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Jacob Machado D, White RA, Kofsky J, Janies DA. Fundamentals of genomic epidemiology, lessons learned from the coronavirus disease 2019 (COVID-19) pandemic, and new directions. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2021; 1:e60. [PMID: 36168505 PMCID: PMC9495640 DOI: 10.1017/ash.2021.222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 04/19/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic was one of the significant causes of death worldwide in 2020. The disease is caused by severe acute coronavirus syndrome (SARS) coronavirus 2 (SARS-CoV-2), an RNA virus of the subfamily Orthocoronavirinae related to 2 other clinically relevant coronaviruses, SARS-CoV and MERS-CoV. Like other coronaviruses and several other viruses, SARS-CoV-2 originated in bats. However, unlike other coronaviruses, SARS-CoV-2 resulted in a devastating pandemic. The SARS-CoV-2 pandemic rages on due to viral evolution that leads to more transmissible and immune evasive variants. Technology such as genomic sequencing has driven the shift from syndromic to molecular epidemiology and promises better understanding of variants. The COVID-19 pandemic has exposed critical impediments that must be addressed to develop the science of pandemics. Much of the progress is being applied in the developed world. However, barriers to the use of molecular epidemiology in low- and middle-income countries (LMICs) remain, including lack of logistics for equipment and reagents and lack of training in analysis. We review the molecular epidemiology literature to understand its origins from the SARS epidemic (2002-2003) through influenza events and the current COVID-19 pandemic. We advocate for improved genomic surveillance of SARS-CoV and understanding the pathogen diversity in potential zoonotic hosts. This work will require training in phylogenetic and high-performance computing to improve analyses of the origin and spread of pathogens. The overarching goals are to understand and abate zoonosis risk through interdisciplinary collaboration and lowering logistical barriers.
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Affiliation(s)
- Denis Jacob Machado
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
- Author for correspondence: Denis Jacob Machado, PhD, Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, BINF 224, Charlotte, NC28223. E-mail:
| | - Richard Allen White
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
- University of North Carolina at Charlotte, North Carolina Research Campus (NCRC), Kannapolis, North Carolina
| | - Janice Kofsky
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
| | - Daniel A. Janies
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
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Álvarez A, Ercoli MD, Olivares AI, De Santi NA, Verzi DH. Evolutionary Patterns of Mandible Shape Diversification of Caviomorph Rodents. J MAMM EVOL 2020. [DOI: 10.1007/s10914-020-09511-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Janies D. Phylogenetic Concepts and Tools Applied to Epidemiologic Investigations of Infectious Diseases. Microbiol Spectr 2019; 7:10.1128/microbiolspec.ame-0006-2018. [PMID: 31325287 PMCID: PMC10956736 DOI: 10.1128/microbiolspec.ame-0006-2018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Indexed: 01/13/2023] Open
Abstract
In this review, which is a part of the Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases, I present an overview of the principles used to classify organisms in the field of phylogenetics, highlight the methods used to infer the interrelationships of organisms, and summarize how these concepts are applied to molecular epidemiologic analyses. I present steps in analyses that come downstream of the assembly of a set of genomes or genes and the production of a multiple-sequence alignment or other matrices of putative orthologs for comparison. I focus on the history of the problem of phylogenetic reconstruction and debates within the field about the most appropriate methods. I illustrate methods that bridge the gap between molecular epidemiology and traditional epidemiology, including phylogenetic character evolution and geographic visualization. Finally, I provide practical advice on how to conduct an example analysis in the appendix. *This article is part of a curated collection.
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Affiliation(s)
- Daniel Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223
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Muscat KM, Ladiges PY, Bayly MJ. Molecular phylogenetic relationships reveal taxonomic and biogeographic clades inDianella(flax lilies; Asphodelaceae, Hemerocallidoideae). SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1607617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Karen M. Muscat
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010 Australia
| | - Pauline Y. Ladiges
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010 Australia
| | - Michael J. Bayly
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, 3010 Australia
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Tahsin T, Weissenbacher D, Rivera R, Beard R, Firago M, Wallstrom G, Scotch M, Gonzalez G. A high-precision rule-based extraction system for expanding geospatial metadata in GenBank records. J Am Med Inform Assoc 2016; 23:934-41. [PMID: 26911818 PMCID: PMC4997033 DOI: 10.1093/jamia/ocv172] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 10/22/2015] [Accepted: 10/22/2015] [Indexed: 01/09/2023] Open
Abstract
OBJECTIVE The metadata reflecting the location of the infected host (LOIH) of virus sequences in GenBank often lacks specificity. This work seeks to enhance this metadata by extracting more specific geographic information from related full-text articles and mapping them to their latitude/longitudes using knowledge derived from external geographical databases. MATERIALS AND METHODS We developed a rule-based information extraction framework for linking GenBank records to the latitude/longitudes of the LOIH. Our system first extracts existing geospatial metadata from GenBank records and attempts to improve it by seeking additional, relevant geographic information from text and tables in related full-text PubMed Central articles. The final extracted locations of the records, based on data assimilated from these sources, are then disambiguated and mapped to their respective geo-coordinates. We evaluated our approach on a manually annotated dataset comprising of 5728 GenBank records for the influenza A virus. RESULTS We found the precision, recall, and f-measure of our system for linking GenBank records to the latitude/longitudes of their LOIH to be 0.832, 0.967, and 0.894, respectively. DISCUSSION Our system had a high level of accuracy for linking GenBank records to the geo-coordinates of the LOIH. However, it can be further improved by expanding our database of geospatial data, incorporating spell correction, and enhancing the rules used for extraction. CONCLUSION Our system performs reasonably well for linking GenBank records for the influenza A virus to the geo-coordinates of their LOIH based on record metadata and information extracted from related full-text articles.
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Affiliation(s)
- Tasnia Tahsin
- Department of Biomedical Informatics, Arizona State University, 13212 E Shea Blvd, Scottsdale, AZ 85259, USA
| | - Davy Weissenbacher
- Department of Biomedical Informatics, Arizona State University, 13212 E Shea Blvd, Scottsdale, AZ 85259, USA
| | - Robert Rivera
- Department of Biomedical Informatics, Arizona State University, 13212 E Shea Blvd, Scottsdale, AZ 85259, USA
| | - Rachel Beard
- Department of Biomedical Informatics, Arizona State University, 13212 E Shea Blvd, Scottsdale, AZ 85259, USA
| | - Mari Firago
- Department of Biomedical Informatics, Arizona State University, 13212 E Shea Blvd, Scottsdale, AZ 85259, USA
| | - Garrick Wallstrom
- Department of Biomedical Informatics, Arizona State University, 13212 E Shea Blvd, Scottsdale, AZ 85259, USA
| | - Matthew Scotch
- Department of Biomedical Informatics, Arizona State University, 13212 E Shea Blvd, Scottsdale, AZ 85259, USA
| | - Graciela Gonzalez
- Department of Biomedical Informatics, Arizona State University, 13212 E Shea Blvd, Scottsdale, AZ 85259, USA
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Macrosystematics of Didymodon sensu lato (Pottiaceae, Bryophyta) using an analytic key and information theory. UKRAINIAN BOTANICAL JOURNAL 2016. [DOI: 10.15407/ukrbotj73.04.319] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Young AD, Lemmon AR, Skevington JH, Mengual X, Ståhls G, Reemer M, Jordaens K, Kelso S, Lemmon EM, Hauser M, De Meyer M, Misof B, Wiegmann BM. Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae). BMC Evol Biol 2016; 16:143. [PMID: 27357120 PMCID: PMC4928351 DOI: 10.1186/s12862-016-0714-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 06/15/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly diverse nature, importance as pollinators, and historical instability with regard to subfamilial and tribal classification, Syrphidae (flower flies or hoverflies) are an ideal candidate for anchored hybrid enrichment-based phylogenetics, especially since recent molecular phylogenies of the syrphids using only a few markers have resulted in highly unresolved topologies. Over 6200 syrphids are currently known and uncovering their phylogeny will help us to understand how these species have diversified, providing insight into an array of ecological processes, from the development of adult mimicry, the origin of adult migration, to pollination patterns and the evolution of larval resource utilization. RESULTS We present the first use of anchored hybrid enrichment in insect phylogenetics on a dataset containing 30 flower fly species from across all four subfamilies and 11 tribes out of 15. To produce a phylogenetic hypothesis, 559 loci were sampled to produce a final dataset containing 217,702 sites. We recovered a well resolved topology with bootstrap support values that were almost universally >95 %. The subfamily Eristalinae is recovered as paraphyletic, with the strongest support for this hypothesis to date. The ant predators in the Microdontinae are sister to all other syrphids. Syrphinae and Pipizinae are monophyletic and sister to each other. Larval predation on soft-bodied hemipterans evolved only once in this family. CONCLUSIONS Anchored hybrid enrichment was successful in producing a robustly supported phylogenetic hypothesis for the syrphids. Subfamilial reconstruction is concordant with recent phylogenetic hypotheses, but with much higher support values. With the newly designed probe kit this analysis could be rapidly expanded with further sampling, opening the door to more comprehensive analyses targeting problem areas in syrphid phylogenetics and ecology.
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Affiliation(s)
- Andrew Donovan Young
- />Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, K.W. Neatby Building, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
- />Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6 Canada
| | - Alan R. Lemmon
- />Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4102 USA
| | - Jeffrey H. Skevington
- />Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, K.W. Neatby Building, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
- />Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6 Canada
| | - Ximo Mengual
- />Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institute for Animal Biodiversity, Adenauerallee 160, Bonn, D-53113 Germany
| | - Gunilla Ståhls
- />Finnish Museum of Natural History, University of Helsinki, Zoology unit, P.O.Box 17, FIN-00014 Helsinki, Finland
| | - Menno Reemer
- />Naturalis Biodiversity Center, EIS, P.O. Box 9517, 2300 RA Leiden, The Netherlands
| | - Kurt Jordaens
- />Invertebrates Section, Royal Museum for Central Africa, Leuvensesteenweg 13, 3080 Tervuren, Belgium
| | - Scott Kelso
- />Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, K.W. Neatby Building, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
| | - Emily Moriarty Lemmon
- />Department of Biological Science, Florida State University, 319 Stadium Dr., P.O. Box 3064295, Tallahassee, FL 32306-4295 USA
| | - Martin Hauser
- />Plant Pest Diagnostics Branch, California Department of Food & Agriculture, 3294 Meadowview Road, Sacramento, CA 95832-1448 USA
| | - Marc De Meyer
- />Invertebrates Section, Royal Museum for Central Africa, Leuvensesteenweg 13, 3080 Tervuren, Belgium
| | - Bernhard Misof
- />Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für molekulare Biodiversitätsforschung, Adenauerallee 160, Bonn, D-53113 Germany
| | - Brian M. Wiegmann
- />Department of Entomology, North Carolina State University, Raleigh, NC 27695 USA
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Pei N, Erickson DL, Chen B, Ge X, Mi X, Swenson NG, Zhang JL, Jones FA, Huang CL, Ye W, Hao Z, Hsieh CF, Lum S, Bourg NA, Parker JD, Zimmerman JK, McShea WJ, Lopez IC, Sun IF, Davies SJ, Ma K, Kress WJ. Closely-related taxa influence woody species discrimination via DNA barcoding: evidence from global forest dynamics plots. Sci Rep 2015; 5:15127. [PMID: 26456472 PMCID: PMC4601009 DOI: 10.1038/srep15127] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 09/17/2015] [Indexed: 11/09/2022] Open
Abstract
To determine how well DNA barcodes from the chloroplast region perform in forest dynamics plots (FDPs) from global CTFS-ForestGEO network, we analyzed DNA barcoding sequences of 1277 plant species from a wide phylogenetic range (3 FDPs in tropics, 5 in subtropics and 5 in temperate zone) and compared the rates of species discrimination (RSD). We quantified RSD by two DNA barcode combinations (rbcL + matK and rbcL + matK + trnH-psbA) using a monophyly-based method (GARLI). We defined two indexes of closely-related taxa (Gm/Gt and S/G ratios) and correlated these ratios with RSD. The combination of rbcL + matK averagely discriminated 88.65%, 83.84% and 72.51% at the local, regional and global scales, respectively. An additional locus trnH-psbA increased RSD by 2.87%, 1.49% and 3.58% correspondingly. RSD varied along a latitudinal gradient and were negatively correlated with ratios of closely-related taxa. Successes of species discrimination generally depend on scales in global FDPs. We suggested that the combination of rbcL + matK + trnH-psbA is currently applicable for DNA barcoding-based phylogenetic studies on forest communities.
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Affiliation(s)
- Nancai Pei
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, PR China
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, PR China
| | - David L. Erickson
- Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012, USA
| | - Bufeng Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, PR China
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, PR China
| | - Xuejun Ge
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Xiangcheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - Nathan G. Swenson
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Jin-Long Zhang
- Flora Conservation Department, Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, N.T., Hong Kong
| | - Frank A. Jones
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR, 97331, USA
| | - Chun-Lin Huang
- Laboratory of Molecular Phylogenetics, Department of Biology, National Museum of Natural Science, Taichung, Taiwan
| | - Wanhui Ye
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Zhanqing Hao
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, PR China
| | - Chang-Fu Hsieh
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Roosevelt Road 1, Taipei, Taiwan
| | - Shawn Lum
- National Institute of Education of Nanyang Technological University, Singapore 637616
| | - Norman A. Bourg
- Smithsonian Conservation Biology Institute, Front Royal, VA, USA
| | - John D. Parker
- Smithsonian Environmental Research Center, Edgewater, Maryland, USA
| | - Jess K. Zimmerman
- Institute for Tropical Ecosystem Studies, University of Puerto Rico, San Juan Puerto Rico, 00936-8377, USA
| | | | - Ida C. Lopez
- Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012, USA
| | - I-Fang Sun
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien, Taiwan
| | - Stuart J. Davies
- Center for Tropical Forest Science-Forest Global Earth Observatory, Smithsonian Tropical Research Institute, P.O. Box 37012, Washington, DC 20013-7012, USA
| | - Keping Ma
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - W. John Kress
- Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012, USA
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Janies DA, Pomeroy LW, Krueger C, Zhang Y, Senturk IF, Kaya K, Çatalyürek ÜV. Phylogenetic visualization of the spread of H7 influenza A viruses. Cladistics 2015; 31:679-691. [DOI: 10.1111/cla.12107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- Daniel A. Janies
- Department of Bioinformatics and Genomics University of North Carolina at Charlotte 9201 University City Blvd Charlotte NC 28223 USA
| | - Laura W. Pomeroy
- Department of Veterinary Preventative Medicine Ohio State University A100 Sisson Hall 1920 Coffey Road Columbus OH 43210 USA
| | - Chris Krueger
- Department of Bioinformatics and Genomics University of North Carolina at Charlotte 9201 University City Blvd Charlotte NC 28223 USA
| | - Yuqi Zhang
- College of Medicine and Life Sciences University of Toledo Toledo OH 43606 USA
| | - Izzet F. Senturk
- Department of Biomedical Informatics Ohio State University College of Medicine Columbus OH 43210 USA
| | - Kamer Kaya
- Faculty of Engineering and Natural Sciences Sabanci University Orta Mahalle Tuzla 34956 İstanbul Turkey
| | - Ümit V. Çatalyürek
- Department of Biomedical Informatics Ohio State University College of Medicine Columbus OH 43210 USA
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Sandie R, Aris-Brosou S. Predicting the emergence of H3N2 influenza viruses reveals contrasted modes of evolution of HA and NA antigens. J Mol Evol 2013; 78:1-12. [PMID: 24343641 DOI: 10.1007/s00239-013-9608-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 12/06/2013] [Indexed: 02/01/2023]
Abstract
Vaccine design for rapidly changing viruses is based on empirical surveillance of strains circulating in a given season to assess those that will most likely spread during the next season. The choice of which strains to include in the vaccine is critical, as an erroneous decision can lead to a nonimmunized human population that will then be at risk in the face of an epidemic or, worse, a pandemic. Here, we present the first steps toward a very general phylogenetic approach to predict the emergence of novel viruses. Our genomic model builds upon natural features of viral evolution such as selection and recombination / reassortment, and incorporates episodic bursts of evolution and or of recombination. As a proof-of-concept, we assess the performance of this model in a retrospective study, focusing: (i) on the emergence of an unexpected H3N2 influenza strain in 2007, and (ii) on a longitudinal design. Based on the analysis of hemagglutinin (HA) and neuraminidase (NA) genes, our results show a lack of predictive power in both experimental designs, but shed light on the mode of evolution of these two antigens: (i) supporting the lack of significance of recombination in the evolution of this influenza virus, and (ii) showing that HA evolves episodically while NA changes gradually.
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Affiliation(s)
- Reatha Sandie
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
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Cameron SL. Insect mitochondrial genomics: implications for evolution and phylogeny. ANNUAL REVIEW OF ENTOMOLOGY 2013; 59:95-117. [PMID: 24160435 DOI: 10.1146/annurev-ento-011613-162007] [Citation(s) in RCA: 853] [Impact Index Per Article: 77.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The mitochondrial (mt) genome is, to date, the most extensively studied genomic system in insects, outnumbering nuclear genomes tenfold and representing all orders versus very few. Phylogenomic analysis methods have been tested extensively, identifying compositional bias and rate variation, both within and between lineages, as the principal issues confronting accurate analyses. Major studies at both inter- and intraordinal levels have contributed to our understanding of phylogenetic relationships within many groups. Genome rearrangements are an additional data type for defining relationships, with rearrangement synapomorphies identified across multiple orders and at many different taxonomic levels. Hymenoptera and Psocodea have greatly elevated rates of rearrangement offering both opportunities and pitfalls for identifying rearrangement synapomorphies in each group. Finally, insects are model systems for studying aberrant mt genomes, including truncated tRNAs and multichromosomal genomes. Greater integration of nuclear and mt genomic studies is necessary to further our understanding of insect genomic evolution.
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Affiliation(s)
- Stephen L Cameron
- Earth, Environmental & Biological Sciences School, Science & Engineering Faculty, Queensland University of Technology, Brisbane, QLD 4001, Australia;
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12
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Lavoie CA, Platt RN, Novick PA, Counterman BA, Ray DA. Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera. Mob DNA 2013; 4:21. [PMID: 24088337 PMCID: PMC4016481 DOI: 10.1186/1759-8753-4-21] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 09/27/2013] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) have the potential to impact genome structure, function and evolution in profound ways. In order to understand the contribution of transposable elements (TEs) to Heliconius melpomene, we queried the H. melpomene draft sequence to identify repetitive sequences. RESULTS We determined that TEs comprise ~25% of the genome. The predominant class of TEs (~12% of the genome) was the non-long terminal repeat (non-LTR) retrotransposons, including a novel SINE family. However, this was only slightly higher than content derived from DNA transposons, which are diverse, with several families having mobilized in the recent past. Compared to the only other well-studied lepidopteran genome, Bombyx mori, H. melpomene exhibits a higher DNA transposon content and a distinct repertoire of retrotransposons. We also found that H. melpomene exhibits a high rate of TE turnover with few older elements accumulating in the genome. CONCLUSIONS Our analysis represents the first complete, de novo characterization of TE content in a butterfly genome and suggests that, while TEs are able to invade and multiply, TEs have an overall deleterious effect and/or that maintaining a small genome is advantageous. Our results also hint that analysis of additional lepidopteran genomes will reveal substantial TE diversity within the group.
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Affiliation(s)
- Christine A Lavoie
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State, MS 39762, USA
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi, MS 39762, USA
| | - Roy N Platt
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State, MS 39762, USA
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi, MS 39762, USA
| | - Peter A Novick
- Department of Biological Sciences and Geology, Queensborough Community College, Bayside, New York, NY 11364, USA
| | | | - David A Ray
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State, MS 39762, USA
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi, MS 39762, USA
- Current Address: Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
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Nardi JB, Delgado JA, Collantes F, Miller LA, Bee CM, Kathirithamby J. Sperm Cells of a Primitive Strepsipteran. INSECTS 2013; 4:463-75. [PMID: 26462430 PMCID: PMC4553476 DOI: 10.3390/insects4030463] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 08/07/2013] [Accepted: 08/15/2013] [Indexed: 12/02/2022]
Abstract
The unusual life style of Strepsiptera has presented a long-standing puzzle in establishing its affinity to other insects. Although Strepsiptera share few structural similarities with other insect orders, all members of this order share a parasitic life style with members of two distinctive families in the Coleoptera-the order now considered the most closely related to Strepsiptera based on recent genomic evidence. Among the structural features of several strepsipteran families and other insect families that have been surveyed are the organization of testes and ultrastructure of sperm cells. For comparison with existing information on insect sperm structure, this manuscript presents a description of testes and sperm of a representative of the most primitive extant strepsipteran family Mengenillidae, Eoxenos laboulbenei. We compare sperm structure of E. laboulbenei from this family with that of the three other families of Strepsiptera in the other strepsipteran suborder Stylopidia that have been studied as well as with members of the beetle families Meloidae and Rhipiphoridae that share similar life histories with Strepsiptera. Meloids, Rhipiphorids and Strepsipterans all begin larval life as active and viviparous first instar larvae. This study examines global features of these insects' sperm cells along with specific ultrastructural features of their organelles.
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Affiliation(s)
- James B Nardi
- Department of Entomology, University of Illinois, 320 Morrill Hall, 505 S. Goodwin Avenue, Urbana, IL 61801, USA.
| | - Juan A Delgado
- Department of Zoology and Physical Anthropology, Faculty of Biology, University of Murcia, Murcia 30100, Spain.
| | - Francisco Collantes
- Department of Zoology and Physical Anthropology, Faculty of Biology, University of Murcia, Murcia 30100, Spain.
| | - Lou Ann Miller
- Biological Electron Microscopy, Frederick Seitz Materials Research Laboratory, Room 125, University of Illinois, 104 South Goodwin Avenue, Urbana, IL 61801, USA.
| | - Charles M Bee
- Imaging Technology Group, Beckman Institute for Advanced Science and Technology, University of Illinois, 405 N. Mathews Avenue, Urbana, IL 61801, USA.
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Fleming L. The Notion of Limited Perfect Adaptedness in Darwin's Principle of Divergence. ACTA ACUST UNITED AC 2013. [DOI: 10.1162/posc_a_00084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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15
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Zanno LE, Makovicky PJ. No evidence for directional evolution of body mass in herbivorous theropod dinosaurs. Proc Biol Sci 2013; 280:20122526. [PMID: 23193135 PMCID: PMC3574415 DOI: 10.1098/rspb.2012.2526] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 10/30/2012] [Indexed: 11/12/2022] Open
Abstract
The correlation between large body size and digestive efficiency has been hypothesized to have driven trends of increasing mass in herbivorous clades by means of directional selection. Yet, to date, few studies have investigated this relationship from a phylogenetic perspective, and none, to our knowledge, with regard to trophic shifts. Here, we reconstruct body mass in the three major subclades of non-avian theropod dinosaurs whose ecomorphology is correlated with extrinsic evidence of at least facultative herbivory in the fossil record--all of which also achieve relative gigantism (more than 3000 kg). Ordinary least-squares regressions on natural log-transformed mean mass recover significant correlations between increasing mass and geological time. However, tests for directional evolution in body mass find no support for a phylogenetic trend, instead favouring passive models of trait evolution. Cross-correlation of sympatric taxa from five localities in Asia reveals that environmental influences such as differential habitat sampling and/or taphonomic filtering affect the preserved record of dinosaurian body mass in the Cretaceous. Our results are congruent with studies documenting that behavioural and/or ecological factors may mitigate the benefit of increasing mass in extant taxa, and suggest that the hypothesis can be extrapolated to herbivorous lineages across geological time scales.
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Affiliation(s)
- Lindsay E Zanno
- Paleontology and Geology Laboratory, Nature Research Center, North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA.
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16
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Identification of cortex herbs using the DNA barcode nrITS2. J Nat Med 2012; 67:296-302. [PMID: 22802133 DOI: 10.1007/s11418-012-0681-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2011] [Accepted: 06/08/2012] [Indexed: 10/28/2022]
Abstract
To discriminate the cortex herbs of Chinese Pharmacopoeia, the second internal transcribed spacer (ITS2) of ribosomal DNA of 51 samples belonging to 19 kinds of cortex herbs were analyzed in this paper. Sequence assembly was performed using the CodonCode Aligner. Phylogenetic study was performed using the molecular evolutionary genetics analysis (MEGA) 4.0 software in accordance with the Kimura 2-Parameter (K2P) model. Phylogenetic tree was constructed using the neighbor-joining (NJ) method. We found that the ITS2 sequences of the studied samples ranged from 207 to 256 bp in length and easy to be amplified. The intraspecific genetic distance of the cortex herbs was between 0 and 0.073, which was lower than their interspecific genetic distance (mean, 0.868; minimum, 0.101). In the cluster dendrogram, all the studied medicinal materials with several samples, were monophyletic. It is concluded that ITS2 barcode is suitable for the identification of cortex herbs of Chinese Pharmacopoeia, and it will play an important role in the field of identification of traditional Chinese medicine (TCM).
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Gauthier JA, Kearney M, Maisano JA, Rieppel O, Behlke AD. Assembling the Squamate Tree of Life: Perspectives from the Phenotype and the Fossil Record. BULLETIN OF THE PEABODY MUSEUM OF NATURAL HISTORY 2012. [DOI: 10.3374/014.053.0101] [Citation(s) in RCA: 352] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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18
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Radomski JP, Slonimski PP. Alignment free characterization of the influenza-A hemagglutinin genes by the ISSCOR method. C R Biol 2012; 335:180-93. [PMID: 22464426 DOI: 10.1016/j.crvi.2012.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 10/26/2011] [Accepted: 01/11/2012] [Indexed: 12/23/2022]
Abstract
Analyses and visualizations by the ISSCOR method of the influenza virus hemagglutinin genes of three different A-subtypes revealed some rather striking temporal (for A/H3N3), and spatial relationships (for A/H5N1) between groups of individual gene subsets. The application to the A/H1N1 set revealed also relationships between the seasonal H1, and the swine-like novel 2009 H1v variants in a quick and unambiguous manner. Based on these examples we consider the application of the ISSCOR method for analysis of large sets of homologous genes as a worthwhile addition to a toolbox of genomics-it allows a rapid diagnostics of trends, and possibly can even aid an early warning of newly emerging epidemiological threats.
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Affiliation(s)
- Jan P Radomski
- Interdisciplinary Center for Mathematical and Computational Modeling, Warsaw University, Warsaw, Poland.
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19
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Newman SH, Hill NJ, Spragens KA, Janies D, Voronkin IO, Prosser DJ, Yan B, Lei F, Batbayar N, Natsagdorj T, Bishop CM, Butler PJ, Wikelski M, Balachandran S, Mundkur T, Douglas DC, Takekawa JY. Eco-virological approach for assessing the role of wild birds in the spread of avian influenza H5N1 along the Central Asian Flyway. PLoS One 2012; 7:e30636. [PMID: 22347393 PMCID: PMC3274535 DOI: 10.1371/journal.pone.0030636] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 12/20/2011] [Indexed: 11/18/2022] Open
Abstract
A unique pattern of highly pathogenic avian influenza (HPAI) H5N1 outbreaks has emerged along the Central Asia Flyway, where infection of wild birds has been reported with steady frequency since 2005. We assessed the potential for two hosts of HPAI H5N1, the bar-headed goose (Anser indicus) and ruddy shelduck (Tadorna tadorna), to act as agents for virus dispersal along this 'thoroughfare'. We used an eco-virological approach to compare the migration of 141 birds marked with GPS satellite transmitters during 2005-2010 with: 1) the spatio-temporal patterns of poultry and wild bird outbreaks of HPAI H5N1, and 2) the trajectory of the virus in the outbreak region based on phylogeographic mapping. We found that biweekly utilization distributions (UDs) for 19.2% of bar-headed geese and 46.2% of ruddy shelduck were significantly associated with outbreaks. Ruddy shelduck showed highest correlation with poultry outbreaks owing to their wintering distribution in South Asia, where there is considerable opportunity for HPAI H5N1 spillover from poultry. Both species showed correlation with wild bird outbreaks during the spring migration, suggesting they may be involved in the northward movement of the virus. However, phylogeographic mapping of HPAI H5N1 clades 2.2 and 2.3 did not support dissemination of the virus in a northern direction along the migration corridor. In particular, two subclades (2.2.1 and 2.3.2) moved in a strictly southern direction in contrast to our spatio-temporal analysis of bird migration. Our attempt to reconcile the disciplines of wild bird ecology and HPAI H5N1 virology highlights prospects offered by both approaches as well as their limitations.
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Affiliation(s)
- Scott H Newman
- EMPRES Wildlife Unit, Emergency Centre for Transboundary Animal Diseases, Animal Production and Health Division, Food and Agriculture Organization of the United Nations, Rome, Italy
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Trautwein MD, Wiegmann BM, Beutel R, Kjer KM, Yeates DK. Advances in insect phylogeny at the dawn of the postgenomic era. ANNUAL REVIEW OF ENTOMOLOGY 2012; 57:449-468. [PMID: 22149269 DOI: 10.1146/annurev-ento-120710-100538] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Most species on Earth are insects and thus, understanding their evolutionary relationships is key to understanding the evolution of life. Insect relationships are increasingly well supported, due largely to technological advances in molecular sequencing and phylogenetic computational analysis. In this postgenomic era, insect systematics will be furthered best by integrative methods aimed at hypothesis corroboration from molecular, morphological, and paleontological evidence. This review of the current consensus of insect relationships provides a foundation for comparative study and offers a framework to evaluate incoming genomic evidence. Notable recent phylogenetic successes include the resolution of Holometabola, including the identification of the enigmatic Strepsiptera as a beetle relative and the early divergence of Hymenoptera; the recognition of hexapods as a crustacean lineage within Pancrustacea; and the elucidation of Dictyoptera orders, with termites placed as social cockroaches. Regions of the tree that require further investigation include the earliest winged insects (Palaeoptera) and Polyneoptera (orthopteroid lineages).
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Affiliation(s)
- Michelle D Trautwein
- Department of Entomology, North Carolina State University, Raleigh, North Carolina 27695, USA.
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21
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Bapteste E, Bouchard F, Burian RM. Philosophy and evolution: minding the gap between evolutionary patterns and tree-like patterns. Methods Mol Biol 2012; 856:81-110. [PMID: 22399456 DOI: 10.1007/978-1-61779-585-5_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Ever since Darwin, the familiar genealogical pattern known as the Tree of Life (TOL) has been prominent in evolutionary thinking and has dominated not only systematics, but also the analysis of the units of evolution. However, recent findings indicate that the evolution of DNA, especially in prokaryotes and such DNA vehicles as viruses and plasmids, does not follow a unique tree-like pattern. Because evolutionary patterns track a greater range of processes than those captured in genealogies, genealogical patterns are in fact only a subset of a broader set of evolutionary patterns. This fact suggests that evolutionists who focus exclusively on genealogical patterns are blocked from providing a significant range of genuine evolutionary explanations. Consequently, we highlight challenges to tree-based approaches, and point the way toward more appropriate methods to study evolution (although we do not present them in technical detail). We argue that there is significant benefit in adopting wider range of models, evolutionary representations, and evolutionary explanations, based on an analysis of the full range of evolutionary processes. We introduce an ecosystem orientation into evolutionary thinking that highlights the importance of "type 1 coalitions" (functionally related units with genetic exchanges, aka "friends with genetic benefits"), "type 2 coalitions" (functionally related units without genetic exchanges), "communal interactions," and "emergent evolutionary properties." On this basis, we seek to promote the study of (especially prokaryotic) evolution with dynamic evolutionary networks, which are less constrained than the TOL, and to provide new ways to analyze an expanded range of evolutionary units (genetic modules, recombined genes, plasmids, phages and prokaryotic genomes, pangenomes, microbial communities) and evolutionary processes. Finally, we discuss some of the conceptual and practical questions raised by such network-based representation.
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Ronquist F, Sanmartín I. Phylogenetic Methods in Biogeography. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2011. [DOI: 10.1146/annurev-ecolsys-102209-144710] [Citation(s) in RCA: 192] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Fredrik Ronquist
- Department of Biodiversity Informatics, Swedish Museum of Natural History, SE-10405 Stockholm, Sweden;
| | - Isabel Sanmartín
- Department of Biodiversity and Conservation, Real Jardín Botanico, RJB-CSIC, ES-28014 Madrid, Spain;
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Talavera G, Vila R. What is the phylogenetic signal limit from mitogenomes? The reconciliation between mitochondrial and nuclear data in the Insecta class phylogeny. BMC Evol Biol 2011; 11:315. [PMID: 22032248 PMCID: PMC3213125 DOI: 10.1186/1471-2148-11-315] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 10/27/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Efforts to solve higher-level evolutionary relationships within the class Insecta by using mitochondrial genomic data are hindered due to fast sequence evolution of several groups, most notably Hymenoptera, Strepsiptera, Phthiraptera, Hemiptera and Thysanoptera. Accelerated rates of substitution on their sequences have been shown to have negative consequences in phylogenetic inference. In this study, we tested several methodological approaches to recover phylogenetic signal from whole mitochondrial genomes. As a model, we used two classical problems in insect phylogenetics: The relationships within Paraneoptera and within Holometabola. Moreover, we assessed the mitochondrial phylogenetic signal limits in the deeper Eumetabola dataset, and we studied the contribution of individual genes. RESULTS Long-branch attraction (LBA) artefacts were detected in all the datasets. Methods using Bayesian inference outperformed maximum likelihood approaches, and LBA was avoided in Paraneoptera and Holometabola when using protein sequences and the site-heterogeneous mixture model CAT. The better performance of this method was evidenced by resulting topologies matching generally accepted hypotheses based on nuclear and/or morphological data, and was confirmed by cross-validation and simulation analyses. Using the CAT model, the order Strepsiptera was recovered as sister to Coleoptera for the first time using mitochondrial sequences, in agreement with recent results based on large nuclear and morphological datasets. Also the Hymenoptera-Mecopterida association was obtained, leaving Coleoptera and Strepsiptera as the basal groups of the holometabolan insects, which coincides with one of the two main competing hypotheses. For the Paraneroptera, the currently accepted non-monophyly of Homoptera was documented as a phylogenetic novelty for mitochondrial data. However, results were not satisfactory when exploring the entire Eumetabola, revealing the limits of the phylogenetic signal that can be extracted from Insecta mitogenomes. Based on the combined use of the five best topology-performing genes we obtained comparable results to whole mitogenomes, highlighting the important role of data quality. CONCLUSION We show for the first time that mitogenomic data agrees with nuclear and morphological data for several of the most controversial insect evolutionary relationships, adding a new independent source of evidence to study relationships among insect orders. We propose that deeper divergences cannot be inferred with the current available methods due to sequence saturation and compositional bias inconsistencies. Our exploratory analysis indicates that the CAT model is the best dealing with LBA and it could be useful for other groups and datasets with similar phylogenetic difficulties.
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Affiliation(s)
- Gerard Talavera
- Institut de Biologia Evolutiva (CSIC-UPF), Pg. Marítim de la Barceloneta 37, 08003 Barcelona, Spain
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Edifici C, 08193 Bellaterra, Spain
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), Pg. Marítim de la Barceloneta 37, 08003 Barcelona, Spain
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Béthoux O, Cui Y, Kondratieff B, Stark B, Ren D. At last, a Pennsylvanian stem-stonefly (Plecoptera) discovered. BMC Evol Biol 2011; 11:248. [PMID: 21880126 PMCID: PMC3225047 DOI: 10.1186/1471-2148-11-248] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 08/31/2011] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Stem-relatives of many winged insect orders have been identified among Pennsylvanian fossils (Carboniferous Period). Owing to their presumed 'basal' position in insect phylogeny, stoneflies were expected to occur at this period. However, no relative has ever been designated convincingly. RESULTS In this paper, we report specimens belonging to a new fossil insect species collected from the Tupo Formation (Pennsylvanian; China). The wing venation of Gulou carpenteri gen. et sp. nov. exhibits character states diagnostic of the order Plecoptera, but lack character states shared by unequivocal representatives of the order. Derived from this identification, the delimitation of the fossil species is ascertained based on comparison of several extant stonefly species. This comparative analysis allowed a trait present in G. carpenteri gen. et sp. nov., but rarely occurring in extant species, to be documented and highlighted as atavistic. Affinities of taxa formerly proposed as putative stem-stoneflies are reconsidered in the light of the new discovery. CONCLUSIONS Gulou carpenteri gen. et sp. nov. is considered the only genuine Plecoptera reported from the Pennsylvanian. Continuing efforts on the systematics of Pennsylvanian winged insects indicate a fauna more diverse than previously appreciated. It suggests that insects already had a long, yet undocumented, history by this time.
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Affiliation(s)
- Olivier Béthoux
- Key Laboratory of Insect Evolution and Environmental Changes, College of Life Science, Capital Normal University,105 Xisanhuanbeilu, Beijing, 100048, China
- 40 rue d'Aveillans, La Motte d'Aveillans, 38770, France
| | - Yingying Cui
- Key Laboratory of Insect Evolution and Environmental Changes, College of Life Science, Capital Normal University,105 Xisanhuanbeilu, Beijing, 100048, China
| | - Boris Kondratieff
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
| | - Bill Stark
- Department of Biology, Mississippi College, Clinton, MS 39058, USA
| | - Dong Ren
- Key Laboratory of Insect Evolution and Environmental Changes, College of Life Science, Capital Normal University,105 Xisanhuanbeilu, Beijing, 100048, China
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Abstract
BACKGROUND Genome sequencing has revolutionized our view of the relationships among genomes, particularly in revealing the confounding effects of lateral genetic transfer (LGT). Phylogenomic techniques have been used to construct purported trees of microbial life. Although such trees are easily interpreted and allow the use of a subset of genomes as "proxies" for the full set, LGT and other phenomena impact the positioning of different groups in genome trees, confounding and potentially invalidating attempts to construct a phylogeny-based taxonomy of microorganisms. Network and graph approaches can reveal complex sets of relationships, but applying these techniques to large data sets is a significant challenge. Notwithstanding the question of what exactly it might represent, generating and interpreting a Tree or Network of All Genomes will only be feasible if current algorithms can be improved upon. RESULTS Complex relationships among even the most-similar genomes demonstrate that proxy-based approaches to simplifying large sets of genomes are not alone sufficient to solve the analysis problem. A phylogenomic analysis of 1173 sequenced bacterial and archaeal genomes generated phylogenetic trees for 159,905 distinct homologous gene sets. The relationships inferred from this set can be heavily dependent on the inclusion of other taxa: for example, phyla such as Spirochaetes, Proteobacteria and Firmicutes are recovered as cohesive groups or split depending on the presence of other specific lineages. Furthermore, named groups such as Acidithiobacillus, Coprothermobacter and Brachyspira show a multitude of affiliations that are more consistent with their ecology than with small subunit ribosomal DNA-based taxonomy. Network and graph representations can illustrate the multitude of conflicting affinities, but all methods impose constraints on the input data and create challenges of construction and interpretation. CONCLUSIONS These complex relationships highlight the need for an inclusive approach to genomic data, and current methods with minor alterations will likely scale to allow the analysis of data sets with 10,000 or more genomes. The main challenges lie in the visualization and interpretation of genomic relationships, and the redefinition of microbial taxonomy when subsets of genomic data are so evidently in conflict with one another, and with the "canonical" molecular taxonomy.
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Affiliation(s)
- Robert G Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, NS B3H 1W5 Canada.
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Janies DA, Treseder T, Alexandrov B, Habib F, Chen JJ, Ferreira R, Çatalyürek Ü, Varón A, Wheeler WC. The Supramap project: linking pathogen genomes with geography to fight emergent infectious diseases. Cladistics 2011; 27:61-66. [PMID: 32313364 PMCID: PMC7162175 DOI: 10.1111/j.1096-0031.2010.00314.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2010] [Indexed: 11/27/2022] Open
Abstract
Novel pathogens have the potential to become critical issues of national security, public health and economic welfare. As demonstrated by the response to Severe Acute Respiratory Syndrome (SARS) and influenza, genomic sequencing has become an important method for diagnosing agents of infectious disease. Despite the value of genomic sequences in characterizing novel pathogens, raw data on their own do not provide the information needed by public health officials and researchers. One must integrate knowledge of the genomes of pathogens with host biology and geography to understand the etiology of epidemics. To these ends, we have created an application called Supramap (http://supramap.osu.edu) to put information on the spread of pathogens and key mutations across time, space and various hosts into a geographic information system (GIS). To build this application, we created a web service for integrated sequence alignment and phylogenetic analysis as well as methods to describe the tree, mutations, and host shifts in Keyhole Markup Language (KML). We apply the application to 239 sequences of the polymerase basic 2 (PB2) gene of recent isolates of avian influenza (H5N1). We map a mutation, glutamic acid to lysine at position 627 in the PB2 protein (E627K), in H5N1 influenza that allows for increased replication of the virus in mammals. We use a statistical test to support the hypothesis of a correlation of E627K mutations with avian-mammalian host shifts but reject the hypothesis that lineages with E627K are moving westward. Data, instructions for use, and visualizations are included as supplemental materials at: http://supramap.osu.edu/sm/supramap/publications. © The Willi Hennig Society 2010.
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Affiliation(s)
- Daniel A Janies
- Department of Biomedical Informatics, The Ohio State University, College of Medicine, Columbus, OH 43210, USA
| | - Travis Treseder
- Department of Biomedical Informatics, The Ohio State University, College of Medicine, Columbus, OH 43210, USA
| | - Boyan Alexandrov
- Department of Biomedical Informatics, The Ohio State University, College of Medicine, Columbus, OH 43210, USA
| | - Farhat Habib
- Indian Institute of Science Education and Research (IISER) Garware Circle, Sutarwadi, Pashan Pune, Maharashtra 411021, India
| | - Jennifer J Chen
- Department of Biomedical Informatics, The Ohio State University, College of Medicine, Columbus, OH 43210, USA
| | - Renato Ferreira
- Universidade Federal de Minas Gerais, Departamento de Ciência da Computação, Belo Horizonte, MG, Brazil
| | - Ümit Çatalyürek
- Department of Biomedical Informatics, The Ohio State University, College of Medicine, Columbus, OH 43210, USA
| | - Andrés Varón
- Division of Invertebrate Zoology, The American Museum of Natural History, New York, NY 10024, USA
- Computer Science Department, The Graduate Center, The City University of New York, New York, NY 10016, USA
| | - Ward C Wheeler
- Division of Invertebrate Zoology, The American Museum of Natural History, New York, NY 10024, USA
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Lu SE, Gross DC. Drippy Pod of White Lupine: A New Bacterial Disease Caused by a Pathovar of Brenneria quercina. PLANT DISEASE 2010; 94:1431-1440. [PMID: 30743385 DOI: 10.1094/pdis-05-10-0365] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Drippy pod is a unique bacterial disease of Mediterranean white lupine (Lupinus albus) that first appeared in commercial fields in Eastern Washington State in the mid-1980s. The disease is most noticeable in the field as water-soaked lesions on lupine pods that produce an abundance of whitish-colored ooze with a sticky and foamy consistency. As the disease progresses, yellowing of lupine plants occurs with ooze characteristically dripping down the infected pods and stems and solidifying. A gram-negative rod-shaped bacterium with facultative anaerobic growth was repeatedly isolated from infected lupine tissues, and subsequently confirmed by Koch's postulates to infect lupines. Physiological and biochemical tests, including the API 20E and 50CHE strip assays, showed a highly uniform phenotype for the lupine strains that was distinctive for the genus Brenneria and most closely resembled the oak pathogen Brenneria quercina. Furthermore, sequence analyses of the 16S rDNA gene and the 16S-23S intergenic region of lupine strains revealed the highest similarity (>97%) to the corresponding regions of B. quercina and less similarity to the next closest species, B. salicis. Fatty acid profiling demonstrated that lupine strains were qualitatively similar in composition to Brenneria spp., and supported placement of the drippy pod bacterium in the species B. quercina. Oak strains of B. quercina, however, did not incite drippy pod disease on lupine. Consequently, the lupine strains that cause bacterial drippy pod disease were classified as B. quercina pv. lupinicola pv. nov.
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Affiliation(s)
- Shi-En Lu
- Department of Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762
| | - Dennis C Gross
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843-2132
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Haase M, Starick E, Fereidouni S, Strebelow G, Grund C, Seeland A, Scheuner C, Cieslik D, Smietanka K, Minta Z, Zorman-Rojs O, Mojzis M, Goletic T, Jestin V, Schulenburg B, Pybus O, Mettenleiter T, Beer M, Harder T. Possible sources and spreading routes of highly pathogenic avian influenza virus subtype H5N1 infections in poultry and wild birds in Central Europe in 2007 inferred through likelihood analyses. INFECTION GENETICS AND EVOLUTION 2010; 10:1075-84. [DOI: 10.1016/j.meegid.2010.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Revised: 07/01/2010] [Accepted: 07/02/2010] [Indexed: 12/09/2022]
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Bittner L, Halary S, Payri C, Cruaud C, de Reviers B, Lopez P, Bapteste E. Some considerations for analyzing biodiversity using integrative metagenomics and gene networks. Biol Direct 2010; 5:47. [PMID: 20673351 PMCID: PMC2921367 DOI: 10.1186/1745-6150-5-47] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 07/30/2010] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Improving knowledge of biodiversity will benefit conservation biology, enhance bioremediation studies, and could lead to new medical treatments. However there is no standard approach to estimate and to compare the diversity of different environments, or to study its past, and possibly, future evolution. PRESENTATION OF THE HYPOTHESIS We argue that there are two conditions for significant progress in the identification and quantification of biodiversity. First, integrative metagenomic studies - aiming at the simultaneous examination (or even better at the integration) of observations about the elements, functions and evolutionary processes captured by the massive sequencing of multiple markers - should be preferred over DNA barcoding projects and over metagenomic projects based on a single marker. Second, such metagenomic data should be studied with novel inclusive network-based approaches, designed to draw inferences both on the many units and on the many processes present in the environments. TESTING THE HYPOTHESIS We reached these conclusions through a comparison of the theoretical foundations of two molecular approaches seeking to assess biodiversity: metagenomics (mostly used on prokaryotes and protists) and DNA barcoding (mostly used on multicellular eukaryotes), and by pragmatic considerations of the issues caused by the 'species problem' in biodiversity studies. IMPLICATIONS OF THE HYPOTHESIS Evolutionary gene networks reduce the risk of producing biodiversity estimates with limited explanatory power, biased either by unequal rates of LGT, or difficult to interpret due to (practical) problems caused by type I and type II grey zones. Moreover, these networks would easily accommodate additional (meta)transcriptomic and (meta)proteomic data.
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Affiliation(s)
- Lucie Bittner
- UMR CNRS 7138 Systématique, Adaptation, Evolution, Muséum National d'Histoire Naturelle, Paris, France
| | - Sébastien Halary
- UMR CNRS 7138 Systématique, Adaptation, Evolution, Université Pierre et Marie Curie, Paris, France
| | - Claude Payri
- UR227, IRD-BPA5, Nouméa, Nouvelle-Calédonie, France
| | | | - Bruno de Reviers
- UMR CNRS 7138 Systématique, Adaptation, Evolution, Muséum National d'Histoire Naturelle, Paris, France
| | - Philippe Lopez
- UMR CNRS 7138 Systématique, Adaptation, Evolution, Université Pierre et Marie Curie, Paris, France
| | - Eric Bapteste
- UMR CNRS 7138 Systématique, Adaptation, Evolution, Université Pierre et Marie Curie, Paris, France
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30
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Genome informatics of influenza A: from data sharing to shared analytical capabilities. Anim Health Res Rev 2010; 11:73-9. [DOI: 10.1017/s1466252310000083] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
AbstractEmerging infectious diseases are critical issues of public health and the economic and social stability of nations. As demonstrated by the international response to the severe acute respiratory syndrome (SARS) and influenza A, rapid genomic sequencing is a crucial tool to understand diseases that occur at the interface of human and animal populations. However, our ability to make sense of sequence data lags behind our ability to acquire the data. The potential of sequence data on pathogens is not fully realized until raw data are translated into public health intelligence. Sequencing technologies have become highly mechanized. If the political will for data sharing remains strong, the frontier for progress in emerging infectious diseases will be in analysis of sequence data and translation of results into better public health science and policy. For example, applying analytical tools such as Supramap (http://supramap.osu.edu) to genomic data for pathogens, public health scientists can track specific mutations in pathogens that confer the ability to infect humans or resist drugs. The results produced by the Supramap application are compelling visualizations of pathogen lineages and features mapped into geographic information systems that can be used to test hypotheses and to follow the spread of diseases across geography and hosts and communicate the results to a wide audience.
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