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Mupamhadzi TL, Machona O, Chidzwondo F, Mangoyi R. Molecular Detection and Phylogenetic Analysis of the alkB Gene in Klebsiella oxytoca Strains Isolated from the Gut of Tenebrio molitor. ScientificWorldJournal 2024; 2024:3350591. [PMID: 38756480 PMCID: PMC11098606 DOI: 10.1155/2024/3350591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 04/17/2024] [Accepted: 04/29/2024] [Indexed: 05/18/2024] Open
Abstract
The challenge in polystyrene disposal has caused researchers to look for urgent innovative and ecofriendly solutions for plastic degradation. Some insects have been reported to use polystyrene as their sole carbon source, and this has been linked to the presence of microbes in their guts that aid in plastic digestion. Thus, this study focuses on the molecular detection and phylogenetic analysis of the alkane-1-monooxygenase (alkB) gene in Klebsiella oxytoca strains isolated from the gut of Tenebrio molitor. The alkB gene encodes for alkane-1-monooxygenase, an enzyme involved in the oxidation of inactivated alkanes. This gene can be used as a marker to assess bacteria's ability to biodegrade polystyrene. Three bacterial strains were isolated from the guts of T. molitor mealworms and were confirmed using polymerase chain reaction (PCR) of the 16S ribosomal RNA gene. The primers used in the amplification of the 16S ribosomal RNA region were designed using NCBI, a bioinformatics tool. To detect the presence of the alkB gene in the isolated bacterial strains, a set of primers used in the amplification of this gene was manually designed from the conserved regions of the alkB nucleotide sequences of eleven bacterial species from GenBank. TCOFFE online tool was used to align the alkB sequences of the bacteria, while Jalview and ConSurf were used to view the alignment. The amplified alkB gene was then sequenced using the Sanger sequencing technique, blasted on NCBI to look for similar sequences, and a phylogenetic tree was constructed. Based on the 16S ribosomal RNA gene sequences, the isolated bacterial strains were confirmed to be Klebsiella oxytoca NBRC 102593, Klebsiella oxytoca JCM 1665, and Klebsiella oxytoca ATCC 13182. The alkB gene sequence identical to fourteen alkB gene sequences derived from Actinobacteria whole genome was detected in Klebsiella oxytoca for the first time to the best of our knowledge. The novel nucleotide sequence was published in the NCBI database under accession number OP959069. This gene sequence was found to be for the enzyme alkane-1-monooxygenase and may be one of the enzymes responsible for polystyrene degradation by the putative Klebsiella oxytoca ATCC 13182 in T. molitor.
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Affiliation(s)
| | - Oleen Machona
- Department of Biotechnology and Biochemistry, University of Zimbabwe, Harare, Zimbabwe
| | - Farisai Chidzwondo
- Department of Biotechnology and Biochemistry, University of Zimbabwe, Harare, Zimbabwe
| | - Rumbidzai Mangoyi
- Department of Biotechnology and Biochemistry, University of Zimbabwe, Harare, Zimbabwe
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Tapia R, Brito B, Saavedra M, Mena J, García-Salum T, Rathnasinghe R, Barriga G, Tapia K, García V, Bucarey S, Jang Y, Wentworth D, Torremorell M, Neira V, Medina RA. Novel influenza A viruses in pigs with zoonotic potential, Chile. Microbiol Spectr 2024; 12:e0218123. [PMID: 38446039 PMCID: PMC10986610 DOI: 10.1128/spectrum.02181-23] [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: 05/30/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Abstract
Novel H1N2 and H3N2 swine influenza A viruses (IAVs) have recently been identified in Chile. The objective of this study was to evaluate their zoonotic potential. We perform phylogenetic analyses to determine the genetic origin and evolution of these viruses, and a serological analysis to determine the level of cross-protective antibodies in the human population. Eight genotypes were identified, all with pandemic H1N1 2009-like internal genes. H1N1 and H1N2 were the subtypes more commonly detected. Swine H1N2 and H3N2 IAVs had hemagglutinin and neuraminidase lineages genetically divergent from IAVs reported worldwide, including human vaccine strains. These genes originated from human seasonal viruses were introduced into the swine population since the mid-1980s. Serological data indicate that the general population is susceptible to the H3N2 virus and that elderly and young children also lack protective antibodies against the H1N2 strains, suggesting that these viruses could be potential zoonotic threats. Continuous IAV surveillance and monitoring of the swine and human populations is strongly recommended.IMPORTANCEIn the global context, where swine serve as crucial intermediate hosts for influenza A viruses (IAVs), this study addresses the pressing concern of the zoonotic potential of novel reassortant strains. Conducted on a large scale in Chile, it presents a comprehensive account of swine influenza A virus diversity, covering 93.8% of the country's industrialized swine farms. The findings reveal eight distinct swine IAV genotypes, all carrying a complete internal gene cassette of pandemic H1N1 2009 origin, emphasizing potential increased replication and transmission fitness. Genetic divergence of H1N2 and H3N2 IAVs from globally reported strains raises alarms, with evidence suggesting introductions from human seasonal viruses since the mid-1980s. A detailed serological analysis underscores the zoonotic threat, indicating susceptibility in the general population to swine H3N2 and a lack of protective antibodies in vulnerable demographics. These data highlight the importance of continuous surveillance, providing crucial insights for global health organizations.
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Affiliation(s)
| | - Bárbara Brito
- Universidad de Chile, Santiago, Chile
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- University of Technology Sydney, Sydney, New South Wales, Australia
| | - Marco Saavedra
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan Mena
- Universidad de Chile, Santiago, Chile
| | - Tamara García-Salum
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Raveen Rathnasinghe
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gonzalo Barriga
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Karla Tapia
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | | | - Yunho Jang
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - David Wentworth
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | | | | | - Rafael A. Medina
- Department of Pediatric Infectious Diseases and Immunology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Pathology and Experimental Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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3
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Freind MC, Tallón de Lara C, Kouyos RD, Wimmersberger D, Kuster H, Aceto L, Kovari H, Flepp M, Schibli A, Hampel B, Grube C, Braun DL, Günthard HF. Cohort Profile: The Zurich Primary HIV Infection Study. Microorganisms 2024; 12:302. [PMID: 38399706 PMCID: PMC10893142 DOI: 10.3390/microorganisms12020302] [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: 12/15/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
The Zurich Primary HIV Infection (ZPHI) study is a longitudinal cohort study established in 2002, aiming to study the clinical, epidemiological, and biological characteristics of primary HIV infection. The ZPHI enrolls individuals with documented primary HIV-1 infection. At the baseline and thereafter, the socio-demographic, clinical, and laboratory data are systematically collected, and regular blood sampling is performed for biobanking. By the end of December 2022, 486 people were enrolled, of which 353 were still undergoing active follow-up. Of the 486 participants, 86% had an acute infection, and 14% a recent HIV-1 infection. Men who have sex with men accounted for 74% of the study population. The median time from the estimated date of infection to diagnosis was 32 days. The median time from diagnosis to the initiation of antiretroviral therapy was 11 days, and this has consistently decreased over the last two decades. During the seroconversion phase, 447 (92%) patients reported having symptoms, of which only 73% of the patients were classified as having typical acute retroviral syndrome. The ZPHI study is a well-characterized cohort belonging to the most extensively studied primary HIV infection cohort. Its findings contribute to advancing our understanding of the early stages of HIV infection and pathogenesis, and it is paving the way to further improve HIV translational research and HIV medicine.
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Affiliation(s)
- Matt C. Freind
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (M.C.F.); (C.T.d.L.); (R.D.K.); (D.W.); (H.K.); (D.L.B.)
| | - Carmen Tallón de Lara
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (M.C.F.); (C.T.d.L.); (R.D.K.); (D.W.); (H.K.); (D.L.B.)
| | - Roger D. Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (M.C.F.); (C.T.d.L.); (R.D.K.); (D.W.); (H.K.); (D.L.B.)
- Institute of Medical Virology, University of Zurich, 8006 Zurich, Switzerland
| | - David Wimmersberger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (M.C.F.); (C.T.d.L.); (R.D.K.); (D.W.); (H.K.); (D.L.B.)
| | - Hebert Kuster
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (M.C.F.); (C.T.d.L.); (R.D.K.); (D.W.); (H.K.); (D.L.B.)
| | - Leonardo Aceto
- Center for Infectious Diseases, Klinik im Park, 8027 Zurich, Switzerland; (L.A.); (H.K.); (M.F.)
| | - Helen Kovari
- Center for Infectious Diseases, Klinik im Park, 8027 Zurich, Switzerland; (L.A.); (H.K.); (M.F.)
| | - Markus Flepp
- Center for Infectious Diseases, Klinik im Park, 8027 Zurich, Switzerland; (L.A.); (H.K.); (M.F.)
| | - Adrian Schibli
- Department of Infectious Diseases, Hospital Epidemiology and Occupational Health, City Hospital Zurich, 8091 Zurich, Switzerland;
| | | | | | - Dominique L. Braun
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (M.C.F.); (C.T.d.L.); (R.D.K.); (D.W.); (H.K.); (D.L.B.)
- Institute of Medical Virology, University of Zurich, 8006 Zurich, Switzerland
| | - Huldrych F. Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland; (M.C.F.); (C.T.d.L.); (R.D.K.); (D.W.); (H.K.); (D.L.B.)
- Institute of Medical Virology, University of Zurich, 8006 Zurich, Switzerland
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4
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Li YQ, Ghafari M, Holbrook AJ, Boonen I, Amor N, Catalano S, Webster JP, Li YY, Li HT, Vergote V, Maes P, Chong YL, Laudisoit A, Baelo P, Ngoy S, Mbalitini SG, Gembu GC, Musaba AP, Goüy de Bellocq J, Leirs H, Verheyen E, Pybus OG, Katzourakis A, Alagaili AN, Gryseels S, Li YC, Suchard MA, Bletsa M, Lemey P. The evolutionary history of hepaciviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.30.547218. [PMID: 37425679 PMCID: PMC10327235 DOI: 10.1101/2023.06.30.547218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
In the search for natural reservoirs of hepatitis C virus (HCV), a broad diversity of non-human viruses within the Hepacivirus genus has been uncovered. However, the evolutionary dynamics that shaped the diversity and timescale of hepaciviruses evolution remain elusive. To gain further insights into the origins and evolution of this genus, we screened a large dataset of wild mammal samples (n = 1,672) from Africa and Asia, and generated 34 full-length hepacivirus genomes. Phylogenetic analysis of these data together with publicly available genomes emphasizes the importance of rodents as hepacivirus hosts and we identify 13 rodent species and 3 rodent genera (in Cricetidae and Muridae families) as novel hosts of hepaciviruses. Through co-phylogenetic analyses, we demonstrate that hepacivirus diversity has been affected by cross-species transmission events against the backdrop of detectable signal of virus-host co-divergence in the deep evolutionary history. Using a Bayesian phylogenetic multidimensional scaling approach, we explore the extent to which host relatedness and geographic distances have structured present-day hepacivirus diversity. Our results provide evidence for a substantial structuring of mammalian hepacivirus diversity by host as well as geography, with a somewhat more irregular diffusion process in geographic space. Finally, using a mechanistic model that accounts for substitution saturation, we provide the first formal estimates of the timescale of hepacivirus evolution and estimate the origin of the genus to be about 22 million years ago. Our results offer a comprehensive overview of the micro- and macroevolutionary processes that have shaped hepacivirus diversity and enhance our understanding of the long-term evolution of the Hepacivirus genus.
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Affiliation(s)
- YQ Li
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - M Ghafari
- Department of Biology, University of Oxford, Oxford, OX1, UK
| | - AJ Holbrook
- Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
| | - I Boonen
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - N Amor
- Laboratory of Biodiversity, Parasitology, and Ecology of Aquatic Ecosystems, Department of Biology - Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, 2092, Tunisia
| | - S Catalano
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK
- Department of Pathobiology and Population Sciences, the Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - JP Webster
- Department of Pathobiology and Population Sciences, the Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - YY Li
- College of Life Sciences, Linyi University, Linyi, 276000, China
- Marine College, Shandong University (Weihai), Weihai, 264209, China
| | - HT Li
- College of Life Sciences, Liaocheng University, Liaocheng, 252000, China
- Marine College, Shandong University (Weihai), Weihai, 264209, China
| | - V Vergote
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - P Maes
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - YL Chong
- Animal Resource Science and Management Group, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak (UNIMAS), 94300, Malaysia
- Department of Science and Environmental Studies, The Education University of Hong Kong, Hong Kong, 999077, China
| | - A Laudisoit
- EcoHealth Alliance, New York, NY 10018, USA
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - P Baelo
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - S Ngoy
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - SG Mbalitini
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - GC Gembu
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Akawa P Musaba
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - J Goüy de Bellocq
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic
| | - H Leirs
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - E Verheyen
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - OG Pybus
- Department of Biology, University of Oxford, Oxford, OX1, UK
- Department of Pathobiology and Population Sciences, the Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - A Katzourakis
- Department of Biology, University of Oxford, Oxford, OX1, UK
| | - AN Alagaili
- Laboratory of Biodiversity, Parasitology, and Ecology of Aquatic Ecosystems, Department of Biology - Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, 2092, Tunisia
| | - S Gryseels
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - YC Li
- Marine College, Shandong University (Weihai), Weihai, 264209, China
| | - MA Suchard
- Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
| | - M Bletsa
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, 11527, Greece
| | - P Lemey
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
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5
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Yassin A, Gidaszewski N, Debat V, David JR. Long-term evolution of quantitative traits in the Drosophila melanogaster species subgroup. Genetica 2022; 150:343-353. [PMID: 36242716 DOI: 10.1007/s10709-022-00171-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 10/04/2022] [Indexed: 11/26/2022]
Abstract
Quantitative genetics aims at untangling the genetic and environmental effects on phenotypic variation. Trait heritability, which summarizes the relative importance of genetic effects, is estimated at the intraspecific level, but theory predicts that heritability could influence long-term evolution of quantitative traits. The phylogenetic signal concept bears resemblance to heritability and it has often been called species-level heritability. Under certain conditions, such as trait neutrality or contribution to phylogenesis, within-species heritability and between-species phylogenetic signal should be correlated. Here, we investigate the potential relationship between these two concepts by examining the evolution of multiple morphological traits for which heritability has been estimated in Drosophila melanogaster. Specifically, we analysed 42 morphological traits in both sexes on a phylogeny inferred from 22 nuclear genes for nine species of the melanogaster subgroup. We used Pagel's λ as a measurement of phylogenetic signal because it is the least influenced by the number of analysed taxa. Pigmentation traits showed the strongest concordance with the phylogeny, but no correlation was found between phylogenetic signal and heritability estimates mined from the literature. We obtained data for multiple climatic variables inferred from the geographical distribution of each species. Phylogenetic regression of quantitative traits on climatic variables showed a significantly positive correlation with heritability. Convergent selection, the response to which depends on the trait heritability, may have led to the null association between phylogenetic signal and heritability for morphological traits in Drosophila. We discuss the possible causes of discrepancy between both statistics and caution against their confusion in evolutionary biology.
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Affiliation(s)
- Amir Yassin
- Laboratoire Évolution, Génomes, Comportement et Écologie, CNRS, IRD, Université Paris-Saclay - Institut Diversité, Ecologie et Evolution du Vivant (IDEEV), 12 route 128, 91190, Gif- sur-Yvette, France.
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP50, 75005, Paris, France.
| | - Nelly Gidaszewski
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP50, 75005, Paris, France
| | - Vincent Debat
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP50, 75005, Paris, France
| | - Jean R David
- Laboratoire Évolution, Génomes, Comportement et Écologie, CNRS, IRD, Université Paris-Saclay - Institut Diversité, Ecologie et Evolution du Vivant (IDEEV), 12 route 128, 91190, Gif- sur-Yvette, France
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6
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Lecocq de Pletincx N, Dellicour S, Aron S. The evolution of ant worker polymorphism correlates with multiple social traits. Behav Ecol Sociobiol 2021. [DOI: 10.1007/s00265-021-03049-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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7
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Towards a more healthy conservation paradigm: integrating disease and molecular ecology to aid biological conservation †. J Genet 2021. [PMID: 33622992 PMCID: PMC7371965 DOI: 10.1007/s12041-020-01225-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Parasites, and the diseases they cause, are important from an ecological and evolutionary perspective because they can negatively affect host fitness and can regulate host populations. Consequently, conservation biology has long recognized the vital role that parasites can play in the process of species endangerment and recovery. However, we are only beginning to understand how deeply parasites are embedded in ecological systems, and there is a growing recognition of the important ways in which parasites affect ecosystem structure and function. Thus, there is an urgent need to revisit how parasites are viewed from a conservation perspective and broaden the role that disease ecology plays in conservation-related research and outcomes. This review broadly focusses on the role that disease ecology can play in biological conservation. Our review specifically emphasizes on how the integration of tools and analytical approaches associated with both disease and molecular ecology can be leveraged to aid conservation biology. Our review first concentrates on disease-mediated extinctions and wildlife epidemics. We then focus on elucidating how host–parasite interactions has improved our understanding of the eco-evolutionary dynamics affecting hosts at the individual, population, community and ecosystem scales. We believe that the role of parasites as drivers and indicators of ecosystem health is especially an exciting area of research that has the potential to fundamentally alter our view of parasites and their role in biological conservation. The review concludes with a broad overview of the current and potential applications of modern genomic tools in disease ecology to aid biological conservation.
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Bastide P, Ho LST, Baele G, Lemey P, Suchard MA. Efficient Bayesian inference of general Gaussian models on large phylogenetic trees. Ann Appl Stat 2021. [DOI: 10.1214/20-aoas1419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
| | - Lam Si Tung Ho
- Department of Mathematics and Statistics, Dalhousie University
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven
| | - Marc A. Suchard
- Departments of Biostatistics, Biomathematics, and Human Genetics, University of California, Los Angeles
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9
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Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART. Nat Commun 2020; 11:5542. [PMID: 33139735 PMCID: PMC7608612 DOI: 10.1038/s41467-020-19198-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/23/2020] [Indexed: 12/02/2022] Open
Abstract
The HIV-1 reservoir is the major hurdle to curing HIV-1. However, the impact of the viral genome on the HIV-1 reservoir, i.e. its heritability, remains unknown. We investigate the heritability of the HIV-1 reservoir size and its long-term decay by analyzing the distribution of those traits on viral phylogenies from both partial-pol and viral near full-length genome sequences. We use a unique nationwide cohort of 610 well-characterized HIV-1 subtype-B infected individuals on suppressive ART for a median of 5.4 years. We find that a moderate but significant fraction of the HIV-1 reservoir size 1.5 years after the initiation of ART is explained by genetic factors. At the same time, we find more tentative evidence for the heritability of the long-term HIV-1 reservoir decay. Our findings indicate that viral genetic factors contribute to the HIV-1 reservoir size and hence the infecting HIV-1 strain may affect individual patients’ hurdle towards a cure. The HIV reservoir is a major hurdle for a cure of HIV, but the factors determining its size and dynamics remain unclear. Here the authors show in a large cohort of 610 HIV-1 infected individuals, who are on suppressive ART for a median of 5.4 years, that viral genetic factors contribute substantially to the HIV-1 reservoir size.
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Hassler G, Tolkoff MR, Allen WL, Ho LST, Lemey P, Suchard MA. Inferring Phenotypic Trait Evolution on Large Trees With Many Incomplete Measurements. J Am Stat Assoc 2020; 117:678-692. [PMID: 36060555 PMCID: PMC9438787 DOI: 10.1080/01621459.2020.1799812] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 05/27/2020] [Accepted: 07/15/2020] [Indexed: 01/03/2023]
Abstract
Comparative biologists are often interested in inferring covariation between multiple biological traits sampled across numerous related taxa. To properly study these relationships, we must control for the shared evolutionary history of the taxa to avoid spurious inference. An additional challenge arises as obtaining a full suite of measurements becomes increasingly difficult with increasing taxa. This generally necessitates data imputation or integration, and existing control techniques typically scale poorly as the number of taxa increases. We propose an inference technique that integrates out missing measurements analytically and scales linearly with the number of taxa by using a post-order traversal algorithm under a multivariate Brownian diffusion (MBD) model to characterize trait evolution. We further exploit this technique to extend the MBD model to account for sampling error or non-heritable residual variance. We test these methods to examine mammalian life history traits, prokaryotic genomic and phenotypic traits, and HIV infection traits. We find computational efficiency increases that top two orders-of-magnitude over current best practices. While we focus on the utility of this algorithm in phylogenetic comparative methods, our approach generalizes to solve long-standing challenges in computing the likelihood for matrix-normal and multivariate normal distributions with missing data at scale.
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Affiliation(s)
- Gabriel Hassler
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, United States
| | - Max R Tolkoff
- Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, United States
| | - William L Allen
- Department of Biosciences, Swansea University, Swansea, United Kingdom
| | - Lam Si Tung Ho
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, United States
- Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, United States
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Universtiy of California, Los Angeles, United States
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11
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Gupta P, Robin VV, Dharmarajan G. Towards a more healthy conservation paradigm: integrating disease and molecular ecology to aid biological conservation †. J Genet 2020; 99:65. [PMID: 33622992 PMCID: PMC7371965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/23/2020] [Accepted: 05/25/2020] [Indexed: 08/23/2024]
Abstract
Parasites, and the diseases they cause, are important from an ecological and evolutionary perspective because they can negatively affect host fitness and can regulate host populations. Consequently, conservation biology has long recognized the vital role that parasites can play in the process of species endangerment and recovery. However, we are only beginning to understand how deeply parasites are embedded in ecological systems, and there is a growing recognition of the important ways in which parasites affect ecosystem structure and function. Thus, there is an urgent need to revisit how parasites are viewed from a conservation perspective and broaden the role that disease ecology plays in conservation-related research and outcomes. This review broadly focusses on the role that disease ecology can play in biological conservation. Our review specifically emphasizes on how the integration of tools and analytical approaches associated with both disease and molecular ecology can be leveraged to aid conservation biology. Our review first concentrates on disease mediated extinctions and wildlife epidemics. We then focus on elucidating how host-parasite interactions has improved our understanding of the eco-evolutionary dynamics affecting hosts at the individual, population, community and ecosystem scales. We believe that the role of parasites as drivers and indicators of ecosystem health is especially an exciting area of research that has the potential to fundamentally alter our view of parasites and their role in biological conservation. The review concludes with a broad overview of the current and potential applications of modern genomic tools in disease ecology to aid biological conservation.
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Affiliation(s)
- Pooja Gupta
- Savannah River Ecology Laboratory, University of Georgia, PO Drawer E, Aiken, SC 29801, USA.
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12
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Tolkoff MR, Alfaro ME, Baele G, Lemey P, Suchard MA. Phylogenetic Factor Analysis. Syst Biol 2018; 67:384-399. [PMID: 28950376 DOI: 10.1093/sysbio/syx066] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 07/21/2017] [Indexed: 11/14/2022] Open
Abstract
Phylogenetic comparative methods explore the relationships between quantitative traits adjusting for shared evolutionary history. This adjustment often occurs through a Brownian diffusion process along the branches of the phylogeny that generates model residuals or the traits themselves. For high-dimensional traits, inferring all pair-wise correlations within the multivariate diffusion is limiting. To circumvent this problem, we propose phylogenetic factor analysis (PFA) that assumes a small unknown number of independent evolutionary factors arise along the phylogeny and these factors generate clusters of dependent traits. Set in a Bayesian framework, PFA provides measures of uncertainty on the factor number and groupings, combines both continuous and discrete traits, integrates over missing measurements and incorporates phylogenetic uncertainty with the help of molecular sequences. We develop Gibbs samplers based on dynamic programming to estimate the PFA posterior distribution, over 3-fold faster than for multivariate diffusion and a further order-of-magnitude more efficiently in the presence of latent traits. We further propose a novel marginal likelihood estimator for previously impractical models with discrete data and find that PFA also provides a better fit than multivariate diffusion in evolutionary questions in columbine flower development, placental reproduction transitions and triggerfish fin morphometry.
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Affiliation(s)
- Max R Tolkoff
- Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, 650 Charles E. Young Dr. South Los Angeles, CA 90095-1772, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, 610 Charles E. Young Drive South Los Angeles, CA 90095-1606, USA
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Minderbroederstraat 10 BE-3000 Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Minderbroederstraat 10 BE-3000 Leuven, Belgium
| | - Marc A Suchard
- Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, 650 Charles E. Young Dr. South Los Angeles, CA 90095-1772, USA.,Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, 650 Charles E. Young Dr., South Los Angeles, CA 90095-1766, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, 695 Charles E. Young Drive South Los Angeles, CA 90095-7088, USA
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13
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Dellicour S, Vrancken B, Trovão NS, Fargette D, Lemey P. On the importance of negative controls in viral landscape phylogeography. Virus Evol 2018; 4:vey023. [PMID: 30151241 PMCID: PMC6101606 DOI: 10.1093/ve/vey023] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Phylogeographic reconstructions are becoming an established procedure to evaluate the factors that could impact virus spread. While a discrete phylogeographic approach can be used to test predictors of transition rates among discrete locations, alternative continuous phylogeographic reconstructions can also be exploited to investigate the impact of underlying environmental layers on the dispersal velocity of a virus. The two approaches are complementary tools for studying pathogens' spread, but in both cases, care must be taken to avoid misinterpretations. Here, we analyse rice yellow mottle virus (RYMV) sequence data from West and East Africa to illustrate how both approaches can be used to study the impact of environmental factors on the virus’ dispersal frequency and velocity. While it was previously reported that host connectivity was a major determinant of RYMV spread, we show that this was a false positive result due to the lack of appropriate negative controls. We also discuss and compare the phylodynamic tools currently available for investigating the impact of environmental factors on virus spread.
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Affiliation(s)
- Simon Dellicour
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium.,Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12 50, av. FD Roosevelt, 1050 Bruxelles, Belgium
| | - Bram Vrancken
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Nídia S Trovão
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Denis Fargette
- Institut de Recherche pour le Développement (IRD), UMR IPME (IRD, CIRAD, Université de Montpellier), BP 64051 34394 Montpellier cedex 5, France
| | - Philippe Lemey
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
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14
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Becker DJ, Streicker DG, Altizer S, Derryberry E. Using host species traits to understand the consequences of resource provisioning for host-parasite interactions. J Anim Ecol 2018; 87:511-525. [PMID: 29023699 PMCID: PMC5836909 DOI: 10.1111/1365-2656.12765] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 08/31/2017] [Indexed: 12/17/2022]
Abstract
Supplemental food provided to wildlife by human activities can be more abundant and predictable than natural resources, and subsequent changes in wildlife ecology can have profound impacts on host-parasite interactions. Identifying traits of species associated with increases or decreases in infection outcomes with resource provisioning could improve assessments of wildlife most prone to disease risks in changing environments. We conducted a phylogenetic meta-analysis of 342 host-parasite interactions across 56 wildlife species and three broad taxonomic groups of parasites to identify host-level traits that influence whether provisioning is associated with increases or decreases in infection. We predicted dietary generalists that capitalize on novel food would show greater infection in provisioned habitats owing to population growth and food-borne exposure to contaminants and parasite infectious stages. Similarly, species with fast life histories could experience stronger demographic and immunological benefits from provisioning that affect parasite transmission. We also predicted that wide-ranging and migratory behaviours could increase infection risks with provisioning if concentrated and non-seasonal foods promote dense aggregations that increase exposure to parasites. We found that provisioning increased infection with bacteria, viruses, fungi and protozoa (i.e. microparasites) most for wide-ranging, dietary generalist host species. Effect sizes for ectoparasites were also highest for host species with large home ranges but were instead lowest for dietary generalists. In contrast, the type of provisioning was a stronger correlate of infection outcomes for helminths than host species traits. Our analysis highlights host traits related to movement and feeding behaviour as important determinants of whether species experience greater infection with supplemental feeding. These results could help prioritize monitoring wildlife with particular trait profiles in anthropogenic habitats to reduce infectious disease risks in provisioned populations.
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Affiliation(s)
- Daniel J. Becker
- Odum School of EcologyUniversity of GeorgiaAthensGAUSA
- Center for the Ecology of Infectious DiseaseUniversity of GeorgiaAthensGAUSA
| | - Daniel G. Streicker
- Odum School of EcologyUniversity of GeorgiaAthensGAUSA
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
- MRC‐University of Glasgow Centre for Virus ResearchGlasgowUK
| | - Sonia Altizer
- Odum School of EcologyUniversity of GeorgiaAthensGAUSA
- Center for the Ecology of Infectious DiseaseUniversity of GeorgiaAthensGAUSA
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15
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Gill MS, Tung Ho LS, Baele G, Lemey P, Suchard MA. A Relaxed Directional Random Walk Model for Phylogenetic Trait Evolution. Syst Biol 2018; 66:299-319. [PMID: 27798403 DOI: 10.1093/sysbio/syw093] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 10/10/2016] [Indexed: 12/26/2022] Open
Abstract
Understanding the processes that give rise to quantitative measurements associated with molecular sequence data remains an important issue in statistical phylogenetics. Examples of such measurements include geographic coordinates in the context of phylogeography and phenotypic traits in the context of comparative studies. A popular approach is to model the evolution of continuously varying traits as a Brownian diffusion process acting on a phylogenetic tree. However, standard Brownian diffusion is quite restrictive and may not accurately characterize certain trait evolutionary processes. Here, we relax one of the major restrictions of standard Brownian diffusion by incorporating a nontrivial estimable mean into the process. We introduce a relaxed directional random walk (RDRW) model for the evolution of multivariate continuously varying traits along a phylogenetic tree. Notably, the RDRW model accommodates branch-specific variation of directional trends while preserving model identifiability. Furthermore, our development of a computationally efficient dynamic programming approach to compute the data likelihood enables scaling of our method to large data sets frequently encountered in phylogenetic comparative studies and viral evolution. We implement the RDRW model in a Bayesian inference framework to simultaneously reconstruct the evolutionary histories of molecular sequence data and associated multivariate continuous trait data, and provide tools to visualize evolutionary reconstructions. We demonstrate the performance of our model on synthetic data, and we illustrate its utility in two viral examples. First, we examine the spatiotemporal spread of HIV-1 in central Africa and show that the RDRW model uncovers a clearer, more detailed picture of the dynamics of viral dispersal than standard Brownian diffusion. Second, we study antigenic evolution in the context of HIV-1 resistance to three broadly neutralizing antibodies. Our analysis reveals evidence of a continuous drift at the HIV-1 population level towards enhanced resistance to neutralization by the VRC01 monoclonal antibody over the course of the epidemic. [Brownian Motion; Diffusion Processes; Phylodynamics; Phylogenetics; Phylogeography; Trait Evolution.].
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Affiliation(s)
- Mandev S Gill
- Department of Statistics, Columbia University, New York, NY 10027, USA
| | - Lam Si Tung Ho
- Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Minderbroedersstaat 10, 3000, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Minderbroedersstaat 10, 3000, Leuven, Belgium
| | - Marc A Suchard
- Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA.,Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, Universtiy of California, Los Angeles, CA, USA
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16
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Rife BD, Mavian C, Chen X, Ciccozzi M, Salemi M, Min J, Prosperi MCF. Phylodynamic applications in 21 st century global infectious disease research. Glob Health Res Policy 2017; 2:13. [PMID: 29202081 PMCID: PMC5683535 DOI: 10.1186/s41256-017-0034-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/31/2017] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Phylodynamics, the study of the interaction between epidemiological and pathogen evolutionary processes within and among populations, was originally defined in the context of rapidly evolving viruses and used to characterize transmission dynamics. The concept of phylodynamics has evolved since the early 21st century, extending its reach to slower-evolving pathogens, including bacteria and fungi, and to the identification of influential factors in disease spread and pathogen population dynamics. RESULTS The phylodynamic approach has now become a fundamental building block for the development of comparative phylogenetic tools capable of incorporating epidemiological surveillance data with molecular sequences into a single statistical framework. These innovative tools have greatly enhanced scientific investigations of the temporal and geographical origins, evolutionary history, and ecological risk factors associated with the growth and spread of viruses such as human immunodeficiency virus (HIV), Zika, and dengue and bacteria such as Methicillin-resistant Staphylococcus aureus. CONCLUSIONS Capitalizing on an extensive review of the literature, we discuss the evolution of the field of infectious disease epidemiology and recent accomplishments, highlighting the advancements in phylodynamics, as well as the challenges and limitations currently facing researchers studying emerging pathogen epidemics across the globe.
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Affiliation(s)
- Brittany D Rife
- Emerging Pathogens Institute and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL USA
| | - Carla Mavian
- Emerging Pathogens Institute and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL USA
| | - Xinguang Chen
- Department of Epidemiology, University of Florida, Gainesville, FL USA
| | - Massimo Ciccozzi
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
- Unit of Clinical Pathology and Microbiology, University Campus Biomedico of Rome, Rome, Italy
| | - Marco Salemi
- Emerging Pathogens Institute and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL USA
| | - Jae Min
- Department of Epidemiology, University of Florida, Gainesville, FL USA
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17
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Santibáñez-López CE, Kriebel R, Sharma PP. eadem figura manet: Measuring morphological convergence in diplocentrid scorpions (Arachnida : Scorpiones : Diplocentridae) under a multilocus phylogenetic framework. INVERTEBR SYST 2017. [DOI: 10.1071/is16078] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Morphology still plays a key role in the systematics and phylogenetics of most of the scorpion families and genera, including the Diplocentridae Karsch, 1880. The monophyly of this family, and the monophyly of its two subfamilies is supported by morphological characters; however, neither hypothesis has been tested using molecular data. The lack of a molecular phylogeny has prevented the study of the evolution of morphology within the family. Here, we examine the morphological evolution of several key character systems in diplocentrid systematics. We tested the monophyly of the Diplocentridae, and subsequently the validity of its two subfamilies using a five-locus phylogeny. We examined the variation and evolution of the shape of the carapace, the external surface of the pedipalp patella and the retrolateral surface of the pedipalp chelae of males and females. We also examined the phylogenetic signal of discrete and continuous characters previously reported. We show that Diplocentridae is monophyletic, but Nebinae is nested within Diplocentrinae. Therefore, Nebinae is synonymised with Diplocentrinae (new synonymy). Finally, we show that a new character system proposed here, tarsal spiniform and macrosetal counts, retains high phylogenetic signal and circumscribes independently evolving substructures within this character system.
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18
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Baele G, Suchard MA, Rambaut A, Lemey P. Emerging Concepts of Data Integration in Pathogen Phylodynamics. Syst Biol 2017; 66:e47-e65. [PMID: 28173504 PMCID: PMC5837209 DOI: 10.1093/sysbio/syw054] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 06/02/2016] [Indexed: 12/24/2022] Open
Abstract
Phylodynamics has become an increasingly popular statistical framework to extract evolutionary and epidemiological information from pathogen genomes. By harnessing such information, epidemiologists aim to shed light on the spatio-temporal patterns of spread and to test hypotheses about the underlying interaction of evolutionary and ecological dynamics in pathogen populations. Although the field has witnessed a rich development of statistical inference tools with increasing levels of sophistication, these tools initially focused on sequences as their sole primary data source. Integrating various sources of information, however, promises to deliver more precise insights in infectious diseases and to increase opportunities for statistical hypothesis testing. Here, we review how the emerging concept of data integration is stimulating new advances in Bayesian evolutionary inference methodology which formalize a marriage of statistical thinking and evolutionary biology. These approaches include connecting sequence to trait evolution, such as for host, phenotypic and geographic sampling information, but also the incorporation of covariates of evolutionary and epidemic processes in the reconstruction procedures. We highlight how a full Bayesian approach to covariate modeling and testing can generate further insights into sequence evolution, trait evolution, and population dynamics in pathogen populations. Specific examples demonstrate how such approaches can be used to test the impact of host on rabies and HIV evolutionary rates, to identify the drivers of influenza dispersal as well as the determinants of rabies cross-species transmissions, and to quantify the evolutionary dynamics of influenza antigenicity. Finally, we briefly discuss how data integration is now also permeating through the inference of transmission dynamics, leading to novel insights into tree-generative processes and detailed reconstructions of transmission trees. [Bayesian inference; birth–death models; coalescent models; continuous trait evolution; covariates; data integration; discrete trait evolution; pathogen phylodynamics.
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Affiliation(s)
- Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - Marc A. Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Department of Biostatistics, School of Public Health, University of California, Los Angeles, CA 90095, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3FL, UK
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Kings Buildings, Edinburgh EH9 3FL, UK
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
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19
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Potential Pitfalls in Estimating Viral Load Heritability. Trends Microbiol 2016; 24:687-698. [PMID: 27185643 DOI: 10.1016/j.tim.2016.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 04/14/2016] [Accepted: 04/15/2016] [Indexed: 01/08/2023]
Abstract
In HIV patients, the set-point viral load (SPVL) is the most widely used predictor of disease severity. Yet SPVL varies over several orders of magnitude between patients. The heritability of SPVL quantifies how much of the variation in SPVL is due to transmissible viral genetics. There is currently no clear consensus on the value of SPVL heritability, as multiple studies have reported apparently discrepant estimates. Here we illustrate that the discrepancies in estimates are most likely due to differences in the estimation methods, rather than the study populations. Importantly, phylogenetic estimates run the risk of being strongly confounded by unrealistic model assumptions. Care must be taken when interpreting and comparing the different estimates to each other.
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Abstract
Human metapneumovirus (HMPV) has been described as an important etiologic agent of upper and lower respiratory tract infections, especially in young children and the elderly. Most of school-aged children might be introduced to HMPVs, and exacerbation with other viral or bacterial super-infection is common. However, our understanding of the molecular evolution of HMPVs remains limited. To address the comprehensive evolutionary dynamics of HMPVs, we report a genome-wide analysis of the eight genes (N, P, M, F, M2, SH, G, and L) using 103 complete genome sequences. Phylogenetic reconstruction revealed that the eight genes from one HMPV strain grouped into the same genetic group among the five distinct lineages (A1, A2a, A2b, B1, and B2). A few exceptions of phylogenetic incongruence might suggest past recombination events, and we detected possible recombination breakpoints in the F, SH, and G coding regions. The five genetic lineages of HMPVs shared quite remote common ancestors ranging more than 220 to 470 years of age with the most recent origins for the A2b sublineage. Purifying selection was common, but most protein genes except the F and M2-2 coding regions also appeared to experience episodic diversifying selection. Taken together, these suggest that the five lineages of HMPVs maintain their individual evolutionary dynamics and that recombination and selection forces might work on shaping the genetic diversity of HMPVs.
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