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Takeuchi H, Matsuishi TF, Hayakawa T. A tradeoff evolution between acoustic fat bodies and skull muscles in toothed whales. Gene 2024; 901:148167. [PMID: 38224921 DOI: 10.1016/j.gene.2024.148167] [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: 10/24/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/17/2024]
Abstract
Toothed whales have developed specialized echolocation abilities that are crucial for underwater activities. Acoustic fat bodies, including the melon, extramandibular fat body, and intramandibular fat body, are vital for echolocation. This study explores the transcriptome of acoustic fat bodies in toothed whales, revealing some insight into their evolutionary origins and ecological significance. Comparative transcriptome analysis of acoustic fat bodies and related tissues in a harbor porpoise and a Pacific white-sided dolphin reveals that acoustic fat bodies possess characteristics of both muscle and adipose tissue, occupying an intermediate position. The melon and extramandibular fat body exhibit specific muscle-related functions, implying an evolutionary connection between acoustic fat bodies and muscle tissue. Furthermore, we suggested that the melon and extramandibular fat body originate from intramuscular adipose tissue, a component of white adipose tissue. The extramandibular fat body has been identified as an evolutionary homolog of the masseter muscle, supported by the specific expression of MYH16, a pivotal protein in masticatory muscles. The intramandibular fat body, located within the mandibular foramen, shows possibilities of the presence of several immune-related functions, likely due to its proximity to bone marrow. Furthermore, this study sheds light on leucine modification in the catabolic pathway, which leads to the accumulation of isovaleric acid in acoustic fat bodies. Swallowing without chewing, a major toothed whale feeding ecology adaptation, makes the masticatory muscle redundant and leads to the formation of the extramandibular fat body. We propose that the intramuscular fat enlargement in facial muscles, which influences acoustic fat body development, is potentially related to the substantial reorganization of head morphology in toothed whales during aquatic adaptation.
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Affiliation(s)
- Hayate Takeuchi
- Division of Biosphere Science, Graduate School of Environmental Science, Hokkaido University, N10W5, Sapporo, Hokkaido 060-0810, Japan
| | - Takashi Fritz Matsuishi
- Global Center for Food, Land and Water Resources, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1, Minato, Hakodate, Hokkaido 041-8611, Japan
| | - Takashi Hayakawa
- Section of Environmental Biology, Faculty of Environmental Earth Science, Hokkaido University, N10W5, Sapporo, Hokkaido 060-0810, Japan.
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2
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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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3
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Courcelle M, Fabre PH, Douzery EJP. Phylogeny, Ecology, and Gene Families Covariation Shaped the Olfactory Subgenome of Rodents. Genome Biol Evol 2023; 15:evad197. [PMID: 37972291 PMCID: PMC10653590 DOI: 10.1093/gbe/evad197] [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] [Accepted: 10/29/2023] [Indexed: 11/19/2023] Open
Abstract
Olfactory receptor (OR) genes represent the largest multigenic family in mammalian genomes and encode proteins that bind environmental odorant molecules. The OR repertoire is extremely variable among species and is subject to many gene duplications and losses, which have been linked to ecological adaptations in mammals. Although they have been studied on a broad taxonomic scale (i.e., placental), finer sampling has rarely been explored in order to better capture the mechanisms that drove the evolution of the OR repertoire. Among placental mammals, rodents are well-suited for this task, as they exhibit diverse life history traits, and genomic data are available for most major families and a diverse array of lifestyles. In this study, 53 rodent published genomes were mined for their OR subgenomes. We retrieved more than 85,000 functional and pseudogene OR sequences that were subsequently classified into phylogenetic clusters. Copy number variation among rodents is similar to that of other mammals. Using our OR counts along with comparative phylogenetic approaches, we demonstrated that ecological niches such as diet, period of activity, and a fossorial lifestyle strongly impacted the proportion of OR pseudogenes. Within the OR subgenome, phylogenetic inertia was the main factor explaining the relative variations of the 13 OR gene families. However, a striking exception was a convergent 10-fold expansion of the OR family 14 among the phylogenetically divergent subterranean mole-rat lineages belonging to Bathyergidae and Spalacidae families. This study illustrates how the diversity of the OR repertoire has evolved among rodents, both shaped by selective forces stemming from species life history traits and neutral evolution along the rodent phylogeny.
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Affiliation(s)
- Maxime Courcelle
- Institutdes Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
- CIRAD, UMR ASTRE, Montpellier, France
| | - Pierre-Henri Fabre
- Institutdes Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
- Mammal Section, Life Sciences, Vertebrate Division, The Natural History Museum, London, United Kingdom
- Institut Universitaire de France (IUF), Section Biologie-Médecine-Santé, Paris, France
| | - Emmanuel J P Douzery
- Institutdes Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
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4
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Kang M, Ahn B, Youk S, Jeon H, Soundarajan N, Cho ES, Park W, Park C. Individual and population diversity of 20 representative olfactory receptor genes in pigs. Sci Rep 2023; 13:18668. [PMID: 37907519 PMCID: PMC10618239 DOI: 10.1038/s41598-023-45784-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: 01/26/2023] [Accepted: 10/24/2023] [Indexed: 11/02/2023] Open
Abstract
Understanding the influence of genetic variations in olfactory receptor (OR) genes on the olfaction-influenced phenotypes such as behaviors, reproduction, and feeding is important in animal biology. However, our understanding of the complexity of the OR subgenome is limited. In this study, we analyzed 1120 typing results of 20 representative OR genes belonging to 13 OR families on 14 pig chromosomes from 56 individuals belonging to seven different breeds using a sequence-based OR typing method. We showed that the presence of copy number variations, conservation of locus-specific diversity, abundance of breed-specific alleles, presence of a loss-of-function allele, and low-level purifying selection in pig OR genes could be common characteristics of OR genes in mammals. The observed nucleotide sequence diversity of pig ORs was higher than that of dogs. To the best of our knowledge, this is the first report on the individual- or population-level characterization of a large number of OR family genes in livestock species.
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Affiliation(s)
- Mingue Kang
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Byeongyong Ahn
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Seungyeon Youk
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hyoim Jeon
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | | | - Eun-Seok Cho
- Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Woncheoul Park
- Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea.
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5
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Christmas MJ, Kaplow IM, Genereux DP, Dong MX, Hughes GM, Li X, Sullivan PF, Hindle AG, Andrews G, Armstrong JC, Bianchi M, Breit AM, Diekhans M, Fanter C, Foley NM, Goodman DB, Goodman L, Keough KC, Kirilenko B, Kowalczyk A, Lawless C, Lind AL, Meadows JRS, Moreira LR, Redlich RW, Ryan L, Swofford R, Valenzuela A, Wagner F, Wallerman O, Brown AR, Damas J, Fan K, Gatesy J, Grimshaw J, Johnson J, Kozyrev SV, Lawler AJ, Marinescu VD, Morrill KM, Osmanski A, Paulat NS, Phan BN, Reilly SK, Schäffer DE, Steiner C, Supple MA, Wilder AP, Wirthlin ME, Xue JR, Birren BW, Gazal S, Hubley RM, Koepfli KP, Marques-Bonet T, Meyer WK, Nweeia M, Sabeti PC, Shapiro B, Smit AFA, Springer MS, Teeling EC, Weng Z, Hiller M, Levesque DL, Lewin HA, Murphy WJ, Navarro A, Paten B, Pollard KS, Ray DA, Ruf I, Ryder OA, Pfenning AR, Lindblad-Toh K, Karlsson EK. Evolutionary constraint and innovation across hundreds of placental mammals. Science 2023; 380:eabn3943. [PMID: 37104599 PMCID: PMC10250106 DOI: 10.1126/science.abn3943] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 12/16/2022] [Indexed: 04/29/2023]
Abstract
Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.
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Affiliation(s)
- Matthew J. Christmas
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Irene M. Kaplow
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | | | - Michael X. Dong
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Graham M. Hughes
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Xue Li
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Patrick F. Sullivan
- Department of Genetics, University of North Carolina Medical School, Chapel Hill, NC 27599, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Allyson G. Hindle
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Gregory Andrews
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Joel C. Armstrong
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Matteo Bianchi
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Ana M. Breit
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
| | - Mark Diekhans
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Cornelia Fanter
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Nicole M. Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Daniel B. Goodman
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | | | - Kathleen C. Keough
- Fauna Bio, Inc., Emeryville, CA 94608, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Bogdan Kirilenko
- Faculty of Biosciences, Goethe-University, 60438 Frankfurt, Germany
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
| | - Amanda Kowalczyk
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Colleen Lawless
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Abigail L. Lind
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Jennifer R. S. Meadows
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Lucas R. Moreira
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Ruby W. Redlich
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Louise Ryan
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ross Swofford
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Alejandro Valenzuela
- Department of Experimental and Health Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Franziska Wagner
- Museum of Zoology, Senckenberg Natural History Collections Dresden, 01109 Dresden, Germany
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Ashley R. Brown
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Joana Damas
- The Genome Center, University of California Davis, Davis, CA 95616, USA
| | - Kaili Fan
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Jenna Grimshaw
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Jeremy Johnson
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Sergey V. Kozyrev
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Alyssa J. Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Department of Biological Sciences, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Voichita D. Marinescu
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Kathleen M. Morrill
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Austin Osmanski
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Nicole S. Paulat
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - BaDoi N. Phan
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Steven K. Reilly
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Daniel E. Schäffer
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Cynthia Steiner
- Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Megan A. Supple
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Aryn P. Wilder
- Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
| | - Morgan E. Wirthlin
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - James R. Xue
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Bruce W. Birren
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Steven Gazal
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | | | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, Washington, DC 20008, USA
- Computer Technologies Laboratory, ITMO University, St. Petersburg 197101, Russia
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630, USA
| | - Tomas Marques-Bonet
- Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08036 Barcelona, Spain
- Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Wynn K. Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Martin Nweeia
- Department of Comprehensive Care, School of Dental Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Vertebrate Zoology, Canadian Museum of Nature, Ottawa, Ontario K2P 2R1, Canada
- Department of Vertebrate Zoology, Smithsonian Institution, Washington, DC 20002, USA
- Narwhal Genome Initiative, Department of Restorative Dentistry and Biomaterials Sciences, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Mark S. Springer
- Department of Evolution, Ecology and Organismal Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Emma C. Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Michael Hiller
- Faculty of Biosciences, Goethe-University, 60438 Frankfurt, Germany
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
| | | | - Harris A. Lewin
- The Genome Center, University of California Davis, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California Davis, Davis, CA 95616, USA
- John Muir Institute for the Environment, University of California Davis, Davis, CA 95616, USA
| | - William J. Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Arcadi Navarro
- Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, 08003 Barcelona, Spain
- BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, 08005 Barcelona, Spain
- CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Benedict Paten
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Katherine S. Pollard
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94158, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - David A. Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Irina Ruf
- Division of Messel Research and Mammalogy, Senckenberg Research Institute and Natural History Museum Frankfurt, 60325 Frankfurt am Main, Germany
| | - Oliver A. Ryder
- Conservation Genetics, San Diego Zoo Wildlife Alliance, Escondido, CA 92027, USA
- Department of Evolution, Behavior and Ecology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92039, USA
| | - Andreas R. Pfenning
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Kerstin Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Elinor K. Karlsson
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA 01605, USA
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6
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Martinez Q, Courcelle M, Douzery E, Fabre PH. When morphology does not fit the genomes: the case of rodent olfaction. Biol Lett 2023; 19:20230080. [PMID: 37042683 PMCID: PMC10092080 DOI: 10.1098/rsbl.2023.0080] [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: 09/20/2022] [Accepted: 03/24/2023] [Indexed: 04/13/2023] Open
Abstract
Linking genes to phenotypes has been a major question in evolutionary biology for the last decades. In the genomic era, few studies attempted to link olfactory-related genes to different anatomical proxies. However, they found very inconsistent results. This study is the first to investigate a potential relation between olfactory turbinals and olfactory receptor (OR) genes. We demonstrated that despite the use of similar methodology in the acquisition of data, OR genes do not correlate with the relative and the absolute surface area of olfactory turbinals. These results challenged the interpretations of several studies based on different proxies related to olfaction and their potential relation to olfactory capabilities.
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Affiliation(s)
- Quentin Martinez
- Institut des Sciences de l'Évolution (ISEM, UMR 5554 CNRS-IRD-UM-EPHE), Université de Montpellier, Place E. Bataillon - CC 064 - 34095, Montpellier Cedex 5, France
- Staatliches Museum für Naturkunde Stuttgart DE-70191, Stuttgart, Germany
| | - Maxime Courcelle
- Institut des Sciences de l'Évolution (ISEM, UMR 5554 CNRS-IRD-UM-EPHE), Université de Montpellier, Place E. Bataillon - CC 064 - 34095, Montpellier Cedex 5, France
| | - Emmanuel Douzery
- Institut des Sciences de l'Évolution (ISEM, UMR 5554 CNRS-IRD-UM-EPHE), Université de Montpellier, Place E. Bataillon - CC 064 - 34095, Montpellier Cedex 5, France
| | - Pierre-Henri Fabre
- Institut des Sciences de l'Évolution (ISEM, UMR 5554 CNRS-IRD-UM-EPHE), Université de Montpellier, Place E. Bataillon - CC 064 - 34095, Montpellier Cedex 5, France
- Mammal Section, Department of Life Sciences, The Natural History Museum, London SW7 5DB, UK
- Institut Universitaire de France (IUF), Paris, France
- Division of Vertebrate Zoology (Mammalogy), American Museum of Natural History, Central Park West, 79th St., New York, NY 10024-5192, USA
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7
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Hu Y, Wang X, Xu Y, Yang H, Tong Z, Tian R, Xu S, Yu L, Guo Y, Shi P, Huang S, Yang G, Shi S, Wei F. Molecular mechanisms of adaptive evolution in wild animals and plants. SCIENCE CHINA. LIFE SCIENCES 2023; 66:453-495. [PMID: 36648611 PMCID: PMC9843154 DOI: 10.1007/s11427-022-2233-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 08/30/2022] [Indexed: 01/18/2023]
Abstract
Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.
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Affiliation(s)
- Yibo Hu
- CAS Key Lab of Animal Ecology and Conservation Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xiaoping Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yongchao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hui Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zeyu Tong
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Ran Tian
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China.
| | - Yalong Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Peng Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Shuangquan Huang
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
| | - Guang Yang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Fuwen Wei
- CAS Key Lab of Animal Ecology and Conservation Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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8
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Noh HJ, Turner-Maier J, Schulberg SA, Fitzgerald ML, Johnson J, Allen KN, Hückstädt LA, Batten AJ, Alfoldi J, Costa DP, Karlsson EK, Zapol WM, Buys ES, Lindblad-Toh K, Hindle AG. The Antarctic Weddell seal genome reveals evidence of selection on cardiovascular phenotype and lipid handling. Commun Biol 2022; 5:140. [PMID: 35177770 PMCID: PMC8854659 DOI: 10.1038/s42003-022-03089-2] [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: 07/10/2020] [Accepted: 01/31/2022] [Indexed: 12/24/2022] Open
Abstract
AbstractThe Weddell seal (Leptonychotes weddellii) thrives in its extreme Antarctic environment. We generated the Weddell seal genome assembly and a high-quality annotation to investigate genome-wide evolutionary pressures that underlie its phenotype and to study genes implicated in hypoxia tolerance and a lipid-based metabolism. Genome-wide analyses included gene family expansion/contraction, positive selection, and diverged sequence (acceleration) compared to other placental mammals, identifying selection in coding and non-coding sequence in five pathways that may shape cardiovascular phenotype. Lipid metabolism as well as hypoxia genes contained more accelerated regions in the Weddell seal compared to genomic background. Top-significant genes were SUMO2 and EP300; both regulate hypoxia inducible factor signaling. Liver expression of four genes with the strongest acceleration signals differ between Weddell seals and a terrestrial mammal, sheep. We also report a high-density lipoprotein-like particle in Weddell seal serum not present in other mammals, including the shallow-diving harbor seal.
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9
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Bouchard B, Barnagaud JY, Verborgh P, Gauffier P, Campagna S, Célérier A. A field study of chemical senses in bottlenose dolphins and pilot whales. Anat Rec (Hoboken) 2021; 305:668-679. [PMID: 34260154 DOI: 10.1002/ar.24703] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/02/2021] [Accepted: 05/26/2021] [Indexed: 11/05/2022]
Abstract
For most marine vertebrates, chemical cues provide crucial information during navigation and foraging, but their use by cetaceans is still poorly understood. In contrast to baleen whales, toothed whales (odontocetes) are scarcely equipped for chemoreception: they lack the conventional anatomical structures (i.e., olfactory epithelium, nerves and bulbs) involved in olfaction and have reduced taste buds on the tongue. Several behavioral studies have however shown that captive dolphins can perceive chemical solutions, including odorants, in their oral cavity. To investigate whether odontocetes could use infochemicals in their foraging ecology, we implemented a behavioral response experiment in wild bottlenose dolphins and long-finned pilot whales. We tested dimethyl sulfide (DMS) as a potentially attractive stimulus since it is a chemical signature of highly productive marine areas, known to attract several marine predators including fishes and seabirds. We assessed cetacean responses to DMS exposure by analyzing their movements and surface behaviors recorded by onboard observers. In both species, results did not reveal any significant attraction or behavioral reaction toward DMS when compared to a control chemical stimulus, apart from a short-distance response in bottlenose dolphins. These results suggest that while odontocetes may perceive DMS in water, it apparently does not play a significant role in their foraging ecology. Testing potentially more attractive compounds such as prey extracts with the present method and analyzing surface, underwater and acoustic responses would provide further insights on odontocete feeding behavior. It would also provide valuable clues to studies on the anatomical structures involved in their chemosenses.
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Affiliation(s)
| | | | - Philippe Verborgh
- CIRCE, Conservation, Information and Research on Cetaceans, Algeciras-Pelayo, Spain
| | - Pauline Gauffier
- CIRCE, Conservation, Information and Research on Cetaceans, Algeciras-Pelayo, Spain
| | - Sylvie Campagna
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Université de Nîmes, Montpellier, France
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10
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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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11
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Tebbe J, Humble E, Stoffel MA, Tewes LJ, Müller C, Forcada J, Caspers B, Hoffman JI. Chemical patterns of colony membership and mother-offspring similarity in Antarctic fur seals are reproducible. PeerJ 2020; 8:e10131. [PMID: 33133782 PMCID: PMC7580581 DOI: 10.7717/peerj.10131] [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] [Received: 04/30/2020] [Accepted: 09/17/2020] [Indexed: 11/20/2022] Open
Abstract
Replication studies are essential for evaluating the validity of previous research findings. However, it has proven challenging to reproduce the results of ecological and evolutionary studies, partly because of the complexity and lability of many of the phenomena being investigated, but also due to small sample sizes, low statistical power and publication bias. Additionally, replication is often considered too difficult in field settings where many factors are beyond the investigator’s control and where spatial and temporal dependencies may be strong. We investigated the feasibility of reproducing original research findings in the field of chemical ecology by performing an exact replication of a previous study of Antarctic fur seals (Arctocephalus gazella). In the original study, skin swabs from 41 mother-offspring pairs from two adjacent breeding colonies on Bird Island, South Georgia, were analyzed using gas chromatography-mass spectrometry. Seals from the two colonies differed significantly in their chemical fingerprints, suggesting that colony membership may be chemically encoded, and mothers were also chemically similar to their pups, hinting at the possible involvement of phenotype matching in mother-offspring recognition. In the current study, we generated and analyzed chemical data from a non-overlapping sample of 50 mother-offspring pairs from the same two colonies 5 years later. The original results were corroborated in both hypothesis testing and estimation contexts, with p-values remaining highly significant and effect sizes, standardized between studies by bootstrapping the chemical data over individuals, being of comparable magnitude. However, exact replication studies are only capable of showing whether a given effect can be replicated in a specific setting. We therefore investigated whether chemical signatures are colony-specific in general by expanding the geographic coverage of our study to include pups from a total of six colonies around Bird Island. We detected significant chemical differences in all but a handful of pairwise comparisons between colonies. This finding adds weight to our original conclusion that colony membership is chemically encoded, and suggests that chemical patterns of colony membership not only persist over time but can also be generalized over space. Our study systematically confirms and extends our previous findings, while also implying more broadly that spatial and temporal heterogeneity need not necessarily negate the reproduction and generalization of ecological research findings.
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Affiliation(s)
- Jonas Tebbe
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
| | - Emily Humble
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany.,Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK.,British Antarctic Survey, Cambridge, UK
| | - Martin Adam Stoffel
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany.,Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Lisa Johanna Tewes
- Department of Chemical Ecology, Bielefeld University, Bielefeld, Germany
| | - Caroline Müller
- Department of Chemical Ecology, Bielefeld University, Bielefeld, Germany
| | | | - Barbara Caspers
- Department of Behavioural Ecology, Bielefeld University, Bielefeld, Germany
| | - Joseph Ivan Hoffman
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany.,British Antarctic Survey, Cambridge, UK
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12
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Abstract
Nervous systems allow animals to acutely respond and behaviorally adapt to changes and recurring patterns in their environment at multiple timescales-from milliseconds to years. Behavior is further shaped at intergenerational timescales by genetic variation, drift, and selection. This sophistication and flexibility of behavior makes it challenging to measure behavior consistently in individual subjects and to compare it across individuals. In spite of these challenges, careful behavioral observations in nature and controlled measurements in the laboratory, combined with modern technologies and powerful genetic approaches, have led to important discoveries about the way genetic variation shapes behavior. A critical mass of genes whose variation is known to modulate behavior in nature is finally accumulating, allowing us to recognize emerging patterns. In this review, we first discuss genetic mapping approaches useful for studying behavior. We then survey how variation acts at different levels-in environmental sensation, in internal neuronal circuits, and outside the nervous system altogether-and then discuss the sources and types of molecular variation linked to behavior and the mechanisms that shape such variation. We end by discussing remaining questions in the field.
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Affiliation(s)
- Natalie Niepoth
- Zuckerman Mind Brain Behavior Institute and Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027, USA; ,
| | - Andres Bendesky
- Zuckerman Mind Brain Behavior Institute and Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027, USA; ,
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13
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Convergent evolution of olfactory and thermoregulatory capacities in small amphibious mammals. Proc Natl Acad Sci U S A 2020; 117:8958-8965. [PMID: 32253313 DOI: 10.1073/pnas.1917836117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Olfaction and thermoregulation are key functions for mammals. The former is critical to feeding, mating, and predator avoidance behaviors, while the latter is essential for homeothermy. Aquatic and amphibious mammals face olfactory and thermoregulatory challenges not generally encountered by terrestrial species. In mammals, the nasal cavity houses a bony system supporting soft tissues and sensory organs implicated in either olfactory or thermoregulatory functions. It is hypothesized that to cope with aquatic environments, amphibious mammals have expanded their thermoregulatory capacity at the expense of their olfactory system. We investigated the evolutionary history of this potential trade-off using a comparative dataset of three-dimensional (3D) CT scans of 189 skulls, capturing 17 independent transitions from a strictly terrestrial to an amphibious lifestyle across small mammals (Afrosoricida, Eulipotyphla, and Rodentia). We identified rapid and repeated loss of olfactory capacities synchronously associated with gains in thermoregulatory capacity in amphibious taxa sampled from across mammalian phylogenetic diversity. Evolutionary models further reveal that these convergences result from faster rates of turbinal bone evolution and release of selective constraints on the thermoregulatory-olfaction trade-off in amphibious species. Lastly, we demonstrated that traits related to vital functions evolved faster to the optimum compared to traits that are not related to vital functions.
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14
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Liu G, Zhao C, Xu D, Zhang H, Monakhov V, Shang S, Gao X, Sha W, Ma J, Zhang W, Tang X, Li B, Hua Y, Cao X, Liu Z, Zhang H. First Draft Genome of the Sable, Martes zibellina. Genome Biol Evol 2020; 12:59-65. [PMID: 32058545 PMCID: PMC7144822 DOI: 10.1093/gbe/evaa029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2020] [Indexed: 11/28/2022] Open
Abstract
Members of genus Martes provide early warning signals about forest ecosystem health and are designated as a Management Indicator Species. As one of the most widespread members in Martes, the sable (Martes zibellina) is a circumboreal small predator found throughout all taiga zoogeographical zones of Eurasia and shows distinct population differentiation and morphological variations. To support further studies on striking local adaptation and population evolution, we present the first sable genome, assembled de novo from an individual originating in the Great Khingan Mountains (China). The assembled genome is 2.42 Gb, consisting of 15,814 scaffolds with a scaffold N50 of 5.20 Mb. Searches for complete Mammalia BUSCO (Benchmarking Universal Single-Copy Ortholog) gene groups found that 95.15% of the curated single-copy orthologs were assembled as complete, suggesting a high level of completeness of the genome. We totally predicted 19,413 protein-coding genes, and 0.82 Gb of repeat sequences was annotated. We also detected 1,257 olfactory receptor genes and found more functional olfactory receptor genes in sable than in other Mustelidae species, which provide a possible genetic explanation for the acute sense of smell of the sable for searching the preys under deep snow. Phylogenetic analyses revealed that the ferret (Mustela putorius furo) and sea otter (Enhydra lutris) form a clade that is sister to the sable, which was dated ∼16.4 Ma. Overall, our study provided the first reference genome for research in a broad range of areas including local adaptations, population evolution, conservation, and management for sable.
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Affiliation(s)
- Guangshuai Liu
- College of Life Science, Qufu Normal University, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chao Zhao
- College of Life Science, Qufu Normal University, China
| | - Dongming Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Huanxin Zhang
- College of Marine Life Science, Ocean University of China, Qingdao, Shandong, China
| | - Vladimir Monakhov
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, Russia
| | - Shuai Shang
- College of Marine Life Science, Ocean University of China, Qingdao, Shandong, China
- College of Biological and Environmental Engineering, Binzhou University, China
| | - Xiaodong Gao
- College of Life Science, Qufu Normal University, China
| | - Weilai Sha
- College of Life Science, Qufu Normal University, China
| | - Jianzhang Ma
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Wei Zhang
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Xuexi Tang
- College of Marine Life Science, Ocean University of China, Qingdao, Shandong, China
| | - Bo Li
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Yan Hua
- College of Wildlife Resources, Northeast Forestry University, Harbin, China
| | - Xiaofang Cao
- Novogene Bioinformatics Institute, Beijing, China
| | - Zhen Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Honghai Zhang
- College of Life Science, Qufu Normal University, China
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15
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Marino L, Rose NA, Visser IN, Rally H, Ferdowsian H, Slootsky V. The harmful effects of captivity and chronic stress on the well-being of orcas (Orcinus orca). J Vet Behav 2020. [DOI: 10.1016/j.jveb.2019.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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16
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Liu A, He F, Shen L, Liu R, Wang Z, Zhou J. Convergent degeneration of olfactory receptor gene repertoires in marine mammals. BMC Genomics 2019; 20:977. [PMID: 31842731 PMCID: PMC6916060 DOI: 10.1186/s12864-019-6290-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 11/14/2019] [Indexed: 11/10/2022] Open
Abstract
Background Olfactory receptors (ORs) can bind odor molecules and play a crucial role in odor sensation. Due to the frequent gains and losses of genes during evolution, the number of OR members varies greatly among different species. However, whether the extent of gene gains/losses varies between marine mammals and related terrestrial mammals has not been clarified, and the factors that might underlie these variations are unknown. Results To address these questions, we identified more than 10,000 members of the OR family in 23 mammals and classified them into 830 orthologous gene groups (OGGs) and 281 singletons. Significant differences occurred in the number of OR repertoires and OGGs among different species. We found that all marine mammals had fewer OR genes than their related terrestrial lineages, with the fewest OR genes found in cetaceans, which may be closely related to olfactory degradation. ORs with more gene duplications or loss events tended to be under weaker purifying selection. The average gain and loss rates of OR genes in terrestrial mammals were higher than those of mammalian gene families, while the average gain and loss rates of OR genes in marine mammals were significantly lower and much higher than those of mammalian gene families, respectively. Additionally, we failed to detect any one-to-one orthologous genes in the focal species, suggesting that OR genes are not well conserved among marine mammals. Conclusions Marine mammals have experienced large numbers of OR gene losses compared with their related terrestrial lineages, which may result from the frequent birth-and-death evolution under varied functional constrains. Due to their independent degeneration, OR genes present in each lineage are not well conserved among marine mammals. Our study provides a basis for future research on the olfactory receptor function in mammals from the perspective of evolutionary trajectories.
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Affiliation(s)
- Ake Liu
- Faculty of Biological Science and Technology, Changzhi University, Changzhi, Shanxi, 046011, People's Republic of China.,School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Funan He
- School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Libing Shen
- Institute of Neuroscience, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China
| | - Ruixiang Liu
- Faculty of Biological Science and Technology, Changzhi University, Changzhi, Shanxi, 046011, People's Republic of China
| | - Zhijun Wang
- Department of Chemistry, Changzhi University, Changzhi, Shanxi, 046011, People's Republic of China.
| | - Jingqi Zhou
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China.
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17
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Beichman AC, Koepfli KP, Li G, Murphy W, Dobrynin P, Kliver S, Tinker MT, Murray MJ, Johnson J, Lindblad-Toh K, Karlsson EK, Lohmueller KE, Wayne RK. Aquatic Adaptation and Depleted Diversity: A Deep Dive into the Genomes of the Sea Otter and Giant Otter. Mol Biol Evol 2019; 36:2631-2655. [PMID: 31212313 PMCID: PMC7967881 DOI: 10.1093/molbev/msz101] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Despite its recent invasion into the marine realm, the sea otter (Enhydra lutris) has evolved a suite of adaptations for life in cold coastal waters, including limb modifications and dense insulating fur. This uniquely dense coat led to the near-extinction of sea otters during the 18th-20th century fur trade and an extreme population bottleneck. We used the de novo genome of the southern sea otter (E. l. nereis) to reconstruct its evolutionary history, identify genes influencing aquatic adaptation, and detect signals of population bottlenecks. We compared the genome of the southern sea otter with the tropical freshwater-living giant otter (Pteronura brasiliensis) to assess common and divergent genomic trends between otter species, and with the closely related northern sea otter (E. l. kenyoni) to uncover population-level trends. We found signals of positive selection in genes related to aquatic adaptations, particularly limb development and polygenic selection on genes related to hair follicle development. We found extensive pseudogenization of olfactory receptor genes in both the sea otter and giant otter lineages, consistent with patterns of sensory gene loss in other aquatic mammals. At the population level, the southern sea otter and the northern sea otter showed extremely low genomic diversity, signals of recent inbreeding, and demographic histories marked by population declines. These declines may predate the fur trade and appear to have resulted in an increase in putatively deleterious variants that could impact the future recovery of the sea otter.
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Affiliation(s)
- Annabel C Beichman
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Gang Li
- College of Life Science, Shaanxi Normal University, Xi’an, Shaanxi, China
| | - William Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
| | - Pasha Dobrynin
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Sergei Kliver
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Martin T Tinker
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA
| | | | - Jeremy Johnson
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Kerstin Lindblad-Toh
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Elinor K Karlsson
- Vertebrate Genome Biology, Broad Institute of MIT and Harvard, Cambridge, MA
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
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18
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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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19
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Kishida T, Go Y, Tatsumoto S, Tatsumi K, Kuraku S, Toda M. Loss of olfaction in sea snakes provides new perspectives on the aquatic adaptation of amniotes. Proc Biol Sci 2019; 286:20191828. [PMID: 31506057 DOI: 10.1098/rspb.2019.1828] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Marine amniotes, a polyphyletic group, provide an excellent opportunity for studying convergent evolution. Their sense of smell tends to degenerate, but this process has not been explored by comparing fully aquatic species with their amphibious relatives in an evolutionary context. Here, we sequenced the genomes of fully aquatic and amphibious sea snakes and identified repertoires of chemosensory receptor genes involved in olfaction. Snakes possess large numbers of the olfactory receptor (OR) genes and the type-2 vomeronasal receptor (V2R) genes, and expression profiling in the olfactory tissues suggests that snakes use the ORs in the main olfactory system (MOS) and the V2Rs in the vomeronasal system (VNS). The number of OR genes has decreased in sea snakes, and fully aquatic species lost MOS which is responsible for detecting airborne odours. By contrast, sea snakes including fully aquatic species retain a number of V2R genes and a well-developed VNS for smelling underwater. This study suggests that the sense of smell also degenerated in sea snakes, particularly in fully aquatic species, but their residual olfactory capability is distinct from that of other fully aquatic amniotes. Amphibious species show an intermediate status between terrestrial and fully aquatic snakes, implying their importance in understanding the process of aquatic adaptation.
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Affiliation(s)
- Takushi Kishida
- Wildlife Research Center, Kyoto University, 2-24 Tanaka Sekiden-cho, Sakyo, Kyoto 606-8203, Japan
| | - Yasuhiro Go
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan.,National Institute for Physiological Science, Okazaki, Aichi 444-8585, Japan
| | - Shoji Tatsumoto
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan.,National Institute for Physiological Science, Okazaki, Aichi 444-8585, Japan
| | - Kaori Tatsumi
- RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Shigehiro Kuraku
- RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Mamoru Toda
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
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20
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Hecker N, Lächele U, Stuckas H, Giere P, Hiller M. Convergent vomeronasal system reduction in mammals coincides with convergent losses of calcium signalling and odorant-degrading genes. Mol Ecol 2019; 28:3656-3668. [PMID: 31332871 DOI: 10.1111/mec.15180] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/16/2019] [Accepted: 06/24/2019] [Indexed: 12/11/2022]
Abstract
The vomeronasal system (VNS) serves crucial functions for detecting olfactory clues often related to social and sexual behaviour. Intriguingly, two of the main components of the VNS, the vomeronasal organ (VNO) and the accessory olfactory bulb, are regressed in aquatic mammals, several bats and primates, likely due to adaptations to different ecological niches. To detect genomic changes that are associated with the convergent reduction of the VNS, we performed the first systematic screen for convergently inactivated protein-coding genes associated with convergent VNS reduction, considering 106 mammalian genomes. Extending previous studies, our results support that Trpc2, a cation channel that is important for calcium signalling in the VNO, is a predictive molecular marker for the presence of a VNS. Our screen also detected the convergent inactivation of the calcium-binding protein S100z, the aldehyde oxidase Aox2 that is involved in odorant degradation, and the uncharacterized Mslnl gene that is expressed in the VNO and olfactory epithelium. Furthermore, we found that Trpc2 and S100z or Aox2 are also inactivated in otters and Phocid seals for which no morphological data about the VNS are available yet. This predicts a VNS reduction in these semi-aquatic mammals. By examining the genomes of 115 species in total, our study provides a detailed picture of how the convergent reduction of the VNS coincides with gene inactivation in placental mammals. These inactivated genes provide experimental targets for studying the evolution and biological significance of the olfactory system under different environmental conditions.
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Affiliation(s)
- Nikolai Hecker
- Center for Systems Biology Dresden, Dresden, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Ulla Lächele
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Heiko Stuckas
- Population Genetics, Senckenberg Natural History Collections Dresden, Dresden, Germany.,Leibniz Institution for Biodiversity and Earth System Research, Dresden, Germany
| | - Peter Giere
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Michael Hiller
- Center for Systems Biology Dresden, Dresden, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
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21
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Hu Z, Sackton TB, Edwards SV, Liu JS. Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees. Mol Biol Evol 2019; 36:1086-1100. [PMID: 30851112 PMCID: PMC6501877 DOI: 10.1093/molbev/msz049] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Conservation of DNA sequence over evolutionary time is a strong indicator of function, and gain or loss of sequence conservation can be used to infer changes in function across a phylogeny. Changes in evolutionary rates on particular lineages in a phylogeny can indicate shared functional shifts, and thus can be used to detect genomic correlates of phenotypic convergence. However, existing methods do not allow easy detection of patterns of rate variation, which causes challenges for detecting convergent rate shifts or other complex evolutionary scenarios. Here we introduce PhyloAcc, a new Bayesian method to model substitution rate changes in conserved elements across a phylogeny. The method assumes several categories of substitution rate for each branch on the phylogenetic tree, estimates substitution rates per category, and detects changes of substitution rate as the posterior probability of a category switch. Simulations show that PhyloAcc can detect genomic regions with rate shifts in multiple target species better than previous methods and has a higher accuracy of reconstructing complex patterns of substitution rate changes than prevalent Bayesian relaxed clock models. We demonstrate the utility of PhyloAcc in two classic examples of convergent phenotypes: loss of flight in birds and the transition to marine life in mammals. In each case, our approach reveals numerous examples of conserved nonexonic elements with accelerations specific to the phenotypically convergent lineages. Our method is widely applicable to any set of conserved elements where multiple rate changes are expected on a phylogeny.
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Affiliation(s)
- Zhirui Hu
- Department of Statistics, Harvard University, Cambridge, MA
| | | | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA
| | - Jun S Liu
- Department of Statistics, Harvard University, Cambridge, MA
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22
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Bird DJ, Murphy WJ, Fox-Rosales L, Hamid I, Eagle RA, Van Valkenburgh B. Olfaction written in bone: cribriform plate size parallels olfactory receptor gene repertoires in Mammalia. Proc Biol Sci 2019. [PMID: 29540522 DOI: 10.1098/rspb.2018.0100] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The evolution of mammalian olfaction is manifested in a remarkable diversity of gene repertoires, neuroanatomy and skull morphology across living species. Olfactory receptor genes (ORGs), which initiate the conversion of odorant molecules into odour perceptions and help an animal resolve the olfactory world, range in number from a mere handful to several thousand genes across species. Within the snout, each of these ORGs is exclusively expressed by a discrete population of olfactory sensory neurons (OSNs), suggesting that newly evolved ORGs may be coupled with new OSN populations in the nasal epithelium. Because OSN axon bundles leave high-fidelity perforations (foramina) in the bone as they traverse the cribriform plate (CP) to reach the brain, we predicted that taxa with larger ORG repertoires would have proportionately expanded footprints in the CP foramina. Previous work found a correlation between ORG number and absolute CP size that disappeared after accounting for body size. Using updated, digital measurement data from high-resolution CT scans and re-examining the relationship between CP and body size, we report a striking linear correlation between relative CP area and number of functional ORGs across species from all mammalian superorders. This correlation suggests strong developmental links in the olfactory pathway between genes, neurons and skull morphology. Furthermore, because ORG number is linked to olfactory discriminatory function, this correlation supports relative CP size as a viable metric for inferring olfactory capacity across modern and extinct species. By quantifying CP area from a fossil sabertooth cat (Smilodon fatalis), we predicted a likely ORG repertoire for this extinct felid.
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Affiliation(s)
- Deborah J Bird
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA 90095-8347, USA
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843-4458, USA
| | - Lester Fox-Rosales
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA 90095-8347, USA
| | - Iman Hamid
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA 90095-8347, USA
| | - Robert A Eagle
- Department of Atmospheric and Oceanic Sciences, Institute of the Environment and Sustainability, University of California Los Angeles, 520 Portola Plaza, Math Sciences Building 7127, Los Angeles, CA 90095, USA
| | - Blaire Van Valkenburgh
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA 90095-8347, USA
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23
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Kutsuma R, Sasai T, Kishida T. How Snakes Find Prey Underwater: Sea Snakes Use Visual and Chemical Cues for Foraging. Zoolog Sci 2018; 35:483-486. [DOI: 10.2108/zs180059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Ryo Kutsuma
- Wildlife Research Center, Kyoto University, 2-24 Tanaka Sekiden-cho, Sakyo, Kyoto 606-8203, Japan
| | - Takahide Sasai
- Suma Aqualife Park, Wakamiya 1-3-5, Suma, Kobe 654-0049, Japan
| | - Takushi Kishida
- Wildlife Research Center, Kyoto University, 2-24 Tanaka Sekiden-cho, Sakyo, Kyoto 606-8203, Japan
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24
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Boessenecker RW, Geisler JH. New records of the archaic dolphin Agorophius (Mammalia: Cetacea) from the upper Oligocene Chandler Bridge Formation of South Carolina, USA. PeerJ 2018; 6:e5290. [PMID: 30280011 PMCID: PMC6166619 DOI: 10.7717/peerj.5290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/02/2018] [Indexed: 12/05/2022] Open
Abstract
The stem odontocete Agorophius pygmaeus (Ashley Formation, lower Oligocene, South Carolina; 29.0–26.57 Ma) has been a critical point of comparison for studies of early neocete evolution owing to its early discovery as well as its transitional anatomy relative to archaeocete whales and modern odontocetes. Some time during the late nineteenth century the holotype skull went missing and has never been relocated; supplementary reference specimens have since been recently referred to the species from the Ashley Formation and the overlying Chandler Bridge Formation (upper Oligocene; 24.7–23.5). New crania referable to Agorophius sp. are identifiable to the genus based on several features of the intertemporal region. Furthermore, all published specimens from the Chandler Bridge Formation consistently share larger absolute size and a proportionally shorter exposure of the parietal in the skull roof than specimens from the Ashley Formation (including the holotype). Furthermore, these specimens include well-preserved ethmoid labyrinths and cribriform plates, indicating that Agorophius primitively retained a strong olfactory sense. These new crania suggest that at least two species of Agorophius are present in the Oligocene of South Carolina, revealing a somewhat more complicated taxonomic perspective.
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Affiliation(s)
- Robert W Boessenecker
- Department of Geology and Environmental Geosciences, College of Charleston, Charleston, SC, United States of America.,Museum of Paleontology, University of California, Berkeley, Berkeley, CA, United States of America
| | - Jonathan H Geisler
- Department of Anatomy, College of Osteopathic Medicine, New York Institute of Technology, Old Westbury, NY, United States of America
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25
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Springer MS, Gatesy J. Inactivation of the olfactory marker protein (OMP) gene in river dolphins and other odontocete cetaceans. Mol Phylogenet Evol 2017; 109:375-387. [PMID: 28193458 DOI: 10.1016/j.ympev.2017.01.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/25/2017] [Accepted: 01/29/2017] [Indexed: 11/18/2022]
Abstract
Various toothed whales (Odontoceti) are unique among mammals in lacking olfactory bulbs as adults and are thought to be anosmic (lacking the olfactory sense). At the molecular level, toothed whales have high percentages of pseudogenic olfactory receptor genes, but species that have been investigated to date retain an intact copy of the olfactory marker protein gene (OMP), which is highly expressed in olfactory receptor neurons and may regulate the temporal resolution of olfactory responses. One hypothesis for the retention of intact OMP in diverse odontocete lineages is that this gene is pleiotropic with additional functions that are unrelated to olfaction. Recent expression studies provide some support for this hypothesis. Here, we report OMP sequences for representatives of all extant cetacean families and provide the first molecular evidence for inactivation of this gene in vertebrates. Specifically, OMP exhibits independent inactivating mutations in six different odontocete lineages: four river dolphin genera (Platanista, Lipotes, Pontoporia, Inia), sperm whale (Physeter), and harbor porpoise (Phocoena). These results suggest that the only essential role of OMP that is maintained by natural selection is in olfaction, although a non-olfactory role for OMP cannot be ruled out for lineages that retain an intact copy of this gene. Available genome sequences from cetaceans and close outgroups provide evidence of inactivating mutations in two additional genes (CNGA2, CNGA4), which imply further pseudogenization events in the olfactory cascade of odontocetes. Selection analyses demonstrate that evolutionary constraints on all three genes (OMP, CNGA2, CNGA4) have been greatly reduced in Odontoceti, but retain a signature of purifying selection on the stem Cetacea branch and in Mysticeti (baleen whales). This pattern is compatible with the 'echolocation-priority' hypothesis for the evolution of OMP, which posits that negative selection was maintained in the common ancestor of Cetacea and was not relaxed significantly until the evolution of echolocation in Odontoceti.
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Affiliation(s)
- Mark S Springer
- Department of Biology, University of California, Riverside, CA 92521, USA.
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA.
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26
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Jovancevic N, Wunderlich KA, Haering C, Flegel C, Maßberg D, Weinrich M, Weber L, Tebbe L, Kampik A, Gisselmann G, Wolfrum U, Hatt H, Gelis L. Deep Sequencing of the Human Retinae Reveals the Expression of Odorant Receptors. Front Cell Neurosci 2017; 11:03. [PMID: 28174521 PMCID: PMC5258773 DOI: 10.3389/fncel.2017.00003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 01/09/2017] [Indexed: 01/17/2023] Open
Abstract
Several studies have demonstrated that the expression of odorant receptors (ORs) occurs in various tissues. These findings have served as a basis for functional studies that demonstrate the potential of ORs as drug targets for a clinical application. To the best of our knowledge, this report describes the first evaluation of the mRNA expression of ORs and the localization of OR proteins in the human retina that set a stage for subsequent functional analyses. RNA-Sequencing datasets of three individual neural retinae were generated using Next-generation sequencing and were compared to previously published but reanalyzed datasets of the peripheral and the macular human retina and to reference tissues. The protein localization of several ORs was investigated by immunohistochemistry. The transcriptome analyses detected an average of 14 OR transcripts in the neural retina, of which OR6B3 is one of the most highly expressed ORs. Immunohistochemical stainings of retina sections localized OR2W3 to the photosensitive outer segment membranes of cones, whereas OR6B3 was found in various cell types. OR5P3 and OR10AD1 were detected at the base of the photoreceptor connecting cilium, and OR10AD1 was also localized to the nuclear envelope of all of the nuclei of the retina. The cell type-specific expression of the ORs in the retina suggests that there are unique biological functions for those receptors.
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Affiliation(s)
| | - Kirsten A Wunderlich
- Department of Cell and Matrix Biology, Johannes Gutenberg University of Mainz Mainz, Germany
| | - Claudia Haering
- Department of Cell Physiology, Ruhr-University Bochum Bochum, Germany
| | - Caroline Flegel
- Department of Cell Physiology, Ruhr-University Bochum Bochum, Germany
| | - Désirée Maßberg
- Department of Cell Physiology, Ruhr-University Bochum Bochum, Germany
| | - Markus Weinrich
- Department of Cell Physiology, Ruhr-University Bochum Bochum, Germany
| | - Lea Weber
- Department of Cell Physiology, Ruhr-University Bochum Bochum, Germany
| | - Lars Tebbe
- Department of Cell and Matrix Biology, Johannes Gutenberg University of Mainz Mainz, Germany
| | - Anselm Kampik
- Department of Ophthalmology, Ludwig Maximilian University of Munich Munich, Germany
| | - Günter Gisselmann
- Department of Cell Physiology, Ruhr-University Bochum Bochum, Germany
| | - Uwe Wolfrum
- Department of Cell and Matrix Biology, Johannes Gutenberg University of Mainz Mainz, Germany
| | - Hanns Hatt
- Department of Cell Physiology, Ruhr-University Bochum Bochum, Germany
| | - Lian Gelis
- Department of Cell Physiology, Ruhr-University Bochum Bochum, Germany
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27
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Berta A, Lanzetti A, Ekdale EG, Deméré TA. From Teeth to Baleen and Raptorial to Bulk Filter Feeding in Mysticete Cetaceans: The Role of Paleontological, Genetic, and Geochemical Data in Feeding Evolution and Ecology. Integr Comp Biol 2016; 56:1271-1284. [DOI: 10.1093/icb/icw128] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Samuelson MM, Lauderdale LK, Pulis K, Solangi M, Hoffland T, Lyn H. Olfactory Enrichment in California Sea Lions (Zalophus californianus): An Effective Tool for Captive Welfare? J APPL ANIM WELF SCI 2016; 20:75-85. [PMID: 27827545 DOI: 10.1080/10888705.2016.1246362] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
In the wild, California sea lions (Zalophus californianus) are exposed to a wide variety of sensory information, which cannot be replicated in captive environments. Therefore, unique procedures are necessary for maintaining physiological and psychological health in nonhuman animals in captivity. The effects of introducing natural scents to captive enclosures have been investigated in a variety of species, yet they have not been examined in marine mammals. This project explored the behavioral effect of scent added to the environment, with the goal of improving the welfare of sea lions in captivity. Two scent types were introduced: (a) natural scents, found in their native environment, and (b) non-natural scents, not found in their native environment. This study examined not only scent enrichment but also the possible evolutionary underpinnings of pinniped olfaction. Scent enrichment was found to significantly impact sea lion behavior as demonstrated by a reduction in pattern swimming, an increase in habitat utilization, and a reduction in stereotypical behavior. However, there were no differences in behavior between natural and non-natural scent conditions.
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Affiliation(s)
- Mystera M Samuelson
- a Department of Psychology , The University of Southern Mississippi , Hattiesburg , MS , USA
| | - Lisa K Lauderdale
- a Department of Psychology , The University of Southern Mississippi , Hattiesburg , MS , USA
| | - Kelly Pulis
- b The Institute for Marine Mammal Studies , Gulfport , MS , USA
| | - Moby Solangi
- b The Institute for Marine Mammal Studies , Gulfport , MS , USA
| | - Tim Hoffland
- b The Institute for Marine Mammal Studies , Gulfport , MS , USA
| | - Heidi Lyn
- a Department of Psychology , The University of Southern Mississippi , Hattiesburg , MS , USA.,b The Institute for Marine Mammal Studies , Gulfport , MS , USA
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29
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Ichishima H. The ethmoid and presphenoid of cetaceans. J Morphol 2016; 277:1661-1674. [DOI: 10.1002/jmor.20615] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/27/2016] [Accepted: 08/30/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Hiroto Ichishima
- Fukui Prefectural Dinosaur Museum; Terao 51-11, Muroko Katsuyama Fukui Japan
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30
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Lu Q, Wang K, Lei F, Yu D, Zhao H. Penguins reduced olfactory receptor genes common to other waterbirds. Sci Rep 2016; 6:31671. [PMID: 27527385 PMCID: PMC4985648 DOI: 10.1038/srep31671] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/26/2016] [Indexed: 12/21/2022] Open
Abstract
The sense of smell, or olfaction, is fundamental in the life of animals. However, penguins (Aves: Sphenisciformes) possess relatively small olfactory bulbs compared with most other waterbirds such as Procellariiformes and Gaviiformes. To test whether penguins have a reduced reliance on olfaction, we analyzed the draft genome sequences of the two penguins, which diverged at the origin of the order Sphenisciformes; we also examined six closely related species with available genomes, and identified 29 one-to-one orthologous olfactory receptor genes (i.e. ORs) that are putatively functionally conserved and important across the eight birds. To survey the 29 one-to-one orthologous ORs in penguins and their relatives, we newly generated 34 sequences that are missing from the draft genomes. Through the analysis of totaling 378 OR sequences, we found that, of these functionally important ORs common to other waterbirds, penguins have a significantly greater percentage of OR pseudogenes than other waterbirds, suggesting a reduction of olfactory capability. The penguin-specific reduction of olfactory capability arose in the common ancestor of penguins between 23 and 60 Ma, which may have resulted from the aquatic specializations for underwater vision. Our study provides genetic evidence for a possible reduction of reliance on olfaction in penguins.
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Affiliation(s)
- Qin Lu
- Department of Ecology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Kai Wang
- Department of Ecology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dan Yu
- Department of Ecology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Huabin Zhao
- Department of Ecology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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31
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Prudent X, Parra G, Schwede P, Roscito JG, Hiller M. Controlling for Phylogenetic Relatedness and Evolutionary Rates Improves the Discovery of Associations Between Species' Phenotypic and Genomic Differences. Mol Biol Evol 2016; 33:2135-50. [PMID: 27222536 PMCID: PMC4948712 DOI: 10.1093/molbev/msw098] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The growing number of sequenced genomes allows us now to address a key question in genetics and evolutionary biology: which genomic changes underlie particular phenotypic changes between species? Previously, we developed a computational framework called Forward Genomics that associates phenotypic to genomic differences by focusing on phenotypes that are independently lost in different lineages. However, our previous implementation had three main limitations. Here, we present two new Forward Genomics methods that overcome these limitations by (1) directly controlling for phylogenetic relatedness, (2) controlling for differences in evolutionary rates, and (3) computing a statistical significance. We demonstrate on large-scale simulated data and on real data that both new methods substantially improve the sensitivity to detect associations between phenotypic and genomic differences. We applied these new methods to detect genomic differences involved in the loss of vision in the blind mole rat and the cape golden mole, two independent subterranean mammals. Forward Genomics identified several genes that are enriched in functions related to eye development and the perception of light, as well as genes involved in the circadian rhythm. These new Forward Genomics methods represent a significant advance in our ability to discover the genomic basis underlying phenotypic differences between species. Source code: https://github.com/hillerlab/ForwardGenomics/.
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Affiliation(s)
- Xavier Prudent
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Genis Parra
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Peter Schwede
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Juliana G Roscito
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
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32
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Kremers D, Célérier A, Schaal B, Campagna S, Trabalon M, Böye M, Hausberger M, Lemasson A. Sensory Perception in Cetaceans: Part I—Current Knowledge about Dolphin Senses As a Representative Species. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00049] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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33
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Kremers D, Célérier A, Schaal B, Campagna S, Trabalon M, Böye M, Hausberger M, Lemasson A. Sensory Perception in Cetaceans: Part II—Promising Experimental Approaches to Study Chemoreception in Dolphins. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00050] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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34
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Goh CJ, Choi D, Park DB, Kim H, Hahn Y. MOXD2, a Gene Possibly Associated with Olfaction, Is Frequently Inactivated in Birds. PLoS One 2016; 11:e0152431. [PMID: 27074048 PMCID: PMC4830563 DOI: 10.1371/journal.pone.0152431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 03/14/2016] [Indexed: 11/29/2022] Open
Abstract
Vertebrate MOXD2 encodes a monooxygenase DBH-like 2 protein that could be involved in neurotransmitter metabolism, potentially during olfactory transduction. Loss of MOXD2 in apes and whales has been proposed to be associated with evolution of olfaction in these clades. We analyzed 57 bird genomes to identify MOXD2 sequences and found frequent loss of MOXD2 in 38 birds. Among the 57 birds, 19 species appeared to have an intact MOXD2 that encoded a full-length protein; 32 birds had a gene with open reading frame-disrupting point mutations and/or exon deletions; and the remaining 6 species did not show any MOXD2 sequence, suggesting a whole-gene deletion. Notably, among 10 passerine birds examined, 9 species shared a common genomic deletion that spanned several exons, implying the gene loss occurred in a common ancestor of these birds. However, 2 closely related penguin species, each of which had an inactive MOXD2, did not share any mutation, suggesting an independent loss after their divergence. Distribution of the 38 birds without an intact MOXD2 in the bird phylogenetic tree clearly indicates that MOXD2 loss is widespread and independent in bird lineages. We propose that widespread MOXD2 loss in some bird lineages may be implicated in the evolution of olfactory perception in these birds.
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Affiliation(s)
- Chul Jun Goh
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Republic of Korea
| | - Dongjin Choi
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Republic of Korea
| | - Dong-Bin Park
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Republic of Korea
| | - Hyein Kim
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Republic of Korea
| | - Yoonsoo Hahn
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Republic of Korea
- * E-mail:
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Vandewege MW, Mangum SF, Gabaldón T, Castoe TA, Ray DA, Hoffmann FG. Contrasting Patterns of Evolutionary Diversification in the Olfactory Repertoires of Reptile and Bird Genomes. Genome Biol Evol 2016; 8:470-80. [PMID: 26865070 PMCID: PMC4825420 DOI: 10.1093/gbe/evw013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Olfactory receptors (ORs) are membrane proteins that mediate the detection of odorants in the environment, and are the largest vertebrate gene family. Comparative studies of mammalian genomes indicate that OR repertoires vary widely, even between closely related lineages, as a consequence of frequent OR gains and losses. Several studies also suggest that mammalian OR repertoires are influenced by life history traits. Sauropsida is a diverse group of vertebrates group that is the sister group to mammals, and includes birds, testudines, squamates, and crocodilians, and represents a natural system to explore predictions derived from mammalian studies. In this study, we analyzed olfactory receptor (OR) repertoire variation among several representative species and found that the number of intact OR genes in sauropsid genomes analyzed ranged over an order of magnitude, from 108 in the green anole to over 1,000 in turtles. Our results suggest that different sauropsid lineages have highly divergent OR repertoire composition that derive from lineage-specific combinations of gene expansions, losses, and retentions of ancestral OR genes. These differences also suggest that varying degrees of adaption related to life history have shaped the unique OR repertoires observed across sauropsid lineages.
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Affiliation(s)
- Michael W Vandewege
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University
| | - Sarah F Mangum
- Department of Biological Sciences, Texas Tech University
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington
| | - David A Ray
- Department of Biological Sciences, Texas Tech University
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Institute for Genomics, Biocomputing and Biochemistry, Mississippi State University
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Teeling EC, Jones G, Rossiter SJ. Phylogeny, Genes, and Hearing: Implications for the Evolution of Echolocation in Bats. BAT BIOACOUSTICS 2016. [DOI: 10.1007/978-1-4939-3527-7_2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Chemical fingerprints encode mother-offspring similarity, colony membership, relatedness, and genetic quality in fur seals. Proc Natl Acad Sci U S A 2015; 112:E5005-12. [PMID: 26261311 DOI: 10.1073/pnas.1506076112] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chemical communication underpins virtually all aspects of vertebrate social life, yet remains poorly understood because of its highly complex mechanistic basis. We therefore used chemical fingerprinting of skin swabs and genetic analysis to explore the chemical cues that may underlie mother-offspring recognition in colonially breeding Antarctic fur seals. By sampling mother-offspring pairs from two different colonies, using a variety of statistical approaches and genotyping a large panel of microsatellite loci, we show that colony membership, mother-offspring similarity, heterozygosity, and genetic relatedness are all chemically encoded. Moreover, chemical similarity between mothers and offspring reflects a combination of genetic and environmental influences, the former partly encoded by substances resembling known pheromones. Our findings reveal the diversity of information contained within chemical fingerprints and have implications for understanding mother-offspring communication, kin recognition, and mate choice.
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Khan I, Yang Z, Maldonado E, Li C, Zhang G, Gilbert MTP, Jarvis ED, O’Brien SJ, Johnson WE, Antunes A. Olfactory Receptor Subgenomes Linked with Broad Ecological Adaptations in Sauropsida. Mol Biol Evol 2015. [DOI: 10.1093/molbev/msv155] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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Whitlock KE. The loss of scents: do defects in olfactory sensory neuron development underlie human disease? ACTA ACUST UNITED AC 2015; 105:114-25. [PMID: 26111003 DOI: 10.1002/bdrc.21094] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 05/12/2015] [Indexed: 12/20/2022]
Abstract
The olfactory system is a fascinating and beguiling sensory system: olfactory sensory neurons detect odors underlying behaviors essential for mate choice, food selection, and escape from predators, among others. These sensory neurons are unique in that they have dendrites contacting the outside world, yet their first synapse lies in the central nervous system. The information entering the central nervous system is used to create odor memories that play a profound role in recognition of individuals, places, and appropriate foods. Here, the structure of the olfactory epithelium is given as an overview to discuss the origin of the olfactory placode, the plasticity of the olfactory sensory neurons, and finally the origins of the gonadotropin-releasing hormone neuroendocrine cells. For the purposes of this review, the development of the peripheral sensory system will be analyzed, incorporating recently published studies highlighting the potential novelties in development mechanisms. Specifically, an emerging model where the olfactory epithelium and olfactory bulb develop simultaneously from a continuous neurectoderm patterned at the end of gastrulation, and the multiple origins of the gonadotropin-releasing hormone neuroendocrine cells associated with the olfactory sensory system development will be presented. Advances in the understanding of the basic mechanisms underlying olfactory sensory system development allows for a more thorough understanding of the potential causes of human disease.
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Affiliation(s)
- Kathleen E Whitlock
- Centro Interdisciplinario de Neurociencia de Valparaíso (CINV), Facultad de Ciencias, Universidad de Valparaiso, Valparaiso, Chile
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Bird DJ, Amirkhanian A, Pang B, Van Valkenburgh B. Quantifying the cribriform plate: influences of allometry, function, and phylogeny in Carnivora. Anat Rec (Hoboken) 2015; 297:2080-92. [PMID: 25312366 DOI: 10.1002/ar.23032] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 06/25/2014] [Indexed: 11/12/2022]
Abstract
The small, perforated bony cup of the anterior cranial fossa called the cribriform plate (CP) is perhaps the best-preserved remnant of olfactory anatomy in fossil mammal skulls. The CP and its myriad foramina record the passage of peripheral olfactory nerves from nasal cavity to olfactory bulb. Previous work has suggested that CP surface area reflects aspects of olfactory capacity (as inferred from habitat and observed behavior) in mammals. To further explore the utility of CP as a proxy for olfactory function, we designed novel, nondestructive digital methods to quantify CP morphology from dry skulls. Using CT scans and 3-D imaging software, we quantified CP features from 42 species of Carnivora, a group that represents a wide spectrum of ecologies and sensory demands. Two metrics, CP surface area (CPSA) and cumulative CP foramina area (FXSA), scaled to skull length with negative allometry, and differed between aquatic and terrestrial species, with the former having reduced areas. Number of foramina (NF) was not correlated with skull length but tended to be greater in caniforms than feliforms. Both CPSA and FXSA are well correlated with ethmoturbinal surface area, a known osteological correlate of olfactory function. This suggests that CPSA and FXSA are useful proxies for olfactory ability, especially when studying fossils or skulls in which turbinals are not preserved. Total area of CP foramina (FXSA), an exacting measure of olfactory nerve endocasts, is tightly correlated with CPSA. Because of this, it may be desirable to use CPSA alone as a proxy given that it is easier to measure than FXSA.
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Affiliation(s)
- Deborah J Bird
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, California
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Berta A, Ekdale EG, Zellmer NT, Deméré TA, Kienle SS, Smallcomb M. Eye, nose, hair, and throat: external anatomy of the head of a neonate gray whale (Cetacea, Mysticeti, Eschrichtiidae). Anat Rec (Hoboken) 2015; 298:648-59. [PMID: 25737431 DOI: 10.1002/ar.23112] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 02/28/2014] [Accepted: 09/02/2014] [Indexed: 11/11/2022]
Abstract
Information is scarce on gray whale (Eschrichtius robustus) anatomy and that of mysticetes in general. Dissection of the head of a neonatal gray whale revealed novel anatomical details of the eye, blowhole, incisive papilla with associated nasopalatine ducts, sensory hairs, and throat grooves. Compared to a similar sized right whale calf, the gray whale eyeball is nearly twice as long. The nasal cartilages of the gray whale, located between the blowholes, differ from the bowhead in having accessory cartilages. A small, fleshy incisive papilla bordered by two blind nasopalatine pits near the palate's rostral tip, previously undescribed in gray whales, may be associated with the vomeronasal organ, although histological evidence is needed for definitive identification. Less well known among mysticetes are the numerous elongated, stiff sensory hairs (vibrissae) observed on the gray whale rostrum from the ventral tip to the blowhole and on the mandible. These hairs are concentrated on the chin, and those on the lower jaw are arranged in a V-shaped pattern. We confirm the presence of two primary, anteriorly converging throat grooves, confined to the throat region similar to those of ziphiid and physeteroid odontocetes. A third, shorter groove occurs lateral to the left primary groove. The throat grooves in the gray whale have been implicated in gular expansion during suction feeding.
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Affiliation(s)
- Annalisa Berta
- Department of Biology, San Diego State University, San Diego, California
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Kishida T, Thewissen JGM, Hayakawa T, Imai H, Agata K. Aquatic adaptation and the evolution of smell and taste in whales. ZOOLOGICAL LETTERS 2015; 1:9. [PMID: 26605054 PMCID: PMC4604112 DOI: 10.1186/s40851-014-0002-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 10/23/2014] [Indexed: 06/05/2023]
Abstract
INTRODUCTION While olfaction is one of the most important senses in most terrestrial mammals, it is absent in modern toothed whales (Odontoceti, Cetacea). Furthermore, behavioral evidence suggests that gustation is very limited. In contrast, their aquatic sistergroup, baleen whales (Mysticeti) retain small but functional olfactory organs, and nothing is known about their gustation. It is difficult to investigate mysticete chemosensory abilities because experiments in a controlled setting are impossible. RESULTS Here, we use the functional regionalization of the olfactory bulb (OB) to identify the loss of specific olfactory functions in mysticetes. We provide the whole-genome sequence of a mysticete and show that mysticetes lack the dorsal domain of the OB, an area known to induce innate avoidance behavior against odors of predators and spoiled foods. Genomic and fossil data suggest that mysticetes lost the dorsal domain of the OB before the Odontoceti-Mysticeti split. Furthermore, we found that all modern cetaceans are revealed to have lost the functional taste receptors. CONCLUSION These results strongly indicate that profound changes in the chemosensory capabilities had occurred in the cetacean lineage during the period when ancestral whales migrated from land to water.
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Affiliation(s)
- Takushi Kishida
- />Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo, Kyoto 606-8502 Japan
- />Present affiliation: Wildlife Research Center, Kyoto University, 2-24 Tanaka Sekiden-cho, Sakyo, Kyoto 606-8203 Japan
| | - JGM Thewissen
- />Department of Anatomy and Neurobiology, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH 44272 USA
| | - Takashi Hayakawa
- />Primate Research Institute, Kyoto University, Kanrin, Inuyama, Aichi 484-8506 Japan
- />Japan Society for the Promotion of Science, Kojimachi, Chiyoda, Tokyo 102-0083 Japan
| | - Hiroo Imai
- />Primate Research Institute, Kyoto University, Kanrin, Inuyama, Aichi 484-8506 Japan
| | - Kiyokazu Agata
- />Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo, Kyoto 606-8502 Japan
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Berta A, Ekdale EG, Cranford TW. Review of the Cetacean Nose: Form, Function, and Evolution. Anat Rec (Hoboken) 2014; 297:2205-15. [DOI: 10.1002/ar.23034] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 06/25/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Annalisa Berta
- Department of Biology; San Diego State University; San Diego California USA
| | - Eric G. Ekdale
- Department of Biology; San Diego State University; San Diego California USA
| | - Ted W. Cranford
- Department of Biology; San Diego State University; San Diego California USA
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Zhu K, Zhou X, Xu S, Sun D, Ren W, Zhou K, Yang G. The loss of taste genes in cetaceans. BMC Evol Biol 2014; 14:218. [PMID: 25305673 PMCID: PMC4232718 DOI: 10.1186/s12862-014-0218-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 10/02/2014] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Five basic taste modalities, sour, sweet, bitter, salt and umami, can be distinguished by humans and are fundamental for physical and ecological adaptations in mammals. Molecular genetic studies of the receptor genes for these tastes have been conducted in terrestrial mammals; however, little is known about the evolution and adaptation of these genes in marine mammals. RESULTS Here, all five basic taste modalities, sour, sweet, bitter, salt and umami, were investigated in cetaceans. The sequence characteristics and evolutionary analyses of taste receptor genes suggested that nearly all cetaceans may have lost all taste modalities except for that of salt. CONCLUSIONS This is the first study to comprehensively examine the five basic taste modalities in cetaceans with extensive taxa sampling. Our results suggest that cetaceans have lost four of the basic taste modalities including sour, sweet, umami, and most of the ability to sense bitter tastes. The integrity of the candidate salt taste receptor genes in all the cetaceans examined may be because of their function in Na(+) reabsorption, which is key to osmoregulation and aquatic adaptation.
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Affiliation(s)
- Kangli Zhu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Xuming Zhou
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Di Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Wenhua Ren
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Kaiya Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
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Kim DS, Wang Y, Oh HJ, Lee K, Hahn Y. Frequent loss and alteration of the MOXD2 gene in catarrhines and whales: a possible connection with the evolution of olfaction. PLoS One 2014; 9:e104085. [PMID: 25102179 PMCID: PMC4125168 DOI: 10.1371/journal.pone.0104085] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 07/08/2014] [Indexed: 11/18/2022] Open
Abstract
The MOXD2 gene encodes a membrane-bound monooxygenase similar to dopamine-β-hydroxylase, and has been proposed to be associated with olfaction. In this study, we analyzed MOXD2 genes from 64 mammalian species, and identified loss-of-function mutations in apes (humans, Sumatran and Bornean orangutans, and five gibbon species from the four major gibbon genera), toothed whales (killer whales, bottlenose dolphins, finless porpoises, baijis, and sperm whales), and baleen whales (minke whales and fin whales). We also identified a shared 13-nt deletion in the last exon of Old World cercopithecine monkeys that results in conversion of a membrane-bound protein to a soluble form. We hypothesize that the frequent inactivation and alteration of MOXD2 genes in catarrhines and whales may be associated with the evolution of olfaction in these clades.
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Affiliation(s)
- Dong Seon Kim
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Korea
| | - Yao Wang
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Korea
| | - Hye Ji Oh
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Korea
| | - Kangseok Lee
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Korea
| | - Yoonsoo Hahn
- Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Korea
- * E-mail:
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Niimura Y, Matsui A, Touhara K. Extreme expansion of the olfactory receptor gene repertoire in African elephants and evolutionary dynamics of orthologous gene groups in 13 placental mammals. Genome Res 2014; 24:1485-96. [PMID: 25053675 PMCID: PMC4158756 DOI: 10.1101/gr.169532.113] [Citation(s) in RCA: 210] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Olfactory receptors (ORs) detect odors in the environment, and OR genes constitute the largest multigene family in mammals. Numbers of OR genes vary greatly among species—reflecting the respective species' lifestyles—and this variation is caused by frequent gene gains and losses during evolution. However, whether the extent of gene gains/losses varies among individual gene lineages and what might generate such variation is unknown. To answer these questions, we used a newly developed phylogeny-based method to classify >10,000 intact OR genes from 13 placental mammal species into 781 orthologous gene groups (OGGs); we then compared the OGGs. Interestingly, African elephants had a surprisingly large repertoire (∼2000) of functional OR genes encoded in enlarged gene clusters. Additionally, OR gene lineages that experienced more gene duplication had weaker purifying selection, and Class II OR genes have evolved more dynamically than those in Class I. Some OGGs were highly expanded in a lineage-specific manner, while only three OGGs showed complete one-to-one orthology among the 13 species without any gene gains/losses. These three OGGs also exhibited highly conserved amino acid sequences; therefore, ORs in these OGGs may have physiologically important functions common to every placental mammal. This study provides a basis for inferring OR functions from evolutionary trajectory.
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Affiliation(s)
- Yoshihito Niimura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan; ERATO Touhara Chemosensory Signal Project, JST, The University of Tokyo, Tokyo 113-8657, Japan
| | - Atsushi Matsui
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan; ERATO Touhara Chemosensory Signal Project, JST, 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; ERATO Touhara Chemosensory Signal Project, JST, The University of Tokyo, Tokyo 113-8657, Japan
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McGowen MR, Gatesy J, Wildman DE. Molecular evolution tracks macroevolutionary transitions in Cetacea. Trends Ecol Evol 2014; 29:336-46. [DOI: 10.1016/j.tree.2014.04.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 04/02/2014] [Accepted: 04/03/2014] [Indexed: 10/25/2022]
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Stathopoulos S, Bishop JM, O’Ryan C. Genetic signatures for enhanced olfaction in the African mole-rats. PLoS One 2014; 9:e93336. [PMID: 24699281 PMCID: PMC3974769 DOI: 10.1371/journal.pone.0093336] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 03/03/2014] [Indexed: 01/06/2023] Open
Abstract
The Olfactory Receptor (OR) superfamily, the largest in the vertebrate genome, is responsible for vertebrate olfaction and is traditionally subdivided into 17 OR families. Recent studies characterising whole-OR subgenomes revealed a 'birth and death' model of evolution for a range of species, however little is known about fine-scale evolutionary dynamics within single-OR families. This study reports the first assessment of fine-scale OR evolution and variation in African mole-rats (Bathyergidae), a family of subterranean rodents endemic to sub-Saharan Africa. Because of the selective pressures of life underground, enhanced olfaction is proposed to be fundamental to the evolutionary success of the Bathyergidae, resulting in a highly diversified OR gene-repertoire. Using a PCR-sequencing approach, we analysed variation in the OR7 family across 14 extant bathyergid species, which revealed enhanced levels of functional polymorphisms concentrated across the receptors' ligand-binding region. We propose that mole-rats are able to recognise a broad range of odorants and that this diversity is reflected throughout their OR7 gene repertoire. Using both classic tests and tree-based methods to test for signals of selection, we investigate evolutionary forces across the mole-rat OR7 gene tree. Four well-supported clades emerged in the OR phylogeny, with varying signals of selection; from neutrality to positive and purifying selection. Bathyergid life-history traits and environmental niche-specialisation are explored as possible drivers of adaptive OR evolution, emerging as non-exclusive contributors to the positive selection observed at OR7 genes. Our results reveal unexpected complexity of evolutionary mechanisms acting within a single OR family, providing insightful perspectives into OR evolutionary dynamics.
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Affiliation(s)
- Sofia Stathopoulos
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, Western Cape, South Africa
- * E-mail:
| | - Jacqueline M. Bishop
- Department of Biological Sciences, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Colleen O’Ryan
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, Western Cape, South Africa
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The Genetic Basis of Primate Behavior: Genetics and Genomics in Field-Based Primatology. INT J PRIMATOL 2013; 35:1-10. [PMID: 25013243 DOI: 10.1007/s10764-013-9732-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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50
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Huggenberger S, André M, Oelschläger HHA. An acoustic valve within the nose of sperm whales Physeter macrocephalus. Mamm Rev 2013. [DOI: 10.1111/mam.12017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefan Huggenberger
- Cologne Biocentre; University of Cologne; Cologne 50923 Germany
- Department II of Anatomy; University of Cologne; Cologne 50924 Germany
| | - Michel André
- Laboratori d'Aplicacions Bioacústiques; Universitat Politècnica de Catalunya; Centre Tecnològic de Vilanova i la Geltrú, Avenida.Rambla Exposició, s/n, Vilanova i la Geltrú Barcelona 08800 Spain
| | - Helmut H. A. Oelschläger
- Department of Anatomy III (Dr. Senckenbergische Anatomie); Johann Wolfgang Goethe University Frankfurt am Main; Frankfurt am Main 60590 Germany
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