detecting diverse odor molecules varies extensively among mammals as a result of frequent gene gains and losses that contribute to olfactory specialization. However, how OR expansions/contractions in fish are influenced by habitat and feeding habit and which OR subfamilies are important in each ecological niche is unknown. Here, we report a major OR expansion in a freshwater herbivorous fish, Megalobrama amblycephala, using a highly contiguous, chromosome-level assembly. We evaluate the possible contribution of OR expansion to habitat and feeding specialization by comparing the OR repertoire in 28 phylogenetically and ecologically diverse teleosts. In total, we analyzed > 4,000 ORs including 3,253 intact, 122 truncated, and 913 pseudogenes. The number of intact ORs is highly variable ranging from 20 to 279. We estimate that the most recent common ancestor of Osteichthyes had 62 intact ORs, which declined in most lineages except the freshwater Otophysa clade that has a substantial expansion in subfamily β and ε ORs. Across teleosts, we found a strong association between duplications of β and ε ORs and freshwater habitat. Nearly, all ORs were expressed in the olfactory epithelium (OE) in three tested fish species. Specifically, all the expanded β and ε ORs were highly expressed in OE of M. amblycephala. Together, we provide molecular and functional evidence for how OR repertoires in fish have undergone gain and loss with respect to ecological factors and highlight the role of β and ε OR in freshwater adaptation.
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Affiliation(s)
- Han Liu
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China.,Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Wuhan, 430070, China
| | - Chunhai Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Maolin Lv
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ning Liu
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yafei Hu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hailin Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Erik D Enbody
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE75237, Sweden
| | - Zexia Gao
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China.,Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education/Engineering Technology Research Center for Fish Breeding and Culture in Hubei Province, Wuhan, 430070, China
| | - Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE75237, Sweden.,Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, USA.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Weimin Wang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
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16
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Ali MA, Wang Y, Qin Z, Yuan X, Zhang Y, Zeng C. Odorant and Taste Receptors in Sperm Chemotaxis and Cryopreservation: Roles and Implications in Sperm Capacitation, Motility and Fertility. Genes (Basel) 2021; 12:genes12040488. [PMID: 33801624 PMCID: PMC8065900 DOI: 10.3390/genes12040488] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 11/24/2022] Open
Abstract
Sperm chemotaxis, which guide sperm toward oocyte, is tightly associated with sperm capacitation, motility, and fertility. However, the molecular mechanism of sperm chemotaxis is not known. Reproductive odorant and taste receptors, belong to G-protein-coupled receptors (GPCR) super-family, cause an increase in intracellular Ca2+ concentration which is pre-requisite for sperm capacitation and acrosomal reaction, and result in sperm hyperpolarization and increase motility through activation of Ca2+-dependent Cl¯ channels. Recently, odorant receptors (ORs) in olfactory transduction pathway were thought to be associated with post-thaw sperm motility, freeze tolerance or freezability and cryo-capacitation-like change during cryopreservation. Investigation of the roles of odorant and taste receptors (TRs) is important for our understanding of the freeze tolerance or freezability mechanism and improve the motility and fertility of post-thaw sperm. Here, we reviewed the roles, mode of action, impact of odorant and taste receptors on sperm chemotaxis and post-thaw sperm quality.
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Affiliation(s)
- Malik Ahsan Ali
- College of Animal Science and Technology and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Y.W.); (Z.Q.); (X.Y.); (Y.Z.)
- Department of Theriogenology, Riphah College of Veterinary Sciences, Lahore 54000, Punjab, Pakistan;
- Department of Theriogenology, Faculty of Veterinary Science, University of Agriculture, Faisalabad 38000, Punjab, Pakistan
| | - Yihan Wang
- College of Animal Science and Technology and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Y.W.); (Z.Q.); (X.Y.); (Y.Z.)
| | - Ziyue Qin
- College of Animal Science and Technology and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Y.W.); (Z.Q.); (X.Y.); (Y.Z.)
| | - Xiang Yuan
- College of Animal Science and Technology and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Y.W.); (Z.Q.); (X.Y.); (Y.Z.)
| | - Yan Zhang
- College of Animal Science and Technology and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Y.W.); (Z.Q.); (X.Y.); (Y.Z.)
| | - Changjun Zeng
- College of Animal Science and Technology and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Y.W.); (Z.Q.); (X.Y.); (Y.Z.)
- Correspondence: ; Tel./Fax: +86-28-86291010
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17
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Hoover KC. Sensory disruption and sensory inequities in the Anthropocene. Evol Anthropol 2021; 30:128-140. [PMID: 33580579 DOI: 10.1002/evan.21882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 02/27/2020] [Accepted: 10/21/2020] [Indexed: 12/20/2022]
Abstract
Anthropogenic disruptions to animal sensory ecology are as old as our species. But what about the effect on human sensory ecology? Human sensory dysfunction is increasing globally at great economic and health costs (mental, physical, and social). Contemporary sensory problems are directly tied to human behavioral changes and activity as well as anthropogenic pollution. The evolutionary sensory ecology and anthropogenic disruptions to three human senses (vision, audition, olfaction) are examined along with the economic and health costs of functionally reduced senses and demographic risk factors contributing to impairment. The primary goals of the paper are (a) to sew an evolutionary and ecological thread through clinical narratives on sensory dysfunction that highlights the impact of the built environment on the senses, and (b) to highlight structural, demographic, and environmental injustices that create sensory inequities in risk and that promote health disparities.
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Affiliation(s)
- Kara C Hoover
- Department of Anthropology, University of Alaska, Fairbanks, Alaska, USA
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18
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Bi X, Wang K, Yang L, Pan H, Jiang H, Wei Q, Fang M, Yu H, Zhu C, Cai Y, He Y, Gan X, Zeng H, Yu D, Zhu Y, Jiang H, Qiu Q, Yang H, Zhang YE, Wang W, Zhu M, He S, Zhang G. Tracing the genetic footprints of vertebrate landing in non-teleost ray-finned fishes. Cell 2021; 184:1377-1391.e14. [PMID: 33545088 DOI: 10.1016/j.cell.2021.01.046] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 11/11/2020] [Accepted: 01/27/2021] [Indexed: 01/20/2023]
Abstract
Rich fossil evidence suggests that many traits and functions related to terrestrial evolution were present long before the ancestor of lobe- and ray-finned fishes. Here, we present genome sequences of the bichir, paddlefish, bowfin, and alligator gar, covering all major early divergent lineages of ray-finned fishes. Our analyses show that these species exhibit many mosaic genomic features of lobe- and ray-finned fishes. In particular, many regulatory elements for limb development are present in these fishes, supporting the hypothesis that the relevant ancestral regulation networks emerged before the origin of tetrapods. Transcriptome analyses confirm the homology between the lung and swim bladder and reveal the presence of functional lung-related genes in early ray-finned fishes. Furthermore, we functionally validate the essential role of a jawed vertebrate highly conserved element for cardiovascular development. Our results imply the ancestors of jawed vertebrates already had the potential gene networks for cardio-respiratory systems supporting air breathing.
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Affiliation(s)
- Xupeng Bi
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Liandong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | | | - Haifeng Jiang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Qiwei Wei
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | | | - Hao Yu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Chenglong Zhu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yiran Cai
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yuming He
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaoni Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Honghui Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Daqi Yu
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Youan Zhu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, 142 Xi-zhi-men-wai Street, Beijing 100044, China; CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China
| | - Huifeng Jiang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China; James D. Watson Institute of Genome Sciences, Hangzhou, China; Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen 518120, China
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming 650223, China
| | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming 650223, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
| | - Min Zhu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, 142 Xi-zhi-men-wai Street, Beijing 100044, China; CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China; College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming 650223, China; Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China.
| | - Guojie Zhang
- BGI-Shenzhen, Shenzhen 518083, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming 650223, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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19
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Identification and population genetic analyses of copy number variations in six domestic goat breeds and Bezoar ibexes using next-generation sequencing. BMC Genomics 2020; 21:840. [PMID: 33246410 PMCID: PMC7694352 DOI: 10.1186/s12864-020-07267-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/23/2020] [Indexed: 11/27/2022] Open
Abstract
Background Copy number variations (CNVs) are a major form of genetic variations and are involved in animal domestication and genetic adaptation to local environments. We investigated CNVs in the domestic goat (Capra hircus) using Illumina short-read sequencing data, by comparing our lab data for 38 goats from three Chinese breeds (Chengdu Brown, Jintang Black, and Tibetan Cashmere) to public data for 26 individuals from three other breeds (two Moroccan and one Chinese) and 21samples from Bezoar ibexes. Results We obtained a total of 2394 CNV regions (CNVRs) by merging 208,649 high-confidence CNVs, which spanned ~ 267 Mb of total length and accounted for 10.80% of the goat autosomal genome. Functional analyses showed that 2322 genes overlapping with the CNVRs were significantly enriched in 57 functional GO terms and KEGG pathways, most related to the nervous system, metabolic process, and reproduction system. Clustering patterns of all 85 samples generated separately from duplications and deletions were generally consistent with the results from SNPs, agreeing with the geographical origins of these goats. Based on genome-wide FST at each CNV locus, some genes overlapping with the highly divergent CNVs between domestic and wild goats were mainly enriched for several immunity-related pathways, whereas the genes overlapping with the highly differentiated CNVs between highland and lowland goats were mainly related to vitamin and lipid metabolism. Remarkably, a 507-bp deletion at ~ 14 kb downstream of FGF5 on chromosome 6 showed highly divergent (FST = 0.973) between the highland and lowland goats. Together with an enhancer activity of this sequence shown previously, the function of this duplication in regulating fiber growth deserved to be further investigated in detail. Conclusion We generated a comprehensive map of CNVs in goats. Many genetically differentiated CNVs among various goat populations might be associated with the population characteristics of domestic goat breeds. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07267-6.
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20
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Gisladottir RS, Ivarsdottir EV, Helgason A, Jonsson L, Hannesdottir NK, Rutsdottir G, Arnadottir GA, Skuladottir A, Jonsson BA, Norddahl GL, Ulfarsson MO, Helgason H, Halldorsson BV, Nawaz MS, Tragante V, Sveinbjornsson G, Thorgeirsson T, Oddsson A, Kristjansson RP, Bjornsdottir G, Thorgeirsson G, Jonsdottir I, Holm H, Gudbjartsson DF, Thorsteinsdottir U, Stefansson H, Sulem P, Stefansson K. Sequence Variants in TAAR5 and Other Loci Affect Human Odor Perception and Naming. Curr Biol 2020; 30:4643-4653.e3. [PMID: 33035477 DOI: 10.1016/j.cub.2020.09.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/17/2020] [Accepted: 09/03/2020] [Indexed: 11/17/2022]
Abstract
Olfactory receptor (OR) genes in humans form a special class characterized by unusually high DNA sequence diversity, which should give rise to differences in perception and behavior. In the largest genome-wide association study to date based on olfactory testing, we investigated odor perception and naming with smell tasks performed by 9,122 Icelanders, with replication in a separate sample of 2,204 individuals. We discovered an association between a low-frequency missense variant in TAAR5 and reduced intensity rating of fish odor containing trimethylamine (p.Ser95Pro, pcombined = 5.6 × 10-15). We demonstrate that TAAR5 genotype affects aversion to fish odor, reflected by linguistic descriptions of the odor and pleasantness ratings. We also discovered common sequence variants in two canonical olfactory receptor loci that associate with increased intensity and naming of licorice odor (trans-anethole: lead variant p.Lys233Asn in OR6C70, pcombined = 8.8 × 10-16 and pcombined = 1.4 × 10-9) and enhanced naming of cinnamon (trans-cinnamaldehyde; intergenic variant rs317787-T, pcombined = 5.0 × 10-17). Together, our results show that TAAR5 genotype variation influences human odor responses and highlight that sequence diversity in canonical OR genes can lead to enhanced olfactory ability, in contrast to the view that greater tolerance for mutations in the human OR repertoire leads to diminished function.
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Affiliation(s)
- Rosa S Gisladottir
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland; School of Humanities, University of Iceland, Saemundargata 2, 102 Reykjavik, Iceland.
| | - Erna V Ivarsdottir
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland; School of Engineering and Natural Sciences, University of Iceland, Dunhagi 5, 107 Reykjavik, Iceland
| | - Agnar Helgason
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland; Department of Anthropology, University of Iceland, Saemundargata 10, 102 Reykjavik, Iceland
| | - Lina Jonsson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland; Department of Pharmacology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 13, SE-405 30, Gothenburg, Sweden; The Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Blå Stråket 15, 413 45, Gothenburg, Sweden
| | | | | | | | | | | | | | - Magnus O Ulfarsson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland; Faculty of Electrical and Computer Engineering, University of Iceland, Dunhagi 5, 107 Reykjavik, Iceland
| | - Hannes Helgason
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
| | - Bjarni V Halldorsson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland; School of Technology, Reykjavik University, Menntavegur 1, 101 Reykjavik, Iceland
| | - Muhammad S Nawaz
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
| | | | | | | | - Asmundur Oddsson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
| | | | | | - Gudmundur Thorgeirsson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland; Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, 101 Reykjavik, Iceland; Division of Cardiology, Department of Internal Medicine, Landspitali, The National University Hospital of Iceland, Hringbraut, 101 Reykjavik, Iceland
| | - Ingileif Jonsdottir
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland; Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, 101 Reykjavik, Iceland; Department of Immunology, Landspitali, The National University Hospital of Iceland, Hringbraut, 101 Reykjavik, Iceland
| | - Hilma Holm
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland; School of Engineering and Natural Sciences, University of Iceland, Dunhagi 5, 107 Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland; Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, 101 Reykjavik, Iceland
| | | | - Patrick Sulem
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland
| | - Kari Stefansson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101 Reykjavik, Iceland; Faculty of Medicine, University of Iceland, Vatnsmyrarvegur 16, 101 Reykjavik, Iceland.
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21
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Baldwin MW, Ko MC. Functional evolution of vertebrate sensory receptors. Horm Behav 2020; 124:104771. [PMID: 32437717 DOI: 10.1016/j.yhbeh.2020.104771] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 04/20/2020] [Accepted: 04/28/2020] [Indexed: 12/15/2022]
Abstract
Sensory receptors enable animals to perceive their external world, and functional properties of receptors evolve to detect the specific cues relevant for an organism's survival. Changes in sensory receptor function or tuning can directly impact an organism's behavior. Functional tests of receptors from multiple species and the generation of chimeric receptors between orthologs with different properties allow for the dissection of the molecular basis of receptor function and identification of the key residues that impart functional changes in different species. Knowledge of these functionally important sites facilitates investigation into questions regarding the role of epistasis and the extent of convergence, as well as the timing of sensory shifts relative to other phenotypic changes. However, as receptors can also play roles in non-sensory tissues, and receptor responses can be modulated by numerous other factors including varying expression levels, alternative splicing, and morphological features of the sensory cell, behavioral validation can be instrumental in confirming that responses observed in heterologous systems play a sensory role. Expression profiling of sensory cells and comparative genomics approaches can shed light on cell-type specific modifications and identify other proteins that may affect receptor function and can provide insight into the correlated evolution of complex suites of traits. Here we review the evolutionary history and diversity of functional responses of the major classes of sensory receptors in vertebrates, including opsins, chemosensory receptors, and ion channels involved in temperature-sensing, mechanosensation and electroreception.
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Affiliation(s)
| | - Meng-Ching Ko
- Max Planck Institute for Ornithology, Seewiesen, Germany
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22
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Drea CM. Design, delivery and perception of condition-dependent chemical signals in strepsirrhine primates: implications for human olfactory communication. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190264. [PMID: 32306880 DOI: 10.1098/rstb.2019.0264] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The study of human chemical communication benefits from comparative perspectives that relate humans, conceptually and empirically, to other primates. All major primate groups rely on intraspecific chemosignals, but strepsirrhines present the greatest diversity and specialization, providing a rich framework for examining design, delivery and perception. Strepsirrhines actively scent mark, possess a functional vomeronasal organ, investigate scents via olfactory and gustatory means, and are exquisitely sensitive to chemically encoded messages. Variation in delivery, scent mixing and multimodality alters signal detection, longevity and intended audience. Based on an integrative, 19-species review, the main scent source used (excretory versus glandular) differentiates nocturnal from diurnal or cathemeral species, reflecting differing socioecological demands and evolutionary trajectories. Condition-dependent signals reflect immutable (species, sex, identity, genetic diversity, immunity and kinship) and transient (health, social status, reproductive state and breeding history) traits, consistent with socio-reproductive functions. Sex reversals in glandular elaboration, marking rates or chemical richness in female-dominant species implicate sexual selection of olfactory ornaments in both sexes. Whereas some compounds may be endogenously produced and modified (e.g. via hormones), microbial analyses of different odorants support the fermentation hypothesis of bacterial contribution. The intimate contexts of information transfer and varied functions provide important parallels applicable to olfactory communication in humans. This article is part of the Theo Murphy meeting issue 'Olfactory communication in humans'.
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Affiliation(s)
- Christine M Drea
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708-0383, USA.,Department of Biology, Duke University, Durham, NC 27708-0383, USA
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23
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Liu A, He F, Shen L, Liu R, Wang Z, Zhou J. Convergent degeneration of olfactory receptor gene repertoires in marine mammals. BMC Genomics 2019; 20:977. [PMID: 31842731 PMCID: PMC6916060 DOI: 10.1186/s12864-019-6290-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 11/14/2019] [Indexed: 11/10/2022] Open
Abstract
Background Olfactory receptors (ORs) can bind odor molecules and play a crucial role in odor sensation. Due to the frequent gains and losses of genes during evolution, the number of OR members varies greatly among different species. However, whether the extent of gene gains/losses varies between marine mammals and related terrestrial mammals has not been clarified, and the factors that might underlie these variations are unknown. Results To address these questions, we identified more than 10,000 members of the OR family in 23 mammals and classified them into 830 orthologous gene groups (OGGs) and 281 singletons. Significant differences occurred in the number of OR repertoires and OGGs among different species. We found that all marine mammals had fewer OR genes than their related terrestrial lineages, with the fewest OR genes found in cetaceans, which may be closely related to olfactory degradation. ORs with more gene duplications or loss events tended to be under weaker purifying selection. The average gain and loss rates of OR genes in terrestrial mammals were higher than those of mammalian gene families, while the average gain and loss rates of OR genes in marine mammals were significantly lower and much higher than those of mammalian gene families, respectively. Additionally, we failed to detect any one-to-one orthologous genes in the focal species, suggesting that OR genes are not well conserved among marine mammals. Conclusions Marine mammals have experienced large numbers of OR gene losses compared with their related terrestrial lineages, which may result from the frequent birth-and-death evolution under varied functional constrains. Due to their independent degeneration, OR genes present in each lineage are not well conserved among marine mammals. Our study provides a basis for future research on the olfactory receptor function in mammals from the perspective of evolutionary trajectories.
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Affiliation(s)
- Ake Liu
- Faculty of Biological Science and Technology, Changzhi University, Changzhi, Shanxi, 046011, People's Republic of China.,School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Funan He
- School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Libing Shen
- Institute of Neuroscience, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China
| | - Ruixiang Liu
- Faculty of Biological Science and Technology, Changzhi University, Changzhi, Shanxi, 046011, People's Republic of China
| | - Zhijun Wang
- Department of Chemistry, Changzhi University, Changzhi, Shanxi, 046011, People's Republic of China.
| | - Jingqi Zhou
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China.
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24
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Janmaat KRL. What animals do not do or fail to find: A novel observational approach for studying cognition in the wild. Evol Anthropol 2019; 28:303-320. [PMID: 31418959 PMCID: PMC6916178 DOI: 10.1002/evan.21794] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 06/17/2019] [Accepted: 07/12/2019] [Indexed: 12/29/2022]
Abstract
To understand how our brain evolved and what it is for, we are in urgent need of knowledge about the cognitive skills of a large variety of animal species and individuals, and their relationships to rapidly disappearing social and ecological conditions. But how do we obtain this knowledge? Studying cognition in the wild is a challenge. Field researchers (and their study subjects) face many factors that can easily interfere with their variables of interest. Although field studies of cognition present unique challenges, they are still invaluable for understanding the evolutionary drivers of cognition. In this review, I discuss the advantages and urgency of field-based studies on animal cognition and introduce a novel observational approach for field research that is guided by three questions: (a) what do animals fail to find?, (b) what do they not do?, and (c) what do they only do when certain conditions are met? My goal is to provide guidance to future field researchers examining primate cognition.
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Affiliation(s)
- Karline R. L. Janmaat
- Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
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25
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An Evolutionary Perspective on the Impact of Genomic Copy Number Variation on Human Health. J Mol Evol 2019; 88:104-119. [PMID: 31522275 DOI: 10.1007/s00239-019-09911-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023]
Abstract
Copy number variants (CNVs), deletions and duplications of segments of DNA, account for at least five times more variable base pairs in humans than single-nucleotide variants. Several common CNVs were shown to change coding and regulatory sequences and thus dramatically affect adaptive phenotypes involving immunity, perception, metabolism, skin structure, among others. Some of these CNVs were also associated with susceptibility to cancer, infection, and metabolic disorders. These observations raise the possibility that CNVs are a primary contributor to human phenotypic variation and consequently evolve under selective pressures. Indeed, locus-specific haplotype-level analyses revealed signatures of natural selection on several CNVs. However, more traditional tests of selection which are often applied to single-nucleotide variation often have diminished statistical power when applied to CNVs because they often do not show strong linkage disequilibrium with nearby variants. Recombination-based formation mechanisms of CNVs lead to frequent recurrence and gene conversion events, breaking the linkage disequilibrium involving CNVs. Similar methodological challenges also prevent routine genome-wide association studies to adequately investigate the impact of CNVs on heritable human disease. Thus, we argue that the full relevance of CNVs to human health and evolution is yet to be elucidated. We further argue that a holistic investigation of formation mechanisms within an evolutionary framework would provide a powerful framework to understand the functional and biomedical impact of CNVs. In this paper, we review several cases where studies reveal diverse evolutionary histories and unexpected functional consequences of CNVs. We hope that this review will encourage further work on CNVs by both evolutionary and medical geneticists.
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26
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Saraiva LR, Riveros-McKay F, Mezzavilla M, Abou-Moussa EH, Arayata CJ, Makhlouf M, Trimmer C, Ibarra-Soria X, Khan M, Van Gerven L, Jorissen M, Gibbs M, O’Flynn C, McGrane S, Mombaerts P, Marioni JC, Mainland JD, Logan DW. A transcriptomic atlas of mammalian olfactory mucosae reveals an evolutionary influence on food odor detection in humans. SCIENCE ADVANCES 2019; 5:eaax0396. [PMID: 31392275 PMCID: PMC6669018 DOI: 10.1126/sciadv.aax0396] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 06/24/2019] [Indexed: 05/07/2023]
Abstract
The mammalian olfactory system displays species-specific adaptations to different ecological niches. To investigate the evolutionary dynamics of olfactory sensory neuron (OSN) subtypes across mammalian evolution, we applied RNA sequencing of whole olfactory mucosa samples from mouse, rat, dog, marmoset, macaque, and human. We find that OSN subtypes, representative of all known mouse chemosensory receptor gene families, are present in all analyzed species. Further, we show that OSN subtypes expressing canonical olfactory receptors are distributed across a large dynamic range and that homologous subtypes can be either highly abundant across all species or species/order specific. Highly abundant mouse and human OSN subtypes detect odorants with similar sensory profiles and sense ecologically relevant odorants, such as mouse semiochemicals or human key food odorants. Together, our results allow for a better understanding of the evolution of mammalian olfaction in mammals and provide insights into the possible functions of highly abundant OSN subtypes.
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Affiliation(s)
- Luis R. Saraiva
- Sidra Medicine, PO Box 26999, Doha, Qatar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton,, Cambridge CB10 1SD, UK
- Monell Chemical Senses Center, Philadelphia, PA 19104, USA
| | | | | | | | | | | | - Casey Trimmer
- Monell Chemical Senses Center, Philadelphia, PA 19104, USA
| | - Ximena Ibarra-Soria
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mona Khan
- Max Planck Research Unit for Neurogenetics, Max von-Laue-Strasse 4, 60438 Frankfurt, Germany
| | - Laura Van Gerven
- Department of ENT-HNS, UZ Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Mark Jorissen
- Department of ENT-HNS, UZ Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Matthew Gibbs
- Waltham Centre for Pet Nutrition, Leicestershire LE14 4RT, UK
| | - Ciaran O’Flynn
- Waltham Centre for Pet Nutrition, Leicestershire LE14 4RT, UK
| | - Scott McGrane
- Waltham Centre for Pet Nutrition, Leicestershire LE14 4RT, UK
| | - Peter Mombaerts
- Max Planck Research Unit for Neurogenetics, Max von-Laue-Strasse 4, 60438 Frankfurt, Germany
| | - John C. Marioni
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton,, Cambridge CB10 1SD, UK
- CRUK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Joel D. Mainland
- Monell Chemical Senses Center, Philadelphia, PA 19104, USA
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Darren W. Logan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Monell Chemical Senses Center, Philadelphia, PA 19104, USA
- Waltham Centre for Pet Nutrition, Leicestershire LE14 4RT, UK
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27
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Bu P, Jian Z, Koshy J, Shen Y, Yue B, Fan Z. The olfactory subgenome and specific odor recognition in forest musk deer. Anim Genet 2019; 50:358-366. [DOI: 10.1111/age.12796] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2019] [Indexed: 12/27/2022]
Affiliation(s)
- P. Bu
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education) College of Life Sciences Sichuan University Chengdu 610064 China
| | - Z. Jian
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education) College of Life Sciences Sichuan University Chengdu 610064 China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife College of Life Sciences Sichuan University Chengdu 610064 China
| | - J. Koshy
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education) College of Life Sciences Sichuan University Chengdu 610064 China
| | - Y. Shen
- Sichuan Engineering Research Center for Medicinal Animals Xichang 615000 China
| | - B. Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education) College of Life Sciences Sichuan University Chengdu 610064 China
| | - Z. Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education) College of Life Sciences Sichuan University Chengdu 610064 China
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28
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Niimura Y, Matsui A, Touhara K. Acceleration of Olfactory Receptor Gene Loss in Primate Evolution: Possible Link to Anatomical Change in Sensory Systems and Dietary Transition. Mol Biol Evol 2019; 35:1437-1450. [PMID: 29659972 DOI: 10.1093/molbev/msy042] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Primates have traditionally been regarded as vision-oriented animals with low olfactory ability, though this "microsmatic primates" view has been challenged recently. To clarify when and how degeneration of the olfactory system occurred and to specify the relevant factors during primate evolution, we here examined the olfactory receptor (OR) genes from 24 phylogenetically and ecologically diverse primate species. The results revealed that strepsirrhines with curved noses had functional OR gene repertoires that were nearly twice as large as those for haplorhines with simple noses. Neither activity pattern (nocturnal/diurnal) nor color vision system showed significant correlation with the number of functional OR genes while phylogeny and nose structure (haplorhine/strepsirrhine) are statistically controlled, but extent of folivory did. We traced the evolutionary fates of individual OR genes by identifying orthologous gene groups, demonstrating that the rates of OR gene losses were accelerated at the ancestral branch of haplorhines, which coincided with the acquisition of acute vision. The highest rate of OR gene loss was observed at the ancestral branch of leaf-eating colobines; this reduction is possibly linked with the dietary transition from frugivory to folivory because odor information is essential for fruit foraging but less so for leaf foraging. Intriguingly, we found accelerations of OR gene losses in an external branch to every hominoid species examined. These findings suggest that the current OR gene repertoire in each species has been shaped by a complex interplay of phylogeny, anatomy, and habitat; therefore, multiple factors may contribute to the olfactory degeneration in primates.
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Affiliation(s)
- Yoshihito Niimura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,ERATO Touhara Chemosensory Signal Project, JST, The University of Tokyo, Tokyo, Japan.,Lead Contact
| | - Atsushi Matsui
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,ERATO Touhara Chemosensory Signal Project, JST, The University of Tokyo, Tokyo, Japan
| | - Kazushige Touhara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,ERATO Touhara Chemosensory Signal Project, JST, The University of Tokyo, Tokyo, Japan
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29
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Jacobs LF. The navigational nose: a new hypothesis for the function of the human external pyramid. ACTA ACUST UNITED AC 2019; 222:222/Suppl_1/jeb186924. [PMID: 30728230 DOI: 10.1242/jeb.186924] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
One of the outstanding questions in evolution is why Homo erectus became the first primate species to evolve the external pyramid, i.e. an external nose. The accepted hypothesis for this trait has been its role in respiration, to warm and humidify air as it is inspired. However, new studies testing the key assumptions of the conditioning hypothesis, such as the importance of turbulence to enhance heat and moisture exchange, have called this hypothesis into question. The human nose has two functions, however, respiration and olfaction. It is thus also possible that the external nose evolved in response to selection for olfaction. The genus Homo had many adaptations for long-distance locomotion, which allowed Homo erectus to greatly expand its species range, from Africa to Asia. Long-distance navigation in birds and other species is often accomplished by orientation to environmental odors. Such olfactory navigation, in turn, is enhanced by stereo olfaction, made possible by the separation of the olfactory sensors. By these principles, the human external nose could have evolved to separate olfactory inputs to enhance stereo olfaction. This could also explain why nose shape later became so variable: as humans became more sedentary in the Neolithic, a decreasing need for long-distance movements could have been replaced by selection for other olfactory functions, such as detecting disease, that would have been critical to survival in newly dense human settlements.
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Affiliation(s)
- Lucia F Jacobs
- Department of Psychology and Helen Wills Neuroscience Institute, University of California, 2121 Berkeley Way, Berkeley, CA 94720-1650, USA
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30
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Bird DJ, Murphy WJ, Fox-Rosales L, Hamid I, Eagle RA, Van Valkenburgh B. Olfaction written in bone: cribriform plate size parallels olfactory receptor gene repertoires in Mammalia. Proc Biol Sci 2019. [PMID: 29540522 DOI: 10.1098/rspb.2018.0100] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The evolution of mammalian olfaction is manifested in a remarkable diversity of gene repertoires, neuroanatomy and skull morphology across living species. Olfactory receptor genes (ORGs), which initiate the conversion of odorant molecules into odour perceptions and help an animal resolve the olfactory world, range in number from a mere handful to several thousand genes across species. Within the snout, each of these ORGs is exclusively expressed by a discrete population of olfactory sensory neurons (OSNs), suggesting that newly evolved ORGs may be coupled with new OSN populations in the nasal epithelium. Because OSN axon bundles leave high-fidelity perforations (foramina) in the bone as they traverse the cribriform plate (CP) to reach the brain, we predicted that taxa with larger ORG repertoires would have proportionately expanded footprints in the CP foramina. Previous work found a correlation between ORG number and absolute CP size that disappeared after accounting for body size. Using updated, digital measurement data from high-resolution CT scans and re-examining the relationship between CP and body size, we report a striking linear correlation between relative CP area and number of functional ORGs across species from all mammalian superorders. This correlation suggests strong developmental links in the olfactory pathway between genes, neurons and skull morphology. Furthermore, because ORG number is linked to olfactory discriminatory function, this correlation supports relative CP size as a viable metric for inferring olfactory capacity across modern and extinct species. By quantifying CP area from a fossil sabertooth cat (Smilodon fatalis), we predicted a likely ORG repertoire for this extinct felid.
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Affiliation(s)
- Deborah J Bird
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA 90095-8347, USA
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843-4458, USA
| | - Lester Fox-Rosales
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA 90095-8347, USA
| | - Iman Hamid
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA 90095-8347, USA
| | - Robert A Eagle
- Department of Atmospheric and Oceanic Sciences, Institute of the Environment and Sustainability, University of California Los Angeles, 520 Portola Plaza, Math Sciences Building 7127, Los Angeles, CA 90095, USA
| | - Blaire Van Valkenburgh
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA 90095-8347, USA
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31
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Eyun SI. Accelerated pseudogenization of trace amine-associated receptor genes in primates. GENES BRAIN AND BEHAVIOR 2019; 18:e12543. [PMID: 30536583 PMCID: PMC6849804 DOI: 10.1111/gbb.12543] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 12/03/2018] [Accepted: 12/05/2018] [Indexed: 01/03/2023]
Abstract
Trace amines (TAs) in the mammalian brain have been investigated for four decades. Trace amine‐associated receptors (TAARs) were discovered during the search for receptors activated by TAs. TAARs are considered a second class of vertebrate olfactory receptors and successfully proliferated in conjunction with adaptation to living on the ground to detect carnivore odors. Thus, therian mammals have a high number of TAAR genes due to rapid species‐specific gene duplications. In primate lineages, however, their genomes have significantly smaller numbers of TAAR genes than do other mammals. To elucidate the evolutionary force driving these patterns, exhaustive data mining of TAAR genes was performed for 13 primate genomes (covering all four infraorders) and two nonprimate euarchontan genomes. This study identified a large number of pseudogenes in many of these primate genomes and thus investigated the pseudogenization event process for the TAAR repertoires. The degeneration of TAARs is likely associated with arboreal inhabitants reducing their exposure to carnivores, and this was accelerated by the change in the nose shape of haplorhines after their divergence from strepsirrhines. Arboreal life may have decreased the reliance on the chemosensing of predators, suggestive of leading to the depauperation of TAAR subfamilies. The evolutionary deterioration of TAARs in primates has been reestablished in recently derived primates due to high selection pressure and probably functional diversity.
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Affiliation(s)
- Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul, Korea
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Matsumura K, Imai H, Go Y, Kusuhara M, Yamaguchi K, Shirai T, Ohshima K. Transcriptional activation of a chimeric retrogene PIPSL in a hominoid ancestor. Gene 2018; 678:318-323. [PMID: 30096459 DOI: 10.1016/j.gene.2018.08.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/05/2018] [Accepted: 08/07/2018] [Indexed: 01/09/2023]
Abstract
Retrogenes are a class of functional genes derived from the mRNA of various intron-containing genes. PIPSL was created through a unique mechanism, whereby distinct genes were assembled at the RNA level, and the resulting chimera was then reverse transcribed and integrated into the genome by the L1 retrotransposon. Expression of PIPSL RNA via its transcription start sites (TSSs) has been confirmed in the testes of humans and chimpanzee. Here, we demonstrated that PIPSL RNA is expressed in the testis of the white-handed gibbon. The 5'-end positions of gibbon RNAs were confined to a narrow range upstream of the PIPSL start codon and overlapped with those of orangutan and human, suggesting that PIPSL TSSs are similar among hominoid species. Reporter assays using a luciferase gene and the flanking sequences of human PIPSL showed that an upstream sequence exhibits weak promoter activity in human cells. Our findings suggest that PIPSL might have acquired a promoter at an early stage of hominoid evolution before the divergence of gibbons and ultimately retained similar TSSs in all of the lineages. Moreover, the upstream sequence derived from the phosphatidylinositol-4-phosphate 5-kinase, type I, alpha 5' untranslated region and/or neighboring repetitive sequences in the genome possibly exhibits promoter activity. Furthermore, we observed that a TATA-box-like sequence has emerged by nucleotide substitution in a lineage leading to humans, with this possibly responsible for a broader distribution of the human PIPSL TSSs.
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Affiliation(s)
- Kenya Matsumura
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan; Shizuoka Cancer Center Research Institute, Sunto, Shizuoka, Japan
| | - Hiroo Imai
- Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan
| | - Yasuhiro Go
- Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Physiological Sciences, National Institute for Physiological Sciences, Okazaki, Aichi, Japan; School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | | | - Ken Yamaguchi
- Shizuoka Cancer Center Research Institute, Sunto, Shizuoka, Japan
| | - Tsuyoshi Shirai
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan
| | - Kazuhiko Ohshima
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan.
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Jiao H, Wang Y, Zhang L, Jiang P, Zhao H. Lineage-specific duplication and adaptive evolution of bitter taste receptor genes in bats. Mol Ecol 2018; 27:4475-4488. [PMID: 30230081 DOI: 10.1111/mec.14873] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 08/22/2018] [Accepted: 09/07/2018] [Indexed: 01/30/2023]
Abstract
By generating raw genetic material and diverse biological functions, gene duplication represents a major evolutionary mechanism that is of fundamental importance in ecological adaptation. The lineage-specific duplication events of bitter taste receptor genes (Tas2rs) have been identified in a number of vertebrates, but functional evolution of new Tas2r copies after duplication remains largely unknown. Here, we present the largest data set of bat Tas2rs to date, identified from existing genome sequences of 15 bat species and newly sequenced from 17 bat species, and demonstrate lineage-specific duplications of Tas2r16, Tas2r18 and Tas2r41 that only occurred in Myotis bats. Myotis bats are highly speciose and represent the only mammalian genus that is naturally distributed on every continent except Antarctica. The occupation of such diverse habitats might have driven the Tas2r gene expansion. New copies of Tas2rs in Myotis bats have shown molecular adaptation and functional divergence. For example, three copies of Tas2r16 in Myotis davidii showed differential sensitivities to arbutin and salicin that may occur in their insect prey, as suggested by cell-based functional assays. We hypothesize that functional differences among Tas2r copies in Myotis bats would increase their survival rate through preventing the ingestion of an elevated number of bitter-tasting dietary toxins from their insect prey, which may have facilitated their adaptation to diverse habitats. Our study demonstrates functional changes of new Tas2r copies after lineage-specific duplications in Myotis bats and highlights the potential role of taste perception in exploiting new environments.
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Affiliation(s)
- Hengwu Jiao
- Department of Ecology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yi Wang
- Department of Ecology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Peihua Jiang
- Monell Chemical Senses Center, Philadelphia, Pennsylvania
| | - Huabin Zhao
- Department of Ecology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
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Henkel S, Setchell JM. Group and kin recognition via olfactory cues in chimpanzees ( Pan troglodytes). Proc Biol Sci 2018; 285:rspb.2018.1527. [PMID: 30355708 DOI: 10.1098/rspb.2018.1527] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/01/2018] [Indexed: 01/10/2023] Open
Abstract
Primates were traditionally thought to have a reduced sense of smell. Although there is now evidence that olfaction plays a greater role in primate social life than previously assumed, research on the sense of smell in non-human apes is scarce. Chimpanzees sniff the ground and vegetation on boundary patrols, but the function of this behaviour is unclear. Since chimpanzees are highly territorial and can kill individuals that do not belong to their own community, sniffing might function to gather information about conspecifics, particularly concerning group membership and kinship. To investigate whether chimpanzees recognize group members and kin via olfactory cues, we conducted behavioural bioassays on two groups of chimpanzees at Leipzig Zoo. In a pilot study, we found that chimpanzees responded more strongly to urine than to faeces or body odour. We then presented urine from group members, outgroup individuals and an unscented control in aerated boxes using a simultaneous discrimination task. The first behaviour after a chimpanzee first approached a box was related to olfaction (sniffing, nose within 20 cm, licking) in 83% of cases, highlighting the importance of olfaction as a general investigation mechanism in this species. Chimpanzees sniffed significantly longer at urine stimuli than the control and significantly longer at odours from outgroup individuals than those from group members. Furthermore, the duration of sniffing was positively correlated with relatedness. Our results suggest that chimpanzees use olfactory cues to obtain information about social relationships and fill a gap in our understanding of primate chemical communication.
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Affiliation(s)
- Stefanie Henkel
- Institute of Biology, Faculty of Bioscience, Pharmacy and Psychology, University of Leipzig, Talstrasse 33, 04103 Leipzig, Germany .,Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Joanna M Setchell
- Department of Anthropology and Behaviour Ecology and Evolution Research (BEER) Centre, Durham University, Durham, UK
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Jänig S, Weiß BM, Widdig A. Comparing the sniffing behavior of great apes. Am J Primatol 2018; 80:e22872. [PMID: 29756687 DOI: 10.1002/ajp.22872] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/28/2018] [Accepted: 04/19/2018] [Indexed: 02/03/2023]
Abstract
The importance of smell in humans is well established but we know little about it in regard to our closest relatives, the great apes, as systematic studies on their olfactory behavior are still lacking. Olfaction has long been considered to be of lesser importance in hominids given their relatively smaller olfactory bulbs, fewer functional olfactory receptor genes than other species and absence of a functional vomeronasal organ. Therefore, the aim of this study was to evaluate the use of olfaction in hominids. In particular, we observed sniffing behavior in captive groups of four species (Sumatran orangutans, Pongo abelii; Western lowland gorillas, Gorilla gorilla gorilla; Western chimpanzees, Pan troglodytes verus; bonobos, Pan paniscus) and evaluated in which contexts sniffing was used. Our results show that all investigated species frequently used the sense of smell, and that the sniffing frequency varied with species, sex, age, and context. Most sniffing events were observed in gorillas in comparison to the three other species. Sniffing frequencies were also influenced by sex, with males sniffing slightly more often than females. Furthermore, our results revealed an effect of age, with younger individuals sniffing more often than older individuals. All species mainly sniffed in the non-social context (i.e., toward food and other environmental items) rather than in the social context (i.e., at conspecifics), suggesting that the evaluation of the environment and the nutritional value of food items is of major importance to all great ape species investigated here. In contrast to the other species and female chimpanzees, however, male chimpanzees most often used olfaction to inspect their conspecifics. Together, our study suggests that olfaction is likely to be more important in great apes than previously appreciated.
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Affiliation(s)
- Susann Jänig
- Behavioural Ecology Research Group, Institute of Biology, University of Leipzig, Leipzig, Germany.,Jr. Research Group of Primate Kin Selection, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Brigitte M Weiß
- Behavioural Ecology Research Group, Institute of Biology, University of Leipzig, Leipzig, Germany.,Jr. Research Group of Primate Kin Selection, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anja Widdig
- Behavioural Ecology Research Group, Institute of Biology, University of Leipzig, Leipzig, Germany.,Jr. Research Group of Primate Kin Selection, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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Weiß BM, Kücklich M, Thomsen R, Henkel S, Jänig S, Kulik L, Birkemeyer C, Widdig A. Chemical composition of axillary odorants reflects social and individual attributes in rhesus macaques. Behav Ecol Sociobiol 2018; 72:65. [PMID: 29606788 PMCID: PMC5871651 DOI: 10.1007/s00265-018-2479-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 03/07/2018] [Accepted: 03/12/2018] [Indexed: 02/03/2023]
Abstract
Abstract Scents play an important role in the life of most terrestrial mammals and may transmit valuable information about conspecifics. Olfaction was long considered of low importance in Old World monkeys due to their relative reduction of olfactory structures and low incidence of scent-marking behavior but has been increasingly recognized for mediating social relationships in recent years. Yet, studies investigating the composition of their chemical cues remain scarce. In the present study, we analyzed the potential information content of chemicals present on the skin of rhesus macaques (Macaca mulatta). We collected axillary secretions from 60 animals of the semifree-ranging population on Cayo Santiago (Puerto Rico, USA) with precleaned cotton swabs from which the secretions were subsequently extracted and analyzed by gas chromatography-mass spectrometry. Rhesus macaque axillary odorants varied in their overall similarity and composition. This variation was attributable to differences in sex, group membership, and kinship and further appeared to reflect age and rank in parts of our sample. The compounds most strongly associated with this variation primarily comprised larger molecular weight aldehydes and steroids. Such compounds are considered to be perceivable by the primate olfactory system through close-range interactions or through breakdown into smaller molecules by bacterial fermentation. Overall, our results provide additional evidence that odors of Old World monkeys reflect a wealth of potential information about their carrier, which provides the basis for chemical communication via body odors; however, its use by conspecifics needs to be confirmed in bioassays. Significance statement One prerequisite for olfactory communication is the presence of systematic variation in animal odors that is related to attributes such as age, sex, or kinship. The composition of odors has been examined in numerous mammals but, with the exception of humans, remains poorly understood in Old World monkeys and apes, taxonomic groups in which most species do not show scent-marking behavior. In the present study, we show that the composition of axillary secretions of an Old World monkey, the rhesus macaque, reflects sex, group membership, relatedness, and possibly also age and rank. This variation thus provides a basis for olfactory communication in Old World monkeys.
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Affiliation(s)
- Brigitte M. Weiß
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, Faculty of Life Sciences, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
| | - Marlen Kücklich
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, Faculty of Life Sciences, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
| | - Ruth Thomsen
- Research Group of Behavioural Ecology, Institute of Biology, Faculty of Life Sciences, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
- Department of Anthropology, University College London, Gower Street, London, WC1E 6BT UK
| | - Stefanie Henkel
- Research Group of Behavioural Ecology, Institute of Biology, Faculty of Life Sciences, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
- Department of Developmental and Comparative Psychology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Susann Jänig
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, Faculty of Life Sciences, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
| | - Lars Kulik
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, Faculty of Life Sciences, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
| | - Claudia Birkemeyer
- Institute of Analytical Chemistry, Mass Spectrometry Research Group, University of Leipzig, Linnéstrasse 3, 04103 Leipzig, Germany
| | - Anja Widdig
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, Faculty of Life Sciences, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
- German Center for Integrative Biodiversity Research (iDiv), Deutscher Platz 5E, 04103 Leipzig, Germany
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Majid A, Kruspe N. Hunter-Gatherer Olfaction Is Special. Curr Biol 2018; 28:409-413.e2. [DOI: 10.1016/j.cub.2017.12.014] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/04/2017] [Accepted: 12/07/2017] [Indexed: 02/07/2023]
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Abstract
It is commonly believed that humans have a poor sense of smell compared to other mammalian species. However, this idea derives not from empirical studies of human olfaction but from a famous 19th-century anatomist's hypothesis that the evolution of human free will required a reduction in the proportional size of the brain's olfactory bulb. The human olfactory bulb is actually quite large in absolute terms and contains a similar number of neurons to that of other mammals. Moreover, humans have excellent olfactory abilities. We can detect and discriminate an extraordinary range of odors, we are more sensitive than rodents and dogs for some odors, we are capable of tracking odor trails, and our behavioral and affective states are influenced by our sense of smell.
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Affiliation(s)
- John P McGann
- Behavioral and Systems Neuroscience, Psychology Department, Rutgers University, 152 Frelinghuysen Road, Piscataway, NJ 08854, USA.
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Abstract
Evolution sculpts the olfactory nervous system in response to the unique sensory challenges facing each species. In vertebrates, dramatic and diverse adaptations to the chemical environment are possible because of the hierarchical structure of the olfactory receptor (OR) gene superfamily: expansion or contraction of OR subfamilies accompanies major changes in habitat and lifestyle; independent selection on OR subfamilies can permit local adaptation or conserved chemical communication; and genetic variation in single OR genes can alter odor percepts and behaviors driven by precise chemical cues. However, this genetic flexibility contrasts with the relatively fixed neural architecture of the vertebrate olfactory system, which requires that new olfactory receptors integrate into segregated and functionally distinct neural pathways. This organization allows evolution to couple critical chemical signals with selectively advantageous responses, but also constrains relationships between olfactory receptors and behavior. The coevolution of the OR repertoire and the olfactory system therefore reveals general principles of how the brain solves specific sensory problems and how it adapts to new ones.
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Moriya-Ito K, Hayakawa T, Suzuki H, Hagino-Yamagishi K, Nikaido M. Evolution of vomeronasal receptor 1 (V1R) genes in the common marmoset (Callithrix jacchus). Gene 2017; 642:343-353. [PMID: 29155331 DOI: 10.1016/j.gene.2017.11.048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/23/2017] [Accepted: 11/15/2017] [Indexed: 10/18/2022]
Abstract
Pheromones are crucial for eliciting innate responses and inducing social and sexual behaviors in mammals. The vomeronasal receptor 1 genes, V1Rs, encode members of a pheromone receptor family that are mainly expressed in the vomeronasal organ (VNO). The V1R family shows extraordinary variety in gene number among vertebrates owing to successive gene gains and losses during evolution. Such diversity is believed to reflect a degree of dependence on the VNO. We investigated V1R evolution in primate lineages closely related to humans because these VNOs show a trend toward degeneration. We performed extensive phylogenetic analyses for V1Rs from a broad range of primate species. Although the decline of intact genes was evident in anthropoids (hominoids, Old World monkeys and New World monkeys), we found that a certain number of intact genes persist in New World monkeys. In one New World monkey species, the common marmoset (Callithrix jacchus), we examined seven putatively functional V1Rs using in situ hybridization and reverse transcription-PCR. Based on their mRNA expression patterns in the VNO and other organs, two types of V1Rs emerged: the canonical class with VNO-specific expression, and a second group having more ubiquitous expression in various organs as well as VNO. Furthermore, phylogenetic analysis revealed that the class with the more widespread expression had been retained longer in evolution than the VNO-specific type. We propose that the acquisition of a novel non-VNO-related function(s) may have led to the survival of a small but persistent number of V1Rs in anthropoid primates.
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Affiliation(s)
- Keiko Moriya-Ito
- Department of Brain Development and Neural Regeneration, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan.
| | - Takashi Hayakawa
- Department of Wildlife Science (Nagoya Railroad Co., Ltd.), Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan; Japan Monkey Centre, Inuyama, Aichi 484-0081, Japan
| | - Hikoyu Suzuki
- Nihon BioData Corporation, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan.; School of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Kimiko Hagino-Yamagishi
- Department of Brain Development and Neural Regeneration, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Masato Nikaido
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan.
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Yohe LR, Abubakar R, Giordano C, Dumont E, Sears KE, Rossiter SJ, Dávalos LM. Trpc2 pseudogenization dynamics in bats reveal ancestral vomeronasal signaling, then pervasive loss. Evolution 2017; 71:923-935. [PMID: 28128447 DOI: 10.1111/evo.13187] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 12/30/2016] [Indexed: 01/08/2023]
Abstract
Comparative methods are often used to infer loss or gain of complex phenotypes, but few studies take advantage of genes tightly linked with complex traits to test for shifts in the strength of selection. In mammals, vomerolfaction detects chemical cues mediating many social and reproductive behaviors and is highly conserved, but all bats exhibit degraded vomeronasal structures with the exception of two families (Phyllostomidae and Miniopteridae). These families either regained vomerolfaction after ancestral loss, or there were many independent losses after diversification from an ancestor with functional vomerolfaction. In this study, we use the Transient receptor potential cation channel 2 (Trpc2) as a molecular marker for testing the evolutionary mechanisms of loss and gain of the mammalian vomeronasal system. We sequenced Trpc2 exon 2 in over 100 bat species across 17 of 20 chiropteran families. Most families showed independent pseudogenizing mutations in Trpc2, but the reading frame was highly conserved in phyllostomids and miniopterids. Phylogeny-based simulations suggest loss of function occurred after bat families diverged, and purifying selection in two families has persisted since bats shared a common ancestor. As most bats still display pheromone-mediated behavior, they might detect pheromones through the main olfactory system without using the Trpc2 signaling mechanism.
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Affiliation(s)
- Laurel R Yohe
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794
| | - Ramatu Abubakar
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794
| | - Christina Giordano
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794
| | - Elizabeth Dumont
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, 01003
| | - Karen E Sears
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, 61801.,School of Integrative Biology, Institute for Genome Biology, University of Illinois, Urbana, Illinois, 61801
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794.,Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, New York, 11794
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Belloir C, Miller-Leseigneur ML, Neiers F, Briand L, Le Bon AM. Biophysical and functional characterization of the human olfactory receptor OR1A1 expressed in a mammalian inducible cell line. Protein Expr Purif 2017; 129:31-43. [DOI: 10.1016/j.pep.2016.09.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/07/2016] [Accepted: 09/15/2016] [Indexed: 10/21/2022]
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Kawamura S, Melin AD. Evolution of Genes for Color Vision and the Chemical Senses in Primates. EVOLUTION OF THE HUMAN GENOME I 2017. [DOI: 10.1007/978-4-431-56603-8_10] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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45
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Ligand Specificity and Evolution of Mammalian Musk Odor Receptors: Effect of Single Receptor Deletion on Odor Detection. J Neurosci 2016; 36:4482-91. [PMID: 27098692 DOI: 10.1523/jneurosci.3259-15.2016] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 03/01/2016] [Indexed: 01/20/2023] Open
Abstract
UNLABELLED Musk odors have been used widely for fragrance and medicine for >2000 years because of their fascinating scent and physiological effects. Therefore, fragrance manufacturers have been eager to develop high-quality musk compounds that are safe and easily synthesized. We recently identified muscone-responsive olfactory receptors (ORs) MOR215-1 and OR5AN1 in mice and humans, respectively (Shirasu et al., 2014). In this study, we identified musk ORs that are evolutionarily closely related to MOR215-1 or OR5AN1 in various primates and investigated structure-activity relationships for various musk odorants and related compounds. We found that each species has one or two functional musk ORs that exhibit specific ligand spectra to musk compounds. Some of them, including the human OR5AN1, responded to nitro musks with chemical properties distinct from muscone. The ligand specificity of OR5AN1 reflects the perception of musk odors in humans. Genetic deletion of MOR215-1 in mice resulted in drastic reduction of sensitivity to muscone, suggesting that MOR215-1 plays a critical role in muscone perception. Therefore, the current study reveals a clear link between the identified OR and muscone perception. Moreover, the strategy established for screening ligands for the muscone OR may facilitate the development of novel and commercially useful musk odors. SIGNIFICANCE STATEMENT The long-sought musk odor receptor family in mammals was discovered and found to be well conserved and narrowly tuned to musk odors. In mice, deletion of the most sensitive musk receptor resulted in drastic reduction in sensitivity to muscone, demonstrating a strong link between receptor and odor perception. In humans, we found one musk receptor that recognized both macrocyclic and nitro musks that had distinct chemical structures. The structure-activity relationships were in a good agreement with human sensory perception and therefore may be used to develop novel musk aroma in fragrance fields. Finally, identification of a natural ligand(s) for musk receptors in mammals other than musk deer would reveal an evolutionarily pivotal role in each species in the future.
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El Mountassir F, Belloir C, Briand L, Thomas-Danguin T, Le Bon AM. Encoding odorant mixtures by human olfactory receptors. FLAVOUR FRAG J 2016. [DOI: 10.1002/ffj.3331] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fouzia El Mountassir
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRA; Univ. Bourgogne Franche-Comté; F-21000 Dijon France
| | - Christine Belloir
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRA; Univ. Bourgogne Franche-Comté; F-21000 Dijon France
| | - Loïc Briand
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRA; Univ. Bourgogne Franche-Comté; F-21000 Dijon France
| | - Thierry Thomas-Danguin
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRA; Univ. Bourgogne Franche-Comté; F-21000 Dijon France
| | - Anne-Marie Le Bon
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRA; Univ. Bourgogne Franche-Comté; F-21000 Dijon France
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Eyun SI, Moriyama H, Hoffmann FG, Moriyama EN. Molecular Evolution and Functional Divergence of Trace Amine-Associated Receptors. PLoS One 2016; 11:e0151023. [PMID: 26963722 PMCID: PMC4786312 DOI: 10.1371/journal.pone.0151023] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 02/09/2016] [Indexed: 12/31/2022] Open
Abstract
Trace amine-associated receptors (TAARs) are a member of the G-protein-coupled receptor superfamily and are known to be expressed in olfactory sensory neurons. A limited number of molecular evolutionary studies have been done for TAARs so far. To elucidate how lineage-specific evolution contributed to their functional divergence, we examined 30 metazoan genomes. In total, 493 TAAR gene candidates (including 84 pseudogenes) were identified from 26 vertebrate genomes. TAARs were not identified from non-vertebrate genomes. An ancestral-type TAAR-like gene appeared to have emerged in lamprey. We found four therian-specific TAAR subfamilies (one eutherian-specific and three metatherian-specific) in addition to previously known nine subfamilies. Many species-specific TAAR gene duplications and losses contributed to a large variation of TAAR gene numbers among mammals, ranging from 0 in dolphin to 26 in flying fox. TAARs are classified into two groups based on binding preferences for primary or tertiary amines as well as their sequence similarities. Primary amine-detecting TAARs (TAAR1-4) have emerged earlier, generally have single-copy orthologs (very few duplication or loss), and have evolved under strong functional constraints. In contrast, tertiary amine-detecting TAARs (TAAR5-9) have emerged more recently and the majority of them experienced higher rates of gene duplications. Protein members that belong to the tertiary amine-detecting TAAR group also showed the patterns of positive selection especially in the area surrounding the ligand-binding pocket, which could have affected ligand-binding activities and specificities. Expansions of the tertiary amine-detecting TAAR gene family may have played important roles in terrestrial adaptations of therian mammals. Molecular evolution of the TAAR gene family appears to be governed by a complex, species-specific, interplay between environmental and evolutionary factors.
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Affiliation(s)
- Seong-il Eyun
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, United States of America
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, United States of America
| | - Hideaki Moriyama
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, United States of America
| | - Federico G. Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology and Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS, 39762, United States of America
| | - Etsuko N. Moriyama
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, United States of America
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, United States of America
- * E-mail:
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48
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Vandewege MW, Mangum SF, Gabaldón T, Castoe TA, Ray DA, Hoffmann FG. Contrasting Patterns of Evolutionary Diversification in the Olfactory Repertoires of Reptile and Bird Genomes. Genome Biol Evol 2016; 8:470-80. [PMID: 26865070 PMCID: PMC4825420 DOI: 10.1093/gbe/evw013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Olfactory receptors (ORs) are membrane proteins that mediate the detection of odorants in the environment, and are the largest vertebrate gene family. Comparative studies of mammalian genomes indicate that OR repertoires vary widely, even between closely related lineages, as a consequence of frequent OR gains and losses. Several studies also suggest that mammalian OR repertoires are influenced by life history traits. Sauropsida is a diverse group of vertebrates group that is the sister group to mammals, and includes birds, testudines, squamates, and crocodilians, and represents a natural system to explore predictions derived from mammalian studies. In this study, we analyzed olfactory receptor (OR) repertoire variation among several representative species and found that the number of intact OR genes in sauropsid genomes analyzed ranged over an order of magnitude, from 108 in the green anole to over 1,000 in turtles. Our results suggest that different sauropsid lineages have highly divergent OR repertoire composition that derive from lineage-specific combinations of gene expansions, losses, and retentions of ancestral OR genes. These differences also suggest that varying degrees of adaption related to life history have shaped the unique OR repertoires observed across sauropsid lineages.
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Affiliation(s)
- Michael W Vandewege
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University
| | - Sarah F Mangum
- Department of Biological Sciences, Texas Tech University
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington
| | - David A Ray
- Department of Biological Sciences, Texas Tech University
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing and Biochemistry, Mississippi State University
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Deciphering the Receptor Repertoire Encoding Specific Odorants by Time-Lapse Single-Cell Array Cytometry. Sci Rep 2016; 6:19934. [PMID: 26832639 PMCID: PMC4735795 DOI: 10.1038/srep19934] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/21/2015] [Indexed: 01/12/2023] Open
Abstract
Mammals can recognize a vast number of odorants by using olfactory receptors (ORs) known as G protein-coupled receptors. The OR gene family is one of the most diverse gene families in mammalian genomes. Because of the vast combinations of ORs and odorants, few ORs have thus far been linked to specific odorants. Here, we established a functional screening method for OR genes by using a microchamber array containing >5,400 single olfactory epithelium-derived cells from mice applied to time-lapse single-cell array cytometry. This method facilitated the prompt isolation of single olfactory sensory neurons (OSNs) responding to the odorant of interest. Subsequent single-cell RT-PCR allowed us to isolate the genes encoding respective ORs. By using volatile molecules recognized as biomarkers for lung cancers, this method could deorphanize ORs and thereby reconstitute the OR-mediated signaling cascade in HEK293T cells. Thus, our system could be applied to identify any receptor by using specific ligands in the fields of physiopathology and pharmacology.
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50
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Degl'Innocenti A, Parrilla M, Harr B, Teschke M. The Mouse Solitary Odorant Receptor Gene Promoters as Models for the Study of Odorant Receptor Gene Choice. PLoS One 2016; 11:e0144698. [PMID: 26794459 PMCID: PMC4721658 DOI: 10.1371/journal.pone.0144698] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 11/23/2015] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND In vertebrates, several anatomical regions located within the nasal cavity mediate olfaction. Among these, the main olfactory epithelium detects most conventional odorants. Olfactory sensory neurons, provided with cilia exposed to the air, detect volatile chemicals via an extremely large family of seven-transmembrane chemoreceptors named odorant receptors. Their genes are expressed in a monogenic and monoallelic fashion: a single allele of a single odorant receptor gene is transcribed in a given mature neuron, through a still uncharacterized molecular mechanism known as odorant receptor gene choice. AIM Odorant receptor genes are typically arranged in genomic clusters, but a few are isolated (we call them solitary) from the others within a region broader than 1 Mb upstream and downstream with respect to their transcript's coordinates. The study of clustered genes is problematic, because of redundancy and ambiguities in their regulatory elements: we propose to use the solitary genes as simplified models to understand odorant receptor gene choice. PROCEDURES Here we define number and identity of the solitary genes in the mouse genome (C57BL/6J), and assess the conservation of the solitary status in some mammalian orthologs. Furthermore, we locate their putative promoters, predict their homeodomain binding sites (commonly present in the promoters of odorant receptor genes) and compare candidate promoter sequences with those of wild-caught mice. We also provide expression data from histological sections. RESULTS In the mouse genome there are eight intact solitary genes: Olfr19 (M12), Olfr49, Olfr266, Olfr267, Olfr370, Olfr371, Olfr466, Olfr1402; five are conserved as solitary in rat. These genes are all expressed in the main olfactory epithelium of three-day-old mice. The C57BL/6J candidate promoter of Olfr370 has considerably varied compared to its wild-type counterpart. Within the putative promoter for Olfr266 a homeodomain binding site is predicted. As a whole, our findings favor Olfr266 as a model gene to investigate odorant receptor gene choice.
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Affiliation(s)
- Andrea Degl'Innocenti
- Max-Planck-Institut für Biophysik, Frankfurt am Main, Germany
- Unità di Biologia Cellulare e dello Sviluppo, Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Marta Parrilla
- Max-Planck-Institut für Biophysik, Frankfurt am Main, Germany
| | - Bettina Harr
- Abteilung Evolutionsgenetik, Max-Planck-Institut für Evolutionsbiologie, Plön, Germany
| | - Meike Teschke
- Abteilung Evolutionsgenetik, Max-Planck-Institut für Evolutionsbiologie, Plön, Germany
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