1
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Zhang T, Jing H, Wang J, Zhao L, Liu Y, Rossiter SJ, Lu H, Li G. Evolution of olfactory receptor superfamily in bats based on high throughput molecular modelling. Mol Ecol Resour 2024; 24:e13958. [PMID: 38567648 DOI: 10.1111/1755-0998.13958] [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: 09/21/2023] [Revised: 03/05/2024] [Accepted: 03/25/2024] [Indexed: 04/04/2024]
Abstract
The origin of flight and laryngeal echolocation in bats is likely to have been accompanied by evolutionary changes in other aspects of their sensory biology. Of all sensory modalities in bats, olfaction is perhaps the least well understood. Olfactory receptors (ORs) function in recognizing odour molecules, with crucial roles in evaluating food, as well as in processing social information. Here we compare OR repertoire sizes across taxa and apply a new pipeline that integrates comparative genome data with protein structure modelling and then we employ molecular docking techniques with small molecules to analyse OR functionality based on binding energies. Our results suggest a sharp contraction in odorant recognition of the functional OR repertoire during the origin of bats, consistent with a reduced dependence on olfaction. We also compared bat lineages with contrasting different ecological characteristics and found evidence of differences in OR gene expansion and contraction, and in the composition of ORs with different tuning breadths. The strongest binding energies of ORs in non-echolocating fruit-eating bats were seen to correspond to ester odorants, although we did not detect a quantitative advantage of functional OR repertoires in these bats compared with echolocating insectivorous species. Overall, our findings based on molecular modelling and computational docking suggest that bats have undergone olfactory evolution linked to dietary adaptation. Our results from extant and ancestral bats help to lay the groundwork for targeted experimental functional tests in the future.
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Affiliation(s)
- Tianmin Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Haohao Jing
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Jinhong Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Le Zhao
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Stephen J Rossiter
- School of Biological and Behavioural Sciences, Queen Mary, University of London, London, UK
| | - Huimeng Lu
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
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2
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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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3
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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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4
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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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5
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Liao BY, Weng MP, Chang TY, Chang AYF, Ching YH, Wu CH. Degeneration of the Olfactory System in a Murid Rodent that Evolved Diurnalism. Mol Biol Evol 2024; 41:msae037. [PMID: 38376543 PMCID: PMC10906987 DOI: 10.1093/molbev/msae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/03/2024] [Accepted: 02/13/2024] [Indexed: 02/21/2024] Open
Abstract
In mammalian research, it has been debated what can initiate an evolutionary tradeoff between different senses, and the phenomenon of sensory tradeoff in rodents, the most abundant mammalian clade, is not evident. The Nile rat (Arvicanthis niloticus), a murid rodent, recently adapted to a diurnal niche through an evolutionary acquisition of daylight vision with enhanced visual acuity. As such, this model provides an opportunity for a cross-species investigation where comparative morphological and multi-omic analyses of the Nile rat are made with its closely related nocturnal species, e.g. the mouse (Mus musculus) and the rat (Rattus norvegicus). Thus, morphological examinations were performed, and evolutionary reductions in relative sizes of turbinal bone surfaces, the cribriform plate, and the olfactory bulb were discovered in Nile rats. Subsequently, we compared multiple murid genomes, and profiled olfactory epithelium transcriptomes of mice and Nile rats at various ages with RNA sequencing. The results further demonstrate that, in comparison with mouse olfactory receptor (OR) genes, Nile rat OR genes have experienced less frequent gain, more frequent loss, and more frequent expression reduction during their evolution. Furthermore, functional degeneration of coding sequences in the Nile rat lineage was found in OR genes, yet not in other genes. Taken together, these results suggest that acquisition of improved vision in the Nile rat has been accompanied by degeneration of both olfaction-related anatomical structures and OR gene repertoires, consistent with the hypothesis of an olfaction-vision tradeoff initiated by the switch from a nocturnal to a diurnal lifestyle in mammals.
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Affiliation(s)
- Ben-Yang Liao
- Institute of Population Health Sciences, National Health Research Institutes, Taiwan, Republic of China
| | - Meng-Pin Weng
- Institute of Population Health Sciences, National Health Research Institutes, Taiwan, Republic of China
| | - Ting-Yan Chang
- Institute of Population Health Sciences, National Health Research Institutes, Taiwan, Republic of China
| | - Andrew Ying-Fei Chang
- Institute of Population Health Sciences, National Health Research Institutes, Taiwan, Republic of China
| | - Yung-Hao Ching
- Department of Molecular Biology and Human Genetics, Tzu Chi University, Taiwan, Republic of China
| | - Chia-Hwa Wu
- Laboratory Animal Center, National Health Research Institutes, Taiwan, Republic of China
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6
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Policarpo M, Baldwin MW, Casane D, Salzburger W. Diversity and evolution of the vertebrate chemoreceptor gene repertoire. Nat Commun 2024; 15:1421. [PMID: 38360851 PMCID: PMC10869828 DOI: 10.1038/s41467-024-45500-y] [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: 09/22/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
Chemoreception - the ability to smell and taste - is an essential sensory modality of most animals. The number and type of chemical stimuli that animals can perceive depends primarily on the diversity of chemoreceptors they possess and express. In vertebrates, six families of G protein-coupled receptors form the core of their chemosensory system, the olfactory/pheromone receptor gene families OR, TAAR, V1R and V2R, and the taste receptors T1R and T2R. Here, we study the vertebrate chemoreceptor gene repertoire and its evolutionary history. Through the examination of 1,527 vertebrate genomes, we uncover substantial differences in the number and composition of chemoreceptors across vertebrates. We show that the chemoreceptor gene families are co-evolving, highly dynamic, and characterized by lineage-specific expansions (for example, OR in tetrapods; TAAR, T1R in teleosts; V1R in mammals; V2R, T2R in amphibians) and losses. Overall, amphibians, followed by mammals, are the vertebrate clades with the largest chemoreceptor repertoires. While marine tetrapods feature a convergent reduction of chemoreceptor numbers, the number of OR genes correlates with habitat in mammals and birds and with migratory behavior in birds, and the taste receptor repertoire correlates with diet in mammals and with aquatic environment in fish.
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Affiliation(s)
- Maxime Policarpo
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | - Didier Casane
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette, France
- Université Paris Cité, UFR Sciences du Vivant, Paris, France
| | - Walter Salzburger
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
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Martinez Q, Amson E, Laska M. Does the number of functional olfactory receptor genes predict olfactory sensitivity and discrimination performance in mammals? J Evol Biol 2024; 37:238-247. [PMID: 38297391 DOI: 10.1093/jeb/voae006] [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: 04/20/2023] [Revised: 12/05/2023] [Accepted: 01/04/2024] [Indexed: 02/02/2024]
Abstract
The number of functional genes coding for olfactory receptors differs markedly between species and has repeatedly been suggested to be predictive of a species' olfactory capabilities. To test this assumption, we compiled a database of all published olfactory detection threshold values in mammals and used three sets of data on olfactory discrimination performance that employed the same structurally related monomolecular odour pairs with different mammal species. We extracted the number of functional olfactory receptor genes of the 20 mammal species for which we found data on olfactory sensitivity and/or olfactory discrimination performance from the Chordata Olfactory Receptor Database. We found that the overall olfactory detection thresholds significantly correlate with the number of functional olfactory receptor genes. Similarly, the overall proportion of successfully discriminated monomolecular odour pairs significantly correlates with the number of functional olfactory receptor genes. These results provide the first statistically robust evidence for the relationship between olfactory capabilities and their genomics correlates. However, when analysed individually, of the 44 monomolecular odourants for which data on olfactory sensitivity from at least five mammal species are available, only five yielded a significant correlation between olfactory detection thresholds and the number of functional olfactory receptors genes. Also, for the olfactory discrimination performance, no significant correlation was found for any of the 74 relationships between the proportion of successfully discriminated monomolecular odour pairs and the number of functional olfactory receptor genes. While only a rather limited amount of data on olfactory detection thresholds and olfactory discrimination scores in a rather limited number of mammal species is available so far, we conclude that the number of functional olfactory receptor genes may be a predictor of olfactory sensitivity and discrimination performance in mammals.
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Affiliation(s)
| | - Eli Amson
- Staatliches Museum für Naturkunde Stuttgart, Stuttgart, Germany
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8
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Ferreira JS, Bruschi DP. Tracking the Diversity and Chromosomal Distribution of the Olfactory Receptor Gene Repertoires of Three Anurans Species. J Mol Evol 2023; 91:793-805. [PMID: 37906255 DOI: 10.1007/s00239-023-10135-y] [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: 03/29/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023]
Abstract
Olfaction is a crucial capability for most vertebrates and is realized through olfactory receptors in the nasal cavity. The enormous diversity of olfactory receptors has been created by gene duplication, following a birth-and-death model of evolution. The olfactory receptor genes of the amphibians have received relatively little attention up to now, although recent studies have increased the number of species for which data are available. This study analyzed the diversity and chromosomal distribution of the OR genes of three anuran species (Engystomops pustulosus, Bufo bufo and Hymenochirus boettgeri). The OR genes were identified through searches for homologies, and sequence filtering and alignment using bioinformatic tools and scripts. A high diversity of OR genes was found in all three species, ranging from 917 in B. bufo to 1194 in H. boettgeri, and a total of 2076 OR genes in E. pustulosus. Six OR groups were recognized using an evolutionary gene tree analysis. While E. pustulosus has one of the highest numbers of genes of the gamma group (which detect airborne odorants) yet recorded in an anuran, B. bufo presented the smallest number of pseudogene sequences ever identified, with no pseudogenes in either the beta or epsilon groups. Although H. boettgeri shares many morphological adaptations for an aquatic lifestyle with Xenopus, and presented a similar number of genes related to the detection of water-soluble odorants, it had comparatively far fewer genes related to the detection of airborne odorants. This study is the first to describe the complete OR repertoire of the three study species and represents an important contribution to the understanding of the evolution and function of the sense of smell in vertebrates.
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Affiliation(s)
- Johnny Sousa Ferreira
- Laboratório de Citogenética Evolutiva e Conservação Animal (LabCECA), Departamento de Genética, Universidade Federal do Paraná (UFPR), Paraná, Brazil
| | - Daniel Pacheco Bruschi
- Laboratório de Citogenética Evolutiva e Conservação Animal (LabCECA), Departamento de Genética, Universidade Federal do Paraná (UFPR), Paraná, Brazil.
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9
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Yohe LR, Krell NT. An updated synthesis of and outstanding questions in the olfactory and vomeronasal systems in bats: Genetics asks questions only anatomy can answer. Anat Rec (Hoboken) 2023; 306:2765-2780. [PMID: 37523493 DOI: 10.1002/ar.25290] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 08/02/2023]
Abstract
The extensive diversity observed in bat nasal chemosensory systems has been well-documented at the histological level. Understanding how this diversity evolved and developing hypotheses as to why particular patterns exist require a phylogenetic perspective, which was first outlined in the work of anatomist Kunwar Bhatnagar. With the onset of genetics and genomics, it might be assumed that the puzzling patterns observed in the morphological data have been clarified. However, there is still a widespread mismatch of genetic and morphological correlations among bat chemosensory systems. Novel genomic evidence has set up new avenues to explore that demand more evidence from anatomical structures. Here, we outline the progress that has been made in both morphological and molecular studies on the olfactory and vomeronasal systems in bats since the work of Bhatnagar. Genomic data of olfactory and vomeronasal receptors demonstrate the strong need for further morphological sampling, with a particular focus on receiving brain regions, glands, and ducts.
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Affiliation(s)
- Laurel R Yohe
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
- North Carolina Research Campus, Kannapolis, North Carolina, USA
| | - Nicholas T Krell
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
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10
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Kang J, Ramirez-Calero S, Paula JR, Chen Y, Schunter C. Gene losses, parallel evolution and heightened expression confer adaptations to dedicated cleaning behaviour. BMC Biol 2023; 21:180. [PMID: 37612643 PMCID: PMC10463495 DOI: 10.1186/s12915-023-01682-3] [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: 03/23/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND Cleaning symbioses are captivating interspecific interactions in which a cleaner fish removes ectoparasites from its client, contributing to the health and diversity of natural fish communities and aquaculture systems. However, the genetic signatures underlying this specialized behaviour remain poorly explored. To shed light on this, we generated a high-quality chromosome-scale genome of the bluestreak cleaner wrasse Labroides dimidiatus, a dedicated cleaner with cleaning as primary feeding mechanism throughout its life. RESULTS Compared with facultative and non-cleaner wrasses, L. dimidiatus was found with notable contractions in olfactory receptors implying their limited importance in dedicated cleaning. Instead, given its distinct tactile pre-conflict strategies, L. dimidiatus may rely more heavily on touch sensory perception, with heightened gene expression in the brain in anticipation of cleaning. Additionally, a reduction in NLR family CARD domain-containing protein 3 might enhance innate immunity of L. dimidiatus, probably assisting to reduce the impacts from parasite infections. In addition, convergent substitutions for a taste receptor and bone development genes across cleaners (L. dimidiatus and facultative cleaners) may provide them with evolved food discrimination abilities and jaw morphology that differentiate them from non-cleaners. Moreover, L. dimidiatus may exhibit specialized neural signal transductions for cleaning, as evidenced by positive selection in genes related to the glutamatergic synapse pathway. Interestingly, numerous glutamate receptors also demonstrated significantly higher expression in L. dimidiatus not engaged in cleaning, as compared to those involved in cleaning. Besides, apparent contractions in L. dimidiatus for protocadherins, which are responsible for neuronal development, may further promote specialized neural signal transductions in this species. CONCLUSIONS This study reveals that L. dimidiatus harbours substantial losses in specific gene families, convergent evolutions across cleaners and a large-scale high gene expression in preparation for cleaning, allowing for adaptation to the dedicated cleaning behaviour.
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Affiliation(s)
- Jingliang Kang
- Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Sandra Ramirez-Calero
- Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - José Ricardo Paula
- Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- MARE - Marine and Environmental Sciences Centre & ARNET - Aquatic Research Network, Laboratório Marítimo da Guia, Faculdade de Ciências, Universidade de Lisboa, Av. Nossa Senhora Do Cabo, 939, Cascais, 2750-374, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Yifang Chen
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong, SAR, China
| | - Celia Schunter
- Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong, SAR, China.
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11
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Veilleux CC, Garrett EC, Pajic P, Saitou M, Ochieng J, Dagsaan LD, Dominy NJ, Perry GH, Gokcumen O, Melin AD. Human subsistence and signatures of selection on chemosensory genes. Commun Biol 2023; 6:683. [PMID: 37400713 DOI: 10.1038/s42003-023-05047-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/15/2023] [Indexed: 07/05/2023] Open
Abstract
Chemosensation (olfaction, taste) is essential for detecting and assessing foods, such that dietary shifts elicit evolutionary changes in vertebrate chemosensory genes. The transition from hunting and gathering to agriculture dramatically altered how humans acquire food. Recent genetic and linguistic studies suggest agriculture may have precipitated olfactory degeneration. Here, we explore the effects of subsistence behaviors on olfactory (OR) and taste (TASR) receptor genes among rainforest foragers and neighboring agriculturalists in Africa and Southeast Asia. We analyze 378 functional OR and 26 functional TASR genes in 133 individuals across populations in Uganda (Twa, Sua, BaKiga) and the Philippines (Agta, Mamanwa, Manobo) with differing subsistence histories. We find no evidence of relaxed selection on chemosensory genes in agricultural populations. However, we identify subsistence-related signatures of local adaptation on chemosensory genes within each geographic region. Our results highlight the importance of culture, subsistence economy, and drift in human chemosensory perception.
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Affiliation(s)
- Carrie C Veilleux
- Department of Anatomy, Midwestern University, 19555 N 59th Ave, Glendale, AZ, 85308, USA.
- Department of Anthropology & Archaeology, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada.
| | - Eva C Garrett
- Department of Anthropology & Archaeology, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
- Department of Anthropology, Boston University, 232 Bay State Road, Boston, MA, 02215, USA
| | - Petar Pajic
- Department of Biological Sciences, University at Buffalo, 109 Cooke Hall, Buffalo, NY, 14260, USA
| | - Marie Saitou
- Department of Biological Sciences, University at Buffalo, 109 Cooke Hall, Buffalo, NY, 14260, USA
| | - Joseph Ochieng
- Department of Anatomy, Makerere University College of Health Sciences, Kampala, Uganda
| | - Lilia D Dagsaan
- National Commission for Indigenous Peoples, Botolan, Philippines
| | - Nathaniel J Dominy
- Department of Anthropology, Dartmouth College, 6047 Silsby Hall, Hanover, NH, 03755, USA
| | - George H Perry
- Departments of Anthropology and Biology, The Pennsylvania State University, 410 Carpenter Building, University Park, PA, 16802, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, 109 Cooke Hall, Buffalo, NY, 14260, USA
| | - Amanda D Melin
- Department of Anthropology & Archaeology, University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada.
- Department of Medical Genetics, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada.
- Alberta Children's Hospital Research Institute, 3330 Hospital Dr. NW, Calgary, AB, T2N 4N1, Canada.
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12
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Ye M, Lin X, Zhang Y, Huang Y, Li G, Tian C. Genome-Wide Identification and Characterization of Olfactory Receptor Genes in Silver Sillago (Sillago sihama). Animals (Basel) 2023; 13:ani13071232. [PMID: 37048487 PMCID: PMC10093537 DOI: 10.3390/ani13071232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
Olfactory receptor (OR) genes are essential in the specific recognition of diverse stimuli in fish. In this study, a total of 141 OR genes were identified in silver sillago (Sillago sihama), a marine fish sensitive to environmental stimuli, including 112 intact genes, 26 truncated genes, and three pseudogenes. A phylogenetic tree analysis elucidated that the OR genes of S. sihama were classified into six groups, of which β, γ, δ, ε, and ζ groups belonged to type I, and the η group belonged to type II. The type I OR genes contained almost all conserved motifs (n = 62), while type II OR genes mainly retained conserved motifs 7(3), 1, 10, 4, and 2 (n = 39). OR genes were mainly distributed on LG1, LG9, LG11, and LG12. Of all OR genes, 36.23% (50 genes) showed significant expansion in S. sihama. Ka/Ks analysis demonstrated that 227 sites were under purifying selection, while 12 sites were under positive selection, including eight genes in the OR2A12 gene subfamily. Sixty-one genes (44.20%) displayed differential expression under hypoxic stress. The identified OR genes explored the mechanism of environmental stress and ecological adaptation of S. sihama, and provided valuable genomic resources for further research on the olfaction of teleosts.
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Affiliation(s)
- Minghui Ye
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Xinghua Lin
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yulei Zhang
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China
| | - Yang Huang
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China
| | - Guangli Li
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China
| | - Changxu Tian
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China
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13
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Zhao L, Li XD, Jiang T, Wang H, Dan Z, Xu SQ, Guan DL. The Chromosome-Level Genome of Hestina assimilis (Lepidoptera: Nymphalidae) Reveals the Evolution of Saprophagy-Related Genes in Brush-Footed Butterflies. Int J Mol Sci 2023; 24:ijms24032087. [PMID: 36768416 PMCID: PMC9917059 DOI: 10.3390/ijms24032087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/06/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Most butterflies feed on nectar, while some saprophagous butterflies forage on various non-nectar foods. To date, little is known about the genomic and molecular shifts associated with the evolution of the saprophagous feeding strategy. Here, we assembled the high-quality chromosome-level genome of Hestina assimilis to explore its saprophagous molecular and genetic mechanisms. This chromosome-level genome of H. assimilis is 412.82 Mb, with a scaffold N50 of 15.70 Mb. In total, 98.11% of contigs were anchored to 30 chromosomes. Compared with H. assimilis and other Nymphalidae butterflies, the genes of metabolism and detoxification experienced expansions. We annotated 80 cytochrome P450 (CYP) genes in the H. assimilis genome, among which genes belonging to the CYP4 subfamily were significantly expanded (p < 0.01). These P450 genes were unevenly distributed and mainly concentrated on chromosomes 6-9. We identified 33 olfactory receptor (OR), 20 odorant-binding protein (OBP), and six gustatory receptor (GR) genes in the H. assimilis genome, which were fewer than in the nectarivorous Danaus plexippus. A decreased number of OBP, OR, and GR genes implied that H. assimilis should resort less to olfaction and gustation than their nectarivorous counterparts, which need highly specialized olfactory and gustatory functions. Moreover, we found one site under positive selection occurred in residue 996 (phenylalanine) of GR genes exclusive to H. assimilis, which is conservative in most lineages. Our study provides support for the adaptive evolution of feeding habits in butterflies.
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Affiliation(s)
- Lu Zhao
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Xiao-Dong Li
- School of Chemistry and Bioengineering, Hechi University, Yizhou 546300, China
| | - Tao Jiang
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Hang Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Zhicuo Dan
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
| | - Sheng-Quan Xu
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
- Correspondence: (S.-Q.X.); (D.-L.G.)
| | - De-Long Guan
- College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China
- School of Chemistry and Bioengineering, Hechi University, Yizhou 546300, China
- Correspondence: (S.-Q.X.); (D.-L.G.)
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14
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Veilleux CC, Dominy NJ, Melin AD. The sensory ecology of primate food perception, revisited. Evol Anthropol 2022; 31:281-301. [PMID: 36519416 DOI: 10.1002/evan.21967] [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: 11/17/2021] [Revised: 09/06/2022] [Accepted: 10/23/2022] [Indexed: 12/23/2022]
Abstract
Twenty years ago, Dominy and colleagues published "The sensory ecology of primate food perception," an impactful review that brought new perspectives to understanding primate foraging adaptations. Their review synthesized information on primate senses and explored how senses informed feeding behavior. Research on primate sensory ecology has seen explosive growth in the last two decades. Here, we revisit this important topic, focusing on the numerous new discoveries and lines of innovative research. We begin by reviewing each of the five traditionally recognized senses involved in foraging: audition, olfaction, vision, touch, and taste. For each sense, we provide an overview of sensory function and comparative ecology, comment on the state of knowledge at the time of the original review, and highlight advancements and lingering gaps in knowledge. Next, we provide an outline for creative, multidisciplinary, and innovative future research programs that we anticipate will generate exciting new discoveries in the next two decades.
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Affiliation(s)
- Carrie C Veilleux
- Department of Anatomy, Midwestern University, Glendale, Arizona, USA
| | - Nathaniel J Dominy
- Department of Anthropology, Dartmouth College, Hanover, New Hampshire, USA
| | - 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, University of Calgary, Calgary, Alberta, Canada
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15
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Melin AD, Veilleux CC, Janiak MC, Hiramatsu C, Sánchez-Solano KG, Lundeen IK, Webb SE, Williamson RE, Mah MA, Murillo-Chacon E, Schaffner CM, Hernández-Salazar L, Aureli F, Kawamura S. Anatomy and dietary specialization influence sensory behaviour among sympatric primates. Proc Biol Sci 2022; 289:20220847. [PMID: 35975434 PMCID: PMC9382214 DOI: 10.1098/rspb.2022.0847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Senses form the interface between animals and environments, and provide a window into the ecology of past and present species. However, research on sensory behaviours by wild frugivores is sparse. Here, we examine fruit assessment by three sympatric primates (Alouatta palliata, Ateles geoffroyi and Cebus imitator) to test the hypothesis that dietary and sensory specialization shape foraging behaviours. Ateles and Cebus groups are comprised of dichromats and trichromats, while all Alouatta are trichomats. We use anatomical proxies to examine smell, taste and manual touch, and opsin genotyping to assess colour vision. We find that the frugivorous spider monkeys (Ateles geoffroyi) sniff fruits most often, omnivorous capuchins (Cebus imitator), the species with the highest manual dexterity, use manual touch most often, and that main olfactory bulb volume is a better predictor of sniffing behaviour than nasal turbinate surface area. We also identify an interaction between colour vision phenotype and use of other senses. Controlling for species, dichromats sniff and bite fruits more often than trichromats, and trichromats use manual touch to evaluate cryptic fruits more often than dichromats. Our findings reveal new relationships among dietary specialization, anatomical variation and foraging behaviour, and promote understanding of sensory system evolution.
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Affiliation(s)
- Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, Canada.,Department of Medical Genetics, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.,German Primate Research Center, Gottingen, Germany
| | - Carrie C Veilleux
- Department of Anatomy, Midwestern University, Glendale, AZ, USA.,Department of Anthropology, University of Texas, Austin, TX, USA
| | - Mareike C Janiak
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.,School of Science, Engineering & Environment, University of Salford, Manchester, UK
| | - Chihiro Hiramatsu
- Department of Human Science, Faculty of Design, Kyushu University, Fukuoka 815-8540, Japan
| | | | - Ingrid K Lundeen
- Department of Anthropology, University of Texas, Austin, TX, USA
| | - Shasta E Webb
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, Canada
| | - Rachel E Williamson
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, Canada
| | - Megan A Mah
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, Canada
| | | | | | | | - Filippo Aureli
- Instituto de Neuroetología, Universidad Veracruzana, Xalapa, Veracruz, México.,Research Centre in Evolutionary Anthropology and Palaeoecology, Liverpool John Moores University, Liverpool, UK
| | - Shoji Kawamura
- Department of Integrative Biosciences, University of Tokyo, Kashiwa, Japan
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16
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Unique nasal turbinal morphology reveals Homunculus patagonicus functionally converged on modern platyrrhine olfactory sensitivity. J Hum Evol 2022; 167:103184. [DOI: 10.1016/j.jhevol.2022.103184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 03/02/2022] [Accepted: 03/11/2022] [Indexed: 11/19/2022]
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17
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DePasquale A, Hogan JD, Guadamuz Araya C, Dominy NJ, Melin AD. Aeroscapes and the Sensory Ecology of Olfaction in a Tropical Dry Forest. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.849281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aeroscapes—dynamic patterns of air speed and direction—form a critical component of landscape ecology by shaping numerous animal behaviors, including movement, foraging, and social and/or reproductive interactions. Aeroecology is particularly critical for sensory ecology: air is the medium through which many sensory signals and cues propagate, inherently linking sensory perception to variables such as air speed and turbulence. Yet, aeroscapes are seldom explicitly considered in studies of sensory ecology and evolution. A key first step towards this goal is to describe the aeroscapes of habitats. Here, we quantify the variation in air movement in two successional stages (early and late) of a tropical dry forest in Costa Rica. We recorded air speeds every 10 seconds at five different heights simultaneously. Average air speeds and turbulence increased with height above the ground, generally peaked midday, and were higher overall at the early successional forest site. These patterns of lower air speed and turbulence at ground level and overnight have important implications for olfactory foraging niches, as chemotaxis is most reliable when air movement is low and steady. We discuss our results in the context of possible selective pressures and observed variation in the foraging ecology, behaviors, and associated morphologies of resident vertebrates, with a focus on mammals. However, these data also have relevance to researchers studying socioecology, invertebrate biology, plant evolution, community ecology and more. Further investigation into how animals use different forest types, canopy heights and partition activities across different times of day will further inform our understanding of how landscape and sensory ecology are interrelated. Finally, we emphasize the timeliness of monitoring aeroecology as global wind patterns shift with climate change and human disturbance alters forest structure, which may have important downstream consequences for biological conservation.
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18
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Ruiz Tejada Segura ML, Abou Moussa E, Garabello E, Nakahara TS, Makhlouf M, Mathew LS, Wang L, Valle F, Huang SSY, Mainland JD, Caselle M, Osella M, Lorenz S, Reisert J, Logan DW, Malnic B, Scialdone A, Saraiva LR. A 3D transcriptomics atlas of the mouse nose sheds light on the anatomical logic of smell. Cell Rep 2022; 38:110547. [PMID: 35320714 PMCID: PMC8995392 DOI: 10.1016/j.celrep.2022.110547] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 01/26/2022] [Accepted: 03/01/2022] [Indexed: 12/26/2022] Open
Abstract
The sense of smell helps us navigate the environment, but its molecular architecture and underlying logic remain understudied. The spatial location of odorant receptor genes (Olfrs) in the nose is thought to be independent of the structural diversity of the odorants they detect. Using spatial transcriptomics, we create a genome-wide 3D atlas of the mouse olfactory mucosa (OM). Topographic maps of genes differentially expressed in space reveal that both Olfrs and non-Olfrs are distributed in a continuous and overlapping fashion over at least five broad zones in the OM. The spatial locations of Olfrs correlate with the mucus solubility of the odorants they recognize, providing direct evidence for the chromatographic theory of olfaction. This resource resolves the molecular architecture of the mouse OM and will inform future studies on mechanisms underlying Olfr gene choice, axonal pathfinding, patterning of the nervous system, and basic logic for the peripheral representation of smell.
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Affiliation(s)
- Mayra L Ruiz Tejada Segura
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Feodor-Lynen-Strasse 21, 81377 München, Germany; Institute of Functional Epigenetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | | | - Elisa Garabello
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Feodor-Lynen-Strasse 21, 81377 München, Germany; Physics Department, University of Turin and INFN, Via P. Giuria 1, 10125 Turin, Italy; Department of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Thiago S Nakahara
- Department of Biochemistry, University of São Paulo, São Paulo, Brazil
| | | | | | - Li Wang
- Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Filippo Valle
- Physics Department, University of Turin and INFN, Via P. Giuria 1, 10125 Turin, Italy
| | | | - Joel D Mainland
- Monell Chemical Senses Center, 3500 Market Street, Philadelphia, PA 19104, USA; Department of Neuroscience, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michele Caselle
- Physics Department, University of Turin and INFN, Via P. Giuria 1, 10125 Turin, Italy
| | - Matteo Osella
- Physics Department, University of Turin and INFN, Via P. Giuria 1, 10125 Turin, Italy
| | - Stephan Lorenz
- Sidra Medicine, P.O. Box 26999, Doha, Qatar; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Johannes Reisert
- Monell Chemical Senses Center, 3500 Market Street, Philadelphia, PA 19104, USA
| | - Darren W Logan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bettina Malnic
- Department of Biochemistry, University of São Paulo, São Paulo, Brazil
| | - Antonio Scialdone
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Feodor-Lynen-Strasse 21, 81377 München, Germany; Institute of Functional Epigenetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
| | - Luis R Saraiva
- Sidra Medicine, P.O. Box 26999, Doha, Qatar; Monell Chemical Senses Center, 3500 Market Street, Philadelphia, PA 19104, USA; College of Health and Life Sciences, Hamad Bin Khalifa University, P.O. Box 34110, Doha, Qatar.
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19
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Cockburn G, Ko MC, Sadanandan KR, Miller ET, Nakagita T, Monte A, Cho S, Roura E, Toda Y, Baldwin MW. Synergism, Bifunctionality, and the Evolution of a Gradual Sensory Trade-off in Hummingbird Taste Receptors. Mol Biol Evol 2022; 39:msab367. [PMID: 34978567 PMCID: PMC8826506 DOI: 10.1093/molbev/msab367] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Sensory receptor evolution can imply trade-offs between ligands, but the extent to which such trade-offs occur and the underlying processes shaping their evolution is not well understood. For example, hummingbirds have repurposed their ancestral savory receptor (T1R1-T1R3) to detect sugars, but the impact of this sensory shift on amino acid perception is unclear. Here, we use functional and behavioral approaches to show that the hummingbird T1R1-T1R3 acts as a bifunctional receptor responsive to both sugars and amino acids. Our comparative analyses reveal substantial functional diversity across the hummingbird radiation and suggest an evolutionary timeline for T1R1-T1R3 retuning. Finally, we identify a novel form of synergism between sugars and amino acids in vertebrate taste receptors. This work uncovers an unexplored axis of sensory diversity, suggesting new ways in which nectar chemistry and pollinator preferences can coevolve.
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Affiliation(s)
- Glenn Cockburn
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Meng-Ching Ko
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Keren R Sadanandan
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Eliot T Miller
- Macaulay Library, Cornell Lab of Ornithology, Ithaca, NY, USA
| | - Tomoya Nakagita
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
- Proteo-Science Center, Ehime University, Matsuyama, Ehime, Japan
| | - Amanda Monte
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Sungbo Cho
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Australia
| | - Eugeni Roura
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Australia
| | - Yasuka Toda
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany
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20
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AKHTAR MUHAMMADSHOAIB, ASHINO RYUICHI, OOTA HIROKI, ISHIDA HAJIME, NIIMURA YOSHIHITO, TOUHARA KAZUSHIGE, MELIN AMANDAD, KAWAMURA SHOJI. Genetic variation of olfactory receptor gene family in a Japanese population. ANTHROPOL SCI 2022. [DOI: 10.1537/ase.211024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- MUHAMMAD SHOAIB AKHTAR
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa
| | - RYUICHI ASHINO
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa
| | - HIROKI OOTA
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo
| | - HAJIME ISHIDA
- Department of Human Biology and Anatomy, Faculty of Medicine, University of the Ryukyus, Nishihara
| | - YOSHIHITO NIIMURA
- Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki
| | - KAZUSHIGE TOUHARA
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo
| | - AMANDA D. MELIN
- Department of Anthropology and Archaeology & Department of Medical Genetics, University of Calgary, Calgary
| | - SHOJI KAWAMURA
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa
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21
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Ijichi C, Wakabayashi H, Sugiyama S, Hayashi K, Ihara Y, Nishijima H, Touhara K, Kondo K. Odorant metabolism of the olfactory cleft mucus in idiopathic olfactory impairment patients and healthy volunteers. Int Forum Allergy Rhinol 2021; 12:293-301. [PMID: 34637187 DOI: 10.1002/alr.22897] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND It remains unclear whether the metabolic activity of nasal mucus in the olfactory and respiratory areas is different. Moreover, age- and olfaction-related changes may affect metabolism. METHODS Hexanal, octanal, and 2-methylbutanal were selected for in vitro metabolism analysis and compared between the olfactory cleft and respiratory mucus of participants < 50-year-old with normal olfaction using gas chromatography mass spectrometry. The metabolic activity of hexanal in the olfactory cleft mucus was further compared between three groups, (1) normal olfaction, age < 50 years old, (2) normal olfaction, age ≥50 years old, and (3) idiopathic olfactory impairment. To characterize the enzyme(s) responsible for aldehyde reduction, we also tested if epalr22897estat and 3,5-dichlorosalicylic acid, types of reductase inhibitors, affect metabolism. RESULTS Conversion of aldehydes to their corresponding alcohols was observed in the olfactory cleft and respiratory mucus. The metabolic production of hexanol, octanol, and 2-methybutanol was significantly higher in the olfactory cleft mucus than in the respiratory mucus (p < 0.01). The metabolic conversion of hexanal to hexanol in the mucus of the idiopathic olfactory impairment group was significantly lower than that in the age-matched normal olfaction group. Excluding the nicotinamide adenine dinucleotide phosphate (NADPH) regenerating system from the reaction mixture inhibited metabolism. The addition of either epalr22897estat or 3,5-dichlorosalicylic acid did not inhibit this metabolic conversion. CONCLUSIONS The enzymatic metabolism of odorants in the olfactory cleft mucus is markedly higher than in the respiratory mucus and decreases in patients with idiopathic olfactory impairment.
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Affiliation(s)
- Chiori Ijichi
- Technology and Solution Development Center, Institute of Food Science and Technologies, Food Products Division, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Hidehiko Wakabayashi
- Technology and Solution Development Center, Institute of Food Science and Technologies, Food Products Division, Ajinomoto Co., Inc., Kawasaki, Japan.,College of Bioresource Sciences, Nihon University, Kameino, Fujisawa, Japan
| | - Shingo Sugiyama
- Technology and Solution Development Center, Institute of Food Science and Technologies, Food Products Division, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Kazuhiro Hayashi
- Technology and Solution Development Center, Institute of Food Science and Technologies, Food Products Division, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Yusuke Ihara
- Technology and Solution Development Center, Institute of Food Science and Technologies, Food Products Division, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Hironobu Nishijima
- Department of Otolaryngology-Head and Neck Surgery, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Kazushige Touhara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kenji Kondo
- Department of Otolaryngology-Head and Neck Surgery, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
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22
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Santacà M, Dadda M, Bisazza A. The role of visual and olfactory cues in social decisions of guppies and zebrafish. Anim Behav 2021. [DOI: 10.1016/j.anbehav.2021.08.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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23
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Oteiza P, Baldwin MW. Evolution of sensory systems. Curr Opin Neurobiol 2021; 71:52-59. [PMID: 34600187 DOI: 10.1016/j.conb.2021.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/26/2021] [Indexed: 01/14/2023]
Abstract
Sensory systems evolve and enable organisms to perceive their sensory Umwelt, the unique set of cues relevant for their survival. The multiple components that comprise sensory systems - the receptors, cells, organs, and dedicated high-order circuits - can vary greatly across species. Sensory receptor gene families can expand and contract across lineages, resulting in enormous sensory diversity. Comparative studies of sensory receptor function have uncovered the molecular basis of receptor properties and identified novel sensory receptor classes and noncanonical sensory strategies. Phylogenetically informed comparisons of sensory systems across multiple species can pinpoint when sensory changes evolve and highlight the role of contingency in sensory system evolution.
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Affiliation(s)
- Pablo Oteiza
- Flow Sensing Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany.
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany.
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24
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The genomics of ecological flexibility, large brains, and long lives in capuchin monkeys revealed with fecalFACS. Proc Natl Acad Sci U S A 2021; 118:2010632118. [PMID: 33574059 PMCID: PMC7896301 DOI: 10.1073/pnas.2010632118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Surviving challenging environments, living long lives, and engaging in complex cognitive processes are hallmark human characteristics. Similar traits have evolved in parallel in capuchin monkeys, but their genetic underpinnings remain unexplored. We developed and annotated a reference assembly for white-faced capuchin monkeys to explore the evolution of these phenotypes. By comparing populations of capuchins inhabiting rainforest versus dry forests with seasonal droughts, we detected selection in genes associated with kidney function, muscular wasting, and metabolism, suggesting adaptation to periodic resource scarcity. When comparing capuchins to other mammals, we identified evidence of selection in multiple genes implicated in longevity and brain development. Our research was facilitated by our method to generate high- and low-coverage genomes from noninvasive biomaterials. Ecological flexibility, extended lifespans, and large brains have long intrigued evolutionary biologists, and comparative genomics offers an efficient and effective tool for generating new insights into the evolution of such traits. Studies of capuchin monkeys are particularly well situated to shed light on the selective pressures and genetic underpinnings of local adaptation to diverse habitats, longevity, and brain development. Distributed widely across Central and South America, they are inventive and extractive foragers, known for their sensorimotor intelligence. Capuchins have among the largest relative brain size of any monkey and a lifespan that exceeds 50 y, despite their small (3 to 5 kg) body size. We assemble and annotate a de novo reference genome for Cebus imitator. Through high-depth sequencing of DNA derived from blood, various tissues, and feces via fluorescence-activated cell sorting (fecalFACS) to isolate monkey epithelial cells, we compared genomes of capuchin populations from tropical dry forests and lowland rainforests and identified population divergence in genes involved in water balance, kidney function, and metabolism. Through a comparative genomics approach spanning a wide diversity of mammals, we identified genes under positive selection associated with longevity and brain development. Additionally, we provide a technological advancement in the use of noninvasive genomics for studies of free-ranging mammals. Our intra- and interspecific comparative study of capuchin genomics provides insights into processes underlying local adaptation to diverse and physiologically challenging environments, as well as the molecular basis of brain evolution and longevity.
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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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26
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Policarpo M, Bemis KE, Tyler JC, Metcalfe CJ, Laurenti P, Sandoz JC, Rétaux S, Casane D. Evolutionary dynamics of the OR gene repertoire in teleost fishes: evidence of an association with changes in olfactory epithelium shape. Mol Biol Evol 2021; 38:3742-3753. [PMID: 33950257 PMCID: PMC8661438 DOI: 10.1093/molbev/msab145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Teleost fishes perceive their environment through a range of sensory modalities, among which olfaction often plays an important role. Richness of the olfactory repertoire depends on the diversity of receptors coded by homologous genes classified into four families: OR, TAAR, VR1, and VR2. Herein, we focus on the OR gene repertoire. While independent large contractions of the OR gene repertoire associated with ecological transitions have been found in mammals, little is known about the diversity of the OR gene repertoire and its evolution in teleost fishes, a group that includes more than 34,000 living species. We analyzed genomes of 163 species representing diversity in this large group. We found a large range of variation in the number of functional OR genes, from 15 in the Broad-nose Pipefish Syngnathus typhle and the Ocean Sunfish Mola mola, to 429 in the Zig-zag Eel Mastacembelus armatus. The number of OR genes was higher in species when a multilamellar olfactory rosette was present. Moreover, the number of lamellae was correlated with the richness of the OR gene repertoire. While a slow and balanced birth-and-death process generally drives the evolution of the OR gene repertoire, we inferred several episodes of high rates of gene loss, sometimes followed by large gains in the number of OR genes. These gains coincide with morphological changes of the olfactory organ and suggest a strong functional association between changes in the morphology and the evolution of the OR gene repertoire.
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Affiliation(s)
- Maxime Policarpo
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
| | - Katherine E Bemis
- NOAA National Systematics Laboratory, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20560, U.S.A
| | - James C Tyler
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., 20560, U.S.A
| | | | - Patrick Laurenti
- Université de Paris, Laboratoire Interdisciplinaire des Energies de Demain, Paris, France
| | - Jean-Christophe Sandoz
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
| | - Sylvie Rétaux
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Didier Casane
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France.,Université de Paris, UFR Sciences du Vivant, F-75013 Paris, France
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27
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Abstract
Odors may be pleasant or unpleasant and in practice, pleasant odors are attractive while unpleasant odors are repellent. However, an odor that is noxious to one species may be attractive to another. Plants, predators, and pathogens may enhance their transmission by manipulating these signals. This may be especially significant when odors attract arthropod disease vectors. Odor detection may also be important in small prey species for evasion of macropredators such as large carnivores. Conversely, pleasant odors may identify family members, parents, or sexual partners. They may also generate signals of good health or fitness and contribute to the process of mate selection. In this review, we seek to integrate these odor-driven processes into a coherent pattern of behaviors that serve to complement the innate and adaptive immune systems. It may be considered the 'behavioral immune system'.
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Masuo Y, Satou T, Takemoto H, Koike K. Smell and Stress Response in the Brain: Review of the Connection between Chemistry and Neuropharmacology. Molecules 2021; 26:molecules26092571. [PMID: 33924992 PMCID: PMC8124235 DOI: 10.3390/molecules26092571] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 11/24/2022] Open
Abstract
The stress response in the brain is not fully understood, although stress is one of the risk factors for developing mental disorders. On the other hand, the stimulation of the olfactory system can influence stress levels, and a certain smell has been empirically known to have a stress-suppressing effect, indeed. In this review, we first outline what stress is and previous studies on stress-responsive biomarkers (stress markers) in the brain. Subsequently, we confirm the olfactory system and review previous studies on the relationship between smell and stress response by species, such as humans, rats, and mice. Numerous studies demonstrated the stress-suppressing effects of aroma. There are also investigations showing the effects of odor that induce stress in experimental animals. In addition, we introduce recent studies on the effects of aroma of coffee beans and essential oils, such as lavender, cypress, α-pinene, and thyme linalool on the behavior and the expression of stress marker candidates in the brain. The transfer of volatile components into the brain is also discussed while using the results of thyme linalool as an example. These studies may provide a good opportunity to connect chemical research at the molecular level with neuropharmacological approaches in the future.
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Affiliation(s)
- Yoshinori Masuo
- Laboratory of Neuroscience, Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
- Correspondence: ; Tel.: +81-47-472-5257
| | - Tadaaki Satou
- Department of Pharmacognosy, Faculty of Pharmaceutical Sciences, International University of Health and Welfare, 2600-1 Kitakanemaru, Ohtawara, Tochigi 324-8501, Japan;
| | - Hiroaki Takemoto
- Department of Pharmacognosy, Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan; (H.T.); (K.K.)
| | - Kazuo Koike
- Department of Pharmacognosy, Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan; (H.T.); (K.K.)
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29
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The Chemosensory Repertoire of the Eastern Diamondback Rattlesnake (Crotalus adamanteus) Reveals Complementary Genetics of Olfactory and Vomeronasal-Type Receptors. J Mol Evol 2021; 89:313-328. [PMID: 33881604 DOI: 10.1007/s00239-021-10007-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/22/2021] [Indexed: 01/14/2023]
Abstract
Pitviper sensory perception incorporates diverse stimuli through the integration of trichromatic color vision, bifocal heat-sensing, and dual-system chemoperception. Chemoperception, or olfaction, is mediated by chemoreceptors in the olfactory bulb and the vomeronasal organ, but the true genomic complexity of the gene families and their relative contributions is unknown. A full genomic accounting of pitviper chemoperception directly complements our current understanding of their venoms by generating a more complete polyphenic representation of their predatory arsenal. To characterize the genetic repertoire of pitviper chemoperception, we analyzed a full-genome assembly for Crotalus adamanteus, the eastern diamondback rattlesnake. We identified hundreds of genes encoding both olfactory receptors (ORs; 362 full-length genes) and type-2 vomeronasal receptors (V2Rs; 430 full-length genes). Many chemoreceptor genes are organized into large tandem repeat arrays. Comparative analysis of V2R orthologs across squamates demonstrates how gene array expansion and contraction underlies the evolution of the chemoreceptor repertoire, which likely reflects shifts in life history traits. Chromosomal assignments of chemosensory genes identified sex chromosome specific chemoreceptor genes, providing gene candidates underlying observed sex-specific chemosensory-based behaviors. We detected widespread episodic evolution in the extracellular, ligand-binding domains of both ORs and V2Rs, suggesting the diversification of chemoreceptors is driven by transient periods of positive selection. We provide a robust genetic framework for studying pitviper chemosensory ecology and evolution.
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30
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Cunningham EP, Edmonds D, Stalter L, Janal MN. Ring-tailed lemurs (Lemur catta) use olfaction to locate distant fruit. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 175:300-307. [PMID: 33624841 DOI: 10.1002/ajpa.24255] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 01/28/2021] [Accepted: 02/05/2021] [Indexed: 12/22/2022]
Abstract
OBJECTIVES As many primates live in forests where visibility is limited, the ability to detect the aroma of distant fruit and navigate odor plumes would be highly adaptive. Our study is the first to investigate this ability with strepsirrhine primates. MATERIALS AND METHODS We tested the ability of a group of ring-tailed lemurs to detect hidden fruit from afar using scent alone. We hid containers in the underbrush of a semi-natural forest, some baited with real cantaloupe and some with sham cantaloupe, 4-17 m from a path routinely used by the lemurs. Crucially, the containers were not visible from the path. Therefore, the lemurs had to use olfactory cues, but did not have to prioritize them to locate the bait. RESULTS The lemurs found the real cantaloupe on days that the wind blew the scent of the fruit toward the trail. They did not find the sham cantaloupe. Upon detecting the odor of the bait, the lemurs sniffed the air at one or more locations as they moved toward the bait, a process of navigation known as klinotaxis. DISCUSSION The traditional belief is that primates are unable to track odor plumes. The untrained lemurs in this study were able to detect the odor of the cantaloupe among the complex odors of the forest and navigate the odor plume to the fruit. The results indicate that olfaction may be used to respond to cues from distant sources. The ability to track odor plumes may be a critical foraging skill for strepsirrhines.
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Affiliation(s)
- Elena P Cunningham
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, New York, 10010, USA
| | - Devin Edmonds
- Lemur Conservation Foundation, Myakka City, Florida, USA.,Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Laura Stalter
- Lemur Conservation Foundation, Myakka City, Florida, USA.,University of Vermont, Burlington, Vermont, USA
| | - Malvin N Janal
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, New York, 10010, USA.,Department of Epidemiology and Health Promotion, New York University College of Dentistry, Burlington, Vermont, USA
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31
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Westbury MV, Le Duc D, Duchêne DA, Krishnan A, Prost S, Rutschmann S, Grau JH, Dalen L, Weyrich A, Norén K, Werdelin L, Dalerum F, Schöneberg T, Hofreiter M. Ecological Specialisation and Evolutionary Reticulation in Extant Hyaenidae. Mol Biol Evol 2021; 38:3884-3897. [PMID: 34426844 PMCID: PMC8382907 DOI: 10.1093/molbev/msab055] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
During the Miocene, Hyaenidae was a highly diverse family of Carnivora that has since been severely reduced to four species: the bone-cracking spotted, striped, and brown hyenas, and the specialized insectivorous aardwolf. Previous studies investigated the evolutionary histories of the spotted and brown hyenas, but little is known about the remaining two species. Moreover, the genomic underpinnings of scavenging and insectivory, defining traits of the extant species, remain elusive. Here, we generated an aardwolf genome and analyzed it together with the remaining three species to reveal their evolutionary relationships, genomic underpinnings of their scavenging and insectivorous lifestyles, and their respective genetic diversities and demographic histories. High levels of phylogenetic discordance suggest gene flow between the aardwolf lineage and the ancestral brown/striped hyena lineage. Genes related to immunity and digestion in the bone-cracking hyenas and craniofacial development in the aardwolf showed the strongest signals of selection, suggesting putative key adaptations to carrion and termite feeding, respectively. A family-wide expansion in olfactory receptor genes suggests that an acute sense of smell was a key early adaptation. Finally, we report very low levels of genetic diversity within the brown and striped hyenas despite no signs of inbreeding, putatively linked to their similarly slow decline in effective population size over the last ∼2 million years. High levels of genetic diversity and more stable population sizes through time are seen in the spotted hyena and aardwolf. Taken together, our findings highlight how ecological specialization can impact the evolutionary history, demographics, and adaptive genetic changes of an evolutionary lineage.
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Affiliation(s)
- M V Westbury
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, Germany.,Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Diana Le Duc
- Institute of Human Genetics, University Medical Center Leipzig, Leipzig, 04103, Germany.,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - David A Duchêne
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark.,Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Arunkumar Krishnan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.,Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha, 760010, India
| | - Stefan Prost
- LOEWE-Center for Translational Biodiversity Genomics, Senckenberg, 60325, Germany. Frankfurt.,South African National Biodiversity Institute, National Zoological Garden, Pretoria, 0184, South Africa
| | - Sereina Rutschmann
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, Germany
| | - Jose H Grau
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, Germany.,amedes Genetics, amedes Medizinische Dienstleistungen, Berlin, Germany
| | - Love Dalen
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, Stockholm, 10691, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm, 10405, Sweden
| | - Alexandra Weyrich
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, 10315, Germany
| | - Karin Norén
- Department of Zoology, Stockholm University, Stockholm, 106 91, Sweden
| | - Lars Werdelin
- Department of Palaeobiology, Swedish Museum of Natural History, Box 50007, Stockholm, SE-10405, Sweden
| | - Fredrik Dalerum
- Department of Zoology, Stockholm University, Stockholm, 106 91, Sweden.,Research Unit of Biodiversity (UO-CSIC-PA), Mieres Campus, University of Oviedo, Mieres, Asturias, 33600, Spain.,Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, South Africa
| | - Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, Johannisallee 30, Leipzig, 04103, Germany
| | - Michael Hofreiter
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, Germany
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32
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Bacolla A, Sengupta S, Ye Z, Yang C, Mitra J, De-Paula RB, Hegde ML, Ahmed Z, Mort M, Cooper DN, Mitra S, Tainer JA. Heritable pattern of oxidized DNA base repair coincides with pre-targeting of repair complexes to open chromatin. Nucleic Acids Res 2021; 49:221-243. [PMID: 33300026 PMCID: PMC7797072 DOI: 10.1093/nar/gkaa1120] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/12/2020] [Accepted: 12/07/2020] [Indexed: 12/16/2022] Open
Abstract
Human genome stability requires efficient repair of oxidized bases, which is initiated via damage recognition and excision by NEIL1 and other base excision repair (BER) pathway DNA glycosylases (DGs). However, the biological mechanisms underlying detection of damaged bases among the million-fold excess of undamaged bases remain enigmatic. Indeed, mutation rates vary greatly within individual genomes, and lesion recognition by purified DGs in the chromatin context is inefficient. Employing super-resolution microscopy and co-immunoprecipitation assays, we find that acetylated NEIL1 (AcNEIL1), but not its non-acetylated form, is predominantly localized in the nucleus in association with epigenetic marks of uncondensed chromatin. Furthermore, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) revealed non-random AcNEIL1 binding near transcription start sites of weakly transcribed genes and along highly transcribed chromatin domains. Bioinformatic analyses revealed a striking correspondence between AcNEIL1 occupancy along the genome and mutation rates, with AcNEIL1-occupied sites exhibiting fewer mutations compared to AcNEIL1-free domains, both in cancer genomes and in population variation. Intriguingly, from the evolutionarily conserved unstructured domain that targets NEIL1 to open chromatin, its damage surveillance of highly oxidation-susceptible sites to preserve essential gene function and to limit instability and cancer likely originated ∼500 million years ago during the buildup of free atmospheric oxygen.
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Affiliation(s)
- Albino Bacolla
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shiladitya Sengupta
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA.,Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - Zu Ye
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chunying Yang
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Joy Mitra
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Ruth B De-Paula
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Muralidhar L Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA.,Weill Cornell Medical College, Cornell University, New York, NY 10065, USA.,Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Zamal Ahmed
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Sankar Mitra
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA.,Weill Cornell Medical College, Cornell University, New York, NY 10065, USA.,Houston Methodist Cancer Center, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - John A Tainer
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Kalra S, Mittal A, Bajoria M, Mishra T, Maryam S, Sengupta D, Ahuja G. Challenges and possible solutions for decoding extranasal olfactory receptors. FEBS J 2020; 288:4230-4241. [PMID: 33085840 DOI: 10.1111/febs.15606] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/29/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022]
Abstract
Olfactory receptors are primarily known to be expressed in the olfactory epithelium of the nasal cavity and therefore assist in odor perception. With the advent of high-throughput omics technologies such as tissue microarray or RNA sequencing, a large number of olfactory receptors have been reported to be expressed in the nonolfactory tissues. Although these technologies uncovered the expression of these olfactory receptors in the nonchemosensory tissues, unfortunately, they failed to reveal the information about their cell type of origin. Accurate characterization of the cell types should be the first step towards devising cell type-specific assays for their functional evaluation. Single-cell RNA-sequencing technology resolved some of these apparent limitations and opened new means to interrogate the expression of these extranasal olfactory receptors at the single-cell resolution. Moreover, the availability of large-scale, multi-organ/species single-cell expression atlases offer ample resources for the systematic reannotation of these receptors in a cell type-specific manner. In this Viewpoint article, we discuss some of the technical limitations that impede the in-depth understanding of these extranasal olfactory receptors, with a special focus on odorant receptors. Moreover, we also propose a list of single cell-based omics technologies that could further promulgate the opportunity to decipher the regulatory network that drives the odorant receptors expression at atypical locations.
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Affiliation(s)
- Siddhant Kalra
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India, India
| | - Aayushi Mittal
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India, India
| | - Manisha Bajoria
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India, India
| | - Tripti Mishra
- Pathfinder Research and Training Foundation, Greater Noida, India
| | - Sidrah Maryam
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India, India
| | - Debarka Sengupta
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India, India.,Department of Computer Science and Engineering, Indraprastha Institute of Information Technology, New Delhi, India, India.,Centre for Artificial Intelligence, Indraprastha Institute of Information Technology, New Delhi, India.,Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Gaurav Ahuja
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India, India
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Nevo O, Schmitt MH, Ayasse M, Valenta K. Sweet tooth: Elephants detect fruit sugar levels based on scent alone. Ecol Evol 2020; 10:11399-11407. [PMID: 33144973 PMCID: PMC7593167 DOI: 10.1002/ece3.6777] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/07/2020] [Accepted: 08/18/2020] [Indexed: 11/10/2022] Open
Abstract
The ability to assess food quality is crucial to all organisms. Fleshy fruits are a major source of nutrients to various animals, and unlike most food sources, have evolved to be attractive and to be consumed by animals to promote seed dispersal. It has recently been established that fruit scent-the bouquet of volatile chemicals emitted by ripe fruit-is an evolved communication system between plants and animals. Further, it has been argued that chemicals that are synthesized from sugar and its products may be an honest signal for sugar content and fruit quality. Elephants are important seed dispersers for numerous species and possess an olfactory system that is likely to outperform most other animals. We tested the hypothesis that fruit scent signifies sugar content and that elephants are capable of assessing fruit sugar levels based on scent alone. Using a paired-choice test of marula fruits (Sclerocarya birrea) by semitame African elephants, we show that elephants are capable of identifying more sugar-rich fruits based on scent alone and that this is likely based on two chemical compounds: ethanol and ethyl acetate, both downstream products of sugar fermentation. These results shed light on the mechanisms driving elephant feeding ecology, plant signaling, and the coevolutionary process between angiosperms and animal seed dispersers.
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Affiliation(s)
- Omer Nevo
- Institute of Evolutionary Ecology and Conservation GenomicsUlm UniversityUlmGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of BiodiversityFriedrich Schiller University JenaJenaGermany
| | - Melissa H. Schmitt
- Department of Ecology, Evolution, and Marine BiologyUniversity of California Santa BarbaraSanta BarbaraCAUSA
- South African Environmental Observation NetworkNdlovu NodePhalaborwaSouth Africa
| | - Manfred Ayasse
- Institute of Evolutionary Ecology and Conservation GenomicsUlm UniversityUlmGermany
| | - Kim Valenta
- Department of AnthropologyUniversity of FloridaGainesvilleFLUSA
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35
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Ijichi C, Wakabayashi H, Sugiyama S, Ihara Y, Nogi Y, Nagashima A, Ihara S, Niimura Y, Shimizu Y, Kondo K, Touhara K. Metabolism of Odorant Molecules in Human Nasal/Oral Cavity Affects the Odorant Perception. Chem Senses 2020; 44:465-481. [PMID: 31254383 DOI: 10.1093/chemse/bjz041] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In this study, we examined the mode of metabolism of food odorant molecules in the human nasal/oral cavity in vitro and in vivo. We selected 4 odorants, 2-furfurylthiol (2-FT), hexanal, benzyl acetate, and methyl raspberry ketone, which are potentially important for designing food flavors. In vitro metabolic assays of odorants with saliva/nasal mucus analyzed by gas chromatography mass spectrometry revealed that human saliva and nasal mucus exhibit the following 3 enzymatic activities: (i) methylation of 2-FT into furfuryl methylsulfide (FMS); (ii) reduction of hexanal into hexanol; and (iii) hydrolysis of benzyl acetate into benzyl alcohol. However, (iv) demethylation of methyl raspberry ketone was not observed. Real-time in vivo analysis using proton transfer reaction-mass spectrometry demonstrated that the application of 2-FT and hexanal through 3 different pathways via the nostril or through the mouth generated the metabolites FMS and hexanol within a few seconds. The concentration of FMS and hexanol in the exhaled air was above the perception threshold. A cross-adaptation study based on the activation pattern of human odorant receptors suggested that this metabolism affects odor perception. These results suggest that some odorants in food are metabolized in the human nasal mucus/saliva, and the resulting metabolites are perceived as part of the odor quality of the substrates. Our results help improve the understanding of the mechanism of food odor perception and may enable improved design and development of foods in relation to odor.
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Affiliation(s)
- Chiori Ijichi
- Chemosensory Research Group, Technology Development Center, Institute of Food Science and Technologies, Food Products Division, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Hidehiko Wakabayashi
- Taste & Flavor Technology Group, Technology Development Center, Institute of Food Sciences and Technologies, Food Products Division, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Shingo Sugiyama
- Taste & Flavor Technology Group, Technology Development Center, Institute of Food Sciences and Technologies, Food Products Division, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Yusuke Ihara
- Chemosensory Research Group, Technology Development Center, Institute of Food Science and Technologies, Food Products Division, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Yasuko Nogi
- Chemosensory Research Group, Technology Development Center, Institute of Food Science and Technologies, Food Products Division, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Ayumi Nagashima
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,ERATO Touhara Chemosensory Signal Project, JST, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Sayoko Ihara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,ERATO Touhara Chemosensory Signal Project, JST, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yoshihito Niimura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,ERATO Touhara Chemosensory Signal Project, JST, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yuya Shimizu
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Kenji Kondo
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Kazushige Touhara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,ERATO Touhara Chemosensory Signal Project, JST, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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36
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Nikaido M, Kondo S, Zhang Z, Wu J, Nishihara H, Niimura Y, Suzuki S, Touhara K, Suzuki Y, Noguchi H, Minakuchi Y, Toyoda A, Fujiyama A, Sugano S, Yoneda M, Kai C. Comparative genomic analyses illuminate the distinct evolution of megabats within Chiroptera. DNA Res 2020; 27:5910551. [PMID: 32966557 PMCID: PMC7547651 DOI: 10.1093/dnares/dsaa021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/09/2020] [Indexed: 11/12/2022] Open
Abstract
The revision of the sub-order Microchiroptera is one of the most intriguing outcomes in recent mammalian molecular phylogeny. The unexpected sister–taxon relationship between rhinolophoid microbats and megabats, with the exclusion of other microbats, suggests that megabats arose in a relatively short period of time from a microbat-like ancestor. In order to understand the genetic mechanism underlying adaptive evolution in megabats, we determined the whole-genome sequences of two rousette megabats, Leschenault’s rousette (Rousettus leschenaultia) and the Egyptian fruit bat (R. aegyptiacus). The sequences were compared with those of 22 other mammals, including nine bats, available in the database. We identified that megabat genomes are distinct in that they have extremely low activity of SINE retrotranspositions, expansion of two chemosensory gene families, including the trace amine receptor (TAAR) and olfactory receptor (OR), and elevation of the dN/dS ratio in genes for immunity and protein catabolism. The adaptive signatures discovered in the genomes of megabats may provide crucial insight into their distinct evolution, including key processes such as virus resistance, loss of echolocation, and frugivorous feeding.
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Affiliation(s)
- Masato Nikaido
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Shinji Kondo
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.,Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
| | - Zicong Zhang
- Department of Computational Intelligence and Systems Science, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8502, Japan
| | - Jiaqi Wu
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Hidenori Nishihara
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Yoshihito Niimura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Shunta Suzuki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kazushige Touhara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa City, Chiba 277-0882, Japan
| | - Hideki Noguchi
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.,Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka 411-8540, Japan
| | - Yohei Minakuchi
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.,Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Asao Fujiyama
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa City, Chiba 277-0882, Japan
| | - Misako Yoneda
- Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.,Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo 153-8505, Japan
| | - Chieko Kai
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Tokyo 153-8505, Japan
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37
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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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38
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Valenta K, Daegling DJ, Nevo O, Ledogar J, Sarkar D, Kalbitzer U, Bortolamiol S, Omeja P, Chapman CA, Ayasse M, Kay R, Williams B. Fruit Selectivity in Anthropoid Primates: Size Matters. INT J PRIMATOL 2020. [DOI: 10.1007/s10764-020-00158-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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39
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Freeman AR, Ophir AG, Sheehan MJ. The giant pouched rat (Cricetomys ansorgei) olfactory receptor repertoire. PLoS One 2020; 15:e0221981. [PMID: 32240170 PMCID: PMC7117715 DOI: 10.1371/journal.pone.0221981] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 03/06/2020] [Indexed: 12/12/2022] Open
Abstract
For rodents, olfaction is essential for locating food, recognizing mates and competitors, avoiding predators, and navigating their environment. It is thought that rodents may have expanded olfactory receptor repertoires in order to specialize in olfactory behavior. Despite being the largest clade of mammals and depending on olfaction relatively little work has documented olfactory repertoires outside of conventional laboratory species. Here we report the olfactory receptor repertoire of the African giant pouched rat (Cricetomys ansorgei), a Muroid rodent distantly related to mice and rats. The African giant pouched rat is notable for its large cortex and olfactory bulbs relative to its body size compared to other sympatric rodents, which suggests anatomical elaboration of olfactory capabilities. We hypothesized that in addition to anatomical elaboration for olfaction, these pouched rats might also have an expanded olfactory receptor repertoire to enable their olfactory behavior. We examined the composition of the olfactory receptor repertoire to better understand how their sensory capabilities have evolved. We identified 1145 intact olfactory genes, and 260 additional pseudogenes within 301 subfamilies from the African giant pouched rat genome. This repertoire is similar to mice and rats in terms of size, pseudogene percentage and number of subfamilies. Analyses of olfactory receptor gene trees revealed that the pouched rat has 6 expansions in different subfamilies compared to mice, rats and squirrels. We identified 81 orthologous genes conserved among 4 rodent species and an additional 147 conserved genes within the Muroid rodents. The orthologous genes shared within Muroidea suggests that there may be a conserved Muroid-specific olfactory receptor repertoire. We also note that the description of this repertoire can serve as a complement to other studies of rodent olfaction, as the pouched rat is an outgroup within Muroidea. Thus, our data suggest that African giant pouched rats are capable of both natural and trained olfactory behaviors with a typical Muriod olfactory receptor repertoire.
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Affiliation(s)
- Angela R. Freeman
- Department of Psychology, Cornell University, Ithaca, NY, United States of America
- * E-mail:
| | - Alexander G. Ophir
- Department of Psychology, Cornell University, Ithaca, NY, United States of America
| | - Michael J. Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, United States of America
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40
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Jiang H, Du K, Gan X, Yang L, He S. Massive Loss of Olfactory Receptors But Not Trace Amine-Associated Receptors in the World's Deepest-Living Fish ( Pseudoliparis swirei). Genes (Basel) 2019; 10:E910. [PMID: 31717379 PMCID: PMC6895882 DOI: 10.3390/genes10110910] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/02/2019] [Accepted: 11/05/2019] [Indexed: 12/11/2022] Open
Abstract
Olfactory receptor repertoires show highly dynamic evolution associated with ecological adaptations in different species. The Mariana snailfish (Pseudoliparis swirei) living below a depth of 6000 m in the Mariana Trench evolved degraded vision and occupies a specific feeding habitat in a dark, low-food environment. However, whether such adaptations involve adaptive changes in the chemosensory receptor repertoire is not known. Here, we conducted a comparative analysis of the olfactory receptor (OR) and trace amine-associated receptor (TAAR) gene repertoires in nine teleosts with a focus on the evolutionary divergence between the Mariana snailfish and its shallow-sea relative, Tanaka's snailfish (Liparis tanakae). We found many fewer functional OR genes and a significantly higher fraction of pseudogenes in the Mariana snailfish, but the numbers of functional TAAR genes in the two species were comparable. Phylogenetic analysis showed that the expansion patterns of the gene families were shared by the two species, but that Mariana snailfish underwent massive gene losses in its OR repertoire. Despite an overall decreased size in OR subfamilies and a reduced number of TAAR subfamilies in the Mariana snailfish, expansion of certain subfamilies was observed. Selective pressure analysis indicated greatly relaxed selective strength in ORs but a slightly enhanced selective strength in TAARs of Mariana snailfish. Overall, our study reveals simplified but specific OR and TAAR repertoires in the Mariana snailfish shaped by natural selection with respect to ecological adaptations in the hadal environment. This is the first study on the chemosensation evolution in vertebrates living in the hadal zone, which could provide new insights into evolutionary adaptation to the hadal environment.
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Affiliation(s)
- Haifeng Jiang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (H.J.); (K.D.); (X.G.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China
| | - Kang Du
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (H.J.); (K.D.); (X.G.)
| | - Xiaoni Gan
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (H.J.); (K.D.); (X.G.)
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (H.J.); (K.D.); (X.G.)
| | - Shunping He
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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41
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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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42
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Contraction of the ROS Scavenging Enzyme Glutathione S-Transferase Gene Family in Cetaceans. G3-GENES GENOMES GENETICS 2019; 9:2303-2315. [PMID: 31092607 PMCID: PMC6643896 DOI: 10.1534/g3.119.400224] [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] [Indexed: 02/07/2023]
Abstract
Cetaceans are a group of marine mammals whose ancestors were adaptated for life on land. Life in an aquatic environment poses many challenges for air-breathing mammals. Diving marine mammals have adapted to rapid reoxygenation and reactive oxygen species (ROS)-mediated reperfusion injury. Here, we considered the evolution of the glutathione transferase (GST) gene family which has important roles in the detoxification of endogenously-derived ROS and environmental pollutants. We characterized the cytosolic GST gene family in 21 mammalian species; cetaceans, sirenians, pinnipeds, and their terrestrial relatives. All seven GST classes were identified, showing that GSTs are ubiquitous in mammals. Some GST genes are the product of lineage-specific duplications and losses, in line with a birth-and-death evolutionary model. We detected sites with signatures of positive selection that possibly influence GST structure and function, suggesting that adaptive evolution of GST genes is important for defending mammals from various types of noxious environmental compounds. We also found evidence for loss of alpha and mu GST subclass genes in cetacean lineages. Notably, cetaceans have retained a homolog of at least one of the genes GSTA1, GSTA4, and GSTM1; GSTs that are present in both the cytosol and mitochondria. The observed variation in number and selection pressure on GST genes suggest that the gene family structure is dynamic within cetaceans.
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43
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Melin AD, Nevo O, Shirasu M, Williamson RE, Garrett EC, Endo M, Sakurai K, Matsushita Y, Touhara K, Kawamura S. Fruit scent and observer colour vision shape food-selection strategies in wild capuchin monkeys. Nat Commun 2019; 10:2407. [PMID: 31160592 PMCID: PMC6546703 DOI: 10.1038/s41467-019-10250-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 04/30/2019] [Indexed: 11/29/2022] Open
Abstract
The senses play critical roles in helping animals evaluate foods, including fruits that can change both in colour and scent during ripening to attract frugivores. Although numerous studies have assessed the impact of colour on fruit selection, comparatively little is known about fruit scent and how olfactory and visual data are integrated during foraging. We combine 25 months of behavioural data on 75 wild, white-faced capuchins (Cebus imitator) with measurements of fruit colours and scents from 18 dietary plant species. We show that frequency of fruit-directed olfactory behaviour is positively correlated with increases in the volume of fruit odours produced during ripening. Monkeys with red-green colour blindness sniffed fruits more often, indicating that increased reliance on olfaction is a behavioural strategy that mitigates decreased capacity to detect red-green colour contrast. These results demonstrate a complex interaction among fruit traits, sensory capacities and foraging strategies, which help explain variation in primate behaviour.
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Affiliation(s)
- Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, T2N 1N4, Canada.
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.
| | - Omer Nevo
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Mika Shirasu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
- ERATO Touhara Chemosensory Signal Project, JST, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Rachel E Williamson
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Eva C Garrett
- Department of Anthropology, Boston University, Boston, MA, 02215, USA
| | - Mizuki Endo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Kodama Sakurai
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Yuka Matsushita
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Kazushige Touhara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
- ERATO Touhara Chemosensory Signal Project, JST, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan.
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44
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Lundeen IK, Kirk EC. Internal nasal morphology of the Eocene primate Rooneyia viejaensis and extant Euarchonta: Using μCT scan data to understand and infer patterns of nasal fossa evolution in primates. J Hum Evol 2019; 132:137-173. [PMID: 31203844 DOI: 10.1016/j.jhevol.2019.04.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 04/19/2019] [Accepted: 04/19/2019] [Indexed: 11/18/2022]
Abstract
Primates have historically been viewed as having a diminished sense of smell compared to other mammals. In haplorhines, olfactory reduction has been inferred partly based on the complexity of the bony turbinals within the nasal cavity. Some turbinals are covered in olfactory epithelium, which contains olfactory receptor neurons that detect odorants. Accordingly, turbinal number and complexity has been used as a rough anatomical proxy for the relative importance of olfactory cues for an animal's behavioral ecology. Unfortunately, turbinals are delicate and rarely preserved in fossil specimens, limiting opportunities to make direct observations of the olfactory periphery in extinct primates. Here we describe the turbinal morphology of Rooneyia viejaensis, a late middle Eocene primate of uncertain phylogenetic affinities from the Tornillo Basin of West Texas. This species is currently the oldest fossil primate for which turbinals are preserved with minimal damage or distortion. Microcomputed tomography (μCT) reveals that Rooneyia possessed 1 nasoturbinal, 4 bullar ethmoturbinals, 1 frontoturbinal, 1 interturbinal, and an olfactory recess. This pattern is broadly similar to the condition seen in some extant strepsirrhine primates but differs substantially from the condition seen in extant haplorhines. Crown haplorhines possess only two ethmoturbinals and lack frontoturbinals, interturbinals, and an olfactory recess. Additionally, crown anthropoids have ethmoturbinals that are non-bullar. These observations reinforce the conclusion that Rooneyia is not a stem tarsiiform or stem anthropoid. However, estimated olfactory turbinal surface area in Rooneyia is greater than that of similar-sized haplorhines but smaller than that of similar-sized lemuriforms and lorisiforms. This finding suggests that although Rooneyia was broadly plesiomorphic in retaining a large complement of olfactory turbinals as in living strepsirrhines, Rooneyia may have evolved somewhat diminished olfactory abilities as in living haplorhines.
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Affiliation(s)
- Ingrid K Lundeen
- Department of Anthropology, University of Texas at Austin, SAC 4.102, 2201 Speedway Stop C3200, Austin, TX 78712, USA.
| | - E Christopher Kirk
- Department of Anthropology, University of Texas at Austin, SAC 4.102, 2201 Speedway Stop C3200, Austin, TX 78712, USA; Jackson School Museum of Earth History, University of Texas at Austin, J. J. Pickle Research Campus, 10100 Burnet Road, PRC 6-VPL, R7600, Austin, TX 78758, USA
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45
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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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Nevo O, Razafimandimby D, Jeffrey JAJ, Schulz S, Ayasse M. Fruit scent as an evolved signal to primate seed dispersal. SCIENCE ADVANCES 2018; 4:eaat4871. [PMID: 30306132 PMCID: PMC6170039 DOI: 10.1126/sciadv.aat4871] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 08/28/2018] [Indexed: 05/13/2023]
Abstract
The tremendous diversity of floral and fruit traits is, to a large extent, a set of adaptations that promote plant reproduction through animal pollinators and seed dispersers. Yet, it is still unknown whether fruit scent is a by-product of fruit maturation or an evolved communication channel with animal mutualists. We show that in species that specialize on seed dispersal by lemurs-an olfactorily oriented primate-fruits increase scent production and change their chemical composition significantly more than sympatric species whose seeds are largely dispersed by birds. We further show that lemurs use these shifts in fruit scent to identify ripe fruits. These results show that fruit scent is an evolved communication system that facilitates animal-plant mutualism.
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Affiliation(s)
- Omer Nevo
- University of Ulm, Institute of Evolutionary Ecology and Conservation Genomics, Ulm, Germany
- Corresponding author.
| | - Diary Razafimandimby
- Department of Zoology and Animal Biodiversity, Faculty of Sciences, University of Antananarivo, Antananarivo, Madagascar
| | - Juan Antonio James Jeffrey
- University of Ulm, Institute of Evolutionary Ecology and Conservation Genomics, Ulm, Germany
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Stefan Schulz
- Technische Universität Braunschweig, Institute of Organic Chemistry, Braunschweig, Germany
| | - Manfred Ayasse
- University of Ulm, Institute of Evolutionary Ecology and Conservation Genomics, Ulm, Germany
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Yohe LR, Brand P. Evolutionary ecology of chemosensation and its role in sensory drive. Curr Zool 2018; 64:525-533. [PMID: 30108633 PMCID: PMC6084603 DOI: 10.1093/cz/zoy048] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 06/20/2018] [Indexed: 11/14/2022] Open
Abstract
All behaviors of an organism are rooted in sensory processing of signals from its environment, and natural selection shapes sensory adaptations to ensure successful detection of cues that maximize fitness. Sensory drive, or divergent selection for efficient signal transmission among heterogeneous environments, has been a useful hypothesis for describing sensory adaptations, but its current scope has primarily focused on visual and acoustic sensory modalities. Chemosensation, the most widespread sensory modality in animals that includes the senses of smell and taste, is characterized by rapid evolution and has been linked to sensory adaptations to new environments in numerous lineages. Yet, olfaction and gustation have been largely underappreciated in light of the sensory drive hypothesis. Here, we examine why chemosensory systems have been overlooked and discuss the potential of chemosensation to shed new insight on the sensory drive hypothesis and vice versa. We provide suggestions for developing a framework to better incorporate studies of chemosensory adaptation that have the potential to shape a more complete, coherent, and holistic interpretation of the sensory drive.
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Affiliation(s)
- Laurel R Yohe
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Department of Geology & Geophysics, Yale University, New Haven, CT, USA
| | - Philipp Brand
- Department of Evolution and Ecology, Center for Population Biology, University of California, Davis, CA, USA
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