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Webster CF, Smotherman M, Pippel M, Brown T, Winkler S, Pieri M, Mai M, Myers EW, Teeling EC, Vernes SC. The genome sequence of Tadarida brasiliensis I. Geoffroy Saint-Hilaire, 1824 [Molossidae; Tadarida]. Wellcome Open Res 2024; 9:98. [PMID: 38800517 PMCID: PMC11128047 DOI: 10.12688/wellcomeopenres.20603.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2024] [Indexed: 05/29/2024] Open
Abstract
We present a genome assembly from an individual male Tadarida brasiliensis (The Brazilian free-tailed bat; Chordata; Mammalia; Chiroptera; Molossidae). The genome sequence is 2.28 Gb in span. The majority of the assembly is scaffolded into 25 chromosomal pseudomolecules, with the X and Y sex chromosomes assembled.
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Affiliation(s)
- Cara F. Webster
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Michael Smotherman
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
- Center for Systems Biology, Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
- DRESDEN concept Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universitat, Dresden, 01307 Dresden, Germany
| | - Thomas Brown
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
- Center for Systems Biology, Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
- DRESDEN concept Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universitat, Dresden, 01307 Dresden, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
- Center for Systems Biology, Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
- DRESDEN concept Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universitat, Dresden, 01307 Dresden, Germany
| | - Myrtani Pieri
- Department of Life Sciences, School of Life and Health Sciences, University of Nicosia, Nicosia, Cyprus
| | - Meike Mai
- School of Biology, University of St Andrews, St Andrews, UK
| | - Eugene W. Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
- Center for Systems Biology, Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
- DRESDEN concept Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universitat, Dresden, 01307 Dresden, Germany
| | - Emma C. Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridgeshire, CB10 1SA, UK
| | - Sonja C. Vernes
- School of Biology, University of St Andrews, St Andrews, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - The Bat1K Consortium
- Department of Biology, Texas A&M University, College Station, Texas, USA
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
- Center for Systems Biology, Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
- DRESDEN concept Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universitat, Dresden, 01307 Dresden, Germany
- Department of Life Sciences, School of Life and Health Sciences, University of Nicosia, Nicosia, Cyprus
- School of Biology, University of St Andrews, St Andrews, UK
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridgeshire, CB10 1SA, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
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2
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Gordon WE, Baek S, Nguyen HP, Kuo YM, Bradley R, Fong SL, Kim N, Galazyuk A, Lee I, Ingala MR, Simmons NB, Schountz T, Cooper LN, Georgakopoulos-Soares I, Hemberg M, Ahituv N. Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas. Nat Commun 2024; 15:12. [PMID: 38195585 PMCID: PMC10776631 DOI: 10.1038/s41467-023-44186-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 12/03/2023] [Indexed: 01/11/2024] Open
Abstract
Frugivory evolved multiple times in mammals, including bats. However, the cellular and molecular components driving it remain largely unknown. Here, we use integrative single-cell sequencing (scRNA-seq and scATAC-seq) on insectivorous (Eptesicus fuscus; big brown bat) and frugivorous (Artibeus jamaicensis; Jamaican fruit bat) bat kidneys and pancreases and identify key cell population, gene expression and regulatory differences associated with the Jamaican fruit bat that also relate to human disease, particularly diabetes. We find a decrease in loop of Henle and an increase in collecting duct cells, and differentially active genes and regulatory elements involved in fluid and electrolyte balance in the Jamaican fruit bat kidney. The Jamaican fruit bat pancreas shows an increase in endocrine and a decrease in exocrine cells, and differences in genes and regulatory elements involved in insulin regulation. We also find that these frugivorous bats share several molecular characteristics with human diabetes. Combined, our work provides insights from a frugivorous mammal that could be leveraged for therapeutic purposes.
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Affiliation(s)
- Wei E Gordon
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA
- Department of Biology, Menlo College, 1000 El Camino Real, Atherton, CA, 94027, USA
| | - Seungbyn Baek
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Hai P Nguyen
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Yien-Ming Kuo
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Rachael Bradley
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Sarah L Fong
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Nayeon Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Alex Galazyuk
- Hearing Research Focus Area, Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH, USA
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
- POSTECH Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Melissa R Ingala
- Department of Biological Sciences, Fairleigh Dickinson University, Madison, NJ, 07940, USA
| | - Nancy B Simmons
- Division of Vertebrate Zoology, Department of Mammalogy, American Museum of Natural History, New York, NY, 10024, USA
| | - Tony Schountz
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Lisa Noelle Cooper
- Musculoskeletal Research Focus Area, Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH, 44272, USA
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Martin Hemberg
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94158, USA.
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3
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Yohe LR, Krell NT. An updated synthesis of and outstanding questions in the olfactory and vomeronasal systems in bats: Genetics asks questions only anatomy can answer. Anat Rec (Hoboken) 2023; 306:2765-2780. [PMID: 37523493 DOI: 10.1002/ar.25290] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 08/02/2023]
Abstract
The extensive diversity observed in bat nasal chemosensory systems has been well-documented at the histological level. Understanding how this diversity evolved and developing hypotheses as to why particular patterns exist require a phylogenetic perspective, which was first outlined in the work of anatomist Kunwar Bhatnagar. With the onset of genetics and genomics, it might be assumed that the puzzling patterns observed in the morphological data have been clarified. However, there is still a widespread mismatch of genetic and morphological correlations among bat chemosensory systems. Novel genomic evidence has set up new avenues to explore that demand more evidence from anatomical structures. Here, we outline the progress that has been made in both morphological and molecular studies on the olfactory and vomeronasal systems in bats since the work of Bhatnagar. Genomic data of olfactory and vomeronasal receptors demonstrate the strong need for further morphological sampling, with a particular focus on receiving brain regions, glands, and ducts.
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Affiliation(s)
- Laurel R Yohe
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
- North Carolina Research Campus, Kannapolis, North Carolina, USA
| | - Nicholas T Krell
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
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4
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Mutumi GL, Hall RP, Hedrick BP, Yohe LR, Sadier A, Davies KTJ, Rossiter SJ, Sears KE, Dávalos LM, Dumont ER. Disentangling Mechanical and Sensory Modules in the Radiation of Noctilionoid Bats. Am Nat 2023; 202:216-230. [PMID: 37531274 DOI: 10.1086/725368] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
AbstractWith diverse mechanical and sensory functions, the vertebrate cranium is a complex anatomical structure whose shifts between modularity and integration, especially in mechanical function, have been implicated in adaptive diversification. Yet how mechanical and sensory systems and their functions coevolve, as well as how their interrelationship contributes to phenotypic disparity, remain largely unexplored. To examine the modularity, integration, and evolutionary rates of sensory and mechanical structures within the head, we analyzed hard and soft tissue scans from ecologically diverse bats in the superfamily Noctilionoidea, a clade that ranges from insectivores and carnivores to frugivores and nectarivores. We identified eight regions that evolved in a coordinated fashion, thus recognizable as evolutionary modules: five associated with bite force and three linked to olfactory, visual, and auditory systems. Interrelationships among these modules differ between Neotropical leaf-nosed bats (family Phyllostomidae) and other noctilionoids. Consistent with the hypothesis that dietary transitions begin with changes in the capacity to detect novel food items followed by adaptations to process them, peak rates of sensory module evolution predate those of some mechanical modules. We propose that the coevolution of structures influencing bite force, olfaction, vision, and hearing constituted a structural opportunity that allowed the phyllostomid ancestor to take advantage of existing ecological opportunities and contributed to the clade's remarkable radiation.
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5
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Winchell KM, Losos JB, Verrelli BC. Urban evolutionary ecology brings exaptation back into focus. Trends Ecol Evol 2023:S0169-5347(23)00060-5. [PMID: 37024381 DOI: 10.1016/j.tree.2023.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/12/2023] [Accepted: 03/14/2023] [Indexed: 04/08/2023]
Abstract
The contribution of pre-existing phenotypic variation to evolution in novel environments has long been appreciated. Nevertheless, evolutionary ecologists have struggled with communicating these aspects of the adaptive process. In 1982, Gould and Vrba proposed terminology to distinguish character states shaped via natural selection for the roles they currently serve ('adaptations') from those shaped under preceding selective regimes ('exaptations'), with the intention of replacing the inaccurate 'preadaptation'. Forty years later, we revisit Gould and Vrba's ideas which, while often controversial, continue to be widely debated and highly cited. We use the recent emergence of urban evolutionary ecology as a timely opportunity to reintroduce the ideas of Gould and Vrba as an integrated framework to understand contemporary evolution in novel environments.
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Affiliation(s)
- Kristin M Winchell
- Department of Biology, New York University, New York, NY 10003, USA; Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA; Department of Biology, Washington University, St Louis, MO 63130, USA.
| | - Jonathan B Losos
- Department of Biology, Washington University, St Louis, MO 63130, USA
| | - Brian C Verrelli
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA 23284, USA
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6
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Gordon WE, Baek S, Nguyen HP, Kuo YM, Bradley R, Galazyuk A, Lee I, Ingala MR, Simmons NB, Schountz T, Cooper LN, Georgakopoulos-Soares I, Hemberg M, Ahituv N. Integrative single-cell characterization of frugivory adaptations in the bat kidney and pancreas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.12.528204. [PMID: 36824791 PMCID: PMC9949079 DOI: 10.1101/2023.02.12.528204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Frugivory evolved multiple times in mammals, including bats. However, the cellular and molecular components driving it remain largely unknown. Here, we used integrative single-cell sequencing on insectivorous and frugivorous bat kidneys and pancreases and identified key cell population, gene expression and regulatory element differences associated with frugivorous adaptation that also relate to human disease, particularly diabetes. We found an increase in collecting duct cells and differentially active genes and regulatory elements involved in fluid and electrolyte balance in the frugivore kidney. In the frugivorous pancreas, we observed an increase in endocrine and a decrease in exocrine cells and differences in genes and regulatory elements involved in insulin regulation. Combined, our work provides novel insights into frugivorous adaptation that also could be leveraged for therapeutic purposes.
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7
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Luo H, Luo S, Fang W, Lin Q, Chen X, Zhou X. Genomic insight into the nocturnal adaptation of the black-crowned night heron (Nycticorax nycticorax). BMC Genomics 2022; 23:683. [PMID: 36192687 PMCID: PMC9531477 DOI: 10.1186/s12864-022-08904-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The black-crowned night heron (Nycticorax nycticorax) is an ardeid bird successfully adapted to the nocturnal environment. Previous studies had indicated that the eyes of the night herons have evolved several specialized morphological traits favoring nocturnal vision. However, the molecular mechanisms of the nocturnal vision adaptation of night herons remained inattentions. In this study, the whole genome of N. nycticorax was sequenced and comparative analyses were performed on the vision-related and olfactory receptor (OR) genes to understand the molecular mechanisms of the visual and olfactory adaptation of night herons. RESULTS The results indicated that a number of vision genes were under positive or relaxed selection in N. nycticorax, whereas a number of other vision genes were under relaxed or intensified selection in the boat-billed heron (Cochlearius cochlearius), which suggested that the two species adapt to nocturnality with different genetic mechanisms. The different selections acting on vision genes are probably associated with the enlargement of eye size and the enhancement of visual sensitivity in night herons. The analyses on olfactory receptor (OR) genes indicated that the total number of OR genes in the genomes of N. nycticorax and C. cochlearius were about half those in the little egret (Egretta garzetta), whereas the diversity of their OR genes was not remarkably different. Additionally, the number of expressed OR genes in the transcriptomes of N. nycticorax was also fewer than that in E. garzetta. These results suggest a reduced olfactory capability in night herons compared with E. garzetta. CONCLUSIONS Our results provided evidence that several vision genes of the night herons were subjected to different natural selections, which can contribute to a better understanding of the genetic mechanisms of visual adaptions of the night heron. In addition, the finding of the reduced number of total and expressed OR genes in night herons may reflect a trade-off between olfaction and vision.
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Affiliation(s)
- Haoran Luo
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Site Luo
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Wenzhen Fang
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Qingxian Lin
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China
| | - Xiaolin Chen
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China.
| | - Xiaoping Zhou
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, People's Republic of China.
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8
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Yohe LR, Fabbri M, Lee D, Davies KTJ, Yohe TP, Sánchez MKR, Rengifo EM, Hall RP, Mutumi G, Hedrick BP, Sadier A, Simmons NB, Sears KE, Dumont E, Rossiter SJ, Bhullar BAS, Dávalos LM. Ecological constraints on highly evolvable olfactory receptor genes and morphology in neotropical bats. Evolution 2022; 76:2347-2360. [PMID: 35904467 DOI: 10.1111/evo.14591] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 05/06/2022] [Accepted: 05/13/2022] [Indexed: 01/22/2023]
Abstract
Although evolvability of genes and traits may promote specialization during species diversification, how ecology subsequently restricts such variation remains unclear. Chemosensation requires animals to decipher a complex chemical background to locate fitness-related resources, and thus the underlying genomic architecture and morphology must cope with constant exposure to a changing odorant landscape; detecting adaptation amidst extensive chemosensory diversity is an open challenge. In phyllostomid bats, an ecologically diverse clade that evolved plant visiting from a presumed insectivorous ancestor, the evolution of novel food detection mechanisms is suggested to be a key innovation, as plant-visiting species rely strongly on olfaction, supplementarily using echolocation. If this is true, exceptional variation in underlying olfactory genes and phenotypes may have preceded dietary diversification. We compared olfactory receptor (OR) genes sequenced from olfactory epithelium transcriptomes and olfactory epithelium surface area of bats with differing diets. Surprisingly, although OR evolution rates were quite variable and generally high, they are largely independent of diet. Olfactory epithelial surface area, however, is relatively larger in plant-visiting bats and there is an inverse relationship between OR evolution rates and surface area. Relatively larger surface areas suggest greater reliance on olfactory detection and stronger constraint on maintaining an already diverse OR repertoire. Instead of the typical case in which specialization and elaboration are coupled with rapid diversification of associated genes, here the relevant genes are already evolving so quickly that increased reliance on smell has led to stabilizing selection, presumably to maintain the ability to consistently discriminate among specific odorants-a potential ecological constraint on sensory evolution.
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Affiliation(s)
- Laurel R Yohe
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, 06511, USA.,Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794, USA.,Deaprtment of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, 28223, USA.,North Carolina Research Campus, Kannapolis, North Carolina, 28081, USA
| | - Matteo Fabbri
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, 06511, USA.,Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois, 60605, USA
| | - Daniela Lee
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, 06511, USA.,Harvard School of Medicine, Cambridge, Massachusetts, 02115, USA
| | - Kalina T J Davies
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom
| | | | - Miluska K R Sánchez
- Escuela Profesional de Ciencias Biológicas, Universidad Nacional de Piura, Piura, 20004, Peru
| | - Edgardo M Rengifo
- Programa de Pós-Graduação Interunidades em Ecologia Aplicada, Escola Superior de Agricultura 'Luiz de Queiroz', Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, 13416-970, Brazil.,Centro de Investigación Biodiversidad Sostenible (BioS), Lima, 15073, Peru
| | - Ronald P Hall
- School of Natural Sciences, University of California, Merced, Merced, California, 95344, USA
| | - Gregory Mutumi
- School of Natural Sciences, University of California, Merced, Merced, California, 95344, USA
| | - Brandon P Hedrick
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, 14853, USA
| | - Alexa Sadier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, 90095, USA
| | - Nancy B Simmons
- Department of Mammalogy, American Museum of Natural History, New York, New York, 10024, USA
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, 90095, USA
| | - Elizabeth Dumont
- School of Natural Sciences, University of California, Merced, Merced, California, 95344, USA
| | - Stephen J Rossiter
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom
| | - Bhart-Anjan S Bhullar
- Department of Earth and Planetary Sciences, Yale University, New Haven, Connecticut, 06511, USA.,Yale Peabody Museum of Natural History, Yale University, New Haven, Connecticut, 06511, USA
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794, USA.,Center for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, New York, 11794, USA
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9
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Cornman RS, Cryan PM. Positively selected genes in the hoary bat ( Lasiurus cinereus) lineage: prominence of thymus expression, immune and metabolic function, and regions of ancient synteny. PeerJ 2022; 10:e13130. [PMID: 35317076 PMCID: PMC8934532 DOI: 10.7717/peerj.13130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 02/25/2022] [Indexed: 01/12/2023] Open
Abstract
Background Bats of the genus Lasiurus occur throughout the Americas and have diversified into at least 20 species among three subgenera. The hoary bat (Lasiurus cinereus) is highly migratory and ranges farther across North America than any other wild mammal. Despite the ecological importance of this species as a major insect predator, and the particular susceptibility of lasiurine bats to wind turbine strikes, our understanding of hoary bat ecology, physiology, and behavior remains poor. Methods To better understand adaptive evolution in this lineage, we used whole-genome sequencing to identify protein-coding sequence and explore signatures of positive selection. Gene models were predicted with Maker and compared to seven well-annotated and phylogenetically representative species. Evolutionary rate analysis was performed with PAML. Results Of 9,447 single-copy orthologous groups that met evaluation criteria, 150 genes had a significant excess of nonsynonymous substitutions along the L. cinereus branch (P < 0.001 after manual review of alignments). Selected genes as a group had biased expression, most strongly in thymus tissue. We identified 23 selected genes with reported immune functions as well as a divergent paralog of Steep1 within suborder Yangochiroptera. Seventeen genes had roles in lipid and glucose metabolic pathways, partially overlapping with 15 mitochondrion-associated genes; these adaptations may reflect the metabolic challenges of hibernation, long-distance migration, and seasonal variation in prey abundance. The genomic distribution of positively selected genes differed significantly from background expectation by discrete Kolmogorov-Smirnov test (P < 0.001). Remarkably, the top three physical clusters all coincided with islands of conserved synteny predating Mammalia, the largest of which shares synteny with the human cat-eye critical region (CECR) on 22q11. This observation coupled with the expansion of a novel Tbx1-like gene family may indicate evolutionary innovation during pharyngeal arch development: both the CECR and Tbx1 cause dosage-dependent congenital abnormalities in thymus, heart, and head, and craniodysmorphy is associated with human orthologs of other positively selected genes as well.
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10
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Potter JHT, Davies KTJ, Yohe LR, Sanchez MKR, Rengifo EM, Struebig M, Warren K, Tsagkogeorga G, Lim BK, dos Reis M, Dávalos LM, Rossiter SJ. Dietary Diversification and Specialization in Neotropical Bats Facilitated by Early Molecular Evolution. Mol Biol Evol 2021; 38:3864-3883. [PMID: 34426843 PMCID: PMC8382914 DOI: 10.1093/molbev/msab028] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Dietary adaptation is a major feature of phenotypic and ecological diversification, yet the genetic basis of dietary shifts is poorly understood. Among mammals, Neotropical leaf-nosed bats (family Phyllostomidae) show unmatched diversity in diet; from a putative insectivorous ancestor, phyllostomids have radiated to specialize on diverse food sources including blood, nectar, and fruit. To assess whether dietary diversification in this group was accompanied by molecular adaptations for changing metabolic demands, we sequenced 89 transcriptomes across 58 species and combined these with published data to compare ∼13,000 protein coding genes across 66 species. We tested for positive selection on focal lineages, including those inferred to have undergone dietary shifts. Unexpectedly, we found a broad signature of positive selection in the ancestral phyllostomid branch, spanning genes implicated in the metabolism of all major macronutrients, yet few positively selected genes at the inferred switch to plantivory. Branches corresponding to blood- and nectar-based diets showed selection in loci underpinning nitrogenous waste excretion and glycolysis, respectively. Intriguingly, patterns of selection in metabolism genes were mirrored by those in loci implicated in craniofacial remodeling, a trait previously linked to phyllostomid dietary specialization. Finally, we show that the null model of the widely-used branch-site test is likely to be misspecified, with the implication that the test is too conservative and probably under-reports true cases of positive selection. Our findings point to a complex picture of adaptive radiation, in which the evolution of new dietary specializations has been facilitated by early adaptations combined with the generation of new genetic variation.
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Affiliation(s)
- Joshua H T Potter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Kalina T J Davies
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Laurel R Yohe
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Department of Earth and Planetary Science, Yale University, 210 Whitney Ave, New Haven, CT, USA
| | - Miluska K R Sanchez
- Escuela Profesional de Ciencias Biológicas, Universidad Nacional de Piura, Piura, Peru
| | - Edgardo M Rengifo
- Escola Superior de Agricultura ‘Luiz de Queiroz,’ Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, Brazil
- Centro de Investigación Biodiversidad Sostenible (BioS), Lima, Peru
| | - Monika Struebig
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Kim Warren
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Mario dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY, USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
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11
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Moreno Santillán DD, Lama TM, Gutierrez Guerrero YT, Brown AM, Donat P, Zhao H, Rossiter SJ, Yohe LR, Potter JH, Teeling EC, Vernes SC, Davies KTJ, Myers E, Hughes GM, Huang Z, Hoffmann F, Corthals AP, Ray DA, Dávalos LM. Large-scale genome sampling reveals unique immunity and metabolic adaptations in bats. Mol Ecol 2021; 30:6449-6467. [PMID: 34146369 DOI: 10.1111/mec.16027] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 05/27/2021] [Accepted: 06/03/2021] [Indexed: 11/28/2022]
Abstract
Comprising more than 1,400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species, one generated in this study, encompassing a large number of lineages, with a particular emphasis on multi-gene family evolution across immune and metabolic genes. In agreement with previous analyses, we found lineage-specific expansions of the APOBEC3 and MHC-I gene families, and loss of the proinflammatory PYHIN gene family. We inferred more than 1,000 gene losses unique to bats, including genes involved in the regulation of inflammasome pathways such as epithelial defence receptors, the natural killer gene complex and the interferon-gamma induced pathway. Gene set enrichment analyses revealed genes lost in bats are involved in defence response against pathogen-associated molecular patterns and damage-associated molecular patterns. Gene family evolution and selection analyses indicate bats have evolved fundamental functional differences compared to other mammals in both innate and adaptive immune system, with the potential to enhance antiviral immune response while dampening inflammatory signalling. In addition, metabolic genes have experienced repeated expansions related to convergent shifts to plant-based diets. Our analyses support the hypothesis that, in tandem with flight, ancestral bats had evolved a unique set of immune adaptations whose functional implications remain to be explored.
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Affiliation(s)
| | - Tanya M Lama
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Yocelyn T Gutierrez Guerrero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, Mexico City, Mexico
| | - Alexis M Brown
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Paul Donat
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Huabin Zhao
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Laurel R Yohe
- Department of Earth & Planetary Science, Yale University, New Haven, Connecticut, USA
| | - Joshua H Potter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Sonja C Vernes
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.,School of Biology, The University of St Andrews, Fife, UK
| | - Kalina T J Davies
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Eugene Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Graham M Hughes
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Zixia Huang
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Federico Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, USA
| | - Angelique P Corthals
- Department of Sciences, John Jay College of Criminal Justice, New York, New York, USA
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA.,Consortium for Inter- Disciplinary Environmental Research, Stony Brook University, Stony Brook, New York, USA
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12
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Domingos-Melo A, de Brito VLG, Sérsic A, Cocucci AA, Lunau K, Machado IC. Shining bright in the dusk: How do bat-pollinated flowers reflect light? Ecology 2021; 102:e03416. [PMID: 34042173 DOI: 10.1002/ecy.3416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/05/2021] [Accepted: 03/16/2021] [Indexed: 11/07/2022]
Affiliation(s)
- Arthur Domingos-Melo
- Department of Botany, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | | | - Alicia Sérsic
- Instituto Multidisciplinario de Biología Vegetal, Universidad Nacional de Córdoba, CONICET, Córdoba, Argentina
| | - Andrea A Cocucci
- Instituto Multidisciplinario de Biología Vegetal, Universidad Nacional de Córdoba, CONICET, Córdoba, Argentina
| | - Klaus Lunau
- Institute of Sensory Ecology, Heinrich-Heine-University, Dusseldorf, Germany
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13
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Sadier A, Urban DJ, Anthwal N, Howenstine AO, Sinha I, Sears KE. Making a bat: The developmental basis of bat evolution. Genet Mol Biol 2021; 43:e20190146. [PMID: 33576369 PMCID: PMC7879332 DOI: 10.1590/1678-4685-gmb-2019-0146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 12/11/2020] [Indexed: 11/28/2022] Open
Abstract
Bats are incredibly diverse, both morphologically and taxonomically. Bats are the only mammalian group to have achieved powered flight, an adaptation that is hypothesized to have allowed them to colonize various and diverse ecological niches. However, the lack of fossils capturing the transition from terrestrial mammal to volant chiropteran has obscured much of our understanding of bat evolution. Over the last 20 years, the emergence of evo-devo in non-model species has started to fill this gap by uncovering some developmental mechanisms at the origin of bat diversification. In this review, we highlight key aspects of studies that have used bats as a model for morphological adaptations, diversification during adaptive radiations, and morphological novelty. To do so, we review current and ongoing studies on bat evolution. We first investigate morphological specialization by reviewing current knowledge about wing and face evolution. Then, we explore the mechanisms behind adaptive diversification in various ecological contexts using vision and dentition. Finally, we highlight the emerging work into morphological novelties using bat wing membranes.
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Affiliation(s)
- Alexa Sadier
- University of California at Los Angeles, Department of Ecology and Evolutionary Biology, Los Angeles, USA
| | - Daniel J Urban
- University of California at Los Angeles, Department of Ecology and Evolutionary Biology, Los Angeles, USA.,American Museum of Natural History, Department of Mammalogy, New York, USA
| | - Neal Anthwal
- University of California at Los Angeles, Department of Ecology and Evolutionary Biology, Los Angeles, USA
| | - Aidan O Howenstine
- University of California at Los Angeles, Department of Ecology and Evolutionary Biology, Los Angeles, USA
| | - Ishani Sinha
- University of California at Los Angeles, Department of Ecology and Evolutionary Biology, Los Angeles, USA
| | - Karen E Sears
- University of California at Los Angeles, Department of Ecology and Evolutionary Biology, Los Angeles, USA
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