1
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Hao Q, Yang H, Sun Y, Xu T, Huang H. Evolutionary game on mutually influenceing double-layer network. PLoS One 2025; 20:e0317923. [PMID: 39888920 PMCID: PMC11785339 DOI: 10.1371/journal.pone.0317923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Accepted: 01/07/2025] [Indexed: 02/02/2025] Open
Abstract
In recent years, coupled double-layer networks have played an increasingly critical role in evolutionary game theory. Research indicates that these networks more accurately reflect real-world relationships between individuals. However, current studies mainly focus on unidirectional influence within double-layer networks. Based on this, we propose a strongly coupled double-layer network cooperation evolution model. Strength individuals are located in the upper network layer, influencing the strategy choices of ordinary individuals in the lower layer, and vice versa. Monte Carlo simulations show that strength individuals can effectively enhance overall group cooperation. Under low temptation to defect, the group maintains a high cooperation rate; under high temptation, the presence of strength individuals prevents the group from falling into total defection, helping ordinary individuals escape the defection dilemma and improve cooperation levels.
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Affiliation(s)
- Qinzhi Hao
- Air Force Engineering University, Xi’an, China
| | - Haochun Yang
- School of Computer Science and Engineering, Northwestern Polytechnical University, Xi’an, China
| | - Yao Sun
- Air Force Engineering University, Xi’an, China
| | - Tao Xu
- School of Computer Science and Engineering, Northwestern Polytechnical University, Xi’an, China
| | - Huang Huang
- School of Computer Science and Engineering, Northwestern Polytechnical University, Xi’an, China
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2
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Xia X. Phylogeographic Analysis for Understanding Origin, Speciation, and Biogeographic Expansion of Invasive Asian Hornet, Vespa velutina Lepeletier, 1836 (Hymenoptera, Vespidae). Life (Basel) 2024; 14:1293. [PMID: 39459593 PMCID: PMC11509734 DOI: 10.3390/life14101293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2024] [Revised: 10/08/2024] [Accepted: 10/10/2024] [Indexed: 10/28/2024] Open
Abstract
The Asian hornet, Vespa velutina, is an invasive species that has not only expanded its range in Asia but has also invaded European countries, and it incurs significant costs on local apiculture. This phylogeographic study aims to trace the evolutionary trajectory of V. velutina and its close relatives; it aims to identify features that characterize an invasive species. The last successful invasion of Vespa velutina into France occurred in late May, 2002, and into South Korea in early October, 2002, which were estimated by fitting a logistic equation to the number of observations over time. The instantaneous rate of increase is 1.3667 for V. velutina in France and 0.2812 in South Korea, which are consistent with the interpretation of little competition in France and strong competition from local hornet species in South Korea. The invasive potential of two sister lineages can be compared by their distribution area when proper statistical adjustments are made to account for differences in sample size. V. velutina has a greater invasive potential than its sister lineage. The ancestor of V. velutina split into two lineages, one found in Indonesia/Malaysia and the other colonizing the Asian continent. The second lineage split into a sedentary clade inhabiting Pakistan and India and an invasive lineage colonizing much of Southeast Asia. This latter lineage gave rise to the subspecies V. v. nigrithorax, which invaded France, South Korea, and Japan. My software PGT version 1.5, which generates geophylogenies and computes geographic areas for individual taxa, is useful for understanding biogeography in general and invasive species in particular. I discussed the conceptual formulation of an index of invasiveness for a comparison between sister lineages.
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Affiliation(s)
- Xuhua Xia
- Department of Biology, University of Ottawa, Ottawa, ON K1N 9A7, Canada;
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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3
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Alameh MG, Semon A, Bayard NU, Pan YG, Dwivedi G, Knox J, Glover RC, Rangel PC, Tanes C, Bittinger K, She Q, Hu H, Bonam SR, Maslanka JR, Planet PJ, Moustafa AM, Davis B, Chevrier A, Beattie M, Ni H, Blizard G, Furth EE, Mach RH, Lavertu M, Sellmyer MA, Tam Y, Abt MC, Weissman D, Zackular JP. A multivalent mRNA-LNP vaccine protects against Clostridioides difficile infection. Science 2024; 386:69-75. [PMID: 39361752 PMCID: PMC11719173 DOI: 10.1126/science.adn4955] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 06/11/2024] [Accepted: 08/30/2024] [Indexed: 10/05/2024]
Abstract
Clostridioides difficile infection (CDI) is an urgent public health threat with limited preventative options. In this work, we developed a messenger RNA (mRNA)-lipid nanoparticle (LNP) vaccine targeting C. difficile toxins and virulence factors. This multivalent vaccine elicited robust and long-lived systemic and mucosal antigen-specific humoral and cellular immune responses across animal models, independent of changes to the intestinal microbiota. Vaccination protected mice from lethal CDI in both primary and recurrent infection models, and inclusion of non-toxin cellular and spore antigens improved decolonization of toxigenic C. difficile from the gastrointestinal tract. Our studies demonstrate mRNA-LNP vaccine technology as a promising platform for the development of novel C. difficile therapeutics with potential for limiting acute disease and promoting bacterial decolonization.
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Affiliation(s)
- Mohamad-Gabriel Alameh
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Penn Institute for RNA Innovation, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
| | - Alexa Semon
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
- Division of Protective Immunity, Children’s Hospital of Philadelphia; Philadelphia, PA,USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Nile U. Bayard
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
- Division of Protective Immunity, Children’s Hospital of Philadelphia; Philadelphia, PA,USA
| | - Yi-Gen Pan
- Division of Infectious Disease, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Garima Dwivedi
- Division of Infectious Disease, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - James Knox
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Rochelle C. Glover
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
- Division of Protective Immunity, Children’s Hospital of Philadelphia; Philadelphia, PA,USA
| | - Paula C. Rangel
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
- Division of Protective Immunity, Children’s Hospital of Philadelphia; Philadelphia, PA,USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia; Philadelphia, PA, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia; Philadelphia, PA, USA
- The Center for Microbial Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
| | - Qianxuan She
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia; Philadelphia, PA, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- The Center for Microbial Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
| | - Haitao Hu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Srinivasa Reddy Bonam
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jeffrey R. Maslanka
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, Pennsylvania, USA
| | - Paul J. Planet
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, Pennsylvania, USA
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Comparative Genomics, American Museum of Natural History; New York, NY, USA
- The Center for Microbial Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
| | - Ahmed M. Moustafa
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia; Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- The Center for Microbial Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
| | - Benjamin Davis
- Division of Infectious Disease, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Anik Chevrier
- Chemical Engineering Department, Polytechnique Montreal; Montreal, QC, Canada
| | | | - Houping Ni
- Acuitas Therapeutics; Vancouver, British Columbia, Canada
| | - Gabrielle Blizard
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Emma E. Furth
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Robert H. Mach
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Marc Lavertu
- Chemical Engineering Department, Polytechnique Montreal; Montreal, QC, Canada
| | - Mark A. Sellmyer
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Ying Tam
- Acuitas Therapeutics; Vancouver, British Columbia, Canada
| | - Michael C. Abt
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, Pennsylvania, USA
| | - Drew Weissman
- Division of Infectious Disease, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Penn Institute for RNA Innovation, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, 19104, USA
| | - Joseph P. Zackular
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
- Division of Protective Immunity, Children’s Hospital of Philadelphia; Philadelphia, PA,USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
- The Center for Microbial Medicine, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
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4
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Mason-Gamer RJ, White DM. The phylogeny of the Triticeae: Resolution and phylogenetic conflict based on genomewide nuclear loci. AMERICAN JOURNAL OF BOTANY 2024; 111:e16404. [PMID: 39279223 DOI: 10.1002/ajb2.16404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/07/2024] [Accepted: 06/09/2024] [Indexed: 09/18/2024]
Abstract
PREMISE The wheat tribe, Triticeae, has been the subject of molecular phylogenetic analyses for nearly three decades, and extensive phylogenetic conflict has been apparent from the earliest comparisons among DNA-based data sets. While most previous analyses focused primarily on nuclear vs. chloroplast DNA conflict, the present analysis provides a broader picture of conflict among nuclear loci throughout the tribe. METHODS Exon data were generated from over 1000 nuclear loci using targeted sequence capture with custom baits, and nearly complete chloroplast genome sequences were recovered. Phylogenetic conflict was assessed among the trees from the chloroplast genomes, the concatenated nuclear loci, and a series of nuclear-locus subsets guided by Hordeum chromosome gene maps. RESULTS At the intergeneric level, the analyses collectively revealed a few broadly consistent relationships. However, the prevailing pattern was one of extensive phylogenetic conflict throughout the tribe, among both deep and shallow branches, and with the extent of the conflict varying among data subsets. CONCLUSIONS The results suggest continual introgression or lineage sorting within and among the named lineages of the Triticeae, shaping both deep and shallow relationships in the tribe.
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Affiliation(s)
- Roberta J Mason-Gamer
- Department of Biological Sciences, University of Illinois at Chicago, MC 066, 845 W. Taylor Street, Chicago, 60607 USA, IL
| | - Dawson M White
- Department of Biological Sciences, University of Illinois at Chicago, MC 066, 845 W. Taylor Street, Chicago, 60607 USA, IL
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5
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Waddell PJ, Bouckaert R. An independent base composition of each rate class for improved likelihood-based phylogeny estimation; the 5rf model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.03.610719. [PMID: 39282393 PMCID: PMC11398347 DOI: 10.1101/2024.09.03.610719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/21/2024]
Abstract
The combination of a time reversible Markov process with a "hidden" mixture of gamma distributed relative site rates plus invariant sites have become the most favoured options for likelihood and other probabilistic models of nucleotide evolution (e.g., tr4gi which approximates a gamma with four rate classes). However, these models assume a homogeneous and stationary distribution of nucleotide (character or base) frequencies. Here, we explore the potential benefits and pitfalls of allowing each rate category (rate class) of a 4gi mixture model to have its own base frequencies. This is achieved by starting each of the five rate classes, at the tree's root, with its own free choice of nucleotide frequencies to create a 4gi5rf model or a 5rf model in shorthand. We assess the practical identifiability of this approach with a BEAST 2 implementation, aiming to determine if it can accurately estimate credibility intervals and expected values for a wide range of plausible parameter values. Practical identifiability, as distinguished from mathematical identifiability, gauges the model's ability to identify parameters in real-world scenarios, as opposed to theoretically with infinite data. One of the most common types of phylogenetic data is mitochondrial DNA (mtDNA) protein coding sequence. It is often assumed current models analyse robustly such data and that higher likelihood/posterior probability models do better. However, this abstract shows that vertebrate mtDNA remains a very difficult type of data to fully model, and that dramatically higher likelihoods do not mean a model is measurably more accurate with respect to recovering key parameters of biological interest (e.g., monophyletic groups, their support and their ages). The 4gi5rf model considerably improves marginal likelihoods and seems to reverse some apparent errors exacerbated by the 4gi model, while introducing others. Problems appear to be linked to non-stationary DNA repair processes that alter the mutation/substitution spectra across lineages and time. We also show such problems are not unique to mtDNA and are encountered in analysing nuclear sequences. Non-stationarity of DNA repair processes mutation/substitution spectra thus pose an active challenge to obtaining reliable inferences of relationships and divergence times near the root of placental mammals, for example. An open source implementation is available under the LGPL 3.0 license in the beastbooster package for BEAST 2, available from https://github.com/rbouckaert/beastbooster.
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Affiliation(s)
- Peter J. Waddell
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Remco Bouckaert
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
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6
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Berchtenbreiter L, Mumcu AE, Rackevei AS, Cock JM, Kawai H, Wolf M. 18S and ITS2 rRNA gene sequence-structure phylogeny of the Phaeophyceae (SAR, Stramenopiles) with special reference to Laminariales. Eur J Protistol 2024; 95:126107. [PMID: 39024684 DOI: 10.1016/j.ejop.2024.126107] [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: 04/23/2024] [Revised: 07/11/2024] [Accepted: 07/11/2024] [Indexed: 07/20/2024]
Abstract
The phylogeny of brown algae (Phaeophyceae) has undergone extensive changes in the recent past due to regular new scientific insights. We used nuclear 18S rDNA with an extensive dataset, aiming to increase the accuracy and robustness of the reconstructed phylogenetic trees using a simultaneous sequence-structure approach. Individual secondary structures were generated for all 18S rDNA sequences. The sequence-structure information was encoded and used for an automated simultaneous sequence-structure alignment. Neighbor-joining and profile neighbor-joining trees were calculated based on 186 phaeophycean sequence-structure pairs. Additionally, sequence-structure neighbor-joining, maximum parsimony and maximum likelihood trees were reconstructed on a representative subset. Using a similar approach, ITS2 rDNA sequence-structure information was used to reconstruct a neighbor-joining tree including 604 sequence-structure pairs of the Laminariales. Our study results are in significant agreement with previous single marker 18S and ITS2 rDNA analyses. Moreover, the 18S results are in wide agreement with recent multi-marker analyses. The bootstrap support was significantly higher for our sequence-structure analysis in comparison to sequence-only analyses in this study and the available literature. This study supports the simultaneous inclusion of sequence-structure data at least for 18S to obtain more accurate and robust phylogenetic trees compared to sequence-only analyses.
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Affiliation(s)
- Leon Berchtenbreiter
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Abdullah Emir Mumcu
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | | | - J Mark Cock
- Department UMR 8227, CNRS-UPMC, Station Biologique, Place Georges Teissier, CS 90074, 29688 Roscoff, France
| | - Hiroshi Kawai
- Kobe University Research Center for Inland Seas, Rokkodai, Kobe 657-8501, Japan
| | - Matthias Wolf
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
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7
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Musser G, Clarke JA. A new Paleogene fossil and a new dataset for waterfowl (Aves: Anseriformes) clarify phylogeny, ecological evolution, and avian evolution at the K-Pg Boundary. PLoS One 2024; 19:e0278737. [PMID: 39078833 PMCID: PMC11288464 DOI: 10.1371/journal.pone.0278737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/05/2024] [Indexed: 08/02/2024] Open
Abstract
Despite making up one of the most ecologically diverse groups of living birds, comprising soaring, diving and giant flightless taxa, the evolutionary relationships and ecological evolution of Anseriformes (waterfowl) remain unresolved. Although Anseriformes have a comparatively rich, global Cretaceous and Paleogene fossil record, morphological datasets for this group that include extinct taxa report conflicting relationships for all known extinct taxa. Correct placement of extinct taxa is necessary to understand whether ancestral anseriform feeding ecology was more terrestrial or one of a set of diverse aquatic ecologies and to better understand avian evolution around the K-T boundary. Here, we present a new morphological dataset for Anseriformes that includes more extant and extinct taxa than any previous anseriform-focused dataset and describe a new anseriform species from the early Eocene Green River Formation of North America. The new taxon has a mediolaterally narrow bill which is rarely found in previously described anseriform fossils. The matrix created to assess the placement of this taxon comprises 41 taxa and 719 discrete morphological characters describing skeletal morphology, musculature, syringeal morphology, ecology, and behavior. We additionally combine the morphological dataset with published sequences using Bayesian methods and perform ancestral state reconstruction for select morphological, ecological and behavioral characters. We recover the new Eocene taxon as the sister taxon to (Anseranatidae+Anatidae) across all analyses, and find that the new taxon represents a novel ecology within known Anseriformes and the Green River taxa. Results provide insight into avian evolution during and following the K-Pg mass extinction and indicate that Anseriformes were likely ancestrally aquatic herbivores with rhamphothecal lamellae..
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Affiliation(s)
- Grace Musser
- Department of Vertebrate Zoology, Division of Birds, The Smithsonian National Museum of Natural History, Washington, District of Columbia, United States of America
- Department of Earth and Planetary Sciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Julia A. Clarke
- Department of Earth and Planetary Sciences, The University of Texas at Austin, Austin, Texas, United States of America
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8
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Aziz M, Davis GS, Park DE, Idris AH, Sariya S, Wang Y, Zerbonne S, Nordstrom L, Weaver B, Statham S, Johnson TJ, Campos J, Castro-Nallar E, Crandall KA, Wu Z, Liu CM, DeBiasi RL, Price LB. Pediatric urinary tract infections caused by poultry-associated Escherichia coli. Microbiol Spectr 2024; 12:e0341523. [PMID: 38864635 PMCID: PMC11218530 DOI: 10.1128/spectrum.03415-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 05/05/2024] [Indexed: 06/13/2024] Open
Abstract
Escherichia coli is the leading cause of urinary tract infections (UTIs) in children and adults. The gastrointestinal tract is the primary reservoir of uropathogenic E. coli, which can be acquired from a variety of environmental exposures, including retail meat. In the current study, we used a novel statistical-genomic approach to estimate the proportion of pediatric UTIs caused by foodborne zoonotic E. coli strains. E. coli urine isolates were collected from DC residents aged 2 months to 17 years from the Children's National Medical Center Laboratory, 2013-2014. During the same period, E. coli isolates were collected from retail poultry products purchased from 15 sites throughout DC. A total of 52 urine and 56 poultry isolates underwent whole-genome sequencing, core genome phylogenetic analysis, and host-origin prediction by a Bayesian latent class model that incorporated data on the presence of mobile genetic elements (MGEs) among E. coli isolates from multiple vertebrate hosts. A total of 56 multilocus sequence types were identified among the isolates. Five sequence types-ST10, ST38, ST69, ST117, and ST131-were observed among both urine and poultry isolates. Using the Bayesian latent class model, we estimated that 19% (10/52) of the clinical E. coli isolates in our population were foodborne zoonotic strains. These data suggest that a substantial portion of pediatric UTIs in the Washington DC region may be caused by E. coli strains originating in food animals and likely transmitted via contaminated poultry meat.IMPORTANCEEscherichia coli UTIs are a heavy public health burden and can have long-term negative health consequences for pediatric patients. E. coli has an extremely broad host range, including humans, chickens, turkeys, pigs, and cattle. E. coli derived from food animals is a frequent contaminant of retail meat products, but little is known about the risk these strains pose to pediatric populations. Quantifying the proportion of pediatric UTIs caused by food-animal-derived E. coli, characterizing the highest-risk strains, and identifying their primary reservoir species could inform novel intervention strategies to reduce UTI burden in this vulnerable population. Our results suggest that retail poultry meat may be an important vehicle for pediatric exposure to zoonotic E. coli strains capable of causing UTIs. Vaccinating poultry against the highest-risk strains could potentially reduce poultry colonization, poultry meat contamination, and downstream pediatric infections.
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Affiliation(s)
- Maliha Aziz
- Department of Environmental and Occupational Health, Antibiotic Resistance Action Center, George Washington University, Washington, DC, USA
- Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Gregg S Davis
- Department of Environmental and Occupational Health, Antibiotic Resistance Action Center, George Washington University, Washington, DC, USA
- Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Daniel E Park
- Department of Environmental and Occupational Health, Antibiotic Resistance Action Center, George Washington University, Washington, DC, USA
- Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Azza H Idris
- Division of Pediatric Infectious Diseases, Children's National Health System, Washington, DC, USA
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Sanjeev Sariya
- Department of Environmental and Occupational Health, Antibiotic Resistance Action Center, George Washington University, Washington, DC, USA
- Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Yashan Wang
- Department of Environmental and Occupational Health, Antibiotic Resistance Action Center, George Washington University, Washington, DC, USA
- Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Sarah Zerbonne
- Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Lora Nordstrom
- Translational Genomics Research Institute, Flagstaff, Arizona, USA
| | - Brett Weaver
- Translational Genomics Research Institute, Flagstaff, Arizona, USA
| | - Sally Statham
- Translational Genomics Research Institute, Flagstaff, Arizona, USA
| | - Timothy J Johnson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Joseph Campos
- Division of Pediatric Infectious Diseases, Children's National Health System, Washington, DC, USA
| | - Eduardo Castro-Nallar
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Talca, Chile
- Centro de Ecología Integrativa, Universidad de Talca, Talca, Chile
| | - Keith A Crandall
- Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Zhenke Wu
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Cindy M Liu
- Department of Environmental and Occupational Health, Antibiotic Resistance Action Center, George Washington University, Washington, DC, USA
- Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Roberta L DeBiasi
- Division of Pediatric Infectious Diseases, Children's National Health System, Washington, DC, USA
- Department of Pediatrics and Microbiology, Immunology and Tropical Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Lance B Price
- Department of Environmental and Occupational Health, Antibiotic Resistance Action Center, George Washington University, Washington, DC, USA
- Milken Institute School of Public Health, George Washington University, Washington, DC, USA
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9
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Sánchez-Castro I, Viver T, Martínez-Rodríguez P, Bustos-Caparros E, Ruiz-Fresneda MÁ, Mena-Sanabria MT, Jiménez-García I, Bosch-Estévez G, Descostes M, Merroun ML. Acidovorax bellezanensis sp. nov., a novel bacterium from uranium mill tailings repository sites with selenium bioremediation capabilities. Heliyon 2024; 10:e33171. [PMID: 39005906 PMCID: PMC11239578 DOI: 10.1016/j.heliyon.2024.e33171] [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: 12/02/2023] [Revised: 06/10/2024] [Accepted: 06/14/2024] [Indexed: 07/16/2024] Open
Abstract
A Gram-stain-negative bacterial strain designated Be4T, belonging to the genus Acidovorax, was isolated from mining porewaters sampled in uranium mill tailings repository sites, located in Bellezane, near Bessines-sur-Gartempe (Limousin, France). Cells were facultative anaerobic, rod-shaped, non-endospore-forming and motile with flagella. The mean cell size was 1.25-1.31 μm long and 0.70-0.73 μm wide. Colonies were light yellow, opaque, circular, convex with smooth margins, and 1-2 mm in diameter. Growth occurs at 4-37 °C and between pH 5.5-9.0. It differed from its phylogenetically related strains by phenotypic and physiological characteristics such as growth at 4 °C, presence of acid phosphatase, naphthol-AS-BI-phosphohydrolase and β-glucosidase enzymatic activities, and fermentation of l-xylose and esculin. The major fatty acids were C16:0, C16:1 ω7c/C16:1 ω6c, C17:0 cyclo and C18:1 ω7c. Phylogenetic analysis based on 16S rRNA and 938 core genes, confirmed its placement within the genus Acidovorax as a novel species. Strain Be4T showed highest 16S rRNA sequence similarity to Acidovorax antarcticus (98.2 %), Acidovorax radicis (97.9 %), Acidovorax temperans (97.8 %) and Acidovorax facilis (97.7 %). The genome of strain Be4T is 5,041,667 bp size with a DNA G + C content of 65.15 %. By automatic annotation numerous sequences involved in the interaction with metals/metalloids including some genes related to Se uptake and selenite resistance were detected in its genome. The average nucleotide identity (ANI) values calculated from whole genome sequences between strain Be4T and the most closely related strains A. radicis and A. facilis were below the threshold value of 95 %. Thus, the data from the phylogenetic, physiological, biochemical, and genomic analyses clearly indicates that strain Be4T represents a novel species with the suggested name Acidovorax bellezanensis sp. nov. The type strain is Acidovorax bellezanensis Be4T (=DSM116209T = CECT30865T). This novel species, due to its unique isolation source, genomic analysis, and preliminary laboratory tests where it was able to reduce toxic Se(IV) to less harmful Se(0) in the form of nanoparticles, holds great potential for further investigation in bioremediation, particularly concerning Se.
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Affiliation(s)
- Iván Sánchez-Castro
- Departamento de Microbiología, Campus de Fuentenueva, Universidad de Granada, 18071, Granada, Spain
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Pablo Martínez-Rodríguez
- Departamento de Microbiología, Campus de Fuentenueva, Universidad de Granada, 18071, Granada, Spain
| | - Esteban Bustos-Caparros
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | | | | | - Ignacio Jiménez-García
- Departamento de Microbiología, Campus de Fuentenueva, Universidad de Granada, 18071, Granada, Spain
| | - Germán Bosch-Estévez
- Departamento de Microbiología, Campus de Fuentenueva, Universidad de Granada, 18071, Granada, Spain
| | - Michael Descostes
- Environmental R&D Department, Orano Mining, Chatillon, 92320, France
- Centre de Géosciences, MINES Paris, PSL University, 35 rue St Honoré, 77300, Fontainebleau, France
| | - Mohamed Larbi Merroun
- Departamento de Microbiología, Campus de Fuentenueva, Universidad de Granada, 18071, Granada, Spain
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10
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Rick JA, Brock CD, Lewanski AL, Golcher-Benavides J, Wagner CE. Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses. Syst Biol 2024; 73:76-101. [PMID: 37881861 DOI: 10.1093/sysbio/syad065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 09/20/2023] [Accepted: 10/20/2023] [Indexed: 10/27/2023] Open
Abstract
Molecular phylogenies are a cornerstone of modern comparative biology and are commonly employed to investigate a range of biological phenomena, such as diversification rates, patterns in trait evolution, biogeography, and community assembly. Recent work has demonstrated that significant biases may be introduced into downstream phylogenetic analyses from processing genomic data; however, it remains unclear whether there are interactions among bioinformatic parameters or biases introduced through the choice of reference genome for sequence alignment and variant calling. We address these knowledge gaps by employing a combination of simulated and empirical data sets to investigate the extent to which the choice of reference genome in upstream bioinformatic processing of genomic data influences phylogenetic inference, as well as the way that reference genome choice interacts with bioinformatic filtering choices and phylogenetic inference method. We demonstrate that more stringent minor allele filters bias inferred trees away from the true species tree topology, and that these biased trees tend to be more imbalanced and have a higher center of gravity than the true trees. We find the greatest topological accuracy when filtering sites for minor allele count (MAC) >3-4 in our 51-taxa data sets, while tree center of gravity was closest to the true value when filtering for sites with MAC >1-2. In contrast, filtering for missing data increased accuracy in the inferred topologies; however, this effect was small in comparison to the effect of minor allele filters and may be undesirable due to a subsequent mutation spectrum distortion. The bias introduced by these filters differs based on the reference genome used in short read alignment, providing further support that choosing a reference genome for alignment is an important bioinformatic decision with implications for downstream analyses. These results demonstrate that attributes of the study system and dataset (and their interaction) add important nuance for how best to assemble and filter short-read genomic data for phylogenetic inference.
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Affiliation(s)
- Jessica A Rick
- School of Natural Resources & the Environment, University of Arizona, Tucson, AZ 85719, USA
| | - Chad D Brock
- Department of Biological Sciences, Tarleton State University, Stephenville, TX 76401, USA
| | - Alexander L Lewanski
- Department of Integrative Biology and W.K. Kellogg Biological Station, Michigan State University, East Lansing, MI 48824, USA
| | - Jimena Golcher-Benavides
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA 50011, USA
| | - Catherine E Wagner
- Program in Ecology and Evolution, University of Wyoming, Laramie, WY 82071, USA
- Department of Botany, University of Wyoming, Laramie, WY 82071, USA
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11
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Hewitt TL, Johnson PD, Buntin M, Moore TY, Ó Foighil D. Polymorphism in the aggressive mimicry lure of the parasitic freshwater mussel Lampsilis fasciola. PeerJ 2024; 12:e17359. [PMID: 38803583 PMCID: PMC11129695 DOI: 10.7717/peerj.17359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 04/18/2024] [Indexed: 05/29/2024] Open
Abstract
Unionoid freshwater mussels (Bivalvia: Unionidae) are free-living apart from a brief, obligately parasitic, larval stage that infects fish hosts, and gravid female mussels have evolved a spectrum of strategies to infect fish hosts with their larvae. In many North American species, this involves displaying a mantle lure: a pigmented fleshy extension that acts as an aggressive mimic of a host fish prey, thereby eliciting a feeding response that results in host infection. The mantle lure of Lampsilis fasciola is of particular interest because it is apparently polymorphic, with two distinct primary lure phenotypes. One, described as "darter-like", has "eyespots", a mottled body coloration, prominent marginal extensions, and a distinct "tail". The other, described as "worm-like", lacks those features and has an orange and black coloration. We investigated this phenomenon using genomics, captive rearing, biogeographic, and behavioral analyses. Within-brood lure variation and within-population phylogenomic (ddRAD-seq) analyses of individuals bearing different lures confirmed that this phenomenon is a true polymorphism. The relative abundance of the two morphs appears stable over ecological timeframes: the ratio of the two lure phenotypes in a River Raisin (MI) population in 2017 was consistent with that of museum samples collected at the same site six decades earlier. Within the River Raisin, four main "darter-like" lure motifs visually approximated four co-occurring darter species (Etheostoma blennioides, E. exile, E. microperca, and Percina maculata), and the "worm-like" lure resembled a widespread common leech, Macrobdella decora. Darters and leeches are typical prey of Micropterus dolomieui (smallmouth bass), the primary fish host of L. fasciola. In situ field recordings of the L. fasciola "darter" and "leech" lure display behaviors, and the lure display of co-occurring congener L. cardium, were captured. Despite having putative models in distinct phyla, both L. fasciola lure morphs have largely similar display behaviors that differ significantly from that of sympatric L. cardium individuals. Some minor differences in the behavior between the two L. fasciola morphs were observed, but we found no clear evidence for a behavioral component of the polymorphism given the criteria measured. Discovery of discrete within-brood inheritance of the lure polymorphism implies potential control by a single genetic locus and identifies L. fasciola as a promising study system to identify regulatory genes controlling a key adaptive trait of freshwater mussels.
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Affiliation(s)
- Trevor L. Hewitt
- Ecology and Evolutionary Biology, University of Michigan—Ann Arbor, Ann Arbor, Michigan, United States
| | - Paul D. Johnson
- Alabama Aquatic Biodiversity Center, Marion, Alabama, United States of America
| | - Michael Buntin
- Alabama Aquatic Biodiversity Center, Marion, Alabama, United States of America
| | - Talia Y. Moore
- Ecology and Evolutionary Biology, University of Michigan—Ann Arbor, Ann Arbor, Michigan, United States
- Robotics Department & Mechanical Engineering Department, University of Michigan—Ann Arbor, Ann Arbor, Michigan, United States
| | - Diarmaid Ó Foighil
- Ecology and Evolutionary Biology, University of Michigan—Ann Arbor, Ann Arbor, Michigan, United States
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12
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Takada K, Orba Y, Kida Y, Wu J, Ono C, Matsuura Y, Nakagawa S, Sawa H, Watanabe T. Genes involved in the limited spread of SARS-CoV-2 in the lower respiratory airways of hamsters may be associated with adaptive evolution. J Virol 2024; 98:e0178423. [PMID: 38624229 PMCID: PMC11092350 DOI: 10.1128/jvi.01784-23] [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: 11/14/2023] [Accepted: 03/17/2024] [Indexed: 04/17/2024] Open
Abstract
Novel respiratory viruses can cause a pandemic and then evolve to coexist with humans. The Omicron strain of severe acute respiratory syndrome coronavirus 2 has spread worldwide since its emergence in late 2021, and its sub-lineages are now established in human society. Compared to previous strains, Omicron is markedly less invasive in the lungs and causes less severe disease. One reason for this is that humans are acquiring immunity through previous infection and vaccination, but the nature of the virus itself is also changing. Using our newly established low-volume inoculation system, which reflects natural human infection, we show that the Omicron strain spreads less efficiently into the lungs of hamsters compared with an earlier Wuhan strain. Furthermore, by characterizing chimeric viruses with the Omicron gene in the Wuhan strain genetic background and vice versa, we found that viral genes downstream of ORF3a, but not the S gene, were responsible for the limited spread of the Omicron strain in the lower airways of the virus-infected hamsters. Moreover, molecular evolutionary analysis of SARS-CoV-2 revealed a positive selection of genes downstream of ORF3a (M and E genes). Our findings provide insight into the adaptive evolution of the virus in humans during the pandemic convergence phase.IMPORTANCEThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has spread worldwide since its emergence in late 2021, and its sub-lineages are established in human society. Compared to previous strains, the Omicron strain is less invasive in the lower respiratory tract, including the lungs, and causes less severe disease; however, the mechanistic basis for its restricted replication in the lower airways is poorly understood. In this study, using a newly established low-volume inoculation system that reflects natural human infection, we demonstrated that the Omicron strain spreads less efficiently into the lungs of hamsters compared with an earlier Wuhan strain and found that viral genes downstream of ORF3a are responsible for replication restriction in the lower respiratory tract of Omicron-infected hamsters. Furthermore, we detected a positive selection of genes downstream of ORF3a (especially the M and E genes) in SARS-CoV-2, suggesting that these genes may undergo adaptive changes in humans.
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Grants
- 16H06429, 16K21723, 16H06434, JP22H02521 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21H02736 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP16K21723, JP16H06432 MEXT | Japan Society for the Promotion of Science (JSPS)
- 22K15469, 21J01036 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP20fk0108281, JP19fk0108113, JP20pc0101047 Japan Agency for Medical Research and Development (AMED)
- JP20fk0108401, JP21fk0108493 Japan Agency for Medical Research and Development (AMED)
- JP23wm0125008, JP223fa627005 Japan Agency for Medical Research and Development (AMED)
- JP19fk018113, JP223fa627002h, 22gm1610010h0001 Japan Agency for Medical Research and Development (AMED)
- JPMJMS2025 MEXT | Japan Science and Technology Agency (JST)
- JPMJCR20H6 MEXT | Japan Science and Technology Agency (JST)
- Takeda Science Foundation (TSF)
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Affiliation(s)
- Kosuke Takada
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yurie Kida
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Jiaqi Wu
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Chikako Ono
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
| | - Yoshiharu Matsuura
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hirofumi Sawa
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Hokkaido, Japan
- Global Virus Network, Baltimore, Maryland, USA
| | - Tokiko Watanabe
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Suita, Osaka, Japan
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13
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Pitcher NJ, Feder A, Bolden N, Zirbes CF, Pamatmat AJ, Boyken L, Hill JJ, Bartels AR, Thurman AL, Reeb VC, Porterfield HS, Moustafa AM, Planet PJ, Fischer AJ. Parallel evolution of linezolid-resistant Staphylococcus aureus in patients with cystic fibrosis. Microbiol Spectr 2023; 11:e0208423. [PMID: 37724867 PMCID: PMC10581212 DOI: 10.1128/spectrum.02084-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/10/2023] [Indexed: 09/21/2023] Open
Abstract
Linezolid is an antibiotic used to treat serious Staphylococcus aureus infections. Resistance to linezolid is considered rare but could emerge with repeated dosing. We recently reported widespread prescription of linezolid for a cohort of patients with cystic fibrosis (CF). The goals of this study were to determine the incidence of linezolid-resistant methicillin-resistant Staphylococcus aureus (MRSA) in CF and identify molecular mechanisms for linezolid resistance. We identified patients who cultured S. aureus resistant to linezolid with minimum inhibitory concentration (MIC) >4 at the University of Iowa CF Center between 2008 and 2018. We obtained isolates from these patients and retested susceptibility to linezolid using broth microdilution. We used whole genome sequencing to perform phylogenetic analysis of linezolid-resistant isolates and examine sequences for mutations or accessory genes that confer linezolid resistance. Between 2008 and 2018, 111 patients received linezolid, and 4 of these patients cultured linezolid-resistant S. aureus. We sequenced 11 resistant and 21 susceptible isolates from these 4 subjects. Phylogenetic analysis indicated that linezolid resistance developed in ST5 or ST105 backgrounds. Three individuals had linezolid-resistant S. aureus with a G2576T mutation in 23S rRNA. One of these subjects additionally had a mutS- mutL- hypermutating S. aureus that produced five resistant isolates with multiple ribosomal subunit mutations. In one subject, the genetic basis for linezolid resistance was unclear. We conclude that linezolid resistant S. aureus can occur through multiple genetic mechanisms in patients with repeated exposure to this antibiotic. IMPORTANCE Patients with cystic fibrosis have persistent lung infections with Staphylococcus aureus that require extensive antibiotic treatments. Linezolid, an antibiotic given by oral or intravenous route, is prescribed repeatedly for patients whose lung disease has progressed. After treatment with linezolid, S. aureus strains can evolve antibiotic resistance through multiple genetic mechanisms. In addition to a common mutation in the 23S ribosomal RNA known to confer linezolid resistance, S. aureus strains can evolve novel resistance based on a combination of mutations affecting the bacterial ribosome. This combination of mutations was observed in a strain that exhibited hypermutation owing to the loss of the DNA repair genes mutS and mutL. In this cohort of patients with cystic fibrosis, linezolid resistance was transient, possibly due to the growth disadvantage of resistant strains. However, ongoing chronic exposure to linezolid may create optimal conditions for the future emergence of resistance to this critical antibiotic.
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Affiliation(s)
- Nicholas J. Pitcher
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Andries Feder
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nicholas Bolden
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Christian F. Zirbes
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Anthony J. Pamatmat
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Linda Boyken
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, lowa, USA
| | - Jared J. Hill
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Alyssa R. Bartels
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Andrew L. Thurman
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, lowa, USA
| | - Valerie C. Reeb
- State Hygienic Laboratory at the University of Iowa, Coralville, lowa, USA
| | | | - Ahmed M. Moustafa
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Paul J. Planet
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Anthony J. Fischer
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
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14
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Li S, Qi B, Peng X, Wang W, Wang W, Liu P, Liu B, Peng Z, Wang Q, Li Y. Genome size and GC content of myxomycetes. Eur J Protistol 2023; 90:125991. [PMID: 37331249 DOI: 10.1016/j.ejop.2023.125991] [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: 01/04/2023] [Revised: 05/22/2023] [Accepted: 05/27/2023] [Indexed: 06/20/2023]
Abstract
More than 1272 myxomycetes species have been described, accounting for more than half of all Amoebozoa species. However, the genome size of only three myxomycetes species has been reported. Therefore, we used flow cytometry to present an extensive survey and a phylogeny-based analysis of genome size and GC content evolution in 144 myxomycetes species. The genome size of myxomycetes ranged from 18.7 Mb to 470.3 Mb, and the GC content ranged from 38.7% to 70.1%. Bright-spored clade showed larger genome sizes and more intra-order genome size variations than the dark-spored clade. GC content and genome size were positively correlated in both bright-spored and dark-spored clades, and spore size was positively correlated with genome size and GC content in the bright-spored clade. We provided the first genome size data set in Myxomycetes, and our results will provide helpful information for future Myxomycetes studies, such as genome sequencing.
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Affiliation(s)
- Shu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China; Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Bao Qi
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Xueyan Peng
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Wei Wang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Wan Wang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Pu Liu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Zhanwu Peng
- Information Center, Jilin Agricultural University, Changchun, China.
| | - Qi Wang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
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15
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Campos PE, Pruvost O, Boyer K, Chiroleu F, Cao TT, Gaudeul M, Baider C, Utteridge TMA, Becker N, Rieux A, Gagnevin L. Herbarium specimen sequencing allows precise dating of Xanthomonas citri pv. citri diversification history. Nat Commun 2023; 14:4306. [PMID: 37474518 PMCID: PMC10359311 DOI: 10.1038/s41467-023-39950-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/15/2023] [Indexed: 07/22/2023] Open
Abstract
Herbarium collections are an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography can shed light on the emergence and evolutionary history of plant pathogens. Here, we reconstruct 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected Citrus herbarium specimens. Following authentication based on ancient DNA damage patterns, we compare them with a large set of modern genomes to estimate their phylogenetic relationships, pathogenicity-associated gene content and several evolutionary parameters. Our results indicate that Xci originated in Southern Asia ~11,500 years ago (perhaps in relation to Neolithic climate change and the development of agriculture) and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world (probably via human-driven expansion of citriculture through early East-West trade and colonization).
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Affiliation(s)
- Paola E Campos
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
| | | | - Karine Boyer
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
| | | | - Thuy Trang Cao
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
| | - Myriam Gaudeul
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
- Herbier national, Muséum national d'Histoire naturelle, CP39, 57 rue Cuvier, 75005, Paris, France
| | - Cláudia Baider
- The Mauritius Herbarium, Agricultural Services, Ministry of Agro-Industry and Food Security, R.E. Vaughan Building (MSIRI Compound), Reduit, 80835, Mauritius
| | | | - Nathalie Becker
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
| | - Adrien Rieux
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France.
| | - Lionel Gagnevin
- PHIM Plant Health Institute, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.
- CIRAD, UMR PHIM, Montpellier, France.
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16
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Ruiz-García M, Pinedo-Castro M, Shostell JM. Morphological and Genetics Support for a Hitherto Undescribed Spotted Cat Species (Genus Leopardus; Felidae, Carnivora) from the Southern Colombian Andes. Genes (Basel) 2023; 14:1266. [PMID: 37372446 DOI: 10.3390/genes14061266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/08/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
In 1989, a skin of a small spotted cat, from the Galeras Volcano in southern Colombia (Nariño Department), was donated to the Instituto Alexander von Humboldt (identification, ID 5857) at Villa de Leyva (Boyacá Department, Colombia). Although originally classified as Leopardus tigrinus, its distinctiveness merits a new taxonomic designation. The skin is distinct from all known L. tigrinus holotypes as well as from other Leopardus species. Analysis of the complete mitochondrial genomes from 44 felid specimens (including 18 L. tigrinus and all the current known species of the genus Leopardus), the mtND5 gene from 84 felid specimens (including 30 L. tigrinus and all the species of the genus Leopardus), and six nuclear DNA microsatellites (113 felid specimens of all the current known species of the genus Leopardus) indicate that this specimen does not belong to any previously recognized Leopardus taxon. The mtND5 gene suggests this new lineage (the Nariño cat as we name it) is a sister taxon of Leopardus colocola. The mitogenomic and nuclear DNA microsatellite analyses suggest that this new lineage is the sister taxon to a clade formed by Central American and trans-Andean L. tigrinus + (Leopardus geoffroyi + Leopardus guigna). The temporal split between the ancestor of this new possible species and the most recent ancestor within Leopardus was dated to 1.2-1.9 million years ago. We consider that this new unique lineage is a new species, and we propose the scientific name Leopardus narinensis.
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Affiliation(s)
- Manuel Ruiz-García
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Cra 7A, No 43-82, Bogotá 110231, Colombia
| | - Myreya Pinedo-Castro
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Cra 7A, No 43-82, Bogotá 110231, Colombia
| | - Joseph Mark Shostell
- Math, Science and Technology Department, University of Minnesota Crookston, 2900 University Ave., Crookston, MN 56716, USA
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Pitcher NJ, Feder A, Bolden N, Zirbes CF, Pamatmat AJ, Boyken L, Hill JJ, Thurman AL, Reeb VC, Porterfield HS, Moustafa AM, Planet PJ, Fischer AJ. Parallel Evolution of Linezolid Resistant Staphylococcus aureus in Patients with Cystic Fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539145. [PMID: 37205485 PMCID: PMC10187253 DOI: 10.1101/2023.05.02.539145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Background Linezolid is an antibiotic used to treat serious Staphylococcus aureus infections. Resistance to linezolid is considered rare but could emerge with repeated dosing. We recently reported widespread prescription of linezolid for a cohort of patients with cystic fibrosis (CF). Objectives The goals of this study were to determine the incidence of linezolid resistance in CF and identify molecular mechanisms for linezolid resistance. Methods We identified patients with S. aureus resistant to linezolid (MIC > 4) at the University of Iowa CF Center between 2008 and 2018. We obtained isolates from these patients and retested susceptibility to linezolid using broth microdilution. We used whole genome sequencing to perform phylogenetic analysis of linezolid resistant isolates and examine sequences for mutations or accessory genes that confer linezolid resistance. Main Results Between 2008 and 2018, 111 patients received linezolid and 4 of these patients cultured linezolid resistant S. aureus . We sequenced 11 resistant and 21 susceptible isolates from these 4 subjects. Phylogenetic analysis indicated that linezolid resistance developed in ST5 or ST105 backgrounds. Three individuals had linezolid resistant S. aureus with a G2576T mutation in 23S rRNA. One of these subjects additionally had a mutS - mutL - hypermutating S. aureus that produced 5 resistant isolates with multiple ribosomal subunit mutations. In one subject, the genetic basis for linezolid resistance was unclear. Conclusions Linezolid resistance evolved in 4 of 111 patients in this study. Linezolid resistance occurred by multiple genetic mechanisms. All resistant strains developed in ST5 or ST105 MRSA backgrounds. Key Point Linezolid resistance arises through multiple genetic mechanisms and could be facilitated by mutator phenotypes. Linezolid resistance was transient, possibly due to growth disadvantage.
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Affiliation(s)
- Nicholas J. Pitcher
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Andries Feder
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Nicholas Bolden
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Christian F. Zirbes
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Anthony J. Pamatmat
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Linda Boyken
- Pathology. University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Jared J. Hill
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Andrew L. Thurman
- Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Valérie C. Reeb
- State Hygienic Laboratory at the University of Iowa, Coralville, IA 52241
| | - Harry S. Porterfield
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Ahmed M. Moustafa
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Paul J. Planet
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Comparative Genomics, American Museum of Natural History, New York, NY 10024
| | - Anthony J. Fischer
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, IA 52242
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18
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Nguyen TV, Viver T, Smets I, Bernaerts K, Faust K, Lavigne R, Poughon L, Dussap CG, Springael D. Thermocaproicibacter melissae gen. nov., sp. nov., a thermophilic chain-elongating bacterium, producing n-caproate from polymeric carbohydrates. Int J Syst Evol Microbiol 2023; 73. [PMID: 37200213 DOI: 10.1099/ijsem.0.005893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Abstract
Strain MDTJ8T is a chain-elongating thermophilic bacterium isolated from a thermophilic acidogenic anaerobic digestor treating human waste while producing the high commodity chemical n-caproate. The strain grows and produces formate, acetate, n-butyrate, n-caproate and lactate from mono-, di- and polymeric saccharides at 37-60 °C (optimum, 50-55 °C) and at pH 5.0-7.0 (optimum, pH 6.5). The organism is an obligate anaerobe, is motile and its cells form rods (0.3-0.5×1.0-3.0 µm) that stain Gram-positive and occur primarily as chains. Phylogenetic analysis of both the 16S rRNA gene and full genome sequence shows that strain MDTJ8T belongs to a group that consists of mesophylic chain-elongating bacteria within the family Oscillospiraceae, being nearest to Caproicibacter fermentans EA1T (94.8 %) and Caproiciproducens galactitolivorans BS-1T (93.7 %). Its genome (1.96 Mbp) with a G+C content of 49.6 mol% is remarkably smaller than those of other chain-elongating bacteria of the family Oscillospiraceae. Pairwise average nucleotide identity and DNA-DNA hybridization values between strain MDJT8T and its mesophilic family members are less than 70 and 35 %, respectively, while pairwise average amino acid identity values are less than 68 %. In addition, strain MDJT8T uses far less carbohydrate and non-carbohydrate substrates compared to its nearest family members. The predominant cellular fatty acids of strain MDTJ8T are C14 : 0, C14 : 0 DMA (dimethyl acetal) and C16 : 0, while its polar lipid profile shows three unidentified glycophospholipids, 11 glycolipids, 13 phospholipids and six unidentified lipids. No respiratory quinones and polyamines are detected. Based on its phylogenetic, genotypic, morphological, physiological, biochemical and chemotaxonomic characteristics, strain MDTJ8T represents a novel species and novel genus of the family Oscillospiraceae and Thermocaproicibacter melissae gen. nov., sp. nov. is proposed as its name. The type strain is MDTJ8T (=DSM 114174T=LMG 32615T=NCCB 100883T).
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Affiliation(s)
- Tinh Van Nguyen
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium
- Institut Pascal, Université Clermont Auvergne, Avenue Blaise Pascal 4, F-63178 Aubiére cedex, France
| | - Tomeu Viver
- Marine Microbiology Group, Mediterranean Institute of Advanced Studies (CSIC-UIB), C/Miquel Marquès 21, 07190 Esporles, Spain
| | - Ilse Smets
- Chemical Reactor Engineering and Safety, KU Leuven, Celestijnenlaan 200F, B-3001, Heverlee, Belgium
| | - Kristel Bernaerts
- Chemical Reactor Engineering and Safety, KU Leuven, Celestijnenlaan 200F, B-3001, Heverlee, Belgium
| | - Karoline Faust
- Laboratory of Molecular Bacteriology (Rega Institute), KU Leuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, B-3001 Heverlee, Belgium
| | - Laurent Poughon
- Institut Pascal, Université Clermont Auvergne, Avenue Blaise Pascal 4, F-63178 Aubiére cedex, France
| | - Claude-Gilles Dussap
- Institut Pascal, Université Clermont Auvergne, Avenue Blaise Pascal 4, F-63178 Aubiére cedex, France
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium
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19
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Yang J, Skaro M, Chen J, Zhan D, Lyu L, Gay S, Kandeil A, Ali MA, Kayali G, Stoianova K, Ji P, Alabady M, Bahl J, Liu L, Arnold J. The species coalescent indicates possible bat and pangolin origins of the COVID-19 pandemic. Sci Rep 2023; 13:5571. [PMID: 37019985 PMCID: PMC10074375 DOI: 10.1038/s41598-023-32622-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 03/30/2023] [Indexed: 04/07/2023] Open
Abstract
A consensus species tree is reconstructed from 11 gene trees for human, bat, and pangolin beta coronaviruses from samples taken early in the pandemic (prior to April 1, 2020). Using coalescent theory, the shallow (short branches relative to the hosts) consensus species tree provides evidence of recent gene flow events between bat and pangolin beta coronaviruses predating the zoonotic transfer to humans. The consensus species tree was also used to reconstruct the ancestral sequence of human SARS-CoV-2, which was 2 nucleotides different from the Wuhan sequence. The time to most recent common ancestor was estimated to be Dec 8, 2019 with a bat origin. Some human, bat, and pangolin coronavirus lineages found in China are phylogenetically distinct, a rare example of a class II phylogeography pattern (Avise et al. in Ann Rev Eco Syst 18:489-422, 1987). The consensus species tree is a product of evolutionary factors, providing evidence of repeated zoonotic transfers between bat and pangolin as a reservoir for future zoonotic transfers to humans.
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Affiliation(s)
- Jialin Yang
- Statistics Department, University of Georgia, Athens, GA, USA
| | - Michael Skaro
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Jiani Chen
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Duna Zhan
- Statistics Department, University of Georgia, Athens, GA, USA
| | - Leke Lyu
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Skylar Gay
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- University of Texas School of Public Health, Houston, TX, USA
| | - Ahmed Kandeil
- National Research Centre, Cairo, Egypt
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Ghazi Kayali
- Human-Link DMCC, Dubai, UAE
- University of Texas School of Public Health, Houston, TX, USA
| | - Kateryna Stoianova
- Georgia Genomics and Bioinformatics Center, University of Georgia, Athens, GA, USA
| | - Pensheng Ji
- Statistics Department, University of Georgia, Athens, GA, USA
| | - Magdy Alabady
- Georgia Genomics and Bioinformatics Center, University of Georgia, Athens, GA, USA
- Plant Biology Department, University of Georgia, Athens, GA, USA
| | - Justin Bahl
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, GA, USA
| | - Liang Liu
- Statistics Department, University of Georgia, Athens, GA, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Jonathan Arnold
- Genetics Department, University of Georgia, Athens, GA, USA.
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20
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Patil PB, Gaikwad SM. First report of the beetle Henosepilachna nana (Kapur, 1950) (Coleoptera: Coccinellidae) from Maharashtra with special reference to molecular phylogeny and host plants. JOURNAL OF THREATENED TAXA 2023. [DOI: 10.11609/jott.7664.15.3.22859-22865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023] Open
Abstract
A ladybird beetle, collected from different localities of Kolhapur and Satara districts (Maharashtra) was identified as Henosepilachna nana (Kapur, 1950). The presence of this species in Maharashtra considerably extends its range to the north-west by about 700 km. Since this species is found on vegetables, Pumpkin (Cucurbita spp.), Cucumber (Cucumis spp.), and Karit fruit plant (Cucumis spp.). It is being recorded for the first time that this species is a pest of these vegetables. Also, molecular phylogeny has been studied for the first time in this species in which, this species is the sister taxon of Henosepilachna boisduvali. This species has been described briefly with colour photographs of male genitalia, female coxites and the 6th sternal plate of female, tarsi, & pronotum. Henosepilachna nana is being reported for the first time from Maharashtra and now the molecular data of this species is available.
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21
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Genomic diversity of SARS-CoV-2 can be accelerated by mutations in the nsp14 gene. iScience 2023; 26:106210. [PMID: 36811085 PMCID: PMC9933857 DOI: 10.1016/j.isci.2023.106210] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/23/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), encode a proofreading exonuclease, nonstructural protein 14 (nsp14), that helps ensure replication competence at a low evolutionary rate compared with other RNA viruses. In the current pandemic, SARS-CoV-2 has accumulated diverse genomic mutations including in nsp14. Here, to clarify whether amino acid substitutions in nsp14 affect the genomic diversity and evolution of SARS-CoV-2, we searched for amino acid substitutions in nature that may interfere with nsp14 function. We found that viruses carrying a proline-to-leucine change at position 203 (P203L) have a high evolutionary rate and that a recombinant SARS-CoV-2 virus with the P203L mutation acquired more diverse genomic mutations than wild-type virus during its replication in hamsters. Our findings suggest that substitutions, such as P203L, in nsp14 may accelerate the genomic diversity of SARS-CoV-2, contributing to virus evolution during the pandemic.
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22
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Viver T, Conrad RE, Lucio M, Harir M, Urdiain M, Gago JF, Suárez-Suárez A, Bustos-Caparros E, Sanchez-Martinez R, Mayol E, Fassetta F, Pang J, Mădălin Gridan I, Venter S, Santos F, Baxter B, Llames ME, Cristea A, Banciu HL, Hedlund BP, Stott MB, Kämpfer P, Amann R, Schmitt-Kopplin P, Konstantinidis KT, Rossello-Mora R. Description of two cultivated and two uncultivated new Salinibacter species, one named following the rules of the bacteriological code: Salinibacter grassmerensis sp. nov.; and three named following the rules of the SeqCode: Salinibacter pepae sp. nov., Salinibacter abyssi sp. nov., and Salinibacter pampae sp. nov. Syst Appl Microbiol 2023; 46:126416. [PMID: 36965279 DOI: 10.1016/j.syapm.2023.126416] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/17/2023]
Abstract
Current -omics methods allow the collection of a large amount of information that helps in describing the microbial diversity in nature. Here, and as a result of a culturomic approach that rendered the collection of thousands of isolates from 5 different hypersaline sites (in Spain, USA and New Zealand), we obtained 21 strains that represent two new Salinibacter species. For these species we propose the names Salinibacter pepae sp. nov. and Salinibacter grassmerensis sp. nov. (showing average nucleotide identity (ANI) values < 95.09% and 87.08% with Sal. ruber M31T, respectively). Metabolomics revealed species-specific discriminative profiles. Sal. ruber strains were distinguished by a higher percentage of polyunsaturated fatty acids and specific N-functionalized fatty acids; and Sal. altiplanensis was distinguished by an increased number of glycosylated molecules. Based on sequence characteristics and inferred phenotype of metagenome-assembled genomes (MAGs), we describe two new members of the genus Salinibacter. These species dominated in different sites and always coexisted with Sal. ruber and Sal. pepae. Based on the MAGs from three Argentinian lakes in the Pampa region of Argentina and the MAG of the Romanian lake Fără Fund, we describe the species Salinibacter pampae sp. nov. and Salinibacter abyssi sp. nov. respectively (showing ANI values 90.94% and 91.48% with Sal. ruber M31T, respectively). Sal. grassmerensis sp. nov. name was formed according to the rules of the International Code for Nomenclature of Prokaryotes (ICNP), and Sal. pepae, Sal. pampae sp. nov. and Sal. abyssi sp. nov. are proposed following the rules of the newly published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This work constitutes an example on how classification under ICNP and SeqCode can coexist, and how the official naming a cultivated organism for which the deposit in public repositories is difficult finds an intermediate solution.
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Affiliation(s)
- Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain; Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Roth E Conrad
- Ocean Science & Engineering, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA; School of Civil & Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Marianna Lucio
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, 85764 Neuherberg, Germany
| | - Mourad Harir
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, 85764 Neuherberg, Germany; Chair of Analytical Food Chemistry, Technical University Munich, Maximus-von-Imhof-Forum 2, 85354 Freising, Germany
| | - Mercedes Urdiain
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Juan F Gago
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Ana Suárez-Suárez
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Esteban Bustos-Caparros
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Rodrigo Sanchez-Martinez
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690, San Vicent del Raspeig, Alicante, Spain
| | - Eva Mayol
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690, San Vicent del Raspeig, Alicante, Spain
| | - Federico Fassetta
- Laboratorio de Ecología Acuática, Instituto Tecnológico Chascomús (INTECH)-CONICET-UNSAM, Escuela de Bio y Nanotecnologías -UNSAM, Buenos Aires, Argentina
| | - Jinfeng Pang
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154-4004, USA
| | - Ionuț Mădălin Gridan
- Doctoral School of Integrative Biology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Stephanus Venter
- Department of Biochemistry, Genetics and Microbiology, and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Fernando Santos
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690, San Vicent del Raspeig, Alicante, Spain
| | - Bonnie Baxter
- Great Salt Lake Institute, Westminster College, Salt Lake City, UT, 84105, USA
| | - María E Llames
- Laboratorio de Ecología Acuática, Instituto Tecnológico Chascomús (INTECH)-CONICET-UNSAM, Escuela de Bio y Nanotecnologías -UNSAM, Buenos Aires, Argentina
| | - Adorján Cristea
- Department of Taxonomy and Ecology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj‑Napoca, Romania
| | - Horia L Banciu
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj‑Napoca, Romania; Emil G. Racoviță Institute, Babeș-Bolyai University, Cluj‑Napoca, Romania
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154-4004, USA
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Peter Kämpfer
- Institute of Applied Microbiology (IFZ), Justus Liebig Universität Giessen, Giessen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, 85764 Neuherberg, Germany; Chair of Analytical Food Chemistry, Technical University Munich, Maximus-von-Imhof-Forum 2, 85354 Freising, Germany
| | - Konstantinos T Konstantinidis
- Ocean Science & Engineering, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA; School of Civil & Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
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23
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Di Russo C, Allegrucci G, Rampini M. Molecular and morphological analyses disclose the existence of three species of Dolichopoda (Orthoptera: Rhaphidophoridae) in the Calabria region (Italy). J NAT HIST 2023. [DOI: 10.1080/00222933.2023.2186277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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24
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The Revision of Lichen Flora Around Maxwell Bay, King George Island, Maritime Antarctic. J Microbiol 2023; 61:159-173. [PMID: 36847971 PMCID: PMC9998320 DOI: 10.1007/s12275-023-00015-x] [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: 11/18/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 03/01/2023]
Abstract
Since the floristic study of lichens at the Barton and Weaver Peninsulas of King George Island in 2006, there have been intense investigations of the lichen flora of the two peninsulas as well as that of Fildes Peninsula and Ardley Island in Maxwell Bay, King George Island, South Shetland Islands, maritime Antarctic. In this study, a total of 104 species belonging to 53 genera, are identified from investigations of lichens that were collected in austral summer seasons from 2008 to 2016. Phenotypic and molecular analyses were incorporated for taxonomic identification. In particular, 31 species are found to be endemic to the Antarctic and 22 species are newly recorded to the Maxwell Bay region. Lepra dactylina, Stereocaulon caespitosum, and Wahlenbergiella striatula are newly recorded in the Antarctic, and the previously reported taxon Cladonia furcata is excluded from the formerly recorded list due to misidentification. We also provide ecological and geographical information about lichen associations and habitat preferences.
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25
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Benovics M, Vukić J, Šanda R, Nejat F, Charmpila EA, Buj I, Shumka S, Porcelloti S, Tarkan SA, Aksu S, Emiroğlu O, Šimková A. Monogeneans and chubs: Ancient host-parasite system under the looking glass. Mol Phylogenet Evol 2023; 179:107667. [PMID: 36400419 DOI: 10.1016/j.ympev.2022.107667] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/04/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022]
Abstract
Host-parasite coevolution is one of the fundamentals of evolutionary biology. Due to the intertwined evolutionary history of two interacting species and reciprocal coadaptation processes of hosts and parasites, we can expect that studying parasites will shed more light onto the evolutionary processes of their hosts. Monogenea (ectoparasitic Platyhelminthes) and their cyprinoid fish hosts represent one of the best models for studying host-parasite evolutionary relationships using a cophylogenetic approach. These parasites have developed remarkably high host specificity, where each host species often serves as a potential host for its own host-specific monogenean species. Here, the cophylogenetic relationships in the Dactylogyrus-Squalius system was investigated, as Squalius is one of several cyprinoid genera with puzzling phylogeography and inhabits all four major peri-Mediterranean peninsulas. Of 29 endemic Squalius species examined for the presence of Dactylogyrus parasites, a total of 13 Dactylogyrus species were collected from the gills of 20 Squalius species across a wide range of distribution. Phylogenetic reconstruction revealed a polyphyletic origin for Dactylogyrus species parasitizing congeneric Squalius, with four major clades being recognized. On the basis of the delimitation of host specificity, strict specialists parasitizing single host species, geographic specialists parasitizing congeners in a limited geographical region, and true generalists parasitizing congeners in various geographical regions were recognized in Dactylogyrus species parasitizing Squalius. The phylogenetic reconstruction of Squalius hosts revealed two major clades, the first encompassing only peri-Mediterranean species and the second including species from other Euro-Asian regions. Distance-based cophylogenetic methods did not reveal a statistically significant global cophylogenetic structure in the studied system; however, several host-parasite links among Iberian endemic species contributed significantly to the overall structure. The widest host range and associated genetic variability were recorded for D. folkmanovae, parasitizing nine Squalius species, and D. vistulae, parasitizing 13 Squalius species. Two different dispersion mechanisms and morphological adaptations to Squalius hosts were clearly reflected in the contrasting cophylogenetic patterns for these two species with different levels of host specificity. While host-parasite cospeciation plays an important role in diversification within D. folkmanovae, diversification within D. vistulae is driven mainly by host switching.
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Affiliation(s)
- M Benovics
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic; Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia.
| | - J Vukić
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2 128 44, Czech Republic.
| | - R Šanda
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2 128 44, Czech Republic; Department of Zoology, National Museum, Václavské Náměstí 68, Prague 1 110 00, Czech Republic.
| | - F Nejat
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.
| | - E A Charmpila
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2 128 44, Czech Republic.
| | - I Buj
- Department of Zoology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 100 00 Zagreb, Croatia.
| | - S Shumka
- Department of Biotechnology and Food, Faculty of Biotechnology and Food, Agricultural University of Tirana, Tirana, Albania.
| | - S Porcelloti
- Associazione Ichthyos Italia, Via. A Cecchi 12, 52100 Arezzo, Italy.
| | - S A Tarkan
- Faculty of Fisheries, Muğla Sıtkı Koçman University, Menteşe 480 00, Muğla, Turkey; Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland.
| | - S Aksu
- Vocational School of Health Services, Eskişehir Osmangazi University, Büyükdere Meşelik Yerleşkesi, 26040 Eskişehir, Turkey.
| | - O Emiroğlu
- Vocational School of Health Services, Eskişehir Osmangazi University, Büyükdere Meşelik Yerleşkesi, 26040 Eskişehir, Turkey.
| | - A Šimková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.
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26
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Li Y. Genetic basis underlying Lassa fever endemics in the Mano River region, West Africa. Virology 2023; 579:128-136. [PMID: 36669329 DOI: 10.1016/j.virol.2023.01.006] [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: 11/15/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
Lassa fever (LF), a haemorrhagic fever disease caused by Lassa virus (LASV), is a serious public health burden in West Africa. The Mano River region (Sierra Leone, Guinea, Liberia, and Côte d'Ivoire) has been an endemic focus of the disease over the past decades. Here, we deciphered the genetic basis underlying LF endemics in this region. Clade model and type I functional divergence analyses revealed that the major LASV group, Kenema sub-clade, which is currently circulating in the Eastern Province of Sierra Leone, has been affected by different selective pressure compared to isolates from the other areas with effects on the viral RNA-dependent RNA polymerase (L protein) and probably nucleoprotein (NP). Further, contingency analysis showed that, in the early endemic, the sub-clade has undergone adaptive diversification via acceleration of amino acid substitutions in L protein. These findings highlight the key viral factor and local adaptation regarding the endemicity of LF.
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Affiliation(s)
- Yan Li
- College of Animal Science and Technology, Sichuan Agricultural University, People's Republic of China.
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27
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Soldan S, Su C, Monaco MC, Brown N, Clauze A, Andrada F, Feder A, Planet P, Kossenkov A, Schäffer D, Ohayon J, Auslander N, Jacobson S, Lieberman P. Unstable EBV latency drives inflammation in multiple sclerosis patient derived spontaneous B cells. RESEARCH SQUARE 2023:rs.3.rs-2398872. [PMID: 36778367 PMCID: PMC9915775 DOI: 10.21203/rs.3.rs-2398872/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Epidemiological studies have demonstrated that Epstein-Barr virus (EBV) is a known etiologic risk factor, and perhaps prerequisite, for the development of MS. EBV establishes life-long latent infection in a subpopulation of memory B cells. Although the role of memory B cells in the pathobiology of MS is well established, studies characterizing EBV-associated mechanisms of B cell inflammation and disease pathogenesis in EBV (+) B cells from MS patients are limited. Accordingly, we analyzed spontaneous lymphoblastoid cell lines (SLCLs) from multiple sclerosis patients and healthy controls to study host-virus interactions in B cells, in the context of an individual's endogenous EBV. We identify differences in EBV gene expression and regulation of both viral and cellular genes in SLCLs. Our data suggest that EBV latency is dysregulated in MS SLCLs with increased lytic gene expression observed in MS patient B cells, especially those generated from samples obtained during "active" disease. Moreover, we show increased inflammatory gene expression and cytokine production in MS patient SLCLs and demonstrate that tenofovir alafenamide, an antiviral that targets EBV replication, decreases EBV viral loads, EBV lytic gene expression, and EBV-mediated inflammation in both SLCLs and in a mixed lymphocyte assay. Collectively, these data suggest that dysregulation of EBV latency in MS drives a pro-inflammatory, pathogenic phenotype in memory B cells and that this response can be attenuated by suppressing EBV lytic activation. This study provides further support for the development of antiviral agents that target EBV-infection for use in MS.
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Affiliation(s)
| | | | - Maria Chiara Monaco
- National Institutes of Health - National Institute of Neurological Disorders and Stroke
| | | | | | | | | | | | | | - Daniel Schäffer
- Computational Biology Department, Carnegie Mellon University
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28
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Bianco CM, Moustafa AM, O’Brien K, Martin MA, Read TD, Kreiswirth BN, Planet PJ. Pre-epidemic evolution of the MRSA USA300 clade and a molecular key for classification. Front Cell Infect Microbiol 2023; 13:1081070. [PMID: 36761897 PMCID: PMC9902376 DOI: 10.3389/fcimb.2023.1081070] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/04/2023] [Indexed: 01/26/2023] Open
Abstract
Introduction USA300 has remained the dominant community and healthcare associated methicillin-resistant Staphylococcus aureus (MRSA) clone in the United States and in northern South America for at least the past 20 years. In this time, it has experienced epidemic spread in both of these locations. However, its pre-epidemic evolutionary history and origins are incompletely understood. Large sequencing databases, such as NCBI, PATRIC, and Staphopia, contain clues to the early evolution of USA300 in the form of sequenced genomes of USA300 isolates that are representative of lineages that diverged prior to the establishment of the South American epidemic (SAE) clade and North American epidemic (NAE) clade. In addition, historical isolates collected prior to the emergence of epidemics can help reconstruct early events in the history of this lineage. Methods Here, we take advantage of the accrued, publicly available data, as well as two newly sequenced pre-epidemic historical isolates from 1996, and a very early diverging ACME-negative NAE genome, to understand the pre-epidemic evolution of USA300. We use database mining techniques to emphasize genomes similar to pre-epidemic isolates, with the goal of reconstructing the early molecular evolution of the USA300 lineage. Results Phylogenetic analysis with these genomes confirms that the NAE and SAE USA300 lineages diverged from a most recent common ancestor around 1970 with high confidence, and it also pinpoints the independent acquisition events of the of the ACME and COMER loci with greater precision than in previous studies. We provide evidence for a North American origin of the USA300 lineage and identify multiple introductions of USA300 into South and North America. Notably, we describe a third major USA300 clade (the pre-epidemic branching clade; PEB1) consisting of both MSSA and MRSA isolates circulating around the world that diverged from the USA300 lineage prior to the establishment of the South and North American epidemics. We present a detailed analysis of specific sequence characteristics of each of the major clades, and present diagnostic positions that can be used to classify new genomes.
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Affiliation(s)
- Colleen M. Bianco
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Ahmed M. Moustafa
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Kelsey O’Brien
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Michael A. Martin
- Division of Infectious Diseases & Department of Human Genetics Emory University School of Medicine, Atlanta, GA, United States
| | - Timothy D. Read
- Division of Infectious Diseases & Department of Human Genetics Emory University School of Medicine, Atlanta, GA, United States
| | - Barry N. Kreiswirth
- Center for Discovery & Innovation, Hackensack Meridian Health, Nutley, NJ, United States
| | - Paul J. Planet
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, PA, United States,American Museum of Natural History, New York, NY, United States,*Correspondence: Paul J. Planet,
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29
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Schütte A, Stüben PE, Astrin JJ. Molecular Weevil Identification Project: A thoroughly curated barcode release of 1300 Western Palearctic weevil species (Coleoptera, Curculionoidea). Biodivers Data J 2023; 11:e96438. [PMID: 38357418 PMCID: PMC10865102 DOI: 10.3897/bdj.11.e96438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/08/2022] [Indexed: 01/25/2023] Open
Abstract
The Molecular Weevil Identification project (MWI) studies the systematics of Western Palearctic weevils (superfamily Curculionoidea) in an integrative taxonomic approach of DNA barcoding, morphology and ecology. This barcode release provides almost 3600 curated CO1 sequences linked to morphological vouchers in about 1300 weevil species. The dataset is presented in statistical distance tables and as a Neighbour-Joining tree. Bayesian Inference trees are computed for the subfamilies Cryptorhynchinae, Apioninae and Ceutorhynchinae. Altogether, 18 unresolved taxonomic issues are discussed. A new barcode primer set is presented. Finally, we establish group-specific genetic distances for many weevil genera to serve as a tool in species delineation. These values are statistically based on distances between "good species" and their congeners. With this morphologically calibrated approach, we could resolve most alpha-taxonomic questions within the MWI project.
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Affiliation(s)
- André Schütte
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn Germany
| | - Peter E Stüben
- Curculio Institute, Mönchengladbach, Germany Curculio Institute Mönchengladbach Germany
| | - Jonas J Astrin
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig, Bonn, Germany Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn Germany
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30
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Zeb J, Song B, Senbill H, Aziz MU, Hussain S, Khan MA, Qadri I, Cabezas-Cruz A, de la Fuente J, Sparagano OA. Ticks Infesting Dogs in Khyber Pakhtunkhwa, Pakistan: Detailed Epidemiological and Molecular Report. Pathogens 2023; 12:98. [PMID: 36678446 PMCID: PMC9862609 DOI: 10.3390/pathogens12010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 01/11/2023] Open
Abstract
Ticks and tick-borne diseases are considered a major challenge for human and animal health in tropical, sub-tropical, and temperate regions of the world. However, only scarce information is available on the characterization of tick species infesting dogs in Pakistan. In this study, we present a comprehensive report on the epidemiological and phylogenetic aspects of ticks infesting dogs in Pakistan using the mitochondrial markers i.e. Cytochrome c oxidase subunit 1 (cox1) and 16S ribosomal RNA (16S rRNA) nucleotide sequences. A total of 300 dogs were examined and 1150 ixodid ticks were collected across central Khyber Pakhtunkhwa, Pakistan. The morpho-molecular characterization of hard ticks revealed the presence of two ixodid tick genera on dogs, i.e., Hyalomma and Rhipicephalus, including six tick species viz. Hyalomma dromedarii (15.9%), Hyalomma excavatum (3%), Rhipicephalus sanguineus s.l. (41.3%), Rhipicephalus turanicus s.s. (28.7%), Rhipicephalus haemaphysaloides (10.2%), and Rhipicephalus microplus (2%). The total prevalence of tick infestation in dogs was 61%. The district with the highest tick prevalence rate in dogs was Mardan (14.7%), followed by Peshawar (13%), Swabi (12%), Charsadda (11%), and Malakand (10.3%), respectively. Risk factors analysis indicated that some demographic and host management-associated factors such as host age, breed, exposure to acaricides treatment, and previous tick infestation history were associated with a higher risk of tick infestation on dogs. This is the first molecular report confirming the infestation of Hyalomma and Rhipicephalus tick species in the dog population from the study area. The present study also reported a new tick−host association between Hy. excavatum, Hy. dromedarii, and dogs. Phylogenetic analysis revealed that cox1 partial nucleotide sequences of Hy. excavatum in our dataset were 100% identical to similar tick specimens identified in Turkey, and those of Hy. dromedarii were identical to tick specimens from Iran. Whereas, Rh. haemaphysaloides and Rh. microplus’ cox1 partial nucleotide sequences were identical to sequences previously published from Pakistan. Rhipicephalus turanicus s.s. ‘s cox1 isolates from the present study were 99.8−100% identical to Pakistani-reported isolates, and those of Rh. sanguineus s.l. were 100% identical to Chinese specimens. Results on the genetic characterization of ticks were further confirmed by 16S rRNA partial nucleotide sequences analysis, which revealed 100% identity between the tick isolates of this study and those of Hy. excavatum reported from Turkey; Hy. dromedarii specimens reported from Senegal; Rh. haemaphysaloides, Rh. microplus, and Rh. turanicus s.s., previously published from Pakistan, and Rh. sanguineus s.l., published from China. Furthermore, phylogenetic analysis showed that the Rh. sanguineus s.l. isolates of this study clustered with specimens of the tropical lineage with 7.7−10% nucleotide divergence from the specimens of the temperate lineage. Further molecular works need to be performed throughout Pakistan to present a more detailed map of tick distribution with information about dog host associations, biological characteristics, and pathogen competence.
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Affiliation(s)
- Jehan Zeb
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Sciences, City University of Hong Kong, Hong Kong SAR 999077, China
| | - Baolin Song
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Sciences, City University of Hong Kong, Hong Kong SAR 999077, China
| | - Haytham Senbill
- Department of Applied Entomology and Zoology, Faculty of Agriculture, Alexandria University, Alexandria 21545, Egypt
| | - Muhammad Umair Aziz
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Sciences, City University of Hong Kong, Hong Kong SAR 999077, China
| | - Sabir Hussain
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Sciences, City University of Hong Kong, Hong Kong SAR 999077, China
| | - Munsif Ali Khan
- Vector-Borne Diseases Control Unit, District Health Office, Abbottabad 22010, Pakistan
| | - Ishtiaq Qadri
- Department of Biology, Faculty of Science King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Alejandro Cabezas-Cruz
- ANSES, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, F-94700 Maisons-Alfort, France
| | - José de la Fuente
- SaBio, Instituto de Investigaci’on en Recursos Cineg´eticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo 12, 13005 Ciudad Real, Spain
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74078, USA
| | - Olivier Andre Sparagano
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Sciences, City University of Hong Kong, Hong Kong SAR 999077, China
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31
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Mitochondrial DNA variation of the caracal (Caracal caracal) in Iran and range-wide phylogeographic comparisons. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00328-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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32
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Marcaigh FÓ, Kelly DJ, O’connell DP, Analuddin K, Karya A, Mccloughan J, Tolan E, Lawless N, Marples NM. Small islands and large biogeographic barriers have driven contrasting speciation patterns in Indo-Pacific sunbirds (Aves: Nectariniidae). Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Birds of the Indo-Pacific have provided biologists with many foundationalinsights. This study presents evidence for strong phylogeographic structure in two sunbird species from the heart of this region, the olive-backed sunbird, Cinnyris jugularis, and the black sunbird, Leptocoma aspasia. We assessed population divergence using morphological, plumage, bioacoustic and molecular data (mitochondrial ND2/ND3). Our findings indicate that the olive-backed sunbird should be recognized as multiple species, because birds from Sulawesi and the Sahul Shelf are closely related to each other, but widely separated from those in other regions. In addition, we provide evidence for an endemic species on the Wakatobi Islands, an archipelago of deep-sea islands off south-east Sulawesi. That a small bird could exhibit a range all the way from Sulawesi to Australia, while diverging on a small archipelago within this range, illustrates the complex interplay between dispersal and speciation. Our black sunbird genetic data also suggest unrecognized population structure, despite relatively weak plumage divergence. Black sunbirds in Sulawesi are likely to be a separate species from those in New Guinea, with a mean genetic distance of 9.1%. Current taxonomy suggests these sunbird species transcend classic biogeographic barriers, but our results suggest that these barriers are not easily bypassed.
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Affiliation(s)
- Fionn Ó Marcaigh
- Department of Zoology, School of Natural Sciences, Trinity College Dublin , Dublin D02 CX56 , Ireland
| | - David J Kelly
- Department of Zoology, School of Natural Sciences, Trinity College Dublin , Dublin D02 CX56 , Ireland
| | - Darren P O’connell
- School of Biology and Environmental Science, University College Dublin , Dublin D04 N2E5 , Ireland
| | - Kangkuso Analuddin
- Department of Biology and Biotechnology, Universitas Halu Oleo , Kendari 93132, South-east Sulawesi , Indonesia
| | - Adi Karya
- Department of Biology and Biotechnology, Universitas Halu Oleo , Kendari 93132, South-east Sulawesi , Indonesia
| | - Jennifer Mccloughan
- Department of Zoology, School of Natural Sciences, Trinity College Dublin , Dublin D02 CX56 , Ireland
| | - Ellen Tolan
- Department of Zoology, School of Natural Sciences, Trinity College Dublin , Dublin D02 CX56 , Ireland
| | - Naomi Lawless
- Department of Zoology, School of Natural Sciences, Trinity College Dublin , Dublin D02 CX56 , Ireland
| | - Nicola M Marples
- Department of Zoology, School of Natural Sciences, Trinity College Dublin , Dublin D02 CX56 , Ireland
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Gao H, Chen YJ, Xu XQ, Xu ZY, Xu SJ, Xing JB, Liu J, Zha YF, Sun YK, Zhang GH. Comprehensive phylogeographic and phylodynamic analyses of global Senecavirus A. Front Microbiol 2022; 13:980862. [PMID: 36246286 PMCID: PMC9557172 DOI: 10.3389/fmicb.2022.980862] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Senecavirus A (SVA) is a member of the genus Senecavirus in the family Picornaviridae that infects pigs and shows symptoms similar to foot and mouth diseases and other vesicular diseases. It is difficult to prevent, thus, causing tremendous economic loss to the pig industry. However, the global transmission routes of SVA and its natural origins remain unclear. In this study, we processed representative SVA sequences from the GenBank database along with 10 newly isolated SVA strains from the field samples collected from our lab to explore the origins, population characteristics, and transmission patterns of SVA. The SVA strains were firstly systematically divided into eight clades including Clade I–VII and Clade Ancestor based on the maximum likelihood phylogenetic inference. Phylogeographic and phylodynamics analysis within the Bayesian statistical framework revealed that SVA originated in the United States in the 1980s and afterward spread to different countries and regions. Our analysis of viral transmission routes also revealed its historical spread from the United States and the risk of the global virus prevalence. Overall, our study provided a comprehensive assessment of the phylogenetic characteristics, origins, history, and geographical evolution of SVA on a global scale, unlocking insights into developing efficient disease management strategies.
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Affiliation(s)
- Han Gao
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Yong-jie Chen
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Xiu-qiong Xu
- Guangdong Animal Health and Quarantine Office, Guangdong Animal Disease Prevention and Control Center, Guangzhou, China
| | - Zhi-ying Xu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Si-jia Xu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Jia-bao Xing
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Jing Liu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Yun-feng Zha
- Guangdong Animal Health and Quarantine Office, Guangdong Animal Disease Prevention and Control Center, Guangzhou, China
| | - Yan-kuo Sun
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- *Correspondence: Yan-kuo Sun,
| | - Gui-hong Zhang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- Key Laboratory of Animal Vaccine Development, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- Gui-hong Zhang,
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Ho LST, Dinh V. When can we reconstruct the ancestral state? A unified theory. Theor Popul Biol 2022; 148:22-27. [PMID: 36167107 DOI: 10.1016/j.tpb.2022.09.001] [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: 11/18/2021] [Revised: 09/09/2022] [Accepted: 09/19/2022] [Indexed: 10/14/2022]
Abstract
Ancestral state reconstruction is one of the most important tasks in evolutionary biology. Conditions under which we can reliably reconstruct the ancestral state have been studied for both discrete and continuous traits. However, the connection between these results is unclear, and it seems that each model needs different conditions. In this work, we provide a unifying theory on the consistency of ancestral state reconstruction for various types of trait evolution models. Notably, we show that for a sequence of nested trees with bounded heights, the necessary and sufficient conditions for the existence of a consistent ancestral state reconstruction method under discrete models, the Brownian motion model, and the threshold model are equivalent. When tree heights are unbounded, we provide a simple counter-example to show that this equivalence is no longer valid.
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Affiliation(s)
- Lam Si Tung Ho
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada.
| | - Vu Dinh
- Department of Mathematical Sciences, University of Delaware, USA.
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35
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Robust Phylodynamic Analysis of Genetic Sequencing Data from Structured Populations. Viruses 2022; 14:v14081648. [PMID: 36016270 PMCID: PMC9413058 DOI: 10.3390/v14081648] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/22/2022] [Indexed: 02/04/2023] Open
Abstract
The multi-type birth–death model with sampling is a phylodynamic model which enables the quantification of past population dynamics in structured populations based on phylogenetic trees. The BEAST 2 package bdmm implements an algorithm for numerically computing the probability density of a phylogenetic tree given the population dynamic parameters under this model. In the initial release of bdmm, analyses were computationally limited to trees consisting of up to approximately 250 genetic samples. We implemented important algorithmic changes to bdmm which dramatically increased the number of genetic samples that could be analyzed and which improved the numerical robustness and efficiency of the calculations. Including more samples led to the improved precision of parameter estimates, particularly for structured models with a high number of inferred parameters. Furthermore, we report on several model extensions to bdmm, inspired by properties common to empirical datasets. We applied this improved algorithm to two partly overlapping datasets of the Influenza A virus HA sequences sampled around the world—one with 500 samples and the other with only 175—for comparison. We report and compare the global migration patterns and seasonal dynamics inferred from each dataset. In this way, we show the information that is gained by analyzing the bigger dataset, which became possible with the presented algorithmic changes to bdmm. In summary, bdmm allows for the robust, faster, and more general phylodynamic inference of larger datasets.
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36
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A phylogeographic assessment of the greater kudu (Tragelaphus strepsiceros) across South Africa. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01464-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Gierl C, Dohrmann M, Keith P, Humphreys W, Esmaeili HR, Vukić J, Šanda R, Reichenbacher B. An integrative phylogenetic approach for inferring relationships of fossil gobioids (Teleostei: Gobiiformes). PLoS One 2022; 17:e0271121. [PMID: 35802740 PMCID: PMC9269936 DOI: 10.1371/journal.pone.0271121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 06/23/2022] [Indexed: 11/18/2022] Open
Abstract
The suborder Gobioidei is among the most diverse groups of vertebrates, comprising about 2310 species. In the fossil record gobioids date back to the early Eocene (c. 50 m.y. ago), and a considerable increase in numbers of described species is evident since the middle Miocene (c. 16 m.y. ago). About 40 skeleton-based gobioid species and > 100 otolith-based species have been described until to date. However, assignment of a fossil gobioid species to specific families has often remained tentative, even if well preserved complete specimens are available. The reasons are that synapomorphies that can be recognized in a fossil skeleton are rare (or absent) and that no phylogenetic framework applicable to gobioid fossils exists. Here we aim to overcome this problem by developing a phylogenetic total evidence framework that is suitable to place a fossil skeleton-based gobioid at family level. Using both literature and newly collected data we assembled a morphological character matrix (48 characters) for 29 extant species, representing all extant gobioid families, and ten fossil gobioid species, and we compiled a multi-gene concatenated alignment (supermatrix; 6271 bp) of published molecular sequence data for the extant species. Bayesian and Maximum Parsimony analyses revealed that our selection of extant species was sufficient to achieve a molecular ‘backbone’ that fully conforms to previous molecular work. Our data revealed that inclusion of all fossil species simultaneously produced very poorly resolved trees, even for some extant taxa. In contrast, addition of a single fossil species to the total evidence data set of the extant species provided new insight in its possible placement at family level, especially in a Bayesian framework. Five out of the ten fossil species were recovered in the same family as had been suggested in previous works based on comparative morphology. The remaining five fossil species had hitherto been left as family incertae sedis. Now, based on our phylogenetic framework, new and mostly well supported hypotheses to which clades they could belong can be presented. We conclude that the total evidence framework presented here will be beneficial for all future work dealing with the phylogenetic placement of a fossil skeleton-based gobioid and thus will help to improve our understanding of the evolutionary history of these fascinating fishes. Moreover, our data highlight that increased sampling of fossil taxa in a total-evidence context is not universally beneficial, as might be expected, but strongly depends on the study group and peculiarities of the morphological data.
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Affiliation(s)
- Christoph Gierl
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Martin Dohrmann
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Philippe Keith
- UMR 8067 Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Muséum National d’Histoire Naturelle, CNRS, IRD, SU, Paris, France
| | - William Humphreys
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
- Western Australian Museum, Welshpool, WA, Australia
| | - Hamid R. Esmaeili
- Ichthyology and Molecular Systematics Research Laboratory, Zoology Section, Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran
| | - Jasna Vukić
- Department of Ecology, Charles University, Prague, Czech Republic
| | - Radek Šanda
- Department of Zoology, National Museum, Prague, Czech Republic
| | - Bettina Reichenbacher
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center LMU, Ludwig-Maximilians-Universität München, Munich, Germany
- * E-mail:
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Vanmechelen B, Meurs S, Horemans M, Loosen A, Joly Maes T, Laenen L, Vergote V, Koundouno FR, Magassouba N, Konde MK, Condé IS, Carroll MW, Maes P. The Characterization of Multiple Novel Paramyxoviruses Highlights the Diverse Nature of the Subfamily Orthoparamyxovirinae. Virus Evol 2022; 8:veac061. [PMID: 35854826 PMCID: PMC9290864 DOI: 10.1093/ve/veac061] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/14/2022] [Accepted: 06/29/2022] [Indexed: 11/26/2022] Open
Abstract
The subfamily Orthoparamyxovirinae is a group of single-stranded, negative-sense RNA viruses that contains many human, animal, and zoonotic pathogens. While there are currently only forty-two recognized species in this subfamily, recent research has revealed that much of its diversity remains to be characterized. Using a newly developed nested PCR-based screening assay, we report here the discovery of fifteen orthoparamyxoviruses in rodents and shrews from Belgium and Guinea, thirteen of which are believed to represent new species. Using a combination of nanopore and sanger sequencing, complete genomes could be determined for almost all these viruses, enabling a detailed evaluation of their genome characteristics. While most viruses are thought to belong to the rapidly expanding genus Jeilongvirus, we also identify novel members of the genera Narmovirus, Henipavirus, and Morbillivirus. Together with other recently discovered orthoparamyxoviruses, both henipaviruses and the morbillivirus discovered here appear to form distinct rodent-/shrew-borne clades within their respective genera, clustering separately from all currently classified viruses. In the case of the henipaviruses, a comparison of the different members of this clade revealed the presence of a secondary conserved open reading frame, encoding for a transmembrane protein, within the F gene, the biological relevance of which remains to be established. While the characteristics of the viruses described here shed further light on the complex evolutionary origin of paramyxoviruses, they also illustrate that the diversity of this group of viruses in terms of genome organization appears to be much larger than previously assumed.
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Affiliation(s)
- Bert Vanmechelen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research , Herestraat 49/Box 1040, BE3000 Leuven, Belgium
| | - Sien Meurs
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research , Herestraat 49/Box 1040, BE3000 Leuven, Belgium
| | - Marie Horemans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research , Herestraat 49/Box 1040, BE3000 Leuven, Belgium
| | - Arne Loosen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research , Herestraat 49/Box 1040, BE3000 Leuven, Belgium
| | - Tibe Joly Maes
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research , Herestraat 49/Box 1040, BE3000 Leuven, Belgium
| | - Lies Laenen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research , Herestraat 49/Box 1040, BE3000 Leuven, Belgium
| | - Valentijn Vergote
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research , Herestraat 49/Box 1040, BE3000 Leuven, Belgium
| | - Fara Raymond Koundouno
- Laboratoire des fièvres hémorragiques et virales de Guinée , Conakry Guinea – Direction préfectorale de la santé de Gueckedou
| | - N’Faly Magassouba
- Projet des Fièvres Hémorragiques en Guinée, Laboratoire de Recherche en Virologie , Conakry, Guinea
| | - Mandy Kader Konde
- Center of Excellence for Training, Research on Malaria and Disease Control in Guinea (CEFORPAG) , Quartier Nongo, Ratoma, Conakry, Guinea
| | - Ibrahima Sory Condé
- Center of Excellence for Training, Research on Malaria and Disease Control in Guinea (CEFORPAG) , Quartier Nongo, Ratoma, Conakry, Guinea
| | - Miles W Carroll
- Pandemic Science Centre, Oxford University, Nuffield Department of Medicine, Wellcome Centre for Human Genetics , CCMP1st South, Roosevelt Dr, Headington, Oxford OX3 7BN, United Kingdom
| | - Piet Maes
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research , Herestraat 49/Box 1040, BE3000 Leuven, Belgium
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Van Elslande J, Kerckhofs F, Cuypers L, Wollants E, Potter B, Vankeerberghen A, Cattoir L, Holderbeke A, Behillil S, Gorissen S, Bloemen M, Arnout J, Van Ranst M, Van Weyenbergh J, Maes P, Baele G, Vermeersch P, André E, on behalf of the COG-Belgium Consortium. Two Separate Clusters of SARS-CoV-2 Delta Variant Infections in A Group of 41 Students Travelling from India: An Illustration of the Need for Rigorous Testing and Quarantine. Viruses 2022; 14:v14061198. [PMID: 35746671 PMCID: PMC9229483 DOI: 10.3390/v14061198] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/16/2022] [Accepted: 05/26/2022] [Indexed: 12/24/2022] Open
Abstract
We report two clusters of SARS-CoV-2 B.1.617.2 (Delta variant) infections in a group of 41 Indian nursing students who travelled from New Delhi, India, to Belgium via Paris, France. All students tested negative before departure and had a second negative antigen test upon arrival in Paris. Upon arrival in Belgium, the students were quarantined in eight different houses. Four houses remained COVID-free during the 24 days of follow-up, while all 27 residents of the other four houses developed an infection during quarantine, including the four residents who were fully vaccinated and the two residents who were partially vaccinated. Genome sequencing revealed two distinct clusters affecting one and three houses, respectively. In this group of students, vaccination status did not seem to prevent infection nor decrease the viral load. No severe symptoms were reported. Extensive contact tracing and 3 months of nationwide genomic surveillance confirmed that these outbreaks were successfully contained and did not contribute to secondary community transmission in Belgium. These clusters highlight the importance of repeated testing and quarantine measures among travelers coming from countries experiencing a surge of infections, as all infections were detected 6 days or more after arrival.
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Affiliation(s)
- Jan Van Elslande
- Clinical Department of Laboratory Medicine and National Reference Center for Respiratory Pathogens, University Hospitals Leuven, BE3000 Leuven, Belgium; (J.V.E.); (F.K.); (L.C.); (S.G.); (M.V.R.); (P.V.)
| | - Femke Kerckhofs
- Clinical Department of Laboratory Medicine and National Reference Center for Respiratory Pathogens, University Hospitals Leuven, BE3000 Leuven, Belgium; (J.V.E.); (F.K.); (L.C.); (S.G.); (M.V.R.); (P.V.)
| | - Lize Cuypers
- Clinical Department of Laboratory Medicine and National Reference Center for Respiratory Pathogens, University Hospitals Leuven, BE3000 Leuven, Belgium; (J.V.E.); (F.K.); (L.C.); (S.G.); (M.V.R.); (P.V.)
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, BE3000 Leuven, Belgium;
| | - Elke Wollants
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, BE3000 Leuven, Belgium; (E.W.); (M.B.); (P.M.)
| | - Barney Potter
- Laboratory of Clinical and Evolutionary Virology, Immunology and Transplantation, Department of Microbiology, Rega Institute, KU Leuven, BE3000 Leuven, Belgium; (B.P.); (G.B.)
| | - Anne Vankeerberghen
- Laboratory of Clinical Microbiology, OLV Hospital Aalst, BE9300 Aalst, Belgium; (A.V.); (L.C.); (A.H.)
| | - Lien Cattoir
- Laboratory of Clinical Microbiology, OLV Hospital Aalst, BE9300 Aalst, Belgium; (A.V.); (L.C.); (A.H.)
| | - Astrid Holderbeke
- Laboratory of Clinical Microbiology, OLV Hospital Aalst, BE9300 Aalst, Belgium; (A.V.); (L.C.); (A.H.)
| | - Sylvie Behillil
- Institut Pasteur, Molecular Genetics of RNA Viruses, Université de Paris, CNRS UMR 3569, FR75000 Paris, France;
- Institut Pasteur, National Reference Center for Respiratory Viruses, FR75000 Paris, France
| | - Sarah Gorissen
- Clinical Department of Laboratory Medicine and National Reference Center for Respiratory Pathogens, University Hospitals Leuven, BE3000 Leuven, Belgium; (J.V.E.); (F.K.); (L.C.); (S.G.); (M.V.R.); (P.V.)
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, BE3000 Leuven, Belgium;
| | - Mandy Bloemen
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, BE3000 Leuven, Belgium; (E.W.); (M.B.); (P.M.)
| | - Jef Arnout
- Biomedical Sciences Group Management, KU Leuven, BE3000 Leuven, Belgium;
| | - Marc Van Ranst
- Clinical Department of Laboratory Medicine and National Reference Center for Respiratory Pathogens, University Hospitals Leuven, BE3000 Leuven, Belgium; (J.V.E.); (F.K.); (L.C.); (S.G.); (M.V.R.); (P.V.)
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, BE3000 Leuven, Belgium; (E.W.); (M.B.); (P.M.)
| | - Johan Van Weyenbergh
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, BE3000 Leuven, Belgium;
| | - Piet Maes
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, BE3000 Leuven, Belgium; (E.W.); (M.B.); (P.M.)
| | - Guy Baele
- Laboratory of Clinical and Evolutionary Virology, Immunology and Transplantation, Department of Microbiology, Rega Institute, KU Leuven, BE3000 Leuven, Belgium; (B.P.); (G.B.)
| | - Pieter Vermeersch
- Clinical Department of Laboratory Medicine and National Reference Center for Respiratory Pathogens, University Hospitals Leuven, BE3000 Leuven, Belgium; (J.V.E.); (F.K.); (L.C.); (S.G.); (M.V.R.); (P.V.)
- Department of Cardiovascular Sciences, KU Leuven, BE3000 Leuven, Belgium
| | - Emmanuel André
- Clinical Department of Laboratory Medicine and National Reference Center for Respiratory Pathogens, University Hospitals Leuven, BE3000 Leuven, Belgium; (J.V.E.); (F.K.); (L.C.); (S.G.); (M.V.R.); (P.V.)
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, BE3000 Leuven, Belgium;
- Correspondence:
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Maltseva AL, Lobov AA, Pavlova PA, Panova M, Gafarova ER, Marques JP, Danilov LG, Granovitch AI. Orphan gene in Littorina: An unexpected role of symbionts in the host evolution. Gene 2022; 824:146389. [PMID: 35257790 DOI: 10.1016/j.gene.2022.146389] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/29/2022] [Accepted: 02/28/2022] [Indexed: 11/16/2022]
Abstract
Mechanisms of reproductive isolation between closely related sympatric species are of high evolutionary significance as they may function as initial drivers of speciation and protect species integrity afterwards. Proteins involved in the establishment of reproductive barriers often evolve fast and may be key players in cessation of gene flow between the incipient species. The five Atlantic Littorina (Neritrema) species represent a notable example of recent radiation. The geographic ranges of these young species largely overlap and the mechanisms of reproductive isolation are poorly understood. In this study, we performed a detailed analysis of the reproductive protein LOSP, previously identified in Littorina. We showed that this protein is evolutionary young and taxonomically restricted to the genus Littorina. It has high sequence variation both within and between Littorina species, which is compatible with its presumable role in the reproductive isolation. The strongest differences in the LOSP structure were detected between Littorina subgenera with distinctive repetitive motifs present exclusively in the Neritrema species, but not in L. littorea. Moreover, the sequence of these repetitive structural elements demonstrates a high homology with genetic elements of bacteria, identified as components of Littorina associated microbiomes. We suggest that these elements were acquired from a symbiotic bacterial donor via horizontal genetic transfer (HGT), which is indirectly confirmed by the presence of multiple transposable elements in the LOSP flanking and intronic regions. Furthermore, we hypothesize that this HGT-driven evolutionary innovation promoted LOSP function in reproductive isolation, which might be one of the factors determining the intensive cladogenesis in the Littorina (Neritrema) lineage in contrast to the anagenesis in the L. littorea clade.
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Affiliation(s)
- A L Maltseva
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia.
| | - A A Lobov
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia; Laboratory of Regenerative Biomedicine, Institute of Cytology Russian Academy of Sciences, St Petersburg, Russia
| | - P A Pavlova
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
| | - M Panova
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia; Department of Marine Sciences - Tjärnö, University of Gothenburg, Sweden
| | - E R Gafarova
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
| | - J P Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências do Porto, 4169-007 Porto, Portugal; ISEM, Univ Montpellier, CNRS, EPHE, IRD, 34095 Montpellier, France
| | - L G Danilov
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - A I Granovitch
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
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Osborn RK, Ordóñez ME, Cognato AI. Ecuadorian Coptoborus beetles harbor Fusarium and Graphium fungi previously associated with Euwallacea ambrosia beetles. Mycologia 2022; 114:487-500. [PMID: 35608329 DOI: 10.1080/00275514.2022.2065441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Ambrosia beetles from the scolytine tribe Xyleborini (Curculionidae) are important to the decomposition of woody plant material on every continent except Antarctica. These insects farm fungi on the walls of tunnels they build inside recently dead trees and rely on the fungi for nutrition during all stages of their lives. Such ambrosia fungi rely on the beetles to provide appropriate substrates and environmental conditions for growth. A small minority of xyleborine ambrosia beetle-fungal partnerships cause significant damage to healthy trees. The xyleborine beetle Coptoborus ochromactonus vectors a Fusarium (Hypocreales) fungus that is lethal to balsa (Ochroma pyramidale (Malvaceae)) trees in Ecuador. Although this pathogenic fungus and its associated beetle are not known to be established in the United States, several other non-native ambrosia beetle species are vectors of destructive plant diseases in this country. This fact and the acceleration of trade between South America and the United States demonstrate the importance of understanding fungal plant pathogens before they escape their native ranges. Here we identify the fungi accompanying Coptoborus ambrosia beetles collected in Ecuador. Classification based ribosomal internal transcribed spacer 1 (ITS) sequences revealed the most prevalent fungi associated with Coptoborus are Fusarium sp. and Graphium sp. (Microascales: Microascaceae), which have been confirmed as ambrosia fungi for xyleborine ambrosia beetles, and Clonostsachys sp. (Hypocreales), which is a diverse genus found abundantly in soils and associated with plants. Phylogenetic analyses of the Fusarium strains based on ITS, translation elongation factor (EF1-α), and two subunits of the DNA-directed RNA polymerase II (RPB1 and RPB2) identified them as Fusarium sp. AF-9 in the Ambrosia Fusarium Clade (AFC). This Fusarium species was previously associated with a few xyleborine ambrosia beetles, most notably the species complex Euwallacea fornicatus (Eichhoff 1868) (Curculionidae: Scolytinae: Xyleborini). Examination of ITS and EF1-α sequences showed a close affinity between the Graphium isolated from Coptoborus spp. and other xyleborine-associated Graphium as well as the soil fungus Graphium basitruncatum. This characterization of ambrosia fungi through DNA sequencing confirms the identity of a putative plant pathogen spread by Coptoborus beetles and expands the documented range of Fusarium and Graphium ambrosia fungi.
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Affiliation(s)
- Rachel K Osborn
- Department of Entomology, Michigan State University, East Lansing, Michigan 48823, USA
| | - Maria Eugenia Ordóñez
- Escuela de Ciencias Biológicas, Pontifica Universidad Católica del Ecuador, Quito, Ecuador, 17-01-2184
| | - Anthony I Cognato
- Department of Entomology, Michigan State University, East Lansing, Michigan 48823, USA
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Balamurugan M, Banerjee R, Kasibhatla SM, Achalere A, Joshi R. Understanding the Genetic Diversity of Mycobacterium africanum Using Phylogenetics and Population Genomics Approaches. Front Genet 2022; 13:800083. [PMID: 35495132 PMCID: PMC9043288 DOI: 10.3389/fgene.2022.800083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
A total of two lineages of Mycobacterium tuberculosis var. africanum (Maf), L5 and L6, which are members of the Mycobacterium tuberculosis complex (MTBC), are responsible for causing tuberculosis in West Africa. Regions of difference (RDs) are usually used for delineation of MTBC. With increased data availability, single nucleotide polymorphisms (SNPs) promise to provide better resolution. Publicly available 380 Maf samples were analyzed for identification of “core-cluster-specific-SNPs,” while additional 270 samples were used for validation. RD-based methods were used for lineage-assignment, wherein 31 samples remained unidentified. The genetic diversity of Maf was estimated based on genome-wide SNPs using phylogeny and population genomics approaches. Lineage-based clustering (L5 and L6) was observed in the whole genome phylogeny with distinct sub-clusters. Population stratification using both model-based and de novo approaches supported the same observations. L6 was further delineated into three sub-lineages (L6.1–L6.3), whereas L5 was grouped as L5.1 and L5.2 based on the occurrence of RD711. L5.1 and L5.2 were further divided into two (L5.1.1 and L5.1.2) and four (L5.2.1–L5.2.4) sub-clusters, respectively. Unassigned samples could be assigned to definite lineages/sub-lineages based on clustering observed in phylogeny along with high-confidence posterior membership scores obtained during population stratification. Based on the (sub)-clusters delineated, “core-cluster-specific-SNPs” were derived. Synonymous SNPs (137 in L5 and 128 in L6) were identified as biomarkers and used for validation. Few of the cluster-specific missense variants in L5 and L6 belong to the central carbohydrate metabolism pathway which include His6Tyr (Rv0946c), Glu255Ala (Rv1131), Ala309Gly (Rv2454c), Val425Ala and Ser112Ala (Rv1127c), Gly198Ala (Rv3293) and Ile137Val (Rv0363c), Thr421Ala (Rv0896), Arg442His (Rv1248c), Thr218Ile (Rv1122), and Ser381Leu (Rv1449c), hinting at the differential growth attenuation. Genes harboring multiple (sub)-lineage-specific “core-cluster” SNPs such as Lys117Asn, Val447Met, and Ala455Val (Rv0066c; icd2) present across L6, L6.1, and L5, respectively, hinting at the association of these SNPs with selective advantage or host-adaptation. Cluster-specific SNPs serve as additional markers along with RD-regions for Maf delineation. The identified SNPs have the potential to provide insights into the genotype–phenotype correlation and clues for endemicity of Maf in the African population.
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Hicks JT, Edwards K, Qiu X, Kim DK, Hixson JE, Krauss S, Webby RJ, Webster RG, Bahl J. Host diversity and behavior determine patterns of interspecies transmission and geographic diffusion of avian influenza A subtypes among North American wild reservoir species. PLoS Pathog 2022; 18:e1009973. [PMID: 35417497 PMCID: PMC9037922 DOI: 10.1371/journal.ppat.1009973] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 04/25/2022] [Accepted: 03/07/2022] [Indexed: 11/19/2022] Open
Abstract
Wild birds can carry avian influenza viruses (AIV), including those with pandemic or panzootic potential, long distances. Even though AIV has a broad host range, few studies account for host diversity when estimating AIV spread. We analyzed AIV genomic sequences from North American wild birds, including 303 newly sequenced isolates, to estimate interspecies and geographic viral transition patterns among multiple co-circulating subtypes. Our results show high transition rates within Anseriformes and Charadriiformes, but limited transitions between these orders. Patterns of transition between species were positively associated with breeding habitat range overlap, and negatively associated with host genetic distance. Distance between regions (negative correlation) and summer temperature at origin (positive correlation) were strong predictors of transition between locations. Taken together, this study demonstrates that host diversity and ecology can determine evolutionary processes that underlie AIV natural history and spread. Understanding these processes can provide important insights for effective control of AIV.
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Affiliation(s)
- Joseph T. Hicks
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, Department of Epidemiology and Biostatistics, College of Public Health, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Kimberly Edwards
- Department of Infectious Disease, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Xueting Qiu
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, Department of Epidemiology and Biostatistics, College of Public Health, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Do-Kyun Kim
- University of Texas Health Science Center at Houston School of Public Health, Houston, Texas, United States of America
| | - James E. Hixson
- University of Texas Health Science Center at Houston School of Public Health, Houston, Texas, United States of America
| | - Scott Krauss
- Department of Infectious Disease, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Richard J. Webby
- Department of Infectious Disease, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Robert G. Webster
- Department of Infectious Disease, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, Department of Epidemiology and Biostatistics, College of Public Health, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
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Ruiz-García M, Cáceres AM, Luengas-Villamil K, Aliaga-Rossel E, Zeballos H, Singh MD, Shostell JM. Mitogenomic phylogenetics and population genetics of several taxa of agouties (Dasyprocta sp., Dasyproctidae, Rodentia): molecular nonexistence of some claimed endemic taxa. MAMMAL RES 2022. [DOI: 10.1007/s13364-022-00626-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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45
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Bassett LG, Zughaiyir FE, Richardson DJ, Hammond CI, McAllister CT, Forstner MR. Association of Leeches with the Endangered Houston Toad. SOUTHEAST NAT 2022. [DOI: 10.1656/058.021.0109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
| | | | | | | | - Chris T. McAllister
- Science and Mathematics Division, Eastern Oklahoma State College, Idabel, OK 74745
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46
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Pathogenic potential of bacteria isolated from commercial biostimulants. Arch Microbiol 2022; 204:162. [PMID: 35119529 PMCID: PMC8816496 DOI: 10.1007/s00203-022-02769-1] [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: 07/27/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 11/08/2022]
Abstract
Microbial-based products are a promising alternative to agrochemicals in sustainable agriculture. However, little is known about their impact on human health even if some of them, i.e., Bacillus and Paenibacillus species, have been increasingly implicated in different human diseases. In this study, 18 bacteria were isolated from 2 commercial biostimulants, and they were genotypically and phenotypically characterized to highlight specific virulence properties. Some isolated bacteria were identified as belonging to the genus Bacillus by BLAST and RDP analyses, a genus in-depth studied for plant growth-promoting ability. Moreover, 16S rRNA phylogenetic analysis showed that seven isolates grouped with Bacillus species while two and four clustered, respectively, with Neobacillus and Peribacillus. Unusually, bacterial strains belonging to Franconibacter and Stenotrophomonas were isolated from biostimulants. Although Bacillus species are generally considered nonpathogenic, most of the species have shown to swim, swarm, and produced biofilms, that can be related to bacterial virulence. The evaluation of toxins encoding genes revealed that five isolates had the potential ability to produce the enterotoxin T. In conclusion, the pathogenic potential of microorganisms included in commercial products should be deeply verified, in our opinion. The approach proposed in this study could help in this crucial step.
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Booker WW, Gerhardt HC, Lemmon AR, Ptacek MB, Hassinger ATB, Schul J, Lemmon EM. The Complex History of Genome Duplication and Hybridization in North American Gray Treefrogs. Mol Biol Evol 2022; 39:msab316. [PMID: 34791374 PMCID: PMC8826561 DOI: 10.1093/molbev/msab316] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Polyploid speciation has played an important role in evolutionary history across the tree of life, yet there remain large gaps in our understanding of how polyploid species form and persist. Although systematic studies have been conducted in numerous polyploid complexes, recent advances in sequencing technology have demonstrated that conclusions from data-limited studies may be spurious and misleading. The North American gray treefrog complex, consisting of the diploid Hyla chrysoscelis and the tetraploid H. versicolor, has long been used as a model system in a variety of biological fields, yet all taxonomic studies to date were conducted with only a few loci from nuclear and mitochondrial genomes. Here, we utilized anchored hybrid enrichment and high-throughput sequencing to capture hundreds of loci along with whole mitochondrial genomes to investigate the evolutionary history of this complex. We used several phylogenetic and population genetic methods, including coalescent simulations and testing of polyploid speciation models with approximate Bayesian computation, to determine that H. versicolor was most likely formed via autopolyploidization from a now extinct lineage of H. chrysoscelis. We also uncovered evidence of significant hybridization between diploids and tetraploids where they co-occur, and show that historical hybridization between these groups led to the re-formation of distinct polyploid lineages following the initial whole-genome duplication event. Our study indicates that a wide variety of methods and explicit model testing of polyploid histories can greatly facilitate efforts to uncover the evolutionary history of polyploid complexes.
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Affiliation(s)
- William W Booker
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - H Carl Gerhardt
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, USA
| | - Margaret B Ptacek
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Alyssa T B Hassinger
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, USA
| | - Johannes Schul
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
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Chaber K, Łukomska‐Kowalczyk M, Fells A, Milanowski R, Zakryś B. Toward the robust resolution of taxonomic ambiguity within Lepocinclis (Euglenida) based on DNA sequencing and morphology. JOURNAL OF PHYCOLOGY 2022; 58:105-120. [PMID: 34719033 PMCID: PMC9300208 DOI: 10.1111/jpy.13220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 09/02/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
DNA sequences were analyzed for three groups of species from the Lepocinclis genus (L. acus-like, L. oxyuris-like, and L. tripteris-like) along with cellular morphology. Phylogenetic analyses were based on nuclear SSU rDNA, LSU rDNA, and plastid-encoded LSU rDNA. DNA sequences were obtained from species available in culture collections (L. acus SAG 1224-1a and UTEX 1316) and those isolated directly from the environment in Poland (48 isolates), resulting in 79 new sequences. The obtained phylogenetic tree of Lepocinclis included 27 taxa, five of which are presented for the first time (L. convoluta, L. gracillimoides, L. longissima, L. pseudospiroides, and L. torta) and nine taxonomically verified and described. Based on morphology, literature data, and phylogenetic analyses, the following species were distinguished: in the L. acus-like group, L. longissima and L. acus; in the L. tripteris-like group, L. pseudospiroides, L. torta, and L. tripteris; in the L. oxyuris-like group, L. gracillimoides, L. oxyuris var. oxyuris, and L. oxyuris var. helicoidea. For all verified species, diagnostic descriptions were emended, nomenclatural adjustments were made, and epitypes were designated.
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Affiliation(s)
- Katarzyna Chaber
- Faculty of BiologyInstitute of Evolutionary Biology, Biological and Chemical Research CenterUniversity of Warsawul. Żwirki i Wigury 101Warszawa02‐089Poland
| | - Maja Łukomska‐Kowalczyk
- Faculty of BiologyInstitute of Evolutionary Biology, Biological and Chemical Research CenterUniversity of Warsawul. Żwirki i Wigury 101Warszawa02‐089Poland
| | - Alicja Fells
- Faculty of BiologyInstitute of Evolutionary Biology, Biological and Chemical Research CenterUniversity of Warsawul. Żwirki i Wigury 101Warszawa02‐089Poland
| | - Rafał Milanowski
- Faculty of BiologyInstitute of Evolutionary Biology, Biological and Chemical Research CenterUniversity of Warsawul. Żwirki i Wigury 101Warszawa02‐089Poland
| | - Bożena Zakryś
- Faculty of BiologyInstitute of Evolutionary Biology, Biological and Chemical Research CenterUniversity of Warsawul. Żwirki i Wigury 101Warszawa02‐089Poland
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49
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Framenau VW, de S. Castanheira P, Vink CJ. Taxonomy and systematics of the new Australo-Pacific orb-weaving spider genus Socca (Araneae: Araneidae). NEW ZEALAND JOURNAL OF ZOOLOGY 2022. [DOI: 10.1080/03014223.2021.2014899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Volker W. Framenau
- Harry Butler Institute, Murdoch University, Murdoch, Australia
- Department of Terrestrial Zoology, Western Australian Museum, Perth, Australia
- Zoological Museum Hamburg, Leibnitz Institute for the Analysis of Biodiversity Change (LIB), Centre for Taxonomy & Morphology Hamburg, Germany
| | | | - Cor J. Vink
- Zoological Museum Hamburg, Leibnitz Institute for the Analysis of Biodiversity Change (LIB), Centre for Taxonomy & Morphology Hamburg, Germany
- Department of Pest-management and Conservation, Lincoln University, Lincoln, New Zealand
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50
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Abstract
Over the past three decades, computational capabilities have grown at such a rapid rate that they have given rise to many computationally heavy science fields such as phylogenomics. As increasingly more genomes are sequenced in the three domains of life, larger and more species-complete phylogenetic tree reconstructions are leading to a better understanding of the tree of life and the evolutionary histories in deep times. However, these large datasets pose unique challenges from a modeling and computational perspective: accurately describing the evolutionary process of thousands of species is still beyond the capability of current models, while the computational burden limits our ability to test multiple hypotheses. Thus, it is common practice to reduce the size of a dataset by selecting species to represent a clade (taxon sampling). Unfortunately, this process is subjective, and comparisons of large tree of life studies show that choice and number of species used in a dataset can alter the topology obtained. Thus, taxon sampling is, in itself, a process that needs to be fully investigated to determine its effect on phylogenetic stability. Here, we present the theory and practical application of an automated pipeline that can be easily implemented to explore the effect of taxon sampling on phylogenetic reconstructions. The application of this approach was recently discussed in a study of Terrabacteria and shows its power in investigating the accuracy of deep nodes of a phylogeny.
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Affiliation(s)
| | - Fabia Ursula Battistuzzi
- Department of Biological Sciences, Oakland University, Rochester, MI, USA.
- Center for Data Science and Big Data Analytics, Oakland University, Rochester, MI, USA.
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