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Edwards SV, Cloutier A, Cockburn G, Driver R, Grayson P, Katoh K, Baldwin MW, Sackton TB, Baker AJ. A nuclear genome assembly of an extinct flightless bird, the little bush moa. SCIENCE ADVANCES 2024; 10:eadj6823. [PMID: 38781323 DOI: 10.1126/sciadv.adj6823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 04/17/2024] [Indexed: 05/25/2024]
Abstract
We present a draft genome of the little bush moa (Anomalopteryx didiformis)-one of approximately nine species of extinct flightless birds from Aotearoa, New Zealand-using ancient DNA recovered from a fossil bone from the South Island. We recover a complete mitochondrial genome at 249.9× depth of coverage and almost 900 megabases of a male moa nuclear genome at ~4 to 5× coverage, with sequence contiguity sufficient to identify more than 85% of avian universal single-copy orthologs. We describe a diverse landscape of transposable elements and satellite repeats, estimate a long-term effective population size of ~240,000, identify a diverse suite of olfactory receptor genes and an opsin repertoire with sensitivity in the ultraviolet range, show that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization, and identify potential function-altering coding sequence variants in moa that could be synthesized for future functional assays. This genomic resource should support further studies of avian evolution and morphological divergence.
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Affiliation(s)
- Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Alison Cloutier
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Glenn Cockburn
- Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence, 82319 Seewiesen, Germany
| | - Robert Driver
- Department of Biology, East Carolina University, E 5th Street, Greenville, NC 27605, USA
| | - Phil Grayson
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Kazutaka Katoh
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence, 82319 Seewiesen, Germany
| | - Timothy B Sackton
- Informatics Group, Harvard University, 38 Oxford Street, Cambridge, MA 02138, USA
| | - Allan J Baker
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, ON M5S 3B2, Canada
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON M5S 2C6, Canada
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2
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Yoshida Y, Fujishiro S, Kawai R, Kawabata F. Characterization of taste sensitivities to amino acids and sugars by conditioned taste aversion learning in chickens. Animal 2024; 18:101050. [PMID: 38215678 DOI: 10.1016/j.animal.2023.101050] [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: 07/24/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 01/14/2024] Open
Abstract
Taste plays an essential role in regulating the feeding behaviors of animals. The present study aimed to characterize the taste sensory profiles of amino acids and sugars in chickens. To achieve this, we employed a conditioned taste aversion learning method, which is characterized by a specific pairing of gastrointestinal malaise and taste perception. Our findings revealed that chickens were able to learn to avoid L-Val, L-Lys, and L-His through conditioned taste aversion learning, and exhibited a strong aversion to L-Arg. These results suggest that chickens are primarily sensitive to basic amino acids, including L-Lys, which is a crucial limiting amino acid in feeds. Interstingly, this sensitivity to basic amino acids in chickens contrasts with humans, who are mainly sensitive to acidic amino acids as umami taste. Furthermore, despite the absence of a mammalian sweet taste receptor gene in the chicken genome, we demonstrated that chickens learned to avoid glucose, galactose, sucrose, and maltose by conditioned taste aversion learning. Taken together, the present study provides the idea that chickens possess a gustatory perception toward specific amino acids and sugars for the detection of beneficial nutrients in their feeds.
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Affiliation(s)
- Yuta Yoshida
- Department of Food and Life Sciences, College of Agriculture, Ibaraki University, Ami, Ibaraki 300-0393, Japan.
| | - Shu Fujishiro
- Department of Food and Life Sciences, College of Agriculture, Ibaraki University, Ami, Ibaraki 300-0393, Japan
| | - Ryota Kawai
- Department of Food and Life Sciences, College of Agriculture, Ibaraki University, Ami, Ibaraki 300-0393, Japan
| | - Fuminori Kawabata
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan; The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan
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3
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Nishihara H, Toda Y, Kuramoto T, Kamohara K, Goto A, Hoshino K, Okada S, Kuraku S, Okabe M, Ishimaru Y. A vertebrate-wide catalogue of T1R receptors reveals diversity in taste perception. Nat Ecol Evol 2024; 8:111-120. [PMID: 38093021 PMCID: PMC10781636 DOI: 10.1038/s41559-023-02258-8] [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: 05/06/2023] [Accepted: 10/25/2023] [Indexed: 01/12/2024]
Abstract
Taste is a vital chemical sense for feeding behaviour. In mammals, the umami and sweet taste receptors comprise three members of the taste receptor type 1 (T1R/TAS1R) family: T1R1, T1R2 and T1R3. Because their functional homologues exist in teleosts, only three TAS1R genes generated by gene duplication are believed to have been inherited from the common ancestor of bony vertebrates. Here, we report five previously uncharacterized TAS1R members in vertebrates, TAS1R4, TAS1R5, TAS1R6, TAS1R7 and TAS1R8, based on genome-wide survey of diverse taxa. We show that mammalian and teleost fish TAS1R2 and TAS1R3 genes are paralogues. Our phylogenetic analysis suggests that the bony vertebrate ancestor had nine TAS1Rs resulting from multiple gene duplications. Some TAS1Rs were lost independently in descendent lineages resulting in retention of only three TAS1Rs in mammals and teleosts. Combining functional assays and expression analysis of non-teleost fishes we show that the novel T1Rs form heterodimers in taste-receptor cells and recognize a broad range of ligands such as essential amino acids, including branched-chain amino acids, which have not been previously considered as T1R ligands. This study reveals diversity of taste sensations in both modern vertebrates and their ancestors, which might have enabled vertebrates to adapt to diverse habitats on Earth.
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Affiliation(s)
- Hidenori Nishihara
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan.
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.
| | - Yasuka Toda
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Tae Kuramoto
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan
- Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Kota Kamohara
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Azusa Goto
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Kyoko Hoshino
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Shinji Okada
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shigehiro Kuraku
- Molecular Life History Laboratory, National Institute of Genetics, Mishima, Japan
- Department of Genetics, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan
| | - Masataka Okabe
- Department of Anatomy, The Jikei University School of Medicine, Tokyo, Japan
| | - Yoshiro Ishimaru
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Japan.
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4
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Kumar P, Redel U, Lang T, Korsching SI, Behrens M. Bitter taste receptors of the zebra finch ( Taeniopygia guttata). Front Physiol 2023; 14:1233711. [PMID: 37860623 PMCID: PMC10582322 DOI: 10.3389/fphys.2023.1233711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/20/2023] [Indexed: 10/21/2023] Open
Abstract
Despite the important role of bitter taste for the rejection of potentially harmful food sources, birds have long been suspected to exhibit inferior bitter tasting abilities. Although more recent reports on the bitter recognition spectra of several bird species have cast doubt about the validity of this assumption, the bitter taste of avian species is still an understudied field. Previously, we reported the bitter activation profiles of three zebra finch receptors Tas2r5, -r6, and -r7, which represent orthologs of a single chicken bitter taste receptor, Tas2r1. In order to get a better understanding of the bitter tasting capabilities of zebra finches, we selected another Tas2r gene of this species that is similar to another chicken Tas2r. Using functional calcium mobilization experiments, we screened zebra finch Tas2r1 with 72 bitter compounds and observed responses for 7 substances. Interestingly, all but one of the newly identified bitter agonists were different from those previously identified for Tas2r5, -r6, and -r7 suggesting that the newly investigated receptor fills important gaps in the zebra finch bitter recognition profile. The most potent bitter agonist found in our study is cucurbitacin I, a highly toxic natural bitter substance. We conclude that zebra finch exhibits an exquisitely developed bitter taste with pronounced cucurbitacin I sensitivity suggesting a prominent ecological role of this compound for zebra finch.
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Affiliation(s)
- Praveen Kumar
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Ulrike Redel
- German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Tatjana Lang
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | | | - Maik Behrens
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
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5
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Audet JN, Couture M, Jarvis ED. Songbird species that display more-complex vocal learning are better problem-solvers and have larger brains. Science 2023; 381:1170-1175. [PMID: 37708288 DOI: 10.1126/science.adh3428] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023]
Abstract
Complex vocal learning, a critical component of human spoken language, has been assumed to be associated with more-advanced cognitive abilities. Tests of this hypothesis between individuals within a species have been inconclusive and have not been done across species. In this work, we measured an array of cognitive skills-namely, problem-solving, associative and reversal learning, and self-control-across 214 individuals of 23 bird species, including 19 wild-caught songbird species, two domesticated songbird species, and two wild-caught vocal nonlearning species. We found that the greater the vocal learning abilities of a species, the better their problem-solving skills and the relatively larger their brains. These conclusions held when controlling for noncognitive variables and phylogeny. Our results support a hypothesis of shared genetic and cognitive mechanisms between vocal learning, problem-solving, and bigger brains in songbirds.
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Affiliation(s)
- Jean-Nicolas Audet
- The Rockefeller University Field Research Center, Millbrook, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Mélanie Couture
- The Rockefeller University Field Research Center, Millbrook, NY, USA
- The Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Erich D Jarvis
- The Rockefeller University Field Research Center, Millbrook, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
- The Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
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6
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Niknafs S, Navarro M, Schneider ER, Roura E. The avian taste system. Front Physiol 2023; 14:1235377. [PMID: 37745254 PMCID: PMC10516129 DOI: 10.3389/fphys.2023.1235377] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/30/2023] [Indexed: 09/26/2023] Open
Abstract
Taste or gustation is the sense evolving from the chemo-sensory system present in the oral cavity of avian species, which evolved to evaluate the nutritional value of foods by detecting relevant compounds including amino acids and peptides, carbohydrates, lipids, calcium, salts, and toxic or anti-nutritional compounds. In birds compared to mammals, due to the relatively low retention time of food in the oral cavity, the lack of taste papillae in the tongue, and an extremely limited secretion of saliva, the relevance of the avian taste system has been historically undermined. However, in recent years, novel data has emerged, facilitated partially by the advent of the genomic era, evidencing that the taste system is as crucial to avian species as is to mammals. Despite many similarities, there are also fundamental differences between avian and mammalian taste systems in terms of anatomy, distribution of taste buds, and the nature and molecular structure of taste receptors. Generally, birds have smaller oral cavities and a lower number of taste buds compared to mammals, and their distribution in the oral cavity appears to follow the swallowing pattern of foods. In addition, differences between bird species in the size, structure and distribution of taste buds seem to be associated with diet type and other ecological adaptations. Birds also seem to have a smaller repertoire of bitter taste receptors (T2Rs) and lack some taste receptors such as the T1R2 involved in sweet taste perception. This has opened new areas of research focusing on taste perception mechanisms independent of GPCR taste receptors and the discovery of evolutionary shifts in the molecular function of taste receptors adapting to ecological niches in birds. For example, recent discoveries have shown that the amino acid taste receptor dimer T1R1-T1R3 have mutated to sense simple sugars in almost half of the living bird species, or SGLT1 has been proposed as a part of a T1R2-independent sweet taste sensing in chicken. The aim of this review is to present the scientific data known to date related to the avian taste system across species and its impact on dietary choices including domestic and wild species.
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Affiliation(s)
- Shahram Niknafs
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Marta Navarro
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Eve R. Schneider
- Department of Biology, University of Kentucky, Lexington, KY, United States
| | - Eugeni Roura
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
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7
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Gutiérrez-Ibáñez C, Amaral-Peçanha C, Iwaniuk AN, Wylie DR, Baron J. Online repositories of photographs and videos provide insights into the evolution of skilled hindlimb movements in birds. Commun Biol 2023; 6:781. [PMID: 37582975 PMCID: PMC10427617 DOI: 10.1038/s42003-023-05151-z] [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: 03/06/2023] [Accepted: 07/18/2023] [Indexed: 08/17/2023] Open
Abstract
The ability to manipulate objects with limbs has evolved repeatedly among land tetrapods. Several selective forces have been proposed to explain the emergence of forelimb manipulation, however, work has been largely restricted to mammals, which prevents the testing of evolutionary hypotheses in a comprehensive evolutionary framework. In birds, forelimbs have gained the exclusive function of flight, with grasping transferred predominantly to the beak. In some birds, the feet are also used in manipulative tasks and appear to share some features with manual grasping and prehension in mammals, but this has not been systematically investigated. Here we use large online repositories of photographs and videos to quantify foot manipulative skills across a large sample of bird species (>1000 species). Our results show that a complex interaction between niche, diet and phylogeny drive the evolution of manipulative skills with the feet in birds. Furthermore, we provide strong support for the proposition that an arboreal niche is a key element in the evolution of manipulation in land vertebrates. Our systematic comparison of foot use in birds provides a solid base for understanding morphological and neural adaptations for foot use in birds, and for studying the convergent evolution of manipulative skills in birds and mammals.
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Affiliation(s)
| | - Clara Amaral-Peçanha
- Graduate Program in Physiology and Pharmacology Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Andrew N Iwaniuk
- Department of Neuroscience, Canadian Centre for Behavioural Neuroscience, University of Lethbridge, Lethbridge, Alta., Canada
| | - Douglas R Wylie
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Jerome Baron
- Graduate Program in Physiology and Pharmacology Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Department of Physiology and Biophysics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
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8
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Hao Y, Song G, Zhang YE, Zhai W, Jia C, Ji Y, Tang S, Lv H, Qu Y, Lei F. Divergent contributions of coding and noncoding sequences to initial high-altitude adaptation in passerine birds endemic to the Qinghai-Tibet Plateau. Mol Ecol 2023; 32:3524-3540. [PMID: 37000417 DOI: 10.1111/mec.16942] [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: 12/12/2022] [Revised: 02/27/2023] [Accepted: 03/27/2023] [Indexed: 04/01/2023]
Abstract
Early events in the evolution of an ancestral lineage can shape the adaptive patterns of descendant species, but the evolutionary mechanisms driving initial adaptation from an ancestor remain largely unexplored. High-altitude adaptations have been extensively explored from the viewpoint of protein-coding genes; however, the contribution of noncoding regions remains relatively neglected. Here, we integrate genomic and transcriptomic data to investigate adaptive evolution in the ancestor of three high-altitude snowfinch species endemic to the Qinghai-Tibet Plateau. Our genome-wide scan for adaptation in the snowfinch ancestor identifies strong adaptation signals in functions of development and metabolism for the coding genes, but in functions of the nervous system development for noncoding regions. This pattern is exclusive to the snowfinch ancestor compared to a control ancestral lineage subject to weak selection. Changes in noncoding regions in the snowfinch ancestor, especially those nearest to coding genes, may be disproportionately associated with the differential expression of genes in the brain tissue compared to other tissues. Extensive gene expression in the brain tissue can be further altered via genetic regulatory networks of transcription factors harbouring potential accelerated regulatory regions (e.g., the development-related transcription factor YEATS4). Altogether, our study provides new evidence concerning how coding and noncoding sequences work through decoupled pathways in initial adaptation to the selective pressure of high-altitude environments. The analysis highlights the idea that noncoding sequences may be promising elements in facilitating the rapid evolution and adaptation to high altitudes.
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Affiliation(s)
- Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanzhu Ji
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shiyu Tang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Hongrui Lv
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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9
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Ong S. Japan's rising research stars: Yasuka Toda. Nature 2023; 615:S76-S77. [PMID: 36890386 DOI: 10.1038/d41586-023-00663-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
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10
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Osipova E, Barsacchi R, Brown T, Sadanandan K, Gaede AH, Monte A, Jarrells J, Moebius C, Pippel M, Altshuler DL, Winkler S, Bickle M, Baldwin MW, Hiller M. Loss of a gluconeogenic muscle enzyme contributed to adaptive metabolic traits in hummingbirds. Science 2023; 379:185-190. [PMID: 36634192 DOI: 10.1126/science.abn7050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Hummingbirds possess distinct metabolic adaptations to fuel their energy-demanding hovering flight, but the underlying genomic changes are largely unknown. Here, we generated a chromosome-level genome assembly of the long-tailed hermit and screened for genes that have been specifically inactivated in the ancestral hummingbird lineage. We discovered that FBP2 (fructose-bisphosphatase 2), which encodes a gluconeogenic muscle enzyme, was lost during a time period when hovering flight evolved. We show that FBP2 knockdown in an avian muscle cell line up-regulates glycolysis and enhances mitochondrial respiration, coincident with an increased mitochondria number. Furthermore, genes involved in mitochondrial respiration and organization have up-regulated expression in hummingbird flight muscle. Together, these results suggest that FBP2 loss was likely a key step in the evolution of metabolic muscle adaptations required for true hovering flight.
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Affiliation(s)
- Ekaterina Osipova
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, 01187 Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany.,Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany.,Goethe-University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Rico Barsacchi
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Tom Brown
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany.,DRESDEN concept Genome Center, Technische Universität Dresden, 01062 Dresden, Germany
| | - Keren Sadanandan
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Andrea H Gaede
- University of British Columbia, Vancouver, Vancouver, BC V6T 1Z4, Canada.,Structure and Motion Laboratory, Royal Veterinary College, University of London, London, UK
| | - Amanda Monte
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Julia Jarrells
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Claudia Moebius
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | | | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.,DRESDEN concept Genome Center, Technische Universität Dresden, 01062 Dresden, Germany
| | - Marc Bickle
- Roche Institute for Translational Bioengineering, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, 01187 Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany.,Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany.,Goethe-University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
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11
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Liang Q, Ko MC, Ng NSR, Reh B, Lee JGH, Yamashita A, Nishihara H, Toda Y, Baldwin MW. T1R2-mediated sweet sensing in a lizard. Curr Biol 2022; 32:R1302-R1303. [PMID: 36473437 DOI: 10.1016/j.cub.2022.10.061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sugars are an important class of nutrients found in the flowers and fruits of angiosperms (flowering plants). Although T1R2-T1R3 has been identified as the mammalian sweet receptor, some birds rely on a repurposed T1R1-T1R3 savory receptor to sense sugars. Moreover, as the radiation of flowering plants occurred later than the last common ancestor of amniotes, sugar may not have been an important diet item for amniotes early in evolution, raising the question of whether T1R2-T1R3 is a universal sugar sensor or only a mammalian innovation. Here, using brief-access behavioral tests and functional characterization of taste receptors, we demonstrate that the nectar-taking Madagascar giant day gecko (Phelsuma grandis) can sense sugars through the T1R2-T1R3 receptor. These results reveal the existence of T1R2-based sweet taste in a non-avian reptile, which has important implications for our understanding of the evolutionary history of sugar detection in amniotes.
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Affiliation(s)
- Qiaoyi Liang
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, Seewiesen 82319, Germany; Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence (in foundation), Seewiesen 82319, Germany
| | - Meng-Ching Ko
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, Seewiesen 82319, Germany; Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence (in foundation), Seewiesen 82319, Germany
| | | | - Borja Reh
- Allies for Wildlife, 266 Principe de Vergara, Madrid 28016, Spain
| | | | - Atsuko Yamashita
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Hidenori Nishihara
- School of Life Science and Technology, Tokyo Institute of Technology 4259-S2-17 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Yasuka Toda
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, Seewiesen 82319, Germany; Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence (in foundation), Seewiesen 82319, Germany.
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12
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Hewes AE, Cuban D, Groom DJE, Sargent AJ, Beltrán DF, Rico-Guevara A. Variable evidence for convergence in morphology and function across avian nectarivores. J Morphol 2022; 283:1483-1504. [PMID: 36062802 DOI: 10.1002/jmor.21513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 08/20/2022] [Accepted: 08/24/2022] [Indexed: 01/19/2023]
Abstract
Nectar-feeding birds provide an excellent system in which to examine form-function relationships over evolutionary time. There are many independent origins of nectarivory in birds, and nectar feeding is a lifestyle with many inherent biophysical constraints. We review the morphology and function of the feeding apparatus, the locomotor apparatus, and the digestive and renal systems across avian nectarivores with the goals of synthesizing available information and identifying the extent to which different aspects of anatomy have morphologically and functionally converged. In doing so, we have systematically tabulated the occurrence of putative adaptations to nectarivory across birds and created what is, to our knowledge, the first comprehensive summary of adaptations to nectarivory across body systems and taxa. We also provide the first phylogenetically informed estimate of the number of times nectarivory has evolved within Aves. Based on this synthesis of existing knowledge, we identify current knowledge gaps and provide suggestions for future research questions and methods of data collection that will increase our understanding of the distribution of adaptations across bodily systems and taxa, and the relationship between those adaptations and ecological and evolutionary factors. We hope that this synthesis will serve as a landmark for the current state of the field, prompting investigators to begin collecting new data and addressing questions that have heretofore been impossible to answer about the ecology, evolution, and functional morphology of avian nectarivory.
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Affiliation(s)
- Amanda E Hewes
- Department of Biology, University of Washington, Seattle, Washington, USA.,Burke Museum of Natural History and Culture, Seattle, Washington, USA
| | - David Cuban
- Department of Biology, University of Washington, Seattle, Washington, USA.,Burke Museum of Natural History and Culture, Seattle, Washington, USA
| | - Derrick J E Groom
- Department of Biology, San Francisco State University, San Francisco, California, USA
| | - Alyssa J Sargent
- Department of Biology, University of Washington, Seattle, Washington, USA.,Burke Museum of Natural History and Culture, Seattle, Washington, USA
| | - Diego F Beltrán
- Department of Biology, University of Washington, Seattle, Washington, USA
| | - Alejandro Rico-Guevara
- Department of Biology, University of Washington, Seattle, Washington, USA.,Burke Museum of Natural History and Culture, Seattle, Washington, USA
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13
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Wolsan M, Sato JJ. Role of feeding specialization in taste receptor loss: insights from sweet and umami receptor evolution in Carnivora. Chem Senses 2022; 47:6838703. [PMID: 36433799 PMCID: PMC9680018 DOI: 10.1093/chemse/bjac033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Controversy and misunderstanding surround the role of feeding specialization in taste receptor loss in vertebrates. We refined and tested the hypothesis that this loss is caused by feeding specializations. Specifically, feeding specializations were proposed to trigger time-dependent process of taste receptor loss through deprivation of benefit of using the receptor's gustatory function. We propose that this process may be accelerated by abiotic environmental conditions or decelerated/stopped because of extragustatory functions of the receptor's protein(s). As test case we used evolution of the sweet (TAS1R2+TAS1R3) and umami (TAS1R1+TAS1R3) receptors in Carnivora (dogs, cats, and kin). We predicted these receptors' absence/presence using data on presence/absence of inactivating mutations in these receptors' genes and data from behavioral sweet/umami preference tests. We identified 20 evolutionary events of sweet (11) or umami (9) receptor loss. These events affected species with feeding specializations predicted to favor sweet/umami receptor loss (27 and 22 species, respectively). All species with feeding habits predicted to favor sweet/umami receptor retention (11 and 24, respectively) were found to retain that receptor. Six species retained the sweet (5) or umami (1) receptor despite feeding specialization predicted to favor loss of that receptor, which can be explained by the time dependence of sweet/umami receptor loss process and the possible decelerating effect of TAS1R extragustatory functions so that the sweet/umami receptor process is ongoing in these species. Our findings support the idea that feeding specialization leads to taste receptor loss and is the main if not only triggering factor for evolutionary loss of taste receptors.
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Affiliation(s)
- Mieczyslaw Wolsan
- Corresponding author: Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679 Warszawa, Poland.
| | - Jun J Sato
- Department of Biotechnology, Fukuyama University, Higashimura-cho, Aza, Sanzo, 985-1, Fukuyama 729-0292, Japan
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14
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Cramer JF, Miller ET, Ko MC, Liang Q, Cockburn G, Nakagita T, Cardinale M, Fusani L, Toda Y, Baldwin MW. A single residue confers selective loss of sugar sensing in wrynecks. Curr Biol 2022; 32:4270-4278.e5. [PMID: 35985327 DOI: 10.1016/j.cub.2022.07.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/01/2022] [Accepted: 07/21/2022] [Indexed: 12/14/2022]
Abstract
Sensory receptors evolve, and changes to their response profiles can directly impact sensory perception and affect diverse behaviors, from mate choice to foraging decisions.1-3 Although receptor sensitivities can be highly contingent on changes occurring early in a lineage's evolutionary history,4 subsequent shifts in a species' behavior and ecology may exert selective pressure to modify and even reverse sensory receptor capabilities.5-7 Neither the extent to which sensory reversion occurs nor the mechanisms underlying such shifts is well understood. Using receptor profiling and behavioral tests, we uncover both an early gain and an unexpected subsequent loss of sugar sensing in woodpeckers, a primarily insectivorous family of landbirds.8,9 Our analyses show that, similar to hummingbirds10 and songbirds,4 the ancestors of woodpeckers repurposed their T1R1-T1R3 savory receptor to detect sugars. Importantly, whereas woodpeckers seem to have broadly retained this ability, our experiments demonstrate that wrynecks (an enigmatic ant-eating group sister to all other woodpeckers) selectively lost sugar sensing through a novel mechanism involving a single amino acid change in the T1R3 transmembrane domain. The identification of this molecular microswitch responsible for a sensory shift in taste receptors provides an example of the molecular basis of a sensory reversion in vertebrates and offers novel insights into structure-function relationships during sensory receptor evolution.
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Affiliation(s)
- Julia F Cramer
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Eliot T Miller
- Macaulay Library, Cornell Lab of Ornithology, Ithaca, NY 14850, USA
| | - Meng-Ching Ko
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Qiaoyi Liang
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Glenn Cockburn
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Tomoya Nakagita
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan; Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Massimiliano Cardinale
- Department of Aquatic Resources, Institute of Marine Research, Swedish University of Agricultural Sciences, 453 30 Lysekil, Sweden
| | - Leonida Fusani
- Austrian Ornithological Centre, Konrad-Lorenz Institute of Ethology, University of Veterinary Medicine Vienna, 1160 Wien, Austria; Department of Behavioural and Cognitive Biology, University of Vienna, 1160 Wien, Austria
| | - Yasuka Toda
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany.
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15
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Campagna L, Toews DP. The genomics of adaptation in birds. Curr Biol 2022; 32:R1173-R1186. [DOI: 10.1016/j.cub.2022.07.076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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16
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Protti-Sánchez F, Corrales Parada CD, Mayer U, Rowland HM. Activation of the Nucleus Taeniae of the Amygdala by Umami Taste in Domestic Chicks (Gallus gallus). Front Physiol 2022; 13:897931. [PMID: 35694389 PMCID: PMC9178096 DOI: 10.3389/fphys.2022.897931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
In chickens, the sense of taste plays an important role in detecting nutrients and choosing feed. The molecular mechanisms underlying the taste-sensing system of chickens are well studied, but the neural mechanisms underlying taste reactivity have received less attention. Here we report the short-term taste behaviour of chickens towards umami and bitter (quinine) taste solutions and the associated neural activity in the nucleus taeniae of the amygdala, nucleus accumbens and lateral septum. We found that chickens had more contact with and drank greater volumes of umami than bitter or a water control, and that chicks displayed increased head shaking in response to bitter compared to the other tastes. We found that there was a higher neural activity, measured as c-Fos activation, in response to umami taste in the right hemisphere of the nucleus taeniae of the amygdala. In the left hemisphere, there was a higher c-Fos activation of the nucleus taeniae of the amygdala in response to bitter than in the right hemisphere. Our findings provide clear evidence that chickens respond differently to umami and bitter tastes, that there is a lateralised response to tastes at the neural level, and reveals a new function of the avian nucleus taeniae of the amygdala as a region processing reward information.
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Affiliation(s)
- Francesca Protti-Sánchez
- Max Planck Institute for Chemical Ecology, Jena, Germany
- *Correspondence: Francesca Protti-Sánchez,
| | | | - Uwe Mayer
- Center for Mind/Brain Sciences (CIMeC), University of Trento, Rovereto, Italy
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17
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Brun A, Gutiérrez-Guerrero Y, Magallanes ME, Vidal EC, Karasov WH, Rio CMD. Opportunities lost? Evolutionary causes and ecological consequences of the absence of trehalose digestion in birds. Physiol Biochem Zool 2022; 95:340-349. [DOI: 10.1086/720232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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18
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Frank HER, Amato K, Trautwein M, Maia P, Liman ER, Nichols LM, Schwenk K, Breslin PAS, Dunn RR. The evolution of sour taste. Proc Biol Sci 2022; 289:20211918. [PMID: 35135352 PMCID: PMC8826303 DOI: 10.1098/rspb.2021.1918] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The evolutionary history of sour taste has been little studied. Through a combination of literature review and trait mapping on the vertebrate phylogenetic tree, we consider the origin of sour taste, potential cases of the loss of sour taste, and those factors that might have favoured changes in the valence of sour taste-from aversive to appealing. We reconstruct sour taste as having evolved in ancient fish. By contrast to other tastes, sour taste does not appear to have been lost in any major vertebrate taxa. For most species, sour taste is aversive. Animals, including humans, that enjoy the sour taste triggered by acidic foods are exceptional. We conclude by considering why sour taste evolved, why it might have persisted as vertebrates made the transition to land and what factors might have favoured the preference for sour-tasting, acidic foods, particularly in hominins, such as humans.
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Affiliation(s)
- Hannah E. R. Frank
- Department of Crop and Soil Sciences North Carolina State University, Raleigh, USA
| | - Katie Amato
- Department of Anthropology, Northwestern University, Evanston, IL, USA
| | - Michelle Trautwein
- Entomology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, USA
| | - Paula Maia
- Department of Anthropology, Northwestern University, Evanston, IL, USA
| | - Emily R. Liman
- Department of Biological Sciences, Section of Neurobiology, University of Southern California, Los Angeles, CA, USA
| | - Lauren M. Nichols
- Department of Applied Ecology, North Carolina State University, Raleigh, USA
| | - Kurt Schwenk
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Paul A. S. Breslin
- Department of Nutritional Sciences, Rutgers The State University of New Jersey, New Brunswick, NJ, USA,Monell Chemical Senses Center, Philadelphia, PA, USA
| | - Robert R. Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, USA,Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
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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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Peng J, Svetec N, Zhao L. Intermolecular interactions drive protein adaptive and co-adaptive evolution at both species and population levels. Mol Biol Evol 2021; 39:6456312. [PMID: 34878126 PMCID: PMC8789070 DOI: 10.1093/molbev/msab350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Proteins are the building blocks for almost all the functions in cells. Understanding the molecular evolution of proteins and the forces that shape protein evolution is essential in understanding the basis of function and evolution. Previous studies have shown that adaptation frequently occurs at the protein surface, such as in genes involved in host–pathogen interactions. However, it remains unclear whether adaptive sites are distributed randomly or at regions associated with particular structural or functional characteristics across the genome, since many proteins lack structural or functional annotations. Here, we seek to tackle this question by combining large-scale bioinformatic prediction, structural analysis, phylogenetic inference, and population genomic analysis of Drosophila protein-coding genes. We found that protein sequence adaptation is more relevant to function-related rather than structure-related properties. Interestingly, intermolecular interactions contribute significantly to protein adaptation. We further showed that intermolecular interactions, such as physical interactions, may play a role in the coadaptation of fast-adaptive proteins. We found that strongly differentiated amino acids across geographic regions in protein-coding genes are mostly adaptive, which may contribute to the long-term adaptive evolution. This strongly indicates that a number of adaptive sites tend to be repeatedly mutated and selected throughout evolution in the past, present, and maybe future. Our results highlight the important roles of intermolecular interactions and coadaptation in the adaptive evolution of proteins both at the species and population levels.
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Affiliation(s)
- Junhui Peng
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
| | - Nicolas Svetec
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA
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21
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Toda Y, Hayakawa T, Itoigawa A, Kurihara Y, Nakagita T, Hayashi M, Ashino R, Melin AD, Ishimaru Y, Kawamura S, Imai H, Misaka T. Evolution of the primate glutamate taste sensor from a nucleotide sensor. Curr Biol 2021; 31:4641-4649.e5. [PMID: 34450087 DOI: 10.1016/j.cub.2021.08.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/21/2021] [Accepted: 08/02/2021] [Indexed: 12/19/2022]
Abstract
Taste perception plays an essential role in food selection. Umami (savory) tastes are sensed by a taste receptor complex, T1R1/T1R3, that detects proteinogenic amino acids.1 High sensitivity to l-glutamate (l-Glu) is a characteristic of human T1R1/T1R3, but the T1R1/T1R3 of other vertebrates does not consistently show this l-Glu response.1,2 Here, we demonstrate that the l-Glu sensitivity of T1R1/T1R3 is a derived state that has evolved repeatedly in large primates that rely on leaves as protein sources, after their divergence from insectivorous ancestors. Receptor expression experiments show that common amino acid substitutions at ligand binding sites that render T1R1/T1R3 sensitive to l-Glu occur independently at least three times in primate evolution. Meanwhile T1R1/T1R3 senses 5'-ribonucleotides as opposed to l-Glu in several mammalian species, including insectivorous primates. Our chemical analysis reveal that l-Glu is one of the major free amino acids in primate diets and that insects, but not leaves, contain large amounts of free 5'-ribonucleotides. Altering the ligand-binding preference of T1R1/T1R3 from 5'-ribonucleotides to l-Glu might promote leaf consumption, overcoming bitter and aversive tastes. Altogether, our results provide insight into the foraging ecology of a diverse mammalian radiation and help reveal how evolution of sensory genes facilitates invasion of new ecological niches.
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Affiliation(s)
- Yasuka Toda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan; Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan; Japan Society for the Promotion of Science, Tokyo 102-0083, Japan
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan; Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan; Japan Monkey Centre, Inuyama, Aichi 484-0081, Japan
| | - Akihiro Itoigawa
- Japan Society for the Promotion of Science, Tokyo 102-0083, Japan; Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Yosuke Kurihara
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan; Center for Education and Research in Field Sciences, Faculty of Agriculture, Shizuoka University, Hamamatsu, Shizuoka 431-3532, Japan
| | - Tomoya Nakagita
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan; Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Masahiro Hayashi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Ryuichi Ashino
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Alberta 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
| | - Yoshiro Ishimaru
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.
| | - Hiroo Imai
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan.
| | - Takumi Misaka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan.
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22
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Hiller AE, Brumfield RT, Faircloth BC. A reference genome for the nectar-robbing Black-throated Flowerpiercer ( Diglossa brunneiventris). G3 GENES|GENOMES|GENETICS 2021; 11:6335678. [PMID: 34849784 PMCID: PMC8527499 DOI: 10.1093/g3journal/jkab271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/27/2021] [Indexed: 12/04/2022]
Abstract
Black-throated Flowerpiercers (Diglossa brunneiventris) are one species representing a phenotypically specialized group of tanagers (Thraupidae) that have hooked bills which allow them to feed by stealing nectar from the base of flowers. Members of the genus are widely distributed in montane regions from Mexico to northern Argentina, and previous studies of Diglossa have focused on their systematics, phylogenetics, and interesting natural history. Despite numerous studies of species within the genus, no genome assembly exists to represent these nectivorous tanagers. We described the assembly of a genome sequence representing a museum-vouchered, wild, female D. brunneiventris collected in Peru. By combining Pacific Biosciences Sequel long-read technology with 10× linked-read and reference-based scaffolding, we produced a 1.08 Gbp pseudochromosomal assembly including 600 scaffolds with a scaffold N50 of 67.3 Mbp, a scaffold L50 of 6, and a BUSCO completeness score of 95%. This new assembly improves representation of the diverse species that comprise the tanagers, improves on scaffold lengths and contiguity when compared to existing genomic resources for tanagers, and provides another avenue of research into the genetic basis of adaptations common to a nectivorous lifestyle among vertebrates.
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Affiliation(s)
- Anna E Hiller
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Brant C Faircloth
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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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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Toda Y, Ko MC, Liang Q, Miller ET, Rico-Guevara A, Nakagita T, Sakakibara A, Uemura K, Sackton T, Hayakawa T, Sin SYW, Ishimaru Y, Misaka T, Oteiza P, Crall J, Edwards SV, Buttemer W, Matsumura S, Baldwin MW. Early origin of sweet perception in the songbird radiation. Science 2021; 373:226-231. [PMID: 34244416 DOI: 10.1126/science.abf6505] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/19/2021] [Indexed: 12/24/2022]
Abstract
Early events in the evolutionary history of a clade can shape the sensory systems of descendant lineages. Although the avian ancestor may not have had a sweet receptor, the widespread incidence of nectar-feeding birds suggests multiple acquisitions of sugar detection. In this study, we identify a single early sensory shift of the umami receptor (the T1R1-T1R3 heterodimer) that conferred sweet-sensing abilities in songbirds, a large evolutionary radiation containing nearly half of all living birds. We demonstrate sugar responses across species with diverse diets, uncover critical sites underlying carbohydrate detection, and identify the molecular basis of sensory convergence between songbirds and nectar-specialist hummingbirds. This early shift shaped the sensory biology of an entire radiation, emphasizing the role of contingency and providing an example of the genetic basis of convergence in avian evolution.
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Affiliation(s)
- Yasuka Toda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan.,Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan.,Japan Society for the Promotion of Science, Tokyo 102-0083, Japan
| | - Meng-Ching Ko
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Qiaoyi Liang
- 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
| | - Alejandro Rico-Guevara
- Department of Biology, University of Washington, Seattle, WA 98105, USA.,Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98105, USA
| | - Tomoya Nakagita
- Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Ayano Sakakibara
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
| | - Kana Uemura
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
| | | | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan.,Japan Monkey Centre, Inuyama, Aichi 484-0081, Japan
| | - Simon Yung Wa Sin
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong.,Department of Organismic and Evolutionary Biology and the Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA, USA
| | - Yoshiro Ishimaru
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Takumi Misaka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Pablo Oteiza
- Flow Sensing Research Group, Max Planck Institute for Ornithology, Seewiesen Germany
| | - James Crall
- Department of Organismic and Evolutionary Biology and the Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA, USA.,Department of Entomology, University of Wisconsin-Madison, WI, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and the Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA, USA
| | - William Buttemer
- Centre for Integrative Ecology, Deakin University, Geelong, Victoria, Australia.,School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Shuichi Matsumura
- Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany. .,Department of Organismic and Evolutionary Biology and the Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA, USA
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25
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Barker FK. A shift in taste. Science 2021; 373:154-155. [PMID: 34244394 DOI: 10.1126/science.abj6746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- F Keith Barker
- Department of Ecology, Evolution and Behavior and Bell Museum of Natural History, University of Minnesota, St. Paul, MN, USA.
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