1
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Wang W, Dong Z, Du Z, Wu P. Genome-scale approach to reconstructing the phylogenetic tree of psyllids (superfamily Psylloidea) with account of systematic bias. Mol Phylogenet Evol 2023; 189:107924. [PMID: 37699449 DOI: 10.1016/j.ympev.2023.107924] [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: 05/17/2023] [Revised: 09/05/2023] [Accepted: 09/09/2023] [Indexed: 09/14/2023]
Abstract
Psyllids (class Insecta: order Hemiptera: superfamily Psylloidea) are a taxonomically and phylogenetically challenging clade. Recent studies have largely advanced the phylogeny of this group, yet the family-level relationships among Aphalaridae, Carsidaridae, and others remain unresolved. Genome-scale phylogenetic analysis is known to provide a finer resolution for problems like that. However, such phylogenomics also introduces new problems: incorrect trees with high confidence yielded due to systematic error (bias). Here we addressed these issues using hundreds of single-copy orthologous (SCO) genes in psyllid transcriptomes and genomes. Our analyses revealed conflicts between the nucleotide-based and amino-acid-based phylogenetic trees. While the nucleotide-based phylogeny strongly supported the (Aphalaridae + Carsidaridae) + Others relationship, the amino-acid-based one recovered Aphalaridae + (Carsidaridae + Others) with 100% support. Further inspection revealed significant compositional heterogeneity in nucleotide sequences for 67% of SCO genes, but not in the corresponding translated amino acid sequences. We then used different strategies to combat this compositional bias, and found that using the RY-coding strategy (coding the standard nucleotides as purines and pyrimidines) the nucleotide-based phylogeny became consistent with the amino-acid-based one. We further applied RY-coding to a published concatenated nucleotide dataset and recovered the Aphalaridae monophyly (which is refuted by the original literature on non-recoded sequences) at the base of psyllid tree. Moreover, it was found that variations in evolutionary rate could lead to errors in nucleotide-based phylogeny. The fast-evolving Heteropsylla cubana (Psyllidae: Ciriacreminae) was incorrectly placed within the subfamily Psyllinae. This bias can be avoided by using data removal or RY-coding strategies. Together, our results strongly support the family relationship of Aphalaridae + (Carsidaridae + Others), and show that the amino-acid-based concatenation analysis is more robust than nucleotide-based one. Future phylogenomic analysis of psyllid nucleotide sequences should take into account methods such as the RY-coding scheme to address potential systematic biases arising from composition and rate heterogeneities.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zequn Dong
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhong Du
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengxiang Wu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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2
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Liu GM, Pan Q, Du J, Zhu PF, Liu WQ, Li ZH, Wang L, Hu CY, Dai YC, Zhang XX, Zhang Z, Yu Y, Li M, Wang PC, Wang X, Li M, Zhou XM. Improved mammalian family phylogeny using gap-rare multiple sequence alignment: A timetree of extant placentals and marsupials. Zool Res 2023; 44:1064-1079. [PMID: 37914522 PMCID: PMC10802097 DOI: 10.24272/j.issn.2095-8137.2023.189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/23/2023] [Indexed: 11/03/2023] Open
Abstract
The timing of mammalian diversification in relation to the Cretaceous-Paleogene (KPg) mass extinction continues to be a subject of substantial debate. Previous studies have either focused on limited taxonomic samples with available whole-genome data or relied on short sequence alignments coupled with extensive species samples. In the present study, we improved an existing dataset from the landmark study of Meredith et al. (2011) by filling in missing fragments and further generated another dataset containing 120 taxa and 98 exonic markers. Using these two datasets, we then constructed phylogenies for extant mammalian families, providing improved resolution of many conflicting relationships. Moreover, the timetrees generated, which were calibrated using appropriate molecular clock models and multiple fossil records, indicated that the interordinal diversification of placental mammals initiated before the Late Cretaceous period. Additionally, intraordinal diversification of both extant placental and marsupial lineages accelerated after the KPg boundary, supporting the hypothesis that the availability of numerous vacant ecological niches subsequent to the mass extinction event facilitated rapid diversification. Thus, our results support a scenario of placental radiation characterized by both basal cladogenesis and active interordinal divergences spanning from the Late Cretaceous into the Paleogene.
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Affiliation(s)
- Gao-Ming Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Pan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Juan Du
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping-Fen Zhu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei-Qiang Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zi-Hao Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ling Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chun-Yan Hu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Chen Dai
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiao-Xiao Zhang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhan Zhang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Yu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Meng Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Peng-Cheng Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Xiao Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ming Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xu-Ming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China. E-mail:
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3
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Fisher AA, Ji X, Nishimura A, Baele G, Lemey P, Suchard MA. Shrinkage-based Random Local Clocks with Scalable Inference. Mol Biol Evol 2023; 40:msad242. [PMID: 37950885 PMCID: PMC10665039 DOI: 10.1093/molbev/msad242] [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: 05/31/2023] [Revised: 10/23/2023] [Accepted: 11/07/2023] [Indexed: 11/13/2023] Open
Abstract
Molecular clock models undergird modern methods of divergence-time estimation. Local clock models propose that the rate of molecular evolution is constant within phylogenetic subtrees. Current local clock inference procedures exhibit one or more weaknesses, namely they achieve limited scalability to trees with large numbers of taxa, impose model misspecification, or require a priori knowledge of the existence and location of clocks. To overcome these challenges, we present an autocorrelated, Bayesian model of heritable clock rate evolution that leverages heavy-tailed priors with mean zero to shrink increments of change between branch-specific clocks. We further develop an efficient Hamiltonian Monte Carlo sampler that exploits closed form gradient computations to scale our model to large trees. Inference under our shrinkage clock exhibits a speed-up compared to the popular random local clock when estimating branch-specific clock rates on a variety of simulated datasets. This speed-up increases with the size of the problem. We further show our shrinkage clock recovers known local clocks within a rodent and mammalian phylogeny. Finally, in a problem that once appeared computationally impractical, we investigate the heritable clock structure of various surface glycoproteins of influenza A virus in the absence of prior knowledge about clock placement. We implement our shrinkage clock and make it publicly available in the BEAST software package.
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Affiliation(s)
| | - Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University, New Orleans, LA, USA
| | - Akihiko Nishimura
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Marc A Suchard
- Department of Computational Medicine, University of California, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, CA, USA
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4
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Kalthoff DC, Fejfar O, Kimura Y, Bailey BE, Mörs T. Incisor enamel microstructure places New and Old World Eomyidae outside Geomorpha (Rodentia, Mammalia). ZOOL SCR 2022. [DOI: 10.1111/zsc.12541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Oldrich Fejfar
- Geological‐Paleontological Institute Karls University Prague Czech Republic
| | - Yuri Kimura
- Department of Geology and Paleontology National Museum of Nature and Science Tsukuba Japan
- Institut Català de Paleontologia Miquel Crusafont Universitat Autònoma de Barcelona Barcelona Spain
| | - Bruce E. Bailey
- Division of Vertebrate Paleontology University of Nebraska State Museum Lincoln Nebraska USA
| | - Thomas Mörs
- Department of Paleobiology Swedish Museum of Natural History Stockholm Sweden
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5
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Zhu W, Yang J, Lu S, Jin D, Pu J, Wu S, Luo XL, Liu L, Li Z, Xu J. RNA Virus Diversity in Birds and Small Mammals From Qinghai–Tibet Plateau of China. Front Microbiol 2022; 13:780651. [PMID: 35250920 PMCID: PMC8894885 DOI: 10.3389/fmicb.2022.780651] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/12/2022] [Indexed: 12/20/2022] Open
Abstract
Most emerging and re-emerging viruses causing infectious diseases in humans and domestic animals have originated from wildlife. However, current knowledge of the spectrum of RNA viruses in the Qinghai-Tibet Plateau in China is still limited. Here, we performed metatranscriptomic sequencing on fecal samples from 56 birds and 91 small mammals in Tibet and Qinghai Provinces, China, to delineate their viromes and focused on vertebrate RNA viruses. A total of 184 nearly complete genome RNA viruses belonging to 28 families were identified. Among these, 173 new viruses shared <90% amino acid identity with previously known viral sequences. Several of these viruses, such as those belonging to genera Orthonairovirus and Hepatovirus, could be zoonotic viruses. In addition, host taxonomy and geographical location of these viruses showed new hosts and distribution of several previously discovered viruses. Moreover, 12 invertebrate RNA viruses were identified with <40% amino acid identity to known viruses, indicating that they belong to potentially new taxa. The detection and characterization of RNA viruses from wildlife will broaden our knowledge of virus biodiversity and possible viral diseases in the Qinghai–Tibet Plateau.
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Affiliation(s)
- Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Shusheng Wu
- Yushu Prefecture Center for Disease Control and Prevention, Yushu, China
| | - Xue-Lian Luo
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Zhenjun Li
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
- Research Institute of Public Heath, Nankai University, Tianjin, China
- *Correspondence: Jianguo Xu,
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6
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Du H, Zhang L, Zhang X, Yun F, Chang Y, Tuersun A, Aisaiti K, Ma Z. Metagenome-Assembled Viral Genomes Analysis Reveals Diversity and Infectivity of the RNA Virome of Gerbillinae Species. Viruses 2022; 14:356. [PMID: 35215951 PMCID: PMC8874536 DOI: 10.3390/v14020356] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/04/2022] [Accepted: 02/06/2022] [Indexed: 11/21/2022] Open
Abstract
Rodents are a known reservoir for extensive zoonotic viruses, and also possess a propensity to roost in human habitation. Therefore, it is necessary to identify and catalogue the potentially emerging zoonotic viruses that are carried by rodents. Here, viral metagenomic sequencing was used for zoonotic virus detection and virome characterization on 32 Great gerbils of Rhombomys opimus, Meriones meridianus, and Meiiones Unguiculataus species in Xinjiang, Northwest China. In total, 1848 viral genomes that are potentially pathogenic to rodents and humans, as well as to other wildlife, were identified namely Retro-, Flavi-, Pneumo-, Picobirna-, Nairo-, Arena-, Hepe-, Phenui-, Rhabdo-, Calici-, Reo-, Corona-, Orthomyxo-, Peribunya-, and Picornaviridae families. In addition, a new genotype of rodent Hepacivirus was identified in heart and lung homogenates of seven viscera pools and phylogenetic analysis revealed the closest relationship to rodent Hepacivirus isolate RtMm-HCV/IM2014 that was previously reported to infect rodents from Inner Mongolia, China. Moreover, nine new genotype viral sequences that corresponded to Picobirnaviruses (PBVs), which have a bi-segmented genome and belong to the family Picobirnaviridae, comprising of three segment I and six segment II sequences, were identified in intestines and liver of seven viscera pools. In the two phylogenetic trees that were constructed using ORF1 and ORF2 of segment I, the three segment I sequences were clustered into distinct clades. Additionally, phylogenetic analysis showed that PBV sequences were distributed in the whole tree that was constructed using the RNA-dependent RNA polymerase (RdRp) gene of segment II with high diversity, sharing 68.42-82.67% nucleotide identities with other genogroup I and genogroup II PBV strains based on the partial RdRp gene. By RNA sequencing, we found a high degree of biodiversity of Retro-, Flavi-, Pneumo-, and Picobirnaridae families and other zoonotic viruses in gerbils, indicating that zoonotic viruses are a common presence in gerbils from Xinjiang, China. Therefore, further research is needed to determine the zoonotic potential of these viruses that are carried by other rodent species from different ecosystems and wildlife in general.
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Affiliation(s)
| | | | | | | | | | | | | | - Zhenghai Ma
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China; (H.D.); (L.Z.); (X.Z.); (F.Y.); (Y.C.); (A.T.); (K.A.)
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7
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Gupta RS, Suggett C. Conserved Signatures in Protein Sequences Reliably Demarcate Different Clades of Rodents/Glires Species and Consolidate Their Evolutionary Relationships. Genes (Basel) 2022; 13:genes13020288. [PMID: 35205335 PMCID: PMC8871558 DOI: 10.3390/genes13020288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 01/18/2023] Open
Abstract
The grandorder Glires, consisting of the orders Rodentia and Lagomorpha, encompasses a significant portion of the extant mammalian species including Rat, Mouse, Squirrel, Guinea pig and Beaver. Glires species play an important role in the ecosystem and provide valuable animal models for genetic studies and animal testing. Thus, it is important to reliably determine their evolutionary relationships and identify molecular characteristics that are specific for different species groups within the Glires. In this work, we have constructed a phylogenetic tree for >30 genome sequenced Glires species based on concatenated sequences of 25 conserved proteins. In this tree, members of different orders, suborders, and families within Glires formed strongly supported clades, and their interrelationships were also generally reliably resolved. In parallel, we conducted comparative analyses on more than 1500 protein sequences from Glires species to identify highly conserved molecular markers. These markers were comprised of conserved signature indels (CSIs) in proteins, which are specific for different Rodentia/Glires clades. Of the 41 novel CSIs identified in this work, some are specific for the entire Glires, Rodentia, or Lagomorpha clades, whereas many others reliably demarcate different family/suborder level clades of Rodentia (viz. Myomorpha, Castorimorpha, Sciuromorpha, Hystricomorpha, and Muroidea). Additionally, some of the CSIs also provide information regarding the interrelationships among Rodentia subgroups. Our analysis has also identified one CSI that is commonly shared by the Glires and Scandentia species (tree shrew), however, its evolutionary significance is unclear. Several of the identifed rodents-specific CSIs are present in conserved disease-related proteins. Thus, they provide novel molecular markers for genetic and biochemical studies on the functions of these proteins.
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8
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Wang XP, Balchak DM, Gentilcore C, Clark NL, Kashlan OB. Activation by cleavage of the epithelial Na + channel α and γ subunits independently coevolved with the vertebrate terrestrial migration. eLife 2022; 11:75796. [PMID: 34984981 PMCID: PMC8791634 DOI: 10.7554/elife.75796] [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: 11/23/2021] [Accepted: 12/28/2021] [Indexed: 12/17/2022] Open
Abstract
Vertebrates evolved mechanisms for sodium conservation and gas exchange in conjunction with migration from aquatic to terrestrial habitats. Epithelial Na+ channel (ENaC) function is critical to systems responsible for extracellular fluid homeostasis and gas exchange. ENaC is activated by cleavage at multiple specific extracellular polybasic sites, releasing inhibitory tracts from the channel’s α and γ subunits. We found that proximal and distal polybasic tracts in ENaC subunits coevolved, consistent with the dual cleavage requirement for activation observed in mammals. Polybasic tract pairs evolved with the terrestrial migration and the appearance of lungs, coincident with the ENaC activator aldosterone, and appeared independently in the α and γ subunits. In summary, sites within ENaC for protease activation developed in vertebrates when renal Na+ conservation and alveolar gas exchange were required for terrestrial survival.
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Affiliation(s)
- Xue-Ping Wang
- Department of Medicine, University of Pittsburgh, Pittsburgh, United States
| | - Deidra M Balchak
- Department of Medicine, University of Pittsburgh, Pittsburgh, United States
| | - Clayton Gentilcore
- Department of Medicine, University of Pittsburgh, Pittsburgh, United States
| | - Nathan L Clark
- Department of Human Genetics, University of Utah, Salt Lake City, United States
| | - Ossama B Kashlan
- Department of Medicine, University of Pittsburgh, Pittsburgh, United States.,Computational and Systems Biology, University of Pittsburgh, Pittsburgh, United States
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9
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Bangs MR, Steppan SJ. A rodent anchored hybrid enrichment probe set for a range of phylogenetic utility: From order to species. Mol Ecol Resour 2021; 22:1521-1528. [PMID: 34800355 DOI: 10.1111/1755-0998.13555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/22/2021] [Accepted: 11/10/2021] [Indexed: 11/29/2022]
Abstract
Rodents are the largest order of mammals and contain several model organisms important to scientific research in a variety of fields, yet no large set of genomic markers have been designed for this group to date, hindering evolutionary studies into relationships of the group as a whole. Here we present a genomic probe set designed and optimized for rodents with a protocol that is easy to replicate with little laboratory investment. This design utilizes an anchored hybrid enrichment approach specifically targeting rodents to generate longer loci with a higher substitution rate than existing vertebrate probes to provide utility at various taxonomic levels. Using a test set of rodents from all five suborders, we successfully obtained alignments for 416 of the 418 target loci with an average of 1379 bp per locus and a total alignment of more than half a million base pairs. This genomic data set performed well in all phylogenetic analyses, especially in recent phylogenetic splits, with ample parsimony-informative sites within genera and even within species, showing more than four times as many single nucleotide polymorphisms per locus than a recent vertebrate ultraconserved elements study. Additional support is provided in resolving deeper clades in Rodentia. By providing this probe design, we hope that more laboratories can easily generate data for answering questions in rodents from species delimitation to understanding relationships among families in rapid radiations.
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Affiliation(s)
- Max R Bangs
- Department of Biological Sciences, Florida State University, Tallahassee, Florida, USA
| | - Scott J Steppan
- Department of Biological Sciences, Florida State University, Tallahassee, Florida, USA
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10
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Gutierrez J, Platt R, Opazo JC, Ray DA, Hoffmann F, Vandewege M. Evolutionary history of the vertebrate Piwi gene family. PeerJ 2021; 9:e12451. [PMID: 34760405 PMCID: PMC8574217 DOI: 10.7717/peerj.12451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/18/2021] [Indexed: 11/28/2022] Open
Abstract
PIWIs are regulatory proteins that belong to the Argonaute family. Piwis are primarily expressed in gonads and protect the germline against the mobilization and propagation of transposable elements (TEs) through transcriptional gene silencing. Vertebrate genomes encode up to four Piwi genes: Piwil1, Piwil2, Piwil3 and Piwil4, but their duplication history is unresolved. We leveraged phylogenetics, synteny and expression analyses to address this void. Our phylogenetic analysis suggests Piwil1 and Piwil2 were retained in all vertebrate members. Piwil4 was the result of Piwil1 duplication in the ancestor of gnathostomes, but was independently lost in ray-finned fishes and birds. Further, Piwil3 was derived from a tandem Piwil1 duplication in the common ancestor of marsupial and placental mammals, but was secondarily lost in Atlantogenata (Xenarthra and Afrotheria) and some rodents. The evolutionary rate of Piwil3 is considerably faster than any Piwi among all lineages, but an explanation is lacking. Our expression analyses suggest Piwi expression has mostly been constrained to gonads throughout vertebrate evolution. Vertebrate evolution is marked by two early rounds of whole genome duplication and many multigene families are linked to these events. However, our analyses suggest Piwi expansion was independent of whole genome duplications.
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Affiliation(s)
- Javier Gutierrez
- Department of Biology, Eastern New Mexico University, Portales, NM, United States of America
| | - Roy Platt
- Host Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX, United States of America
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.,Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Valdivia, Chile.,Integrative Biology Group, Universidad Austral de Chile, Valdivia, Chile
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States of America
| | - Federico Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS, United States of America.,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, United States of America
| | - Michael Vandewege
- Department of Biology, Eastern New Mexico University, Portales, NM, United States of America
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11
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Hofmann R, Lehmann T, Warren DL, Ruf I. The squirrel is in the detail: Anatomy and morphometry of the tail in Sciuromorpha (Rodentia, Mammalia). J Morphol 2021; 282:1659-1682. [PMID: 34549832 DOI: 10.1002/jmor.21412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 09/09/2021] [Accepted: 09/15/2021] [Indexed: 11/07/2022]
Abstract
In mammals, the caudal vertebrae are certainly among the least studied elements of their skeleton. However, the tail plays an important role in locomotion (e.g., balance, prehensility) and behavior (e.g., signaling). Previous studies largely focused on prehensile tails in Primates and Carnivora, in which certain osteological features were selected and used to define tail regions (proximal, transitional, distal). Interestingly, the distribution pattern of these anatomical characters and the relative proportions of the tail regions were similar in both orders. In order to test if such tail regionalization can be applied to Rodentia, we investigated the caudal vertebrae of 20 Sciuridae and six Gliridae species. Furthermore, we examined relationships between tail anatomy/morphometry and locomotion. The position of selected characters along the tail was recorded and their distribution was compared statistically using Spearman rank correlation. Vertebral body length (VBL) was measured to calculate the proportions of each tail region and to perform procrustes analysis on the shape of relative vertebral body length (rVBL) progressions. Our results show that tail regionalization, as defined for Primates and Carnivora, can be applied to almost all investigated squirrels, regardless of their locomotor category. Moreover, major locomotor categories can be distinguished by rVBL progression and tail region proportions. In particular, the small flying squirrels Glaucomys volans and Hylopetes sagitta show an extremely short transitional region. Likewise, several semifossorial taxa can be distinguished by their short distal region. Moreover, among flying squirrels, Petaurista petaurista shows differences with the small flying squirrels, mirroring previous observations on locomotory adaptations based on their inner ear morphometry. Our results show furthermore that the tail region proportions of P. petaurista, phylogenetically more basal than the small flying squirrels, are similar to those of bauplan-conservative arboreal squirrels.
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Affiliation(s)
- Rebecca Hofmann
- Abteilung Messelforschung und Mammalogie, Senckenberg Forschungsinstitut und Naturmuseum Frankfurt, Frankfurt am Main, Germany.,Institut für Geowissenschaften, Goethe-Universität, Frankfurt am Main, Germany
| | - Thomas Lehmann
- Abteilung Messelforschung und Mammalogie, Senckenberg Forschungsinstitut und Naturmuseum Frankfurt, Frankfurt am Main, Germany
| | - Dan L Warren
- Senckenberg Biodiversität und Klima Forschungszentrum, Frankfurt am Main, Germany.,Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Irina Ruf
- Abteilung Messelforschung und Mammalogie, Senckenberg Forschungsinstitut und Naturmuseum Frankfurt, Frankfurt am Main, Germany.,Institut für Geowissenschaften, Goethe-Universität, Frankfurt am Main, Germany
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12
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Nadeem R, Barakat AB, Bahgat MM. Cross-reaction between mouse and rat immunoglobulin G: does it matter in sandwich ELISA? J Genet Eng Biotechnol 2021; 19:119. [PMID: 34403025 PMCID: PMC8369443 DOI: 10.1186/s43141-021-00222-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/02/2021] [Indexed: 11/21/2022]
Abstract
Background Sandwich ELISA is an ideal antigen detection and quantification assay. Recently, it was used as the basic concept for high technology diagnostics. The specificity of the assay depends on the exclusion of detection cross-reactivity which arises from using two antibodies developed in different species. Since mice and rats are the common laboratory animals used to develop antigen specific antibodies. Therefore, the questions we addressed here were (1) can one use antigen-specific antibodies raised in mice and rats in the same assay to specifically detect/quantify antigens? and (2) which antibodies of the two rodents should be placed for capturing and for detection in the antigen-detection sandwich? Results Direct ELISA assay was used to assess for the specific reaction of the HRP-conjugated antibody to the target serum. First reaction was to compare between either conjugate anti-rat IgG (homologous) or anti-mouse IgG (heterologous) for the detection of rat sera IgG. Following the dilution factor optimization, the O.D. were 0.744±0.051 and 0.604±0.05, respectively (p= .004). The difference in mean O.D. of 0.14 reflected an unaccepted non-specific reaction. The second reaction was to compare between either conjugate anti-mouse IgG (homologous) and anti-rat IgG (heterologous) for the detection of mouse sera IgG. The recorded O.D. were 0.9414±0.14 and 0.317 ±0.141, respectively (p= .0002). The improved difference in mean O.D. of 0.624 reflecting a minimized cross-reaction. Conclusions Our results suggest that it is possible to use both Swiss albino mice and albino rats in a single sandwich ELISA, given that the captured antibody species to be from the Swiss albino mice and the detection antibody to be from the albino rat. The described working details are limited to the source of the antibodies used in the study. However, the approach stresses on the importance of such optimization steps before making any interpretations based on the antigen detection. To our knowledge, this study is the first to cover the optimal order of the capturing and the detection antibodies in a sandwich ELISA assay. In addition to addressing the possible interfering cross-reactivity that result from using mouse and rat serum antibodies in a single assay. Graphical abstract ![]()
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Affiliation(s)
- Rola Nadeem
- Department of Therapeutic Chemistry, Division of Pharmaceutical and Drug Industries Research, the National Research Center, Cairo, Egypt.,Research Group Immune- and Bio-markers for Infection, The Center of Excellence for Advanced Sciences, the National Research Center, El Buhooth Street (Formerly El Tahrir), Dokki, Cairo, 12622, Egypt
| | - Ahmed B Barakat
- Department of Microbiology, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Mahmoud M Bahgat
- Department of Therapeutic Chemistry, Division of Pharmaceutical and Drug Industries Research, the National Research Center, Cairo, Egypt. .,Research Group Immune- and Bio-markers for Infection, The Center of Excellence for Advanced Sciences, the National Research Center, El Buhooth Street (Formerly El Tahrir), Dokki, Cairo, 12622, Egypt.
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13
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Molecular Evolution of Tooth-Related Genes Provides New Insights into Dietary Adaptations of Mammals. J Mol Evol 2021; 89:458-471. [PMID: 34287664 PMCID: PMC8318974 DOI: 10.1007/s00239-021-10017-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 06/10/2021] [Indexed: 11/01/2022]
Abstract
Mammals have evolved different tooth phenotypes that are hypothesized to be associated with feeding habits. However, the genetic basis for the linkage has not been well explored. In this study, we investigated 13 tooth-related genes, including seven enamel-related genes (AMELX, AMBN, ENAM, AMTN, ODAM, KLK4 and MMP20) and six dentin-related genes (DSPP, COL1A1, DMP1, IBSP, MEPE and SPP1), from 63 mammals to determine their evolutionary history. Our results showed that different evolutionary histories have evolved among divergent feeding habits in mammals. There was stronger positive selection for eight genes (ENAM, AMTN, ODAM, KLK4, DSPP, DMP1, COL1A1, MEPE) in herbivore lineages. In addition, AMELX, AMBN, ENAM, AMTN, MMP20 and COL1A1 underwent accelerated evolution in herbivores. While relatively strong positive selection was detected in IBSP, SPP1, and DSPP, accelerated evolution was only detected for MEPE and SPP1 genes among the carnivorous lineages. We found positive selection on AMBN and ENAM genes for omnivorous primates in the catarrhini clade. Interestingly, a significantly positive association between the evolutionary rate of ENAM, ODAM, KLK4, MMP20 and the average enamel thickness was found in primates. Additionally, we found molecular convergence in some amino acid sites of tooth-related genes among the lineages whose feeding habit are similar. The positive selection of related genes might promote the formation and bio-mineralization of tooth enamel and dentin, which would make the tooth structure stronger. Our results revealed that mammalian tooth-related genes have experienced variable evolutionary histories, which provide some new insights into the molecular basis of dietary adaptation in mammals.
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14
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Fleming PA, Wentzel JJ, Dundas SJ, Kreplins TL, Craig MD, Hardy GESJ. Global meta-analysis of tree decline impacts on fauna. Biol Rev Camb Philos Soc 2021; 96:1744-1768. [PMID: 33955144 DOI: 10.1111/brv.12725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 01/18/2023]
Abstract
Significant portions of the world's forests have been impacted by severe and large-scale tree declines characterised by gradual but widespread loss of vigour and subsequent death of either single or several tree species. Tree deaths represent a threat for fauna that are dependent on forest habitats for their survival. Although tree declines have received considerable scientific attention, surprisingly, little is known about their impacts on fauna. In total, we calculated 631 effect sizes across 59 studies that quantified the impact of tree declines on animal abundance. Data representing 186 bird species indicated an overall increase in bird abundance in response to tree declines (meta-analysis mean ± estimation g = 0.172 ± 0.053 [CI 0.069 to 0.275], P = 0.001); however, there was substantial variability in responses (significant heterogeneity P < 0.001) with a strong influence of diet as well as nesting guild on bird responses. Granivores (especially ground-foraging species, e.g. Passerellidae species), bark-foraging insectivores (e.g. woodpeckers), as well as ground- and cavity-nesting species apparently benefitted from tree declines, while nectarivorous birds [and, although not significant, aerially foraging insectivores (e.g. flycatchers) and leaf-gleaning insectivores (canopy-feeding)] were less common in the presence of tree declines. Data representing 33 mammal species indicate a tendency for detrimental effects of tree declines on mammals that use trees as refuges, while aerial foragers (i.e. bats) may benefit from opening up the canopy. Overall the average effect for mammals was neutral (meta-analysis mean estimation g = -0.150 ± 0.145 [-0.433 to 0.134], P = 0.302). Data representing 20 reptile species showed an insufficient range of responses to determine any diet or foraging effect on their responses. Data for 28 arthropod taxa should be considered with caution, as we could not adequately separate taxa according to their specialisations and reliance on key habitat. The data broadly suggest a detrimental effect of tree declines (meta-analysis mean estimation g = -0.171 ± 0.072 [-0.311 to -0.031], P = 0.017) with ground-foraging arthropods (e.g. detritivores and predators such as spiders and centipedes) more likely to be detrimentally impacted by tree declines. The range of responses to tree declines signifies substantially altered animal communities. In many instances, altered ecosystem function due to loss of key animal services will represent a significant threat to forest health.
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Affiliation(s)
- Patricia A Fleming
- Centre for Terrestrial Ecosystem Science and Sustainability, Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, Perth, WA, 6150, Australia
| | - Jacobus J Wentzel
- Centre for Terrestrial Ecosystem Science and Sustainability, Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, Perth, WA, 6150, Australia
| | - Shannon J Dundas
- Centre for Terrestrial Ecosystem Science and Sustainability, Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, Perth, WA, 6150, Australia.,New South Wales Department of Primary Industries, 1447 Forest Road, Orange, NSW, Australia
| | - Tracey L Kreplins
- Centre for Terrestrial Ecosystem Science and Sustainability, Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, Perth, WA, 6150, Australia
| | - Michael D Craig
- Centre for Terrestrial Ecosystem Science and Sustainability, Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, Perth, WA, 6150, Australia.,School of Biological Sciences, University of Western Australia, Stirling Highway, Nedlands, Perth, WA, 6009, Australia
| | - Giles E St J Hardy
- Centre for Terrestrial Ecosystem Science and Sustainability, Harry Butler Institute, Murdoch University, 90 South Street, Murdoch, Perth, WA, 6150, Australia
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15
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Bertrand OC, Püschel HP, Schwab JA, Silcox MT, Brusatte SL. The impact of locomotion on the brain evolution of squirrels and close relatives. Commun Biol 2021; 4:460. [PMID: 33846528 PMCID: PMC8042109 DOI: 10.1038/s42003-021-01887-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 02/22/2021] [Indexed: 02/01/2023] Open
Abstract
How do brain size and proportions relate to ecology and evolutionary history? Here, we use virtual endocasts from 38 extinct and extant rodent species spanning 50+ million years of evolution to assess the impact of locomotion, body mass, and phylogeny on the size of the brain, olfactory bulbs, petrosal lobules, and neocortex. We find that body mass and phylogeny are highly correlated with relative brain and brain component size, and that locomotion strongly influences brain, petrosal lobule, and neocortical sizes. Notably, species living in trees have greater relative overall brain, petrosal lobule, and neocortical sizes compared to other locomotor categories, especially fossorial taxa. Across millions of years of Eocene-Recent environmental change, arboreality played a major role in the early evolution of squirrels and closely related aplodontiids, promoting the expansion of the neocortex and petrosal lobules. Fossoriality in aplodontiids had an opposing effect by reducing the need for large brains.
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Affiliation(s)
- Ornella C Bertrand
- School of GeoSciences, University of Edinburgh, Grant Institute, Edinburgh, Scotland, UK.
| | - Hans P Püschel
- School of GeoSciences, University of Edinburgh, Grant Institute, Edinburgh, Scotland, UK
| | - Julia A Schwab
- School of GeoSciences, University of Edinburgh, Grant Institute, Edinburgh, Scotland, UK
| | - Mary T Silcox
- Department of Anthropology, University of Toronto Scarborough, Toronto, ON, Canada
| | - Stephen L Brusatte
- School of GeoSciences, University of Edinburgh, Grant Institute, Edinburgh, Scotland, UK
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16
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Chernova OF, Zherebtsova OV. Hair microstructure in some rodent species of Diatomyidae, Ctenodactylidae, and Echimyidae (Ctenohystrica, Rodentia). ZOOL ANZ 2021. [DOI: 10.1016/j.jcz.2021.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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17
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Wu Z, Han Y, Liu B, Li H, Zhu G, Latinne A, Dong J, Sun L, Su H, Liu L, Du J, Zhou S, Chen M, Kritiyakan A, Jittapalapong S, Chaisiri K, Buchy P, Duong V, Yang J, Jiang J, Xu X, Zhou H, Yang F, Irwin DM, Morand S, Daszak P, Wang J, Jin Q. Decoding the RNA viromes in rodent lungs provides new insight into the origin and evolutionary patterns of rodent-borne pathogens in Mainland Southeast Asia. MICROBIOME 2021; 9:18. [PMID: 33478588 PMCID: PMC7818139 DOI: 10.1186/s40168-020-00965-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/06/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND As the largest group of mammalian species, which are also widely distributed all over the world, rodents are the natural reservoirs for many diverse zoonotic viruses. A comprehensive understanding of the core virome of diverse rodents should therefore assist in efforts to reduce the risk of future emergence or re-emergence of rodent-borne zoonotic pathogens. RESULTS This study aimed to describe the viral range that could be detected in the lungs of rodents from Mainland Southeast Asia. Lung samples were collected from 3284 rodents and insectivores of the orders Rodentia, Scandentia, and Eulipotyphla in eighteen provinces of Thailand, Lao PDR, and Cambodia throughout 2006-2018. Meta-transcriptomic analysis was used to outline the unique spectral characteristics of the mammalian viruses within these lungs and the ecological and genetic imprints of the novel viruses. Many mammalian- or arthropod-related viruses from distinct evolutionary lineages were reported for the first time in these species, and viruses related to known pathogens were characterized for their genomic and evolutionary characteristics, host species, and locations. CONCLUSIONS These results expand our understanding of the core viromes of rodents and insectivores from Mainland Southeast Asia and suggest that a high diversity of viruses remains to be found in rodent species of this area. These findings, combined with our previous virome data from China, increase our knowledge of the viral community in wildlife and arthropod vectors in emerging disease hotspots of East and Southeast Asia. Video abstract.
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Affiliation(s)
- Zhiqiang Wu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China.
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China.
| | - Yelin Han
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Bo Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | | | | | - Alice Latinne
- EcoHealth Alliance, New York, NY, USA
- Wildlife Conservation Society, Viet Nam Country Program, Ha Noi, Vietnam
- Wildlife Conservation Society, Health Program, Bronx, NY, USA
| | - Jie Dong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Lilin Sun
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Haoxiang Su
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Liguo Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Jiang Du
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Siyu Zhou
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Mingxing Chen
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Anamika Kritiyakan
- Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand
| | | | | | | | - Veasna Duong
- Virology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Jinyong Jiang
- Yunnan Institute of Parasitic Diseases, Pu'er, PR China
| | - Xiang Xu
- Yunnan Institute of Parasitic Diseases, Pu'er, PR China
| | - Hongning Zhou
- Yunnan Institute of Parasitic Diseases, Pu'er, PR China
| | - Fan Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Serge Morand
- Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand
| | | | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China.
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18
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Bhagat R, Bertrand OC, Silcox MT. Evolution of arboreality and fossoriality in squirrels and aplodontid rodents: Insights from the semicircular canals of fossil rodents. J Anat 2021; 238:96-112. [PMID: 32812227 PMCID: PMC7754939 DOI: 10.1111/joa.13296] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/17/2020] [Accepted: 07/23/2020] [Indexed: 01/03/2023] Open
Abstract
Reconstructing locomotor behaviour for fossil animals is typically done with postcranial elements. However, for species only known from cranial material, locomotor behaviour is difficult to reconstruct. The semicircular canals (SCCs) in the inner ear provide insight into an animal's locomotor agility. A relationship exists between the size of the SCCs relative to body mass and the jerkiness of an animal's locomotion. Additionally, studies have also demonstrated a relationship between SCC orthogonality and angular head velocity. Here, we employ two metrics for reconstructing locomotor agility, radius of curvature dimensions and SCC orthogonality, in a sample of twelve fossil rodents from the families Ischyromyidae, Sciuridae and Aplodontidae. The method utilizing radius of curvature dimensions provided a reconstruction of fossil rodent locomotor behaviour that is more consistent with previous studies assessing fossil rodent locomotor behaviour compared to the method based on SCC orthogonality. Previous work on ischyromyids suggests that this group displayed a variety of locomotor modes. Members of Paramyinae and Ischyromyinae have relatively smaller SCCs and are reconstructed to be relatively slower compared to members of Reithroparamyinae. Early members of the Sciuroidea clade including the sciurid Cedromus wilsoni and the aplodontid Prosciurus relictus are reconstructed to be more agile than ischyromyids, in the range of extant arboreal squirrels. This reconstruction supports previous inferences that arboreality was likely an ancestral trait for this group. Derived members of Sciuridae and Aplodontidae vary in agility scores. The fossil squirrel Protosciurus cf. rachelae is inferred from postcranial material as arboreal, which is in agreement with its high agility, in the range of extant arboreal squirrels. In contrast, the fossil aplodontid Mesogaulus paniensis has a relatively low agility score, similar to the fossorial Aplodontia rufa, the only living aplodontid rodent. This result is in agreement with its postcranial reconstruction as fossorial and with previous indications that early aplodontids were more arboreal than their burrowing descendants.
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Affiliation(s)
- Raj Bhagat
- Department of AnthropologyUniversity of Toronto ScarboroughTorontoONCanada
| | | | - Mary T. Silcox
- Department of AnthropologyUniversity of Toronto ScarboroughTorontoONCanada
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19
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Two hundred and fifty-four metagenome-assembled bacterial genomes from the bank vole gut microbiota. Sci Data 2020; 7:312. [PMID: 32968071 PMCID: PMC7511399 DOI: 10.1038/s41597-020-00656-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/27/2020] [Indexed: 12/12/2022] Open
Abstract
Vertebrate gut microbiota provide many essential services to their host. To better understand the diversity of such services provided by gut microbiota in wild rodents, we assembled metagenome shotgun sequence data from a small mammal, the bank vole Myodes glareolus (Rodentia, Cricetidae). We were able to identify 254 metagenome assembled genomes (MAGs) that were at least 50% (n = 133 MAGs), 80% (n = 77 MAGs) or 95% (n = 44 MAGs) complete. As typical for a rodent gut microbiota, these MAGs are dominated by taxa assigned to the phyla Bacteroidetes (n = 132 MAGs) and Firmicutes (n = 80), with some Spirochaetes (n = 15) and Proteobacteria (n = 11). Based on coverage over contigs, Bacteroidetes were estimated to be most abundant group, followed by Firmicutes, Spirochaetes and Proteobacteria. These draft bacterial genomes can be used freely to determine the likely functions of gut microbiota community composition in wild rodents. Measurement(s) | genome • DNA • gut microbiome measurement • metagenomic data | Technology Type(s) | DNA sequencing | Sample Characteristic - Organism | Bacteroidetes • Firmicutes • Spirochaetes • Proteobacteria • Myodes glareolus |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12936797
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Effect of Dinotefuran, Permethrin, and Pyriproxyfen (Vectra ® 3D) on the Foraging and Blood-Feeding Behaviors of Aedes albopictus Using Laboratory Rodent Model. INSECTS 2020; 11:insects11080507. [PMID: 32764404 PMCID: PMC7469159 DOI: 10.3390/insects11080507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023]
Abstract
Simple Summary Tiger mosquito (Aedes albopictus) is a harmful vector involved in the transmission of several diseases to humans and their pets. Currently, several veterinary products are used to prevent pets against bites of arthropod vectors. However, there is no available information on the effect of these products on feeding and host choice behaviors of Aedes albopictus in the presence of treated and untreated hosts, as is the case of treated dogs present in close physical contact with their owners. The present study investigated the effect of a spot-on product (Vectra® 3D) on the feeding and host choice behaviours of Aedes albopictus when treated and untreated hosts are presents. Laboratory rodent model was performed to simulate the natural conditions. Rat and mouse hosts were alternately treated with Vectra® 3D and exposed simultaneously to starved mosquitoes. Results showed that Vectra® 3D-treated hosts are perfectly protected against up to 82% of mosquitoes. While up to 21% of mosquitoes were repelled from untreated hosts when these latter are present in close physical contact (30 cm) with treated ones suggesting an indirect protection that can allowed the protection of owners who treat their pets with Vectra® 3D. Abstract Dinotefuran-Permethrin-Pyriproxyfen (DPP) is used to kill and repel mosquitoes from dogs. However, the influence of the product on the host-seeking behavior of mosquitoes remains unknown. The interference of DPP with the host selection of unfed female Aedes albopictus was investigated. A total of 18 animals (9 mice and 9 rats) were divided into three groups of six animals each. DU: DPP treated rats (n = 3) with untreated mice (n = 3), UD: DPP treated mice (n = 3) with untreated rats (n = 3) and control UU: untreated mice (n = 3) and untreated rats (n = 3). In each group, the rats and mice were placed 30 cm apart. After sedation, the animals in each group were exposed twice (Day 1 and Day 7 post-treatment) for one hour to 71 ± 3 female mosquitoes. Mosquitoes were categorized after the 2-h post-exposure period as dead or alive. Blood-meal origin was determined from mosquitoes using a newly customized duplex qPCR. The highest values of forage ratio (1.36 ≥ wi ≤ 1.88) and selection index (0.63 ≥ Bi ≤ 0.94) for rat hosts indicates a preference of mosquitoes for this species as compared to mice when co-housed during the exposure. The mosquitoes only seldom fed on mice, even in the untreated group. The anti-feeding effect of DPP was therefore only assessed on rat’s hosts. The results showed that DPP, when directly applied on rats, provided a direct protection of 82% and 61% on Day 1 and Day 7, respectively, while when applied on mice hosts (UD), the DPP provided an indirect protection of 21% and 10% on Day 1 and Day 7, respectively. The results showed also that DPP, when applied on rats, provided a direct protection against Ae. albopictus bites. This effect did not result in increased exposure of the untreated host placed in the same cage at a distance of 30 cm.
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Zherebtsova O, Platonov V. Evolutionary transformation of the subcutaneous muscle in rodents of Ctenohystrica (Rodentia: Diatomyidae, Ctenodactylidae, and Hystricognathi). J Morphol 2020. [DOI: 10.1002/jmor.21221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Olga Zherebtsova
- Laboratory of Theriology Zoological Institute of RAS Saint Petersburg Russia
| | - Vladimir Platonov
- Laboratory of Theriology Zoological Institute of RAS Saint Petersburg Russia
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22
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Babarinde IA, Saitou N. The Dynamics, Causes, and Impacts of Mammalian Evolutionary Rates Revealed by the Analyses of Capybara Draft Genome Sequences. Genome Biol Evol 2020; 12:1444-1458. [PMID: 32835375 DOI: 10.1093/gbe/evaa157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2020] [Indexed: 12/23/2022] Open
Abstract
Capybara (Hydrochoerus hydrochaeri) is the largest species among the extant rodents. The draft genome of capybara was sequenced with the estimated genome size of 2.6 Gb. Although capybara is about 60 times larger than guinea pig, comparative analyses revealed that the neutral evolutionary rates of the two species were not substantially different. However, analyses of 39 mammalian genomes revealed very heterogeneous evolutionary rates. The highest evolutionary rate, 8.5 times higher than the human rate, was found in the Cricetidae-Muridae common ancestor after the divergence of Spalacidae. Muridae, the family with the highest number of species among mammals, emerged after the rate acceleration. Factors responsible for the evolutionary rate heterogeneity were investigated through correlations between the evolutionary rate and longevity, gestation length, litter frequency, litter size, body weight, generation interval, age at maturity, and taxonomic order. The regression analysis of these factors showed that the model with three factors (taxonomic order, generation interval, and litter size) had the highest predictive power (R2 = 0.74). These three factors determine the number of meiosis per unit time. We also conducted transcriptome analysis and found that the evolutionary rate dynamics affects the evolution of gene expression patterns.
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Affiliation(s)
- Isaac Adeyemi Babarinde
- Department of Biological Sciences, Southern University of Science and Technology, Shenzhen, China.,Population Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Naruya Saitou
- Population Genetics Laboratory, National Institute of Genetics, Mishima, Japan.,School of Medicine, University of the Ryukyus, Okinawa, Japan.,Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, Japan.,Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan
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İbiş O. Whole mitochondrial genome sequence and phylogenetic relationships of Williams's jerboa ( Scarturus williamsi) from Turkey. PeerJ 2020; 8:e9569. [PMID: 32742814 PMCID: PMC7369027 DOI: 10.7717/peerj.9569] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/29/2020] [Indexed: 11/29/2022] Open
Abstract
Williams’s jerboa (Scarturus williamsi), a medium-sized jerboa distributed in Anatolia and its adjacent regions, is a member of the four- and five-toed jerboas found mostly in Asia. Disagreements about the taxonomy of this taxon at the genus/species level continue to exist. Here, we report the first effort to sequence and assemble the mitochondrial genome of Williams’s jerboa from Turkey. The mitochondrial genome of S. williamsi was 16,653 bp in total length and contained 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and two non-coding regions (the D-loop and OL region) with intergenic spacer. All of the genes, except ND6 and eight tRNAs, were encoded on the heavy chain strand, similar to the features of mitogenomes of other rodents. When compared with all available rodent mitochondrial genomes, Williams’s jerboa showed (1) a serine deletion at the 3′-end of the ATP8 gene, (2) the ND5 gene terminated with a TAG codon and (3) a tandem repeat cluster (273 bp in length) in the control region. Williams’s jerboa and Siberian jerboa grouped as sister taxa despite the high genetic distance (17.6%) between them, belonging to Allactaginae. This result is consistent with the latest pre-revision, which suggests that Williams’s jerboa and the Siberian jerboa may belong to separate genera, as Scarturus and Orientallactaga, respectively. The present study provides a reference mitochondrial genome for Williams’s jerboa for further molecular studies of other species of Dipodoidea and Rodentia.
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Affiliation(s)
- Osman İbiş
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey.,Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey
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Allen AE, Mouland JW, Rodgers J, Baño-Otálora B, Douglas RH, Jeffery G, Vugler AA, Brown TM, Lucas RJ. Spectral sensitivity of cone vision in the diurnal murid Rhabdomys pumilio. J Exp Biol 2020; 223:jeb215368. [PMID: 32371443 PMCID: PMC7272338 DOI: 10.1242/jeb.215368] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 04/20/2020] [Indexed: 01/14/2023]
Abstract
An animal's temporal niche - the time of day at which it is active - is known to drive a variety of adaptations in the visual system. These include variations in the topography, spectral sensitivity and density of retinal photoreceptors, and changes in the eye's gross anatomy and spectral transmission characteristics. We have characterised visual spectral sensitivity in the murid rodent Rhabdomys pumilio (the four-striped grass mouse), which is in the same family as (nocturnal) mice and rats but exhibits a strong diurnal niche. As is common in diurnal species, the R. pumilio lens acts as a long-pass spectral filter, providing limited transmission of light <400 nm. Conversely, we found strong sequence homologies with the R. pumilio SWS and MWS opsins and those of related nocturnal species (mice and rats) whose SWS opsins are maximally sensitive in the near-UV. We continued to assess in vivo spectral sensitivity of cone vision using electroretinography and multi-channel recordings from the visual thalamus. These revealed that responses across the human visible range could be adequately described by those of a single pigment (assumed to be MWS opsin) maximally sensitive at ∼500 nm, but that sensitivity in the near-UV required inclusion of a second pigment whose peak sensitivity lay well into the UV range (λmax<400 nm, probably ∼360 nm). We therefore conclude that, despite the UV-filtering effects of the lens, R. pumilio retains an SWS pigment with a UV-A λmax In effect, this somewhat paradoxical combination of long-pass lens and UV-A λmax results in narrow-band sensitivity for SWS cone pathways in the UV-A range.
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Affiliation(s)
- Annette E Allen
- Division of Neuroscience and Experimental Psychology, Faculty of Biology Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Joshua W Mouland
- Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Jessica Rodgers
- Division of Neuroscience and Experimental Psychology, Faculty of Biology Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Beatriz Baño-Otálora
- Division of Neuroscience and Experimental Psychology, Faculty of Biology Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Ronald H Douglas
- Department of Optometry and Visual Science, City, University of London, London, EC1V 0HB, UK
| | - Glen Jeffery
- Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
| | - Anthony A Vugler
- Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
| | - Timothy M Brown
- Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Robert J Lucas
- Division of Neuroscience and Experimental Psychology, Faculty of Biology Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
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Swanson MT, Oliveros CH, Esselstyn JA. A phylogenomic rodent tree reveals the repeated evolution of masseter architectures. Proc Biol Sci 2020; 286:20190672. [PMID: 31064307 DOI: 10.1098/rspb.2019.0672] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Understanding the number of times a trait has evolved is a necessary foundation for comprehending its potential relationships with selective regimes, developmental constraints and evolutionary diversification. Rodents make up over 40% of extant mammalian species, and their ecological and evolutionary success has been partially attributed to the increase in biting efficiency that resulted from a forward shift of one or two portions of the masseter muscle from the zygomatic arch onto the rostrum. This forward shift has occurred in three discrete ways, but the number of times it has occurred has never been explicitly quantified. We estimated an ultrametric phylogeny, the first to include all rodent families, using thousands of ultraconserved elements. We examined support for evolutionary relationships among the five rodent suborders and then incorporated relevant fossils, fitted models of character evolution, and used stochastic character mapping to determine that a portion of the masseter muscle has moved forward onto the rostrum at least seven times (with one reversal) during the approximately 70 Myr history of rodents. Combined, the repeated evolution of this key innovation, its increasing prevalence through time, and the species diversity of clades with this character underscores the adaptive value of improved biting efficiency and the relative ease with which some advantageous traits arise.
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Affiliation(s)
- Mark T Swanson
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University , Baton Rouge, LA , USA
| | - Carl H Oliveros
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University , Baton Rouge, LA , USA
| | - Jacob A Esselstyn
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University , Baton Rouge, LA , USA
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Dissecting the differential structural and dynamics features of CCL2 chemokine orthologs. Int J Biol Macromol 2020; 156:239-251. [PMID: 32289428 DOI: 10.1016/j.ijbiomac.2020.04.067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/26/2020] [Accepted: 04/08/2020] [Indexed: 12/29/2022]
Abstract
Chemokines are a sub-group of cytokines that regulate the leukocyte migration. Monocyte chemoattractant protein-1 (MCP/CCL2) is one of the essential CC chemokine that regulates the migration of monocytes into inflamed tissues. It has been observed that the primary sequences of CCL2 orthologs among rodents and primates vary significantly at the C-terminal region. However, no structural details are available for the rodentia family CCL2 proteins. The current study unravelled the structural, dynamics and in-silico functional characteristics of murine CCL2 chemokine using a comprehensive set of NMR spectroscopy techniques and evolutionary approaches. The study unravelled that the N-terminal portion of the murine CCL2 forms a canonical CC chemokine dimer similar to that of human CCL2. However, unlike human CCL2, the murine ortholog exhibits extensive dynamics in the μs-ms timescales. The presence of C-terminal region of the murine CCL2 protein/rodentia family is highly glycosylated, completely disordered, and inhibits the folding of the structured CCL2 regions. Further, it has been observed that the glycosaminoglycan binding surfaces of these orthologs proteins are greatly differed. In a nut shell, this comparative study provided the role of molecular evolution in generating orthologous proteins with differential structural and dynamics characteristics to engage them in specific molecular interactions.
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Cox PG, Faulkes CG, Bennett NC. Masticatory musculature of the African mole-rats (Rodentia: Bathyergidae). PeerJ 2020; 8:e8847. [PMID: 32231887 PMCID: PMC7100595 DOI: 10.7717/peerj.8847] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/03/2020] [Indexed: 12/22/2022] Open
Abstract
The Bathyergidae, commonly known as blesmols or African mole-rats, is a family of rodents well-known for their subterranean lifestyle and tunnelling behaviour. Four of the five extant bathyergid genera (Cryptomys, Fukomys, Georychus and Heliophobius) are chisel-tooth diggers, that is they dig through soil with their enlarged incisors, whereas the remaining genus (Bathyergus) is a scratch-digger, only using its forelimbs for burrowing. Heterocephalus glaber, the naked mole-rat, is also a chisel-tooth digger and was until recently included within the Bathyergidae (as the most basally branching genus), but has now been placed by some researchers into its own family, the Heterocephalidae. Given the importance of the masticatory apparatus in habitat construction in this group, knowledge and understanding of the morphology and arrangement of the jaw-closing muscles in Bathyergidae is vital for future functional analyses. Here, we use diffusible iodine-based contrast-enhanced microCT to reveal and describe the muscles of mastication in representative specimens of each genus of bathyergid mole-rat and to compare them to the previously described musculature of the naked mole-rat. In all bathyergids, as in all rodents, the masseter muscle is the most dominant component of the masticatory musculature. However, the temporalis is also a relatively large muscle, a condition normally associated with sciuromorphous rodents. Unlike their hystricomorphous relatives, the bathyergids do not show an extension of the masseter through the infraorbital foramen on to the rostrum (other than a very slight protrusion in Cryptomys and Fukomys). Thus, morphologically, bathyergids are protrogomorphous, although this is thought to be secondarily derived rather than retained from ancestral rodents. Overall, the relative proportions of the jaw-closing muscles were found to be fairly consistent between genera except in Bathyergus, which was found to have an enlarged superficial masseter and relatively smaller pterygoid muscles. It is concluded that these differences may be a reflection of the behaviour of Bathyergus which, uniquely in the family, does not use its incisors for digging.
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Affiliation(s)
- Philip G Cox
- Department of Archaeology and Hull York Medical School, University of York, York, UK
| | - Chris G Faulkes
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Nigel C Bennett
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
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Dang Y, Wang JY, Liu C, Zhang K, Jinrong P, He J. Evolutionary and Molecular Characterization of liver-enriched gene 1. Sci Rep 2020; 10:4262. [PMID: 32144352 PMCID: PMC7060313 DOI: 10.1038/s41598-020-61208-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 02/24/2020] [Indexed: 11/30/2022] Open
Abstract
Liver-enriched gene 1 (Leg1) is a newly identified gene with little available functional information. To evolutionarily and molecularly characterize Leg1 genes, a phylogenetic study was first conducted, which indicated that Leg1 is a conserved gene that exists from bacteria to mammals. During the evolution of mammals, Leg1s underwent tandem duplications, which gave rise to Leg1a, Leg1b, and Leg1c clades. Analysis of the pig genome showed the presence of all three paralogs of pig Leg1 genes (pLeg1s), whereas only Leg1a could be found in the human (hLeg1a) or mouse (mLeg1a) genomes. Purifying force acts on the evolution of Leg1 genes, likely subjecting them to functional constraint. Molecularly, pLeg1a and its coded protein, pig LEG1a (pLEG1a), displayed high similarities to its human and mouse homologs in terms of gene organization, expression patterns, and structures. Hence, pLeg1a, hLeg1a, and mLeg1a might preserve similar functions. Additionally, expression analysis of the three Leg1as suggested that eutherian Leg1as might have different functions from those of zebrafish and platypus due to subfunctionalization. Therefore, pLeg1a might provide essential information about eutherian Leg1a. Moreover, a preliminary functional study using RNA-seq suggested that pLeg1a is involved in the lipid homeostasis. In conclusion, our study provides some basic information on the aspects of evolution and molecular function, which could be applied for further validation of Leg1 using pig models.
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Affiliation(s)
- Yanna Dang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, PR China
| | - Jin-Yang Wang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, PR China
| | - Chen Liu
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, PR China
| | - Kun Zhang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, PR China
| | - Peng Jinrong
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, PR China
| | - Jin He
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, PR China.
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Potapova EG. Morphological Specificity of the Auditory Capsule of Sciurid (Sciuridae, Rodentia). BIOL BULL+ 2020. [DOI: 10.1134/s1062359019070094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Zherebtsova OV, Potapova EG. Pathways and Level of Morphological Adaptations in Modern Diatomyidae and Ctenodactylidae (Rodentia). BIOL BULL+ 2020. [DOI: 10.1134/s1062359019070124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Moutinho AF, Serén N, Paupério J, Silva TL, Martínez-Freiría F, Sotelo G, Faria R, Mappes T, Alves PC, Brito JC, Boratyński Z. Evolutionary history of two cryptic species of northern African jerboas. BMC Evol Biol 2020; 20:26. [PMID: 32054437 PMCID: PMC7020373 DOI: 10.1186/s12862-020-1592-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 02/03/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Climatic variation and geologic change both play significant roles in shaping species distributions, thus affecting their evolutionary history. In Sahara-Sahel, climatic oscillations shifted the desert extent during the Pliocene-Pleistocene interval, triggering the diversification of several species. Here, we investigated how these biogeographical and ecological events have shaped patterns of genetic diversity and divergence in African Jerboas, desert specialist rodents. We focused on two sister and cryptic species, Jaculus jaculus and J. hirtipes, where we (1) evaluated their genetic differentiation, (2) reconstructed their evolutionary and demographic history; (3) tested the level of gene flow between them, and (4) assessed their ecological niche divergence. RESULTS The analyses based on 231 individuals sampled throughout North Africa, 8 sequence fragments (one mitochondrial and seven single copy nuclear DNA, including two candidate genes for fur coloration: MC1R and Agouti), 6 microsatellite markers and ecological modelling revealed: (1) two distinct genetic lineages with overlapping distributions, in agreement with their classification as different species, J. jaculus and J. hirtipes, with (2) low levels of gene flow and strong species divergence, (3) high haplotypic diversity without evident geographic structure within species, and (4) a low level of large-scale ecological divergence between the two taxa, suggesting species micro-habitat specialization. CONCLUSIONS Overall, our results suggest a speciation event that occurred during the Pliocene-Pleistocene transition. The contemporary distribution of genetic variation suggests ongoing population expansions. Despite the largely overlapping distributions at a macrogeographic scale, our genetic results suggest that the two species remain reproductively isolated, as only negligible levels of gene flow were observed. The overlapping ecological preferences at a macro-geographic scale and the ecological divergence at the micro-habitat scale suggest that local adaptation may have played a crucial role in the speciation process of these species.
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Affiliation(s)
- Ana Filipa Moutinho
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany.
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal.
- Department of Biology, Faculty of Science, University of Porto, Porto, Portugal.
| | - Nina Serén
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
- Department of Biology, Faculty of Science, University of Porto, Porto, Portugal
- Division of Ecology and Evolutionary Biology, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Joana Paupério
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
| | - Teresa Luísa Silva
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
| | - Fernando Martínez-Freiría
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
| | - Graciela Sotelo
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
| | - Rui Faria
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
| | - Tapio Mappes
- Division of Ecology and Evolutionary Biology, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Paulo Célio Alves
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
- Department of Biology, Faculty of Science, University of Porto, Porto, Portugal
| | - José Carlos Brito
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal
- Department of Biology, Faculty of Science, University of Porto, Porto, Portugal
| | - Zbyszek Boratyński
- CIBIO-InBIO Associate Laboratory, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Vairão, Portugal.
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Irwin DM. Variation in the rates of evolution of the insulin and glucagon hormone and receptor genes in rodents. Gene 2020; 728:144296. [DOI: 10.1016/j.gene.2019.144296] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 12/13/2019] [Accepted: 12/13/2019] [Indexed: 02/07/2023]
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Zhou H, Chen Z, Limpanont Y, Hu Y, Ma Y, Huang P, Dekumyoy P, Zhou M, Cheng Y, Lv Z. Necroptosis and Caspase-2-Mediated Apoptosis of Astrocytes and Neurons, but Not Microglia, of Rat Hippocampus and Parenchyma Caused by Angiostrongylus cantonensis Infection. Front Microbiol 2020; 10:3126. [PMID: 32038563 PMCID: PMC6989440 DOI: 10.3389/fmicb.2019.03126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 12/24/2019] [Indexed: 01/18/2023] Open
Abstract
Infection with the roundworm Angiostrongylus cantonensis is the main cause of eosinophilic meningitis worldwide. The underlying molecular basis of the various pathological outcomes in permissive and non-permissive hosts infected with A. cantonensis remains poorly defined. In the present study, the histology of neurological disorders in the central nervous system (CNS) of infected rats was assessed by using hematoxylin and eosin staining. Quantitative reverse transcription polymerase chain reaction (RT-qPCR), western blot and immunofluorescence (IF) were used in evolutions of the transcription and translation levels of the apoptosis-, necroptosis-, autophagy-, and pyroptosis-related genes. The distribution of apoptotic and necroptotic cells in the rat hippocampus and parenchyma was further detected using flow cytometry, and the features of the ultrastructure of the cells were examined by transmission electron microscopy (TEM). The inflammatory response upon CNS infection with A. cantonensis evolved, as characterized by the accumulation of a small number of inflammatory cells under the thickened meninges, which peaked at 21 days post-infection (dpi) and returned to normal by 35 dpi. The transcription levels and translation of caspase-2, caspase-8, RIP1 and RIP3 increased significantly at 21 and 28 dpi but decreased sharply at 35 dpi compared to those in the normal control group. However, the changes in the expression of caspase-1, caspase-3, caspase-11, Beclin-1 and LC3B were not obvious, suggesting that apoptosis and necroptosis but not autophagy or pyroptosis occurred in the brains of infected animals at 21 and 28 dpi. The results of RT-qPCR, western blot analysis, IF, flow cytometry and TEM further illustrated that necroptosis and caspase-2-mediated apoptosis occurred in astrocytes and neurons but not in microglia in the parenchyma and hippocampus of infected animals. This study provides the first evidence that neuronal and astrocytic necroptosis and caspase-2-mediated apoptosis are induced by A. cantonensis infection in the parenchymal and hippocampal regions of rats at 21 and 28 dpi but these processes are negligible at 35 dpi. These findings enhance our understanding of the pathogenesis of A. cantonensis infection and provide new insights into therapeutic approaches targeting the occurrence of cell death in astrocytes and neurons in infected patients.
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Affiliation(s)
- Hongli Zhou
- Joint Program of Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Zhe Chen
- Joint Program of Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Yanin Limpanont
- Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Yue Hu
- Joint Program of Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Yubin Ma
- Joint Program of Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Ping Huang
- Joint Program of Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Paron Dekumyoy
- Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Minyu Zhou
- Joint Program of Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Yixin Cheng
- Joint Program of Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Zhiyue Lv
- Joint Program of Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou, China
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
- Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
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Acrosin is essential for sperm penetration through the zona pellucida in hamsters. Proc Natl Acad Sci U S A 2020; 117:2513-2518. [PMID: 31964830 DOI: 10.1073/pnas.1917595117] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During natural fertilization, mammalian spermatozoa must pass through the zona pellucida before reaching the plasma membrane of the oocyte. It is assumed that this step involves partial lysis of the zona by sperm acrosomal enzymes, but there has been no unequivocal evidence to support this view. Here we present evidence that acrosin, an acrosomal serine protease, plays an essential role in sperm penetration of the zona. We generated acrosin-knockout (KO) hamsters, using an in vivo transfection CRISPR/Cas9 system. Homozygous mutant males were completely sterile. Acrosin-KO spermatozoa ascended the female genital tract and reached ovulated oocytes in the oviduct ampulla, but never fertilized them. In vitro fertilization (IVF) experiments revealed that mutant spermatozoa attached to the zona, but failed to penetrate it. When the zona pellucida was removed before IVF, all oocytes were fertilized. This indicates that in hamsters, acrosin plays an indispensable role in allowing fertilizing spermatozoa to penetrate the zona. This study also suggests that the KO hamster system would be a useful model for identifying new gene functions or analyzing human and animal disorders because of its technical facility and reproducibility.
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Proximal Humerus Morphology Indicates Divergent Patterns of Locomotion in Extinct Giant Kangaroos. J MAMM EVOL 2020. [DOI: 10.1007/s10914-019-09494-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
AbstractSthenurine kangaroos, extinct “giant kangaroos” known predominantly from the Plio-Pleistocene, have been proposed to have used bipedal striding as a mode of locomotion, based on the morphology of their hind limbs. However, sthenurine forelimb morphology has not been considered in this context, and has important bearing as to whether these kangaroos employed quadrupedal or pentapedal locomotion as a slow gait, as in extant kangaroos. Study of the correlation of morphology of the proximal humerus in a broad range of therian mammals shows that humeral morphology is indicative of the degree of weight-bearing on the forelimbs during locomotion, with terrestrial species being distinctly different from arboreal ones. Extant kangaroos have a proximal humeral morphology similar to extant scansorial (semi-arboreal) mammals, but sthenurine humeri resemble those of suspensory arboreal taxa, which rarely bear weight on their forelimbs, supporting the hypothesis that they used bipedal striding rather than quadrupedal locomotion at slow gaits. The humeral morphology of the enigmatic extinct “giant wallaby,” Protemnodon, may be indicative of a greater extent of quadrupedal locomotion than in extant kangaroos.
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Marivaux L, Boivin M. Emergence of hystricognathous rodents: Palaeogene fossil record, phylogeny, dental evolution and historical biogeography. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz048] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractAlthough phylogenetic trees imply Asia as the ancestral homeland of the Hystricognathi clade (Rodentia: Ctenohystrica), curiously the oldest known fossil occurrences of hystricognathous rodents are not from Asia, but from Africa and South America, where they appear suddenly in the fossil record of both landmasses by the Late Middle Eocene. Here we performed cladistic and Bayesian (standard and tip-dating analyses) assessments of the dental evidence documenting early ctenohystricans, including several Asian ‘ctenodactyloids’, virtually all Palaeogene Asian and African hystricognaths known thus far and two representatives of the earliest known South American hystricognaths. Our results provide a phylogenetic context of early hystricognaths (with implications on systematics) and suggest that some Eocene Asian ‘ctenodactyloids’ could be considered as stem hystricognaths and pre-hystricognaths, although they were not recognized as such originally. However, this view does not fill the gap of the Eocene Asian hystricognath record, as the proposed results imply many ghost lineages extending back to the Middle Eocene for several Asian and African taxa. They also imply a complex early historical biogeography of the group, involving multiple dispersal events from Asia to Africa (and possibly from Africa back to Asia) and then to South America sometime during the Middle Eocene. Based on these phylogenetic considerations, we discuss the emergence of hystricognathous rodents from a morpho-anatomical perspective by analysing the differentiation of their masticatory apparatus and chewing movements, notably through the evolution of their dental patterns.
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Affiliation(s)
- Laurent Marivaux
- Laboratoire de Paléontologie, Institut des Sciences de l’Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier, place Eugène Bataillon, France
| | - Myriam Boivin
- Laboratoire de Paléontologie, Institut des Sciences de l’Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier, place Eugène Bataillon, France
- Laboratoire de Planétologie et Géodynamique (LPG, UMR 6112 CNRS, Université de Nantes), France
- Instituto de Ecorregiones Andinas (INECOA), Universidad Nacional de Jujuy, CONICET, Argentina
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Jiao H, Hong W, Nevo E, Li K, Zhao H. Convergent reduction of V1R genes in subterranean rodents. BMC Evol Biol 2019; 19:176. [PMID: 31470793 PMCID: PMC6717356 DOI: 10.1186/s12862-019-1502-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 08/23/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Vomeronasal type 1 receptor genes (V1Rs) are expected to detect intraspecific pheromones. It is believed that rodents rely heavily on pheromonal communication mediated by V1Rs, but pheromonal signals are thought to be confined in subterranean rodents that live in underground burrows. Thus, subterranean rodents may show a contrasting mode of V1R evolution compared with their superterranean relatives. RESULTS We examined the V1R evolution in subterranean rodents by analyzing currently available genomes of 24 rodents, including 19 superterranean and 5 subterranean species from three independent lineages. We identified a lower number of putatively functional V1R genes in each subterranean rodent (a range of 22-40) compared with superterranean species (a range of 63-221). After correcting phylogenetic inertia, the positive correlation remains significant between the small V1R repertoire size and the subterranean lifestyle. To test whether V1Rs have been relaxed from functional constraints in subterranean rodents, we sequenced 22 intact V1Rs in 29 individuals of one subterranean rodent (Spalax galili) from two soil populations, which have been proposed to undergo incipient speciation. We found 12 of the 22 V1Rs to show significant genetic differentiations between the two natural populations, indicative of diversifying selection. CONCLUSION Our study demonstrates convergent reduction of V1Rs in subterranean rodents from three independent lineages. Meanwhile, it is noteworthy that most V1Rs in the two Spalax populations are under diversifying selection rather than relaxed selection, suggesting that functional constraints on these genes may have retained in some subterranean species.
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Affiliation(s)
- Hengwu Jiao
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, 299 Bayi Road, Wuhan, 430072, Hubei, China
| | - Wei Hong
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, 299 Bayi Road, Wuhan, 430072, Hubei, China
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, 31905, Haifa, Israel
| | - Kexin Li
- Institute of Evolution, University of Haifa, Mount Carmel, 31905, Haifa, Israel
| | - Huabin Zhao
- Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, 299 Bayi Road, Wuhan, 430072, Hubei, China.
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Sügis E, Dauvillier J, Leontjeva A, Adler P, Hindie V, Moncion T, Collura V, Daudin R, Loe-Mie Y, Herault Y, Lambert JC, Hermjakob H, Pupko T, Rain JC, Xenarios I, Vilo J, Simonneau M, Peterson H. HENA, heterogeneous network-based data set for Alzheimer's disease. Sci Data 2019; 6:151. [PMID: 31413325 PMCID: PMC6694132 DOI: 10.1038/s41597-019-0152-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 06/18/2019] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease and other types of dementia are the top cause for disabilities in later life and various types of experiments have been performed to understand the underlying mechanisms of the disease with the aim of coming up with potential drug targets. These experiments have been carried out by scientists working in different domains such as proteomics, molecular biology, clinical diagnostics and genomics. The results of such experiments are stored in the databases designed for collecting data of similar types. However, in order to get a systematic view of the disease from these independent but complementary data sets, it is necessary to combine them. In this study we describe a heterogeneous network-based data set for Alzheimer's disease (HENA). Additionally, we demonstrate the application of state-of-the-art graph convolutional networks, i.e. deep learning methods for the analysis of such large heterogeneous biological data sets. We expect HENA to allow scientists to explore and analyze their own results in the broader context of Alzheimer's disease research.
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Affiliation(s)
- Elena Sügis
- Quretec Ltd., Ülikooli 6a, 51003, Tartu, Estonia
- Institute of Computer Science, University of Tartu, J. Liivi 2, 50409, Tartu, Estonia
| | - Jerome Dauvillier
- Swiss Institute of Bioinformatics, Vital-IT group, Unil Quartier Sorge, Genopode building, CH-1015, Lausanne, Switzerland
| | - Anna Leontjeva
- CSIRO Data 61, 5/13 Garden St, Eveleigh, NSW, 2015, Australia
| | - Priit Adler
- Quretec Ltd., Ülikooli 6a, 51003, Tartu, Estonia
- Institute of Computer Science, University of Tartu, J. Liivi 2, 50409, Tartu, Estonia
| | - Valerie Hindie
- Hybrigenics SA, 3-5 Impasse Reille, 75014, Paris, France
| | - Thomas Moncion
- Hybrigenics SA, 3-5 Impasse Reille, 75014, Paris, France
| | | | - Rachel Daudin
- Institut national de la santé et de la recherche médicale, INSERM U894 2 ter rue d'Alésia, 75014, Paris, France
- Laboratoire Aimé Cotton, Centre National Recherche Scientifique, Université Paris-Sud, Ecole Normale Supérieure Paris-Saclay, Université Paris-Saclay, 91405, Orsay, France
| | - Yann Loe-Mie
- (Epi)genomics of Animal Development Unit, Institut Pasteur, CNRS UMR3738, Paris, 75015, France
| | - Yann Herault
- Centre Européen de Recherche en Biologie et Médecine, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Jean-Charles Lambert
- Institut Pasteur de Lille, UMR 744 1 rue du Pr. Calmette BP 245, 59019, Lille cedex, France
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, United Kingdom
| | - Tal Pupko
- George S. Wise Faculty of Life Sciences, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, P.O. Box 39040, 6997801, Tel Aviv, Israel
| | | | - Ioannis Xenarios
- Center for Integrative Genomics University of Lausanne, Genopode, 1015, Lausanne, Switzerland
- Genome Center Health 2030, Analytical Platform Department, Chemin des Mines 9, 1202, Genève, Switzerland
- DFR CHUV, Rue du Bugnon 21, 1011, Lausanne, Switzerland
- Agora Center, LICR/Department of Oncology, Rue du Bugnon 25A, 1005, Lausanne, Switzerland
| | - Jaak Vilo
- Quretec Ltd., Ülikooli 6a, 51003, Tartu, Estonia
- Institute of Computer Science, University of Tartu, J. Liivi 2, 50409, Tartu, Estonia
| | - Michel Simonneau
- Institut national de la santé et de la recherche médicale, INSERM U894 2 ter rue d'Alésia, 75014, Paris, France.
- Laboratoire Aimé Cotton, Centre National Recherche Scientifique, Université Paris-Sud, Ecole Normale Supérieure Paris-Saclay, Université Paris-Saclay, 91405, Orsay, France.
| | - Hedi Peterson
- Quretec Ltd., Ülikooli 6a, 51003, Tartu, Estonia.
- Institute of Computer Science, University of Tartu, J. Liivi 2, 50409, Tartu, Estonia.
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Ghafari SM, Ebadatgar V, Mohammadi S, Ebrahimi S, Bordbar A, Parvizi P. Morphologic, Morphometric and Molecular Comparison of Two Sister Species of Rodents as Potential Reservoir Hosts of Zoonotic Cutaneous Leishmaniasis in the Southwest of Iran. JOURNAL OF MEDICAL MICROBIOLOGY AND INFECTIOUS DISEASES 2019. [DOI: 10.29252/jommid.7.3.79] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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40
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Lang D, Lim BK, Gao Y, Wang X. Adaptive evolutionary expansion of the ribonuclease 6 in Rodentia. Integr Zool 2019; 14:306-317. [PMID: 30688011 DOI: 10.1111/1749-4877.12382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Ribonuclease 6 (RNase6 or RNase K6) is a protein that belongs to a superfamily thought to be the sole verte-brate-specific enzyme known for a wide range of physiological functions, including digestion, cytotoxicity, angiogenesis, male reproduction and host defense. In our study, 51 functional genes and 11 pseudogenes were identified from 27 Rodentia species. Intriguingly, in the 3 main lineages of rodents there were multiple RNase6s identified in all species of Ctenohystrica, whereas only a single RNase6 was observed in other Rodentia species examined except for 2 species in the mouse-related clade. The evolutionary scenario of "birth (gene duplication) and death (gene deactivation)" and gene sorting have been demonstrated in Ctenohystrica. In addition, bursts of positive selection, diversification of isoelectric point and positive net charge have been identified in Ctenohystrica, especially at two key sites that are involved in antimicrobial function. Site Trp30 has undergone positive selection and Ile45 has changed into other residues in Group B and Group C of the Ctenohystrica. Our results demonstrated a complex and intriguing evolutionary pattern of rodent RNase6, and indicated that functional modification may have occurred, which establishes an important theoretical foundation for future functional assays in rodent RNase6.
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Affiliation(s)
- Datian Lang
- Agronomy and Life Science Department, Zhaotong University, Zhaotong, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, China
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Yun Gao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, China
| | - Xiaoping Wang
- School of Life Sciences, Yunnan University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, China.,Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, Yunnan University, Kunming, China
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D’Elía G, Fabre PH, Lessa EP. Rodent systematics in an age of discovery: recent advances and prospects. J Mammal 2019. [DOI: 10.1093/jmammal/gyy179] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Guillermo D’Elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Pierre-Henri Fabre
- Institut des Sciences de l’Evolution (ISEM, UMR 5554 CNRS-UM2-IRD), Université Montpellier, Montpellier Cedex 5, France
| | - Enrique P Lessa
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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Gossmann TI, Shanmugasundram A, Börno S, Duvaux L, Lemaire C, Kuhl H, Klages S, Roberts LD, Schade S, Gostner JM, Hildebrand F, Vowinckel J, Bichet C, Mülleder M, Calvani E, Zelezniak A, Griffin JL, Bork P, Allaine D, Cohas A, Welch JJ, Timmermann B, Ralser M. Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity. Curr Biol 2019; 29:1712-1720.e7. [PMID: 31080084 PMCID: PMC6538971 DOI: 10.1016/j.cub.2019.04.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/16/2019] [Accepted: 04/09/2019] [Indexed: 12/30/2022]
Abstract
Some species responded successfully to prehistoric changes in climate [1, 2], while others failed to adapt and became extinct [3]. The factors that determine successful climate adaptation remain poorly understood. We constructed a reference genome and studied physiological adaptations in the Alpine marmot (Marmota marmota), a large ground-dwelling squirrel exquisitely adapted to the "ice-age" climate of the Pleistocene steppe [4, 5]. Since the disappearance of this habitat, the rodent persists in large numbers in the high-altitude Alpine meadow [6, 7]. Genome and metabolome showed evidence of adaptation consistent with cold climate, affecting white adipose tissue. Conversely, however, we found that the Alpine marmot has levels of genetic variation that are among the lowest for mammals, such that deleterious mutations are less effectively purged. Our data rule out typical explanations for low diversity, such as high levels of consanguineous mating, or a very recent bottleneck. Instead, ancient demographic reconstruction revealed that genetic diversity was lost during the climate shifts of the Pleistocene and has not recovered, despite the current high population size. We attribute this slow recovery to the marmot's adaptive life history. The case of the Alpine marmot reveals a complicated relationship between climatic changes, genetic diversity, and conservation status. It shows that species of extremely low genetic diversity can be very successful and persist over thousands of years, but also that climate-adapted life history can trap a species in a persistent state of low genetic diversity.
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Affiliation(s)
- Toni I Gossmann
- University of Sheffield, Department of Animal and Plant Sciences, Sheffield S10 2TN, UK; Bielefeld University, Department of Animal Behaviour, 33501 Bielefeld, Germany
| | - Achchuthan Shanmugasundram
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
| | - Stefan Börno
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany
| | - Ludovic Duvaux
- IRHS, Université d'Angers, INRA, Agrocampus-Ouest, SFR 4207 QuaSaV, 49071 Beaucouzé, France; BIOGECO, INRA, Université de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
| | - Christophe Lemaire
- IRHS, Université d'Angers, INRA, Agrocampus-Ouest, SFR 4207 QuaSaV, 49071 Beaucouzé, France
| | - Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany; Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, 12587 Berlin, Germany
| | - Sven Klages
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany
| | - Lee D Roberts
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Sophia Schade
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany
| | - Johanna M Gostner
- Division of Medical Biochemistry, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Falk Hildebrand
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK; Gut Health and Microbes Programme, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | | | - Michael Mülleder
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; Department of Biochemistry, Charitè, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Enrica Calvani
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Aleksej Zelezniak
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden; Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm 171 65, Sweden
| | - Julian L Griffin
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Peer Bork
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany; Molecular Medicine Partnership Unit, 69120 Heidelberg, Germany
| | - Dominique Allaine
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, France
| | - Aurélie Cohas
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, France
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany
| | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; Department of Biochemistry, Charitè, Am Chariteplatz 1, 10117 Berlin, Germany.
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Bertrand OC, San Martin‐Flores G, Silcox MT. Endocranial shape variation in the squirrel‐related clade and their fossil relatives using 3D geometric morphometrics: contributions of locomotion and phylogeny to brain shape. J Zool (1987) 2019. [DOI: 10.1111/jzo.12665] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- O. C. Bertrand
- School of GeoSciences University of Edinburgh Grant Institute Edinburgh UK
| | | | - M. T. Silcox
- Department of Anthropology University of Toronto Scarborough Toronto ON Canada
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Neves F, Abrantes J, Lopes AM, Fusinatto LA, Magalhães MJ, van der Loo W, Esteves PJ. Evolution of CCL16 in Glires (Rodentia and Lagomorpha) shows an unusual random pseudogenization pattern. BMC Evol Biol 2019; 19:59. [PMID: 30786851 PMCID: PMC6383237 DOI: 10.1186/s12862-019-1390-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 02/13/2019] [Indexed: 12/16/2022] Open
Abstract
Background The C-C motif chemokine ligand 16 (CCL16) is a potent pro-inflammatory chemokine and a chemoattractant for monocytes and lymphocytes. In normal plasma, it is present at high concentrations and elicits its effects on cells by interacting with cell surface chemokine receptors. In the European rabbit and in rodents such as mouse, rat and guinea pig, CCL16 was identified as a pseudogene, while in the thirteen-lined ground squirrel it appears to be potentially functional. To gain insight into the evolution of this gene in the superorder Glires (rodents and lagomorphs), we amplified the CCL16 gene from eleven Leporidae and seven Ochotonidae species. Results We compared our sequences with CCL16 sequences of twelve rodent species retrieved from public databases. The data show that for all leporid species studied CCL16 is a pseudogene. This is primarily due to mutations at the canonical Cys Cys motif, creating either premature stop codons, or disrupting amino acid replacements. In the Mexican cottontail, CCL16 is pseudogenized due to a frameshift deletion. Additionally, in the exon 1 (signal peptide), there are frameshift deletions present in all leporids studied. In contrast, in Ochotona species, CCL16 is potentially functional, except for an allele in Hoffmann’s pika. In rodents, CCL16 is functional in a number of species, but patterns of pseudogenization similar to those observed in lagomorphs also exist. Conclusions Our results suggest that while functional in the Glires ancestor, CCL16 underwent pseudogenization in some species. This process occurred stochastically or in specific lineages at different moments in the evolution of Glires. These observations suggest that the CCL16 had different evolutionary constrains in the Glires group that could be associated with the CCL16 biological function. Electronic supplementary material The online version of this article (10.1186/s12862-019-1390-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fabiana Neves
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,UMIB/UP - Unidade Multidisciplinar de Investigação Biomédica/Universidade do Porto, Porto, Portugal
| | - Joana Abrantes
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Ana M Lopes
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,UMIB/UP - Unidade Multidisciplinar de Investigação Biomédica/Universidade do Porto, Porto, Portugal
| | - Luciana A Fusinatto
- Departamento de Ecologia, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro (UERJ), R. São Francisco Xavier 524, Rio de Janeiro, RJ, CEP 20550-013, Brazil
| | - Maria J Magalhães
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Wessel van der Loo
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Pedro J Esteves
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal. .,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal. .,CITS - Centro de Investigação em Tecnologias de Saúde, CESPU, Gandra, Portugal.
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Lipka A, Paukszto L, Majewska M, Jastrzebski JP, Panasiewicz G, Szafranska B. De novo characterization of placental transcriptome in the Eurasian beaver (Castor fiber L.). Funct Integr Genomics 2019; 19:421-435. [PMID: 30778795 PMCID: PMC6456477 DOI: 10.1007/s10142-019-00663-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 04/17/2018] [Accepted: 02/04/2019] [Indexed: 12/11/2022]
Abstract
Our pioneering data provide the first comprehensive view of placental transcriptome of the beaver during single and multiple gestation. RNA-Seq and a de novo approach allowed global pattern identification of C. fiber placental transcriptome. Non-redundant beaver transcriptome comprised 211,802,336 nt of placental transcripts, grouped into 128,459 contigs and clustered into 83,951 unigenes. An Ensembl database search revealed 14,487, 14,994, 15,004, 15,267 and 15,892 non-redundant homologs for Ictidomys tridecemlineatus, Rattus norvegicus, Mus musculus, Homo sapiens and Castor canadensis, respectively. Due to expression levels, the identified transcripts were divided into two sets: non-redundant and highly expressed (FPKM > 2 in at least three examined samples), analysed simultaneously. Among 17,009 highly expressed transcripts, 12,147 had BLASTx hits. GO annotations (175,882) were found for 4301 transcripts that were assigned to biological process (16,386), cellular component (9149) and molecular function (8338) categories; 666 unigenes were also classified into 122 KEGG pathways. Comprehensive analyses were performed for 411 and 3078 highly expressed transcripts annotated with a list of processes linked to ‘placenta’ (31 GO terms) or ‘embryo’ (324 GO terms), respectively. Among transcripts with entire CDS annotation, 281 (placenta) and 34 (embryo) alternative splicing events were identified. A total of 8499 putative SNVs (~ 6.2 SNV/transcript and 1.7 SNV/1 kb) were predicted with 0.1 minimum frequency and maximum variant quality (p value 10e−9). Our results provide a broad-based characterization of the global expression pattern of the beaver placental transcriptome. Enhancement of transcriptomic resources for C. fiber should improve understanding of crucial pathways relevant to proper placenta development and successful reproduction.
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Affiliation(s)
- Aleksandra Lipka
- Department of Gynecology and Obstetrics, School of Medicine, Collegium Medicum, University of Warmia and Mazury in Olsztyn, Niepodległości Str 44, 10-045, Olsztyn, Poland.
| | - Lukasz Paukszto
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego Str 1A, 10-719, Olsztyn, Poland
| | - Marta Majewska
- Department of Human Physiology, School of Medicine, Collegium Medicum, University of Warmia and Mazury in Olsztyn, Warszawska Str 30, 10-082, Olsztyn, Poland
| | - Jan Pawel Jastrzebski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego Str 1A, 10-719, Olsztyn, Poland
| | - Grzegorz Panasiewicz
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego Str 1A, 10-719 Olsztyn, Poland
| | - Bozena Szafranska
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego Str 1A, 10-719 Olsztyn, Poland
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Muchlinski MN, Wible JR, Corfe I, Sullivan M, Grant RA. Good Vibrations: The Evolution of Whisking in Small Mammals. Anat Rec (Hoboken) 2018; 303:89-99. [PMID: 30332721 DOI: 10.1002/ar.23989] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/14/2018] [Indexed: 01/11/2023]
Abstract
While most mammals have whiskers, some tactile specialists-mainly small, nocturnal, and arboreal species-can actively move their whiskers in a symmetrical, cyclic movement called whisking. Whisking enables mammals to rapidly, tactually scan their environment to efficiently guide locomotion and foraging in complex habitats. The muscle architecture that enables whisking is preserved from marsupials to primates, prompting researchers to suggest that a common ancestor might have had moveable whiskers. Studying the evolution of whisker touch sensing is difficult, and we suggest that measuring an aspect of skull morphology that correlates with whisking would enable comparisons between extinct and extant mammals. We find that whisking mammals have larger infraorbital foramen (IOF) areas, which indicates larger infraorbital nerves and an increase in sensory acuity. While this relationship is quite variable and IOF area cannot be used to solely predict the presence of whisking, whisking mammals all have large IOF areas. Generally, this pattern holds true regardless of an animal's substrate preferences or activity patterns. Data from fossil mammals and ancestral character state reconstruction and tracing techniques for extant mammals suggest that whisking is not the ancestral state for therian mammals. Instead, whisking appears to have evolved independently as many as seven times across the clades Marsupialia, Afrosoricida, Eulipotyphla, and Rodentia, with Xenarthra the only placental superordinal clade lacking whisking species. However, the term whisking only captures symmetrical and rhythmic movements of the whiskers, rather than all possible whisker movements, and early mammals may still have had moveable whiskers. Anat Rec, 2018. © 2018 American Association for Anatomy.
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Affiliation(s)
- Magdalena N Muchlinski
- Center for Anatomical Sciences, University of North Texas Health Science Center, Fort Worth, Texas
| | - John R Wible
- Section of Mammals, Carnegie Museum of Natural History, Pittsburgh, Pennsylvania
| | - Ian Corfe
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Matthew Sullivan
- Division of Biology and Conservation Ecology, Manchester Metropolitan University, Manchester, UK
| | - Robyn A Grant
- Division of Biology and Conservation Ecology, Manchester Metropolitan University, Manchester, UK
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Smissen PJ, Rowe KC. Repeated biome transitions in the evolution of Australian rodents. Mol Phylogenet Evol 2018; 128:182-191. [DOI: 10.1016/j.ympev.2018.07.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 06/26/2018] [Accepted: 07/16/2018] [Indexed: 12/31/2022]
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Casanovas-Vilar I, Garcia-Porta J, Fortuny J, Sanisidro Ó, Prieto J, Querejeta M, Llácer S, Robles JM, Bernardini F, Alba DM. Oldest skeleton of a fossil flying squirrel casts new light on the phylogeny of the group. eLife 2018; 7:39270. [PMID: 30296996 PMCID: PMC6177260 DOI: 10.7554/elife.39270] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 09/10/2018] [Indexed: 11/29/2022] Open
Abstract
Flying squirrels are the only group of gliding mammals with a remarkable diversity and wide geographical range. However, their evolutionary story is not well known. Thus far, identification of extinct flying squirrels has been exclusively based on dental features, which, contrary to certain postcranial characters, are not unique to them. Therefore, fossils attributed to this clade may indeed belong to other squirrel groups. Here we report the oldest fossil skeleton of a flying squirrel (11.6 Ma) that displays the gliding-related diagnostic features shared by extant forms and allows for a recalibration of the divergence time between tree and flying squirrels. Our phylogenetic analyses combining morphological and molecular data generally support older dates than previous molecular estimates (~23 Ma), being congruent with the inclusion of some of the earliest fossils (~36 Ma) into this clade. They also show that flying squirrels experienced little morphological change for almost 12 million years. Mammals can walk, hop, swim and fly; a few, like marsupial sugar gliders or colugos, can even glide. With 52 species scattered across the Northern hemisphere, flying squirrels are by far the most successful group that adopted this way of going airborne. To drift from tree to tree, these small animals pack their own ‘parachute’: a membrane draping between their lower limbs and the long cartilage rods that extend from their wrists. Tiny specialized wrist bones, which are unique to flying squirrels, help to support the cartilaginous extensions. The origin of flying squirrels is a point of contention: while most genetic studies point towards the group splitting from tree squirrels about 23 million years ago, the oldest remains – mostly cheek teeth – suggest the animals were already soaring through forests 36 million years ago. However, recent studies show that the dental features used to distinguish between gliding and non-gliding squirrels may actually be shared by the two groups. In 2002, the digging of a dump site in Barcelona unearthed a peculiar skeleton: first a tail and two thigh bones, big enough that the researchers thought it could be the fossil of a small primate. In fact, and much to the disappointment of paleoprimatologists, further excavating revealed that it was a rodent. As the specimen – nearly an entire skeleton – was being prepared, paleontologists insisted that all the ‘dirt’ attached to the bones had to be carefully screen-washed. From the mud emerged the minuscule specialized wrist bones: the primate-turned-rodent was in fact Miopetaurista neogrivensis, an extinct flying squirrel. Here, Casanovas-Vilar et al. describe the 11.6 million years old fossil, the oldest ever found. The wrist bones reveal that the animal belongs to the group of flying squirrels that have large sizes. Evolutionary analyses that combined molecular and paleontological data demonstrated that flying squirrels evolved from tree squirrels as far back as 31 to 25 million years ago, and possibly even earlier. In addition, the results show that Miopetaurista is closely related to Petaurista, a modern group of giant flying squirrels. In fact, their skeletons are so similar that the large species that currently inhabit the tropical and subtropical forests of Asia could be considered living fossils. Molecular and paleontological data are often at odds, but this fossil shows that they can be reconciled and combined to retrace history. Discovering older fossils, or even transitional forms, could help to retrace how flying squirrels took a leap from the rest of their evolutionary tree.
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Affiliation(s)
- Isaac Casanovas-Vilar
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Joan Garcia-Porta
- Centre de Recerca Ecològica i Aplicacions Forestals, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Josep Fortuny
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain.,Centre de Recherches sur les Paléoenvironnements et la Paléobiodiversité, Muséum national d'Histoire naturelle, Paris, France
| | - Óscar Sanisidro
- Biodiversity Institute, University of Kansas, Lawrence, United States
| | - Jérôme Prieto
- Department für Geo- und Umweltwissenschaften, Paläontologie, Ludwig-Maximilians-Universität München, Munich, Germany.,Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
| | | | - Sergio Llácer
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Josep M Robles
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Federico Bernardini
- Centro Fermi, Museo Storico della Fisica e Centro Studi e Ricerche Enrico Fermi, Roma, Italy.,Multidisciplinary Laboratory, The 'Abdus Salam' International Centre for Theoretical Physics, Trieste, Italy
| | - David M Alba
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
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Wu Z, Lu L, Du J, Yang L, Ren X, Liu B, Jiang J, Yang J, Dong J, Sun L, Zhu Y, Li Y, Zheng D, Zhang C, Su H, Zheng Y, Zhou H, Zhu G, Li H, Chmura A, Yang F, Daszak P, Wang J, Liu Q, Jin Q. Comparative analysis of rodent and small mammal viromes to better understand the wildlife origin of emerging infectious diseases. MICROBIOME 2018; 6:178. [PMID: 30285857 PMCID: PMC6171170 DOI: 10.1186/s40168-018-0554-9] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 09/05/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Rodents represent around 43% of all mammalian species, are widely distributed, and are the natural reservoirs of a diverse group of zoonotic viruses, including hantaviruses, Lassa viruses, and tick-borne encephalitis viruses. Thus, analyzing the viral diversity harbored by rodents could assist efforts to predict and reduce the risk of future emergence of zoonotic viral diseases. RESULTS We used next-generation sequencing metagenomic analysis to survey for a range of mammalian viral families in rodents and other small animals of the orders Rodentia, Lagomorpha, and Soricomorpha in China. We sampled 3,055 small animals from 20 provinces and then outlined the spectra of mammalian viruses within these individuals and the basic ecological and genetic characteristics of novel rodent and shrew viruses among the viral spectra. Further analysis revealed that host taxonomy plays a primary role and geographical location plays a secondary role in determining viral diversity. Many viruses were reported for the first time with distinct evolutionary lineages, and viruses related to known human or animal pathogens were identified. Phylogram comparison between viruses and hosts indicated that host shifts commonly happened in many different species during viral evolutionary history. CONCLUSIONS These results expand our understanding of the viromes of rodents and insectivores in China and suggest that there is high diversity of viruses awaiting discovery in these species in Asia. These findings, combined with our previous bat virome data, greatly increase our knowledge of the viral community in wildlife in a densely populated country in an emerging disease hotspot.
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Affiliation(s)
- Zhiqiang Wu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People's Republic of China
| | - Liang Lu
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Jiang Du
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Li Yang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Xianwen Ren
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Bo Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Jinyong Jiang
- Yunnan Institute of Parasitic Diseases, Puer, People's Republic of China
| | - Jian Yang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Jie Dong
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Lilian Sun
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Yafang Zhu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Yuhui Li
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Dandan Zheng
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Chi Zhang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Haoxiang Su
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Yuting Zheng
- Yunnan Institute of Parasitic Diseases, Puer, People's Republic of China
| | - Hongning Zhou
- Yunnan Institute of Parasitic Diseases, Puer, People's Republic of China
| | | | | | | | - Fan Yang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | | | - Jianwei Wang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People's Republic of China.
| | - Qiyong Liu
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China.
| | - Qi Jin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People's Republic of China.
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