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Wang H, Liu Z, Yang H, Bai Y, Li Q, Qi X, Li D, Zhao X, Ma Y. Integrated transcriptomics and metabolomics reveal the molecular characteristics and metabolic regulatory mechanisms among different muscles in Minxian black fur sheep. BMC Genomics 2025; 26:412. [PMID: 40301745 PMCID: PMC12039146 DOI: 10.1186/s12864-025-11607-9] [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: 06/19/2024] [Accepted: 04/16/2025] [Indexed: 05/01/2025] Open
Abstract
BACKGROUND Mammalian skeletal muscle is comprised of heterogeneous fibers with various contractile and metabolic properties that affect muscle flavor. Thus, it is of great significance to identify and characterize the potential molecular characteristics and metabolic regulatory mechanisms associated with muscle fiber properties. RESULTS In this study, the muscle samples (Biceps femoris; longissimus dorsi; and infraspinatus) from Minxian black fur sheep were used to perform transcriptome and metabolome analyses. Then, the key genes regulating the metabolism of important flavor precursors (amino acids and lipids) were explored by integrating transcriptome and metabolome. Consequently, we identified 432 differentially expressed genes, which were mainly involved in muscle development and function maintenance (e.g., myofibril, myocyte differentiation, etc.), metabolism (e.g., fatty acid metabolism, arachidonic acid metabolism, PPAR signaling pathway, and PI3K-Akt signaling pathway, etc.), and homeostasis (e.g., regulation of actin cytoskeleton, ECM-receptor interaction, calcium signaling pathway, etc.). A total of 58 key genes affecting muscle fiber properties, including MYL2, HOXA/C/D, MYBPH8, MYH8, etc., were screened, which characterized the molecular differences in muscle fiber metabolic properties between oxidative and glycolytic muscle. Meanwhile, we identified 463 differentially accumulated metabolites. Except for glycerophospholipids, most flavor metabolites were higher in oxidative muscle. Subsequently, key genes highly related to flavor amino acids were identified by weighted gene co-expression network analysis, such as ALDH6A1, BCKDHB, SLC16A7, LDHB, etc. Based on KEGG enrichment analysis, a regulatory network with both lipid metabolism and its crosstalk with other metabolic pathways was constructed. CONCLUSIONS In conclusion, this study provides an in-depth understanding of the molecular mechanism of differences in muscle fiber properties among different muscles of Minxian black fur sheep, and also lays a foundation for further exploration of the regulatory mechanism of key genes on flavor metabolites.
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Affiliation(s)
- Huihui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070, China
| | - Zilong Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Hai Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yaqin Bai
- Animal Husbandry Technology Extension Station of Gansu Province, Lanzhou, 730030, China
| | - Qiao Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xingcai Qi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Dengpan Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xingxu Zhao
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070, China
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China
| | - Youji Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou, 730070, China.
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2
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Allard JB, Sharma S, Patel R, Sanderford M, Tamura K, Vucetic S, Gerhard GS, Kumar S. Evolutionary sparse learning reveals the shared genetic basis of convergent traits. Nat Commun 2025; 16:3217. [PMID: 40185716 PMCID: PMC11971283 DOI: 10.1038/s41467-025-58428-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 03/18/2025] [Indexed: 04/07/2025] Open
Abstract
Cases abound in which nearly identical traits have appeared in distant species facing similar environments. These unmistakable examples of adaptive evolution offer opportunities to gain insight into their genetic origins and mechanisms through comparative analyses. Here, we present an approach to build genetic models that underlie the independent origins of convergent traits using evolutionary sparse learning with paired species contrast (ESL-PSC). We tested the hypothesis that common genes and sites are involved in the convergent evolution of two key traits: C4 photosynthesis in grasses and echolocation in mammals. Genetic models were highly predictive of independent cases of convergent evolution of C4 photosynthesis. Genes contributing to genetic models for echolocation were highly enriched for functional categories related to hearing, sound perception, and deafness, a pattern that has eluded previous efforts applying standard molecular evolutionary approaches. These results support the involvement of sequence substitutions at common genetic loci in the evolution of convergent traits. Benchmarking on empirical and simulated datasets showed that ESL-PSC could be more sensitive in proteome-scale analyses to detect genes with convergent molecular evolution associated with the acquisition of convergent traits. We conclude that phylogeny-informed machine learning naturally excludes apparent molecular convergences due to shared species history, enhances the signal-to-noise ratio for detecting molecular convergence, and empowers the discovery of common genetic bases of trait convergences.
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Affiliation(s)
- John B Allard
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Sudip Sharma
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Ravi Patel
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Maxwell Sanderford
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - Koichiro Tamura
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
- Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Tokyo, Japan
| | - Slobodan Vucetic
- Department of Computer and Information Sciences, Temple University, Philadelphia, PA, USA
| | - Glenn S Gerhard
- Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA.
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.
- Department of Biology, Temple University, Philadelphia, PA, USA.
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Allard JB, Sharma S, Patel R, Sanderford M, Tamura K, Vucetic S, Gerhard GS, Kumar S. Evolutionary sparse learning with paired species contrast reveals the shared genetic basis of convergent traits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.08.631987. [PMID: 39829798 PMCID: PMC11741315 DOI: 10.1101/2025.01.08.631987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
Abstract
Cases abound in which nearly identical traits have appeared in distant species facing similar environments. These unmistakable examples of adaptive evolution offer opportunities to gain insight into their genetic origins and mechanisms through comparative analyses. Here, we present a novel comparative genomics approach to build genetic models that underlie the independent origins of convergent traits using evolutionary sparse learning. We test the hypothesis that common genes and sites are involved in the convergent evolution of two key traits: C4 photosynthesis in grasses and echolocation in mammals. Genetic models were highly predictive of independent cases of convergent evolution of C4 photosynthesis. These results support the involvement of sequence substitutions in many common genetic loci in the evolution of convergent traits studied. Genes contributing to genetic models for echolocation were highly enriched for functional categories related to hearing, sound perception, and deafness (P < 10-6); a pattern that has eluded previous efforts applying standard molecular evolutionary approaches. We conclude that phylogeny-informed machine learning naturally excludes apparent molecular convergences due to shared species history, enhances the signal-to-noise ratio for detecting molecular convergence, and empowers the discovery of common genetic bases of trait convergences.
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Affiliation(s)
- John B. Allard
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Sudip Sharma
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Ravi Patel
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Maxwell Sanderford
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Koichiro Tamura
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
- Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Tokyo, Japan
| | - Slobodan Vucetic
- Department of Computer and Information Sciences, Temple University, Philadelphia PA, United States of America
| | - Glenn S. Gerhard
- Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
- Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
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4
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Morales AE, Burbrink FT, Segall M, Meza M, Munegowda C, Webala PW, Patterson BD, Thong VD, Ruedi M, Hiller M, Simmons NB. Distinct Genes with Similar Functions Underlie Convergent Evolution in Myotis Bat Ecomorphs. Mol Biol Evol 2024; 41:msae165. [PMID: 39116340 PMCID: PMC11371419 DOI: 10.1093/molbev/msae165] [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: 09/08/2023] [Revised: 07/01/2024] [Accepted: 07/24/2024] [Indexed: 08/10/2024] Open
Abstract
Convergence offers an opportunity to explore to what extent evolution can be predictable when genomic composition and environmental triggers are similar. Here, we present an emergent model system to study convergent evolution in nature in a mammalian group, the bat genus Myotis. Three foraging strategies-gleaning, trawling, and aerial hawking, each characterized by different sets of phenotypic features-have evolved independently multiple times in different biogeographic regions in isolation for millions of years. To investigate the genomic basis of convergence and explore the functional genomic changes linked to ecomorphological convergence, we sequenced and annotated 17 new genomes and screened 16,426 genes for positive selection and associations between relative evolutionary rates and foraging strategies across 30 bat species representing all Myotis ecomorphs across geographic regions as well as among sister groups. We identify genomic changes that describe both phylogenetic and ecomorphological trends. We infer that colonization of new environments may have first required changes in genes linked to hearing sensory perception, followed by changes linked to fecundity and development, metabolism of carbohydrates, and heme degradation. These changes may be linked to prey acquisition and digestion and match phylogenetic trends. Our findings also suggest that the repeated evolution of ecomorphs does not always involve changes in the same genes but rather in genes with the same molecular functions such as developmental and cellular processes.
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Affiliation(s)
- Ariadna E Morales
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, USA
- Department of Herpetology, Division of Vertebrate Zoology, American Museum of Natural History, New York, USA
- Centre for Translational Biodiversity Genomics, Frankfurt am Main, Hessen, Germany
- Senckenberg Research Institute, Frankfurt am Main, Hessen, Germany
- Faculty of Biosciences, Goethe-University, Frankfurt am Main, Hessen, Germany
| | - Frank T Burbrink
- Department of Herpetology, Division of Vertebrate Zoology, American Museum of Natural History, New York, USA
| | - Marion Segall
- Department of Herpetology, Division of Vertebrate Zoology, American Museum of Natural History, New York, USA
- Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR 7205, Muséum National d’Histoire Naturelle, CNRS, SU, EPHE, UA, CP 50, Paris, France
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Maria Meza
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, USA
- Escuela de Biología, Universidad Industrial de Santander, Bucaramanga, Santander, Colombia
| | - Chetan Munegowda
- Centre for Translational Biodiversity Genomics, Frankfurt am Main, Hessen, Germany
- Senckenberg Research Institute, Frankfurt am Main, Hessen, Germany
- Faculty of Biosciences, Goethe-University, Frankfurt am Main, Hessen, Germany
| | - Paul W Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok 20500, Kenya
| | - Bruce D Patterson
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, USA
| | - Vu Dinh Thong
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay District, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Road, Cau Giay District, Hanoi, Vietnam
| | - Manuel Ruedi
- Department of Mammalogy and Ornithology, Natural History Museum of Geneva, Geneva 1208, Switzerland
| | - Michael Hiller
- Centre for Translational Biodiversity Genomics, Frankfurt am Main, Hessen, Germany
- Senckenberg Research Institute, Frankfurt am Main, Hessen, Germany
- Faculty of Biosciences, Goethe-University, Frankfurt am Main, Hessen, Germany
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, USA
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5
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Dong Z, Wang C, Qu Q. WGCCRR: a web-based tool for genome-wide screening of convergent indels and substitutions of amino acids. BIOINFORMATICS ADVANCES 2024; 4:vbae070. [PMID: 38808070 PMCID: PMC11132816 DOI: 10.1093/bioadv/vbae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 04/05/2024] [Accepted: 05/23/2024] [Indexed: 05/30/2024]
Abstract
Summary Genome-wide analyses of proteincoding gene sequences are being employed to examine the genetic basis of adaptive evolution in many organismal groups. Previous studies have revealed that convergent/parallel adaptive evolution may be caused by convergent/parallel amino acid changes. Similarly, detailed analysis of lineage-specific amino acid changes has shown correlations with certain lineage-specific traits. However, experimental validation remains the ultimate measure of causality. With the increasing availability of genomic data, a streamlined tool for such analyses would facilitate and expedite the screening of genetic loci that hold potential for adaptive evolution, while alleviating the bioinformatic burden for experimental biologists. In this study, we present a user-friendly web-based tool called WGCCRR (Whole Genome Comparative Coding Region Read) designed to screen both convergent/parallel and lineage-specific amino acid changes on a genome-wide scale. Our tool allows users to replicate previous analyses with just a few clicks, and the exported results are straightforward to interpret. In addition, we have also included amino acid indels that are usually neglected in previous work. Our website provides an efficient platform for screening candidate loci for downstream experimental tests. Availability and Implementation The tool is available at: https://fishevo.xmu.edu.cn/.
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Affiliation(s)
- Zheng Dong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xià-Mén, Fú-Jiàn 361102, China
| | - Chen Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xià-Mén, Fú-Jiàn 361102, China
| | - Qingming Qu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xià-Mén, Fú-Jiàn 361102, China
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6
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Morel M, Zhukova A, Lemoine F, Gascuel O. Accurate Detection of Convergent Mutations in Large Protein Alignments With ConDor. Genome Biol Evol 2024; 16:evae040. [PMID: 38451738 PMCID: PMC10986858 DOI: 10.1093/gbe/evae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 01/30/2024] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
Evolutionary convergences are observed at all levels, from phenotype to DNA and protein sequences, and changes at these different levels tend to be correlated. Notably, convergent mutations can lead to convergent changes in phenotype, such as changes in metabolism, drug resistance, and other adaptations to changing environments. We propose a two-component approach to detect mutations subject to convergent evolution in protein alignments. The "Emergence" component selects mutations that emerge more often than expected, while the "Correlation" component selects mutations that correlate with the convergent phenotype under study. With regard to Emergence, a phylogeny deduced from the alignment is provided by the user and is used to simulate the evolution of each alignment position. These simulations allow us to estimate the expected number of mutations in a neutral model, which is compared to the observed number of mutations in the data studied. In Correlation, a comparative phylogenetic approach, is used to measure whether the presence of each of the observed mutations is correlated with the convergent phenotype. Each component can be used on its own, for example Emergence when no phenotype is available. Our method is implemented in a standalone workflow and a webserver, called ConDor. We evaluate the properties of ConDor using simulated data, and we apply it to three real datasets: sedge PEPC proteins, HIV reverse transcriptase, and fish rhodopsin. The results show that the two components of ConDor complement each other, with an overall accuracy that compares favorably to other available tools, especially on large datasets.
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Affiliation(s)
- Marie Morel
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France
- Université Claude Bernard Lyon 1, LBBE, UMR 5558, CNRS, VAS, Villeurbanne, 69100, France
| | - Anna Zhukova
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Frédéric Lemoine
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
- Institut Pasteur, Université Paris Cité, CNR Virus Des Infections Respiratoires, Paris, France
| | - Olivier Gascuel
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, Paris, France
- Institut de Systématique, Evolution, Biodiversité (UMR 7205—CNRS, Muséum National d’Histoire Naturelle, SU, EPHE, UA), Paris, France
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7
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Usui K, Yamamoto T, Khannoon ER, Tokita M. Musculoskeletal morphogenesis supports the convergent evolution of bat laryngeal echolocation. Proc Biol Sci 2024; 291:20232196. [PMID: 38290542 PMCID: PMC10827442 DOI: 10.1098/rspb.2023.2196] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 12/18/2023] [Indexed: 02/01/2024] Open
Abstract
The order Chiroptera (bats) is the second largest group of mammals. One of the essential adaptations that have allowed bats to dominate the night skies is laryngeal echolocation, where bats emit ultrasonic pulses and listen to the returned echo to produce high-resolution 'images' of their surroundings. There are two possible scenarios for the evolutionary origin of laryngeal echolocation in bats: (1) a single origin in a common ancestor followed by the secondary loss in Pteropodidae, or (2) two convergent origins in Rhinolophoidea and Yangochiroptera. Although data from palaeontological, anatomical, developmental and genomic studies of auditory apparatuses exist, they remain inconclusive concerning the evolutionary origin of bat laryngeal echolocation. Here we compared musculoskeletal morphogenesis of the larynx in several chiropteran lineages and found distinct laryngeal modifications in two echolocating lineages, rhinolophoids and yangochiropterans. Our findings support the second scenario that rhinolophoids and yangochiropterans convergently evolved advanced laryngeal echolocation through anatomical modifications of the larynx for ultrasonic sound generation and refinement of the auditory apparatuses for more detailed sound perception.
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Affiliation(s)
- Kaoru Usui
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Tomoki Yamamoto
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Eraqi R. Khannoon
- Biology Department, College of Science, Taibah University, Al Madinah Al Munawwarah, PO Box 30002, Saudi Arabia
- Zoology Department, Faculty of Science, Fayoum University, Fayoum 63514, Egypt
| | - Masayoshi Tokita
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
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Sadanandan KR, Ko MC, Low GW, Gahr M, Edwards SV, Hiller M, Sackton TB, Rheindt FE, Sin SYW, Baldwin MW. Convergence in hearing-related genes between echolocating birds and mammals. Proc Natl Acad Sci U S A 2023; 120:e2307340120. [PMID: 37844245 PMCID: PMC10614615 DOI: 10.1073/pnas.2307340120] [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: 05/10/2023] [Accepted: 08/18/2023] [Indexed: 10/18/2023] Open
Abstract
Echolocation, the detection of objects by means of sound waves, has evolved independently in diverse animals. Echolocators include not only mammals such as toothed whales and yangochiropteran and rhinolophoid bats but also Rousettus fruit bats, as well as two bird lineages, oilbirds and swiftlets. In whales and yangochiropteran and rhinolophoid bats, positive selection and molecular convergence has been documented in key hearing-related genes, such as prestin (SLC26A5), but few studies have examined these loci in other echolocators. Here, we examine patterns of selection and convergence in echolocation-related genes in echolocating birds and Rousettus bats. Fewer of these loci were under selection in Rousettus or birds compared with classically recognized echolocators, and elevated convergence (compared to outgroups) was not evident across this gene set. In certain genes, however, we detected convergent substitutions with potential functional relevance, including convergence between Rousettus and classic echolocators in prestin at a site known to affect hair cell electromotility. We also detected convergence between Yangochiroptera, Rhinolophidea, and oilbirds in TMC1, an important mechanosensory transduction channel in vertebrate hair cells, and observed an amino acid change at the same site within the pore domain. Our results suggest that although most proteins implicated in echolocation in specialized mammals may not have been recruited in birds or Rousettus fruit bats, certain hearing-related loci may have undergone convergent functional changes. Investigating adaptations in diverse echolocators will deepen our understanding of this unusual sensory modality.
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Affiliation(s)
- Keren R. Sadanandan
- Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence, Seewiesen82319, Germany
| | - Meng-Ching Ko
- Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence, Seewiesen82319, Germany
| | - Gabriel W. Low
- Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence, Seewiesen82319, Germany
| | - Manfred Gahr
- Department of Behavioral Neurobiology, Max Planck Institute for Biological Intelligence, Seewiesen82319, Germany
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA02138
| | - Michael Hiller
- Centre for Translational Biodiversity Genomics, Frankfurt60325, Germany
| | - Timothy B. Sackton
- Informatics Group, Division of Science, Harvard University, Cambridge, MA02138
| | - Frank E. Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore117543, Singapore
| | - Simon Yung Wa Sin
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR999077, China
| | - Maude W. Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Biological Intelligence, Seewiesen82319, Germany
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9
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Vaglietti S, Villeri V, Dell’Oca M, Marchetti C, Cesano F, Rizzo F, Miller D, LaPierre L, Pelassa I, Monje FJ, Colnaghi L, Ghirardi M, Fiumara F. PolyQ length-based molecular encoding of vocalization frequency in FOXP2. iScience 2023; 26:108036. [PMID: 37860754 PMCID: PMC10582585 DOI: 10.1016/j.isci.2023.108036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/18/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
The transcription factor FOXP2, a regulator of vocalization- and speech/language-related phenotypes, contains two long polyQ repeats (Q1 and Q2) displaying marked, still enigmatic length variation across mammals. We found that the Q1/Q2 length ratio quantitatively encodes vocalization frequency ranges, from the infrasonic to the ultrasonic, displaying striking convergent evolution patterns. Thus, species emitting ultrasonic vocalizations converge with bats in having a low ratio, whereas species vocalizing in the low-frequency/infrasonic range converge with elephants and whales, which have higher ratios. Similar, taxon-specific patterns were observed for the FOXP2-related protein FOXP1. At the molecular level, we observed that the FOXP2 polyQ tracts form coiled coils, assembling into condensates and fibrils, and drive liquid-liquid phase separation (LLPS). By integrating evolutionary and molecular analyses, we found that polyQ length variation related to vocalization frequency impacts FOXP2 structure, LLPS, and transcriptional activity, thus defining a novel form of polyQ length-based molecular encoding of vocalization frequency.
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Affiliation(s)
- Serena Vaglietti
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Veronica Villeri
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Marco Dell’Oca
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Chiara Marchetti
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Federico Cesano
- Department of Chemistry, University of Turin, 10125 Turin, Italy
| | - Francesca Rizzo
- Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR 518057, China
| | - Dave Miller
- Cascades Pika Watch, Oregon Zoo, Portland, OR 97221, USA
| | - Louis LaPierre
- Deptartment of Natural Science, Lower Columbia College, Longview, WA 98632, USA
| | - Ilaria Pelassa
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Francisco J. Monje
- Department of Neurophysiology and Neuropharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Luca Colnaghi
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Mirella Ghirardi
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Ferdinando Fiumara
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
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10
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Madsen PT, Siebert U, Elemans CPH. Toothed whales use distinct vocal registers for echolocation and communication. Science 2023; 379:928-933. [PMID: 36862790 DOI: 10.1126/science.adc9570] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Echolocating toothed whales (odontocetes) capture fast-moving prey in dark marine environments, which critically depends on their ability to generate powerful, ultrasonic clicks. How their supposedly air-driven sound source can produce biosonar clicks at depths of >1000 meters, while also producing rich vocal repertoires to mediate complex social communication, remains unknown. We show that odontocetes possess a sound production system based on air driven through nasal passages that is functionally analogous to laryngeal and syringeal sound production. Tissue vibration in different registers produces distinct echolocation and communication signals across all major odontocete clades, and thus provides a physiological basis for classifying their vocal repertoires. The vocal fry register is used by species from porpoises to sperm whales for generating powerful, highly air-efficient echolocation clicks.
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Affiliation(s)
- Peter T Madsen
- Zoophysiology, Department of Biology, Aarhus University, 8000 Aarhus, Denmark
| | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, 25761 Büsum, Germany
| | - Coen P H Elemans
- Sound Communication and Behavior Group, Department of Biology, University of Southern Denmark, 5230 Odense M, Denmark
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11
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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: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [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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12
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Kemfack AM, Hernandez-Morato I, Moayedi Y, Pitman MJ. An optimized method for high-quality RNA extraction from distinctive intrinsic laryngeal muscles in the rat model. Sci Rep 2022; 12:21665. [PMID: 36522411 PMCID: PMC9755529 DOI: 10.1038/s41598-022-25643-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022] Open
Abstract
Challenges related to high-quality RNA extraction from post-mortem tissue have limited RNA-sequencing (RNA-seq) application in certain skeletal muscle groups, including the intrinsic laryngeal muscles (ILMs). The present study identified critical factors contributing to substandard RNA extraction from the ILMs and established a suitable method that permitted high-throughput analysis. Here, standard techniques for tissue processing were adapted, and an effective means to control confounding effects during specimen preparation was determined. The experimental procedure consistently provided sufficient intact total RNA (N = 68) and RIN ranging between 7.0 and 8.6, which was unprecedented using standard RNA purification protocols. This study confirmed the reproducibility of the workflow through repeated trials at different postnatal time points and across the distinctive ILMs. High-throughput diagnostics from 90 RNA samples indicated no sequencing alignment scores below 70%, validating the extraction strategy. Significant differences between the standard and experimental conditions suggest circumvented challenges and broad applicability to other skeletal muscles. This investigation remains ongoing given the prospect of therapeutic insights to voice, swallowing, and airway disorders. The present methodology supports pioneering global transcriptome investigations in the larynx previously unfounded in literature.
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Affiliation(s)
- Angela M Kemfack
- Department of Otolaryngology-Head & Neck Surgery, Columbia University College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Ignacio Hernandez-Morato
- Department of Otolaryngology-Head & Neck Surgery, Columbia University College of Physicians and Surgeons, New York, NY, 10032, USA.
| | - Yalda Moayedi
- Department of Otolaryngology-Head & Neck Surgery, Columbia University College of Physicians and Surgeons, New York, NY, 10032, USA
- Department of Neurology, Irving Medical Center, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Michael J Pitman
- Department of Otolaryngology-Head & Neck Surgery, Columbia University College of Physicians and Surgeons, New York, NY, 10032, USA
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13
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Abstract
Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.
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Affiliation(s)
- Christina Warinner
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Kristine Korzow Richter
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Matthew J. Collins
- Department
of Archaeology, Cambridge University, Cambridge CB2 3DZ, United Kingdom
- Section
for Evolutionary Genomics, Globe Institute,
University of Copenhagen, Copenhagen 1350, Denmark
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14
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Phenotyping in the era of genomics: MaTrics—a digital character matrix to document mammalian phenotypic traits. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00192-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractA new and uniquely structured matrix of mammalian phenotypes, MaTrics (Mammalian Traits for Comparative Genomics) in a digital form is presented. By focussing on mammalian species for which genome assemblies are available, MaTrics provides an interface between mammalogy and comparative genomics.MaTrics was developed within a project aimed to find genetic causes of phenotypic traits of mammals using Forward Genomics. This approach requires genomes and comprehensive and recorded information on homologous phenotypes that are coded as discrete categories in a matrix. MaTrics is an evolving online resource providing information on phenotypic traits in numeric code; traits are coded either as absent/present or with several states as multistate. The state record for each species is linked to at least one reference (e.g., literature, photographs, histological sections, CT scans, or museum specimens) and so MaTrics contributes to digitalization of museum collections. Currently, MaTrics covers 147 mammalian species and includes 231 characters related to structure, morphology, physiology, ecology, and ethology and available in a machine actionable NEXUS-format*. Filling MaTrics revealed substantial knowledge gaps, highlighting the need for phenotyping efforts. Studies based on selected data from MaTrics and using Forward Genomics identified associations between genes and certain phenotypes ranging from lifestyles (e.g., aquatic) to dietary specializations (e.g., herbivory, carnivory). These findings motivate the expansion of phenotyping in MaTrics by filling research gaps and by adding taxa and traits. Only databases like MaTrics will provide machine actionable information on phenotypic traits, an important limitation to genomics. MaTrics is available within the data repository Morph·D·Base (www.morphdbase.de).
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15
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Oteiza P, Baldwin MW. Evolution of sensory systems. Curr Opin Neurobiol 2021; 71:52-59. [PMID: 34600187 DOI: 10.1016/j.conb.2021.08.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/26/2021] [Indexed: 01/14/2023]
Abstract
Sensory systems evolve and enable organisms to perceive their sensory Umwelt, the unique set of cues relevant for their survival. The multiple components that comprise sensory systems - the receptors, cells, organs, and dedicated high-order circuits - can vary greatly across species. Sensory receptor gene families can expand and contract across lineages, resulting in enormous sensory diversity. Comparative studies of sensory receptor function have uncovered the molecular basis of receptor properties and identified novel sensory receptor classes and noncanonical sensory strategies. Phylogenetically informed comparisons of sensory systems across multiple species can pinpoint when sensory changes evolve and highlight the role of contingency in sensory system evolution.
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Affiliation(s)
- Pablo Oteiza
- Flow Sensing Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany.
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany.
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16
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A single mutation underlying phenotypic convergence for hypoxia adaptation on the Qinghai-Tibetan Plateau. Cell Res 2021; 31:1032-1035. [PMID: 34099886 PMCID: PMC8410794 DOI: 10.1038/s41422-021-00517-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 05/10/2021] [Indexed: 02/06/2023] Open
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17
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Alves LQ, Ruivo R, Fonseca MM, Lopes-Marques M, Ribeiro P, Castro L. PseudoChecker: an integrated online platform for gene inactivation inference. Nucleic Acids Res 2020; 48:W321-W331. [PMID: 32449938 PMCID: PMC7319564 DOI: 10.1093/nar/gkaa408] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/22/2020] [Accepted: 05/06/2020] [Indexed: 01/21/2023] Open
Abstract
The rapid expansion of high-quality genome assemblies, exemplified by ongoing initiatives such as the Genome-10K and i5k, demands novel automated methods to approach comparative genomics. Of these, the study of inactivating mutations in the coding region of genes, or pseudogenization, as a source of evolutionary novelty is mostly overlooked. Thus, to address such evolutionary/genomic events, a systematic, accurate and computationally automated approach is required. Here, we present PseudoChecker, the first integrated online platform for gene inactivation inference. Unlike the few existing methods, our comparative genomics-based approach displays full automation, a built-in graphical user interface and a novel index, PseudoIndex, for an empirical evaluation of the gene coding status. As a multi-platform online service, PseudoChecker simplifies access and usability, allowing a fast identification of disruptive mutations. An analysis of 30 genes previously reported to be eroded in mammals, and 30 viable genes from the same lineages, demonstrated that PseudoChecker was able to correctly infer 97% of loss events and 95% of functional genes, confirming its reliability. PseudoChecker is freely available, without login required, at http://pseudochecker.ciimar.up.pt.
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Affiliation(s)
- Luís Q Alves
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Matosinhos, 4450-208, Portugal
| | - Raquel Ruivo
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Matosinhos, 4450-208, Portugal
| | - Miguel M Fonseca
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Matosinhos, 4450-208, Portugal
| | - Mónica Lopes-Marques
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Matosinhos, 4450-208, Portugal
| | - Pedro Ribeiro
- CRACS & INESC-TEC Department of Computer Science, FCUP, Porto, 4169-007, Portugal
| | - L Filipe C Castro
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Matosinhos, 4450-208, Portugal
- Department of Biology, FCUP, Porto, 4169-007, Portugal
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18
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Gutiérrez-Guerrero YT, Ibarra-Laclette E, Martínez del Río C, Barrera-Redondo J, Rebollar EA, Ortega J, León-Paniagua L, Urrutia A, Aguirre-Planter E, Eguiarte LE. Genomic consequences of dietary diversification and parallel evolution due to nectarivory in leaf-nosed bats. Gigascience 2020; 9:giaa059. [PMID: 32510151 PMCID: PMC7276932 DOI: 10.1093/gigascience/giaa059] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/04/2020] [Accepted: 05/10/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The New World leaf-nosed bats (Phyllostomids) exhibit a diverse spectrum of feeding habits and innovations in their nutrient acquisition and foraging mechanisms. However, the genomic signatures associated with their distinct diets are unknown. RESULTS We conducted a genomic comparative analysis to study the evolutionary dynamics related to dietary diversification and specialization. We sequenced, assembled, and annotated the genomes of five Phyllostomid species: one insect feeder (Macrotus waterhousii), one fruit feeder (Artibeus jamaicensis), and three nectar feeders from the Glossophaginae subfamily (Leptonycteris yerbabuenae, Leptonycteris nivalis, and Musonycteris harrisoni), also including the previously sequenced vampire Desmodus rotundus. Our phylogenomic analysis based on 22,388 gene families displayed differences in expansion and contraction events across the Phyllostomid lineages. Independently of diet, genes relevant for feeding strategies and food intake experienced multiple expansions and signatures of positive selection. We also found adaptation signatures associated with specialized diets: the vampire exhibited traits associated with a blood diet (i.e., coagulation mechanisms), whereas the nectarivore clade shares a group of positively selected genes involved in sugar, lipid, and iron metabolism. Interestingly, in fruit-nectar-feeding Phyllostomid and Pteropodids bats, we detected positive selection in two genes: AACS and ALKBH7, which are crucial in sugar and fat metabolism. Moreover, in these two proteins we found parallel amino acid substitutions in conserved positions exclusive to the tribe Glossophagini and to Pteropodids. CONCLUSIONS Our findings illuminate the genomic and molecular shifts associated with the evolution of nectarivory and shed light on how nectar-feeding bats can avoid the adverse effects of diets with high glucose content.
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Affiliation(s)
- Yocelyn T Gutiérrez-Guerrero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, 04510 Coyoacán, Mexico City, Mexico
| | - Enrique Ibarra-Laclette
- Red de Estudios Moleculares Avanzados, Instituto de Ecología AC, 91070 Xalapa, Veracruz, Mexico
| | | | - Josué Barrera-Redondo
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, 04510 Coyoacán, Mexico City, Mexico
| | - Eria A Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Morelos, Mexico
| | - Jorge Ortega
- Departamento de Zoología, Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Instituto Politécnico Nacional-ENCB, 11340 Mexico City, Mexico
| | - Livia León-Paniagua
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Coyoacán, Mexico City, Mexico
| | - Araxi Urrutia
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, 04510 Coyoacán, Mexico City, Mexico
| | - Erika Aguirre-Planter
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, 04510 Coyoacán, Mexico City, Mexico
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, 04510 Coyoacán, Mexico City, Mexico
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19
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He Z, Xu S, Shi S. Adaptive convergence at the genomic level-prevalent, uncommon or very rare? Natl Sci Rev 2020; 7:947-951. [PMID: 34692116 PMCID: PMC8289048 DOI: 10.1093/nsr/nwaa076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 02/17/2020] [Accepted: 04/21/2020] [Indexed: 12/31/2022] Open
Affiliation(s)
- Ziwen He
- School of Life Sciences, Sun Yat-sen University, China
| | - Shaohua Xu
- School of Life Sciences, Sun Yat-sen University, China
| | - Suhua Shi
- School of Life Sciences, Sun Yat-sen University, China
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20
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Hao Y, Qu Y, Song G, Lei F. Genomic Insights into the Adaptive Convergent Evolution. Curr Genomics 2019; 20:81-89. [PMID: 31555059 PMCID: PMC6728901 DOI: 10.2174/1389202920666190313162702] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 01/10/2019] [Accepted: 03/07/2019] [Indexed: 11/22/2022] Open
Abstract
Adaptive convergent evolution, which refers to the same or similar phenotypes produced by species from independent lineages under similar selective pressures, has been widely examined for a long time. Accumulating studies on the adaptive convergent evolution have been reported from many different perspectives (cellular, anatomical, morphological, physiological, biochemical, and behavioral). Recent advances in the genomic technologies have demonstrated that adaptive convergence can arise from specific genetic mechanisms in different hierarchies, ranging from the same nucleotide or amino acid substitutions to the biological functions or pathways. Among these genetic mechanisms, the same amino acid changes in protein-coding genes play an important role in adaptive phenotypic convergence. Methods for detecting adaptive convergence at the protein sequence level have been constantly debated and developed. Here, we review recent progress on using genomic approaches to evaluate the genetic mechanisms of adaptive convergent evolution, summarize the research methods for identifying adaptive amino acid convergence, and discuss the future perspectives for researching adaptive convergent evolu-tion.
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Affiliation(s)
| | | | | | - Fumin Lei
- Address correspondence to this author at the Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, P.O. Box: 100101, Beijing, China; Fax: +86-10-64807159; E-mail:
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