1
|
Trobisch A, Schweintzger NA, Kohlfürst DS, Sagmeister MG, Sperl M, Grisold AJ, Feierl G, Herberg JA, Carrol ED, Paulus SC, Emonts M, van der Flier M, de Groot R, Cebey-López M, Rivero-Calle I, Boeddha NP, Agapow PM, Secka F, Anderson ST, Behrends U, Wintergerst U, Reiter K, Martinon-Torres F, Levin M, Zenz W. Osteoarticular Infections in Pediatric Hospitals in Europe: A Prospective Cohort Study From the EUCLIDS Consortium. Front Pediatr 2022; 10:744182. [PMID: 35601438 PMCID: PMC9114665 DOI: 10.3389/fped.2022.744182] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 03/16/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Pediatric osteoarticular infections (POAIs) are serious diseases requiring early diagnosis and treatment. METHODS In this prospective multicenter cohort study, children with POAIs were selected from the European Union Childhood Life-threatening Infectious Diseases Study (EUCLIDS) database to analyze their demographic, clinical, and microbiological data. RESULTS A cohort of 380 patients with POAIs, 203 with osteomyelitis (OM), 158 with septic arthritis (SA), and 19 with both OM and SA, was analyzed. Thirty-five patients were admitted to the Pediatric Intensive Care Unit; out of these, six suffered from shock, one needed an amputation of the right foot and of four left toes, and two had skin transplantation. According to the Pediatric Overall Performance Score, 36 (10.5%) showed a mild overall disability, 3 (0.8%) a moderate, and 1 (0.2%) a severe overall disability at discharge. A causative organism was detected in 65% (247/380) of patients. Staphylococcus aureus (S. aureus) was identified in 57.1% (141/247) of microbiological confirmed cases, including 1 (0.7%) methicillin-resistant S. aureus (MRSA) and 6 (4.2%) Panton-Valentine leukocidin (PVL)-producing S. aureus, followed by Group A Streptococcus (18.2%) and Kingella kingae (8.9%). K. kingae and PVL production in S. aureus were less frequently reported than expected from the literature. CONCLUSION POAIs are associated with a substantial morbidity in European children, with S. aureus being the major detected pathogen. In one-third of patients, no causative organism is identified. Our observations show an urgent need for the development of a vaccine against S. aureus and for the development of new microbiologic diagnostic guidelines for POAIs in European pediatric hospitals.
Collapse
Affiliation(s)
- Andreas Trobisch
- Department of Pediatrics and Adolescent Medicine, Division of General Pediatrics, Medical University of Graz, Graz, Austria.,Division of Neonatology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria.,Research Group for Neonatal Infectious Diseases, Medical University of Graz, Graz, Austria
| | - Nina A Schweintzger
- Department of Pediatrics and Adolescent Medicine, Division of General Pediatrics, Medical University of Graz, Graz, Austria
| | - Daniela S Kohlfürst
- Department of Pediatrics and Adolescent Medicine, Division of General Pediatrics, Medical University of Graz, Graz, Austria
| | - Manfred G Sagmeister
- Department of Pediatrics and Adolescent Medicine, Division of General Pediatrics, Medical University of Graz, Graz, Austria
| | - Matthias Sperl
- Department of Orthopedics and Traumatology, Pediatric Orthopedic Unit, Medical University of Graz, Graz, Austria
| | - Andrea J Grisold
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Gebhard Feierl
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Jethro A Herberg
- Section of Pediatric Infectious Disease, Imperial College London, London, United Kingdom
| | - Enitan D Carrol
- Department of Clinical Infection Microbiology and Immunology, University of Liverpool Institute of Infection, Veterinary and Ecological Sciences, Liverpool, United Kingdom
| | - Stephane C Paulus
- Department of Clinical Infection Microbiology and Immunology, University of Liverpool Institute of Infection, Veterinary and Ecological Sciences, Liverpool, United Kingdom
| | - Marieke Emonts
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom.,National Institute for Health Research (NIHR) Newcastle Biomedical Research Centre Based at Newcastle upon Tyne Hospitals NHS Trust and Newcastle University, Newcastle upon Tyne, United Kingdom.,Pediatric Infectious Diseases and Immunology Department, Newcastle upon Tyne Hospitals Foundation Trust, Great North Children's Hospital, Newcastle upon Tyne, United Kingdom
| | - Michiel van der Flier
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology and Laboratory of Infectious Diseases, Radboud Institute of Molecular Life Sciences, Nijmegen, Netherlands.,Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital University Medical Center Utrecht, Utrecht, Netherlands
| | - Ronald de Groot
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology and Laboratory of Infectious Diseases, Radboud Institute of Molecular Life Sciences, Nijmegen, Netherlands
| | - Miriam Cebey-López
- Translational Pediatrics and Infectious Diseases Section- Pediatrics Department, Santiago de Compostela, Spain.,Instituto de Investigación Sanitaria de Santiago (IDIS), Genetics- Vaccines- Infectious Diseases and Pediatrics Research Group (GENVIP), Santiago de Compostela, Spain
| | - Irene Rivero-Calle
- Translational Pediatrics and Infectious Diseases Section- Pediatrics Department, Santiago de Compostela, Spain.,Instituto de Investigación Sanitaria de Santiago (IDIS), Genetics- Vaccines- Infectious Diseases and Pediatrics Research Group (GENVIP), Santiago de Compostela, Spain
| | - Navin P Boeddha
- Department of Pediatrics, Erasmus MC-Sophia Children's Hospital, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Paul-Michael Agapow
- Section of Pediatric Infectious Disease, Imperial College London, London, United Kingdom
| | - Fatou Secka
- Medical Research Council Unit the Gambia, Banjul, Gambia
| | | | - Uta Behrends
- Department of Pediatrics and of Pediatric Surgery, Technische Universität München, Munich, Germany
| | - Uwe Wintergerst
- Department of Pediatrics, Hospital St. Josef, Braunau, Austria
| | - Karl Reiter
- Department of Pediatric Intensive Care, University Children's Hospital at Dr. von Haunersche Kinderklinik, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Federico Martinon-Torres
- Translational Pediatrics and Infectious Diseases Section- Pediatrics Department, Santiago de Compostela, Spain.,Instituto de Investigación Sanitaria de Santiago (IDIS), Genetics- Vaccines- Infectious Diseases and Pediatrics Research Group (GENVIP), Santiago de Compostela, Spain
| | - Michael Levin
- Section of Pediatric Infectious Disease, Imperial College London, London, United Kingdom
| | - Werner Zenz
- Department of Pediatrics and Adolescent Medicine, Division of General Pediatrics, Medical University of Graz, Graz, Austria
| | | |
Collapse
|
2
|
Yang GD, Agapow PM, Yedid G. Correction: The tree balance signature of mass extinction is erased by continued evolution in clades of constrained size with trait-dependent speciation. PLoS One 2018; 13:e0197191. [PMID: 29734368 PMCID: PMC5937746 DOI: 10.1371/journal.pone.0197191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
3
|
Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow PM, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Lavender CA, Turaga SC, Alexandari AM, Lu Z, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Boca SM, Swamidass SJ, Huang A, Gitter A, Greene CS. Opportunities and obstacles for deep learning in biology and medicine. J R Soc Interface 2018; 15:20170387. [PMID: 29618526 PMCID: PMC5938574 DOI: 10.1098/rsif.2017.0387] [Citation(s) in RCA: 764] [Impact Index Per Article: 127.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 03/07/2018] [Indexed: 11/12/2022] Open
Abstract
Deep learning describes a class of machine learning algorithms that are capable of combining raw inputs into layers of intermediate features. These algorithms have recently shown impressive results across a variety of domains. Biology and medicine are data-rich disciplines, but the data are complex and often ill-understood. Hence, deep learning techniques may be particularly well suited to solve problems of these fields. We examine applications of deep learning to a variety of biomedical problems-patient classification, fundamental biological processes and treatment of patients-and discuss whether deep learning will be able to transform these tasks or if the biomedical sphere poses unique challenges. Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art. Even though improvements over previous baselines have been modest in general, the recent progress indicates that deep learning methods will provide valuable means for speeding up or aiding human investigation. Though progress has been made linking a specific neural network's prediction to input features, understanding how users should interpret these models to make testable hypotheses about the system under study remains an open challenge. Furthermore, the limited amount of labelled data for training presents problems in some domains, as do legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning enabling changes at both bench and bedside with the potential to transform several areas of biology and medicine.
Collapse
Affiliation(s)
- Travers Ching
- Molecular Biosciences and Bioengineering Graduate Program, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Daniel S Himmelstein
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Brett K Beaulieu-Jones
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexandr A Kalinin
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Gregory P Way
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Enrico Ferrero
- Computational Biology and Stats, Target Sciences, GlaxoSmithKline, Stevenage, UK
| | | | - Michael Zietz
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael M Hoffman
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Wei Xie
- Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Gail L Rosen
- Ecological and Evolutionary Signal-processing and Informatics Laboratory, Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, USA
| | - Benjamin J Lengerich
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Johnny Israeli
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Jack Lanchantin
- Department of Computer Science, University of Virginia, Charlottesville, VA, USA
| | - Stephen Woloszynek
- Ecological and Evolutionary Signal-processing and Informatics Laboratory, Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, USA
| | - Anne E Carpenter
- Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Avanti Shrikumar
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Jinbo Xu
- Toyota Technological Institute at Chicago, Chicago, IL, USA
| | - Evan M Cofer
- Department of Computer Science, Trinity University, San Antonio, TX, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Christopher A Lavender
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Srinivas C Turaga
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA
| | - Amr M Alexandari
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Zhiyong Lu
- National Center for Biotechnology Information and National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - David J Harris
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA
| | | | - Yanjun Qi
- Department of Computer Science, University of Virginia, Charlottesville, VA, USA
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Yifan Peng
- National Center for Biotechnology Information and National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Laura K Wiley
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Marwin H S Segler
- Institute of Organic Chemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Simina M Boca
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA
| | - S Joshua Swamidass
- Department of Pathology and Immunology, Washington University in Saint Louis, St Louis, MO, USA
| | - Austin Huang
- Department of Medicine, Brown University, Providence, RI, USA
| | - Anthony Gitter
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
4
|
Abstract
Biodiversity assessment demands objective measures, because ultimately conservation decisions must prioritize the use of limited resources for preserving taxa. The most general framework for the objective assessment of conservation worth are those that assess evolutionary distinctiveness, e.g. Genetic ( Crozier 1992 ) and Phylogenetic Diversity ( Faith 1992 ), and Evolutionary History ( Nee & May 1997 ). These measures all attempt to assess the conservation worth of any scheme based on how much of the encompassing phylogeny of organisms is preserved. However, their general applicability is limited by the small proportion of taxa that have been reliably placed in a phylogeny. Given that phylogenizaton of many interesting taxa or important is unlikely to occur soon, we present a framework for using taxonomy as a reasonable surrogate for phylogeny. Combining this framework with exhaustive searches for combinations of sites containing maximal diversity, we provide a proof-of-concept for assessing conservation schemes for systematized but un-phylogenised taxa spread over a series of sites. This is illustrated with data from four studies, on North Queensland flightless insects ( Yeates et al. 2002 ), ants from a Florida Transect ( Lubertazzi & Tschinkel 2003 ), New England bog ants ( Gotelli & Ellison 2002 ) and a simulated distribution of the known New Zealand Lepidosauria ( Daugherty et al. 1994 ). The results support this approach, indicating that species, genus and site numbers predict evolutionary history, to a degree depending on the size of the data set.
Collapse
Affiliation(s)
- Ross H Crozier
- School of Tropical Biology, James Cook University, Townsville, Queensland, Australia
| | - Lisa J Dunnett
- School of Information Technology, James Cook University, Townsville, Queensland, Australia
| | | |
Collapse
|
5
|
Abstract
The kind and duration of phylogenetic topological “signatures” left in the wake of macroevolutionary events remain poorly understood. To this end, we examined a broad range of simulated phylogenies generated using trait-biased, heritable speciation probabilities and mass extinction that could be either random or selective on trait value, but also using background extinction and diversity-dependence to constrain clade sizes. In keeping with prior results, random mass extinction increased imbalance of clades that recovered to pre-extinction size, but was a relatively weak effect. Mass extinction that was selective on trait values tended to produce clades of similar or greater balance compared to random extinction or controls. Allowing evolution to continue past the point of clade-size recovery resulted in erosion and eventual erasure of this signal, with all treatments converging on similar values of imbalance, except for very intense extinction regimes targeted at taxa with high speciation rates. Return to a more balanced state with extended post-extinction evolution was also associated with loss of the previous phylogenetic root in most treatments. These results further demonstrate that while a mass extinction event can produce a recognizable phylogenetic signal, its effects become increasingly obscured the further an evolving clade gets from that event, with any sharp imbalance due to unrelated evolutionary factors.
Collapse
Affiliation(s)
- Guan-Dong Yang
- Department of Zoology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Paul-Michael Agapow
- Data Science Institute, William Penney Laboratory, Imperial College, South Kensington, London, United Kingdom
| | - Gabriel Yedid
- Department of Zoology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
- * E-mail:
| |
Collapse
|
6
|
Yedid G, Stredwick J, Ofria CA, Agapow PM. A comparison of the effects of random and selective mass extinctions on erosion of evolutionary history in communities of digital organisms. PLoS One 2012; 7:e37233. [PMID: 22693570 PMCID: PMC3365035 DOI: 10.1371/journal.pone.0037233] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 04/18/2012] [Indexed: 11/19/2022] Open
Abstract
The effect of mass extinctions on phylogenetic diversity and branching history of clades remains poorly understood in paleobiology. We examined the phylogenies of communities of digital organisms undergoing open-ended evolution as we subjected them to instantaneous “pulse” extinctions, choosing survivors at random, and to prolonged “press” extinctions involving a period of low resource availability. We measured age of the phylogenetic root and tree stemminess, and evaluated how branching history of the phylogenetic trees was affected by the extinction treatments. We found that strong random (pulse) and strong selective extinction (press) both left clear long-term signatures in root age distribution and tree stemminess, and eroded deep branching history to a greater degree than did weak extinction and control treatments. The widely-used Pybus-Harvey gamma statistic showed a clear short-term response to extinction and recovery, but differences between treatments diminished over time and did not show a long-term signature. The characteristics of post-extinction phylogenies were often affected as much by the recovery interval as by the extinction episode itself.
Collapse
Affiliation(s)
- Gabriel Yedid
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway.
| | | | | | | |
Collapse
|
7
|
Paredes UM, Prys-Jones R, Adams M, Groombridge J, Kundu S, Agapow PM, Abel RL. Micro-CT X-rays do not fragment DNA in preserved bird skins. J ZOOL SYST EVOL RES 2012. [DOI: 10.1111/j.1439-0469.2012.00657.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
|
8
|
Galiano M, Agapow PM, Thompson C, Platt S, Underwood A, Ellis J, Myers R, Green J, Zambon M. Evolutionary pathways of the pandemic influenza A (H1N1) 2009 in the UK. PLoS One 2011; 6:e23779. [PMID: 21887318 PMCID: PMC3161082 DOI: 10.1371/journal.pone.0023779] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2011] [Accepted: 07/25/2011] [Indexed: 12/20/2022] Open
Abstract
The emergence of the influenza (H1N1) 2009 virus provided a unique opportunity to study the evolution of a pandemic virus following its introduction into the human population. Virological and clinical surveillance in the UK were comprehensive during the first and second waves of the pandemic in 2009, with extensive laboratory confirmation of infection allowing a detailed sampling of representative circulating viruses. We sequenced the complete coding region of the haemagglutinin (HA) segment of 685 H1N1 pandemic viruses selected without bias during two waves of pandemic in the UK (April-December 2009). Phylogenetic analysis showed that although temporal accumulation of amino acid changes was observed in the HA sequences, the overall diversity was less than that typically seen for seasonal influenza A H1N1 or H3N2. There was co-circulation of multiple variants as characterised by signature amino acid changes in the HA. A specific substitution (S203T) became predominant both in UK and global isolates. No antigenic drift occurred during 2009 as viruses with greater than four-fold reduction in their haemagglutination inhibition (HI) titre ("low reactors") were detected in a low proportion (3%) and occurred sporadically. Although some limited antigenic divergence in viruses with four-fold reduction in HI titre might be related to the presence of 203T, additional studies are needed to test this hypothesis.
Collapse
Affiliation(s)
- Monica Galiano
- Centre for Infections, Health Protection Agency, London, United Kingdom.
| | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Agapow PM, Sluys R. The reality of taxonomic change. Trends Ecol Evol 2007; 20:278-80; author reply 280-1. [PMID: 16701382 DOI: 10.1016/j.tree.2005.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2005] [Revised: 03/23/2005] [Accepted: 04/04/2005] [Indexed: 11/29/2022]
|
10
|
Crozier RH, Dunnett LJ, Agapow PM. Phylogenetic biodiversity assessment based on systematic nomenclature. Evol Bioinform Online 2007; 1:11-36. [PMID: 19325850 PMCID: PMC2658867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Biodiversity assessment demands objective measures, because ultimately conservation decisions must prioritize the use of limited resources for preserving taxa. The most general framework for the objective assessment of conservation worth are those that assess evolutionary distinctiveness, e.g. Genetic (Crozier 1992) and Phylogenetic Diversity (Faith 1992), and Evolutionary History (Nee & May 1997). These measures all attempt to assess the conservation worth of any scheme based on how much of the encompassing phylogeny of organisms is preserved. However, their general applicability is limited by the small proportion of taxa that have been reliably placed in a phylogeny. Given that phylogenizaton of many interesting taxa or important is unlikely to occur soon, we present a framework for using taxonomy as a reasonable surrogate for phylogeny. Combining this framework with exhaustive searches for combinations of sites containing maximal diversity, we provide a proof-of-concept for assessing conservation schemes for systematized but un-phylogenised taxa spread over a series of sites. This is illustrated with data from four studies, on North Queensland flightless insects (Yeates et al. 2002), ants from a Florida Transect (Lubertazzi & Tschinkel 2003), New England bog ants (Gotelli & Ellison 2002) and a simulated distribution of the known New Zealand Lepidosauria (Daugherty et al. 1994). The results support this approach, indicating that species, genus and site numbers predict evolutionary history, to a degree depending on the size of the data set.
Collapse
Affiliation(s)
- Ross H Crozier
- School of Tropical Biology, James Cook University, Townsville, Queensland, Australia,Correspondence: Ross Crozier, School of Tropical Biology, James Cook Univeristy, Townsville, Queensland 4811, Australia.
| | - Lisa J Dunnett
- School of Information Technology, James Cook University, Townsville, Queensland, Australia
| | | |
Collapse
|
11
|
|
12
|
Azevedo RBR, Lohaus R, Braun V, Gumbel M, Umamaheshwar M, Agapow PM, Houthoofd W, Platzer U, Borgonie G, Meinzer HP, Leroi AM. The simplicity of metazoan cell lineages. Nature 2005; 433:152-6. [PMID: 15650738 DOI: 10.1038/nature03178] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2004] [Accepted: 11/09/2004] [Indexed: 11/09/2022]
Abstract
Developmental processes are thought to be highly complex, but there have been few attempts to measure and compare such complexity across different groups of organisms. Here we introduce a measure of biological complexity based on the similarity between developmental and computer programs. We define the algorithmic complexity of a cell lineage as the length of the shortest description of the lineage based on its constituent sublineages. We then use this measure to estimate the complexity of the embryonic lineages of four metazoan species from two different phyla. We find that these cell lineages are significantly simpler than would be expected by chance. Furthermore, evolutionary simulations show that the complexity of the embryonic lineages surveyed is near that of the simplest lineages evolvable, assuming strong developmental constraints on the spatial positions of cells and stabilizing selection on cell number. We propose that selection for decreased complexity has played a major role in moulding metazoan cell lineages.
Collapse
Affiliation(s)
- Ricardo B R Azevedo
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Petalcorin MIR, Joshua GW, Agapow PM, Dolphin CT. The fmo genes of Caenorhabditis elegans and C. briggsae: characterisation, gene expression and comparative genomic analysis. Gene 2004; 346:83-96. [PMID: 15716098 DOI: 10.1016/j.gene.2004.09.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2004] [Revised: 08/18/2004] [Accepted: 09/28/2004] [Indexed: 10/26/2022]
Abstract
The flavin-containing monooxygenase (FMO) gene family is conserved and ancient with representatives present in almost all phyla so far examined. The genes encode FAD-, NADP- and O(2)-dependent enzymes that catalyse oxygenation of soft-nucleophilic heteroatom centres in a range of substrates. Although usually classified as xenobiotic-metabolising enzymes, examples of FMOs exist that have evolved to metabolise specific endogenous substrates as part of a discrete physiological process. The genome of Caenorhabditis elegans contains five predicted genes encoding putative homologs of mammalian FMOs, K08C7.2, K08C7.5, Y39A1A.19, F53F4.5 and H24K24.5, which we have named fmo and numbered fmo-1 to fmo-5, respectively. As a first step towards determining their functional role(s), we have experimentally characterised these C. elegans fmo genes including analysing reporter gene expression patterns and RNAi phenotypes. Two major gene expression patterns were observed, either intestinal or hypodermal, but no gross RNAi phenotypes were found possibly due to functional redundancy. The internal structures of fmo-2, fmo-3 and fmo-4 have been compared with orthologs identified in the related nematode C. briggsae. For each orthologous pair, a global comparison of the paired upstream intergenic regions was performed and a number of conserved noncoding sequences, which may represent potential cis-regulatory elements, identified. Phylogenetic analysis reveals that several of the fmo homologs are the result of gene duplication along the lineage leading to the nematodes.
Collapse
Affiliation(s)
- Mark I R Petalcorin
- Section of Molecular Genetics, Pharmaceutical Science Research Division, Franklin-Wilkins Building, 150 Stamford Street, King's College London, London SE1 9NN, UK
| | | | | | | |
Collapse
|
14
|
Agapow PM, Bininda-Emonds OR, Crandall KA, Gittleman JL, Mace GM, Marshall JC, Purvis A. The Impact of Species Concept on Biodiversity Studies. The Quarterly Review of Biology 2004; 79:161-79. [PMID: 15232950 DOI: 10.1086/383542] [Citation(s) in RCA: 265] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Species are defined using a variety of different operational techniques. While discussion of the various methodologies has previously been restricted mostly to taxonomists, the demarcation of species is also crucial for conservation biology. Unfortunately, different methods of diagnosing species can arrive at different entities. Most prominently, it is widely thought that use of a phylogenetic species concept may lead to recognition of a far greater number of much less inclusive units. As a result, studies of the same group of organisms can produce not only different species identities but also different species range and number of individuals. To assess the impact of different definitions on conservation issues, we collected instances from the literature where a group of organisms was categorized both under phylogenetic and nonphylogenetic concepts. Our results show a marked difference, with surveys based on a phylogenetic species concept showing more species (48%) and an associated decrease in population size and range. We discuss the serious consequences of this trend for conservation, including an apparent change in the number of endangered species, potential political fallout, and the difficulty of deciding what should be conserved.
Collapse
Affiliation(s)
- Paul-Michael Agapow
- Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, United Kingdom.
| | | | | | | | | | | | | |
Collapse
|
15
|
Johnson RN, Agapow PM, Crozier RH. A tree island approach to inferring phylogeny in the ant subfamily Formicinae, with especial reference to the evolution of weaving. Mol Phylogenet Evol 2003; 29:317-30. [PMID: 13678687 DOI: 10.1016/s1055-7903(03)00114-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The ant subfamily Formicinae is a large assemblage (2458 species (J. Nat. Hist. 29 (1995) 1037), including species that weave leaf nests together with larval silk and in which the metapleural gland-the ancestrally defining ant character-has been secondarily lost. We used sequences from two mitochondrial genes (cytochrome b and cytochrome oxidase 2) from 18 formicine and 4 outgroup taxa to derive a robust phylogeny, employing a search for tree islands using 10000 randomly constructed trees as starting points and deriving a maximum likelihood consensus tree from the ML tree and those not significantly different from it. Non-parametric bootstrapping showed that the ML consensus tree fit the data significantly better than three scenarios based on morphology, with that of Bolton (Identification Guide to the Ant Genera of the World, Harvard University Press, Cambridge, MA) being the best among these alternative trees. Trait mapping showed that weaving had arisen at least four times and possibly been lost once. A maximum likelihood analysis showed that loss of the metapleural gland is significantly associated with the weaver life-pattern. The graph of the frequencies with which trees were discovered versus their likelihood indicates that trees with high likelihoods have much larger basins of attraction than those with lower likelihoods. While this result indicates that single searches are more likely to find high- than low-likelihood tree islands, it also indicates that searching only for the single best tree may lose important information.
Collapse
Affiliation(s)
- Rebecca N Johnson
- Department of Genetics and Evolution, La Trobe University, Bundoora, Vic 3083, Australia
| | | | | |
Collapse
|
16
|
Isaac NJB, Agapow PM, Harvey PH, Purvis A. PHYLOGENETICALLY NESTED COMPARISONS FOR TESTING CORRELATES OF SPECIES RICHNESS: A SIMULATION STUDY OF CONTINUOUS VARIABLES. Evolution 2003. [DOI: 10.1554/0014-3820(2003)057[0018:pncftc]2.0.co;2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
17
|
Isaac NJB, Agapow PM, Harvey PH, Purvis A. Phylogenetically nested comparisons for testing correlates of species richness: a simulation study of continuous variables. Evolution 2003; 57:18-26. [PMID: 12643564 DOI: 10.1111/j.0014-3820.2003.tb00212.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Explaining the uneven distribution of species among lineages is one of the oldest questions in evolution. Proposed correlations between biological traits and species diversity are routinely tested by making comparisons between phylogenetic sister clades. Several recent studies have used nested sister-clade comparisons to test hypotheses linking continuously varying traits, such as body size, with diversity. Evaluating the findings of these studies is complicated because they differ in the index of species richness difference used, the way in which trait differences were treated, and the statistical tests employed. In this paper, we use simulations to compare the performance of four species richness indices, two choices about the branch lengths used to estimate trait values for internal nodes and two statistical tests under a range of models of clade growth and character evolution. All four indices returned appropriate Type I error rates when the assumptions of the method were met and when branch lengths were set proportional to time. Only two of the indices were robust to the different evolutionary models and to different choices of branch lengths and statistical tests. These robust indices had comparable power under one nonnull scenario. Regression through the origin was consistently more powerful than the t-test, and the choice of branch lengths exerts a strong effect on both the validity and power. In the light of our simulations, we re-evaluate the findings of those who have previously used nested comparisons in the context of species richness. We provide a set of simple guidelines to maximize the performance of phylogenetically nested comparisons in tests of putative correlates of species richness.
Collapse
Affiliation(s)
- Nick J B Isaac
- Department of Biological Sciences, Imperial College, Silwood Park, Ascot, Berks SL5 7PY, United Kingdom
| | | | | | | |
Collapse
|
18
|
Agapow PM, Purvis A. Power of eight tree shape statistics to detect nonrandom diversification: a comparison by simulation of two models of cladogenesis. Syst Biol 2002; 51:866-72. [PMID: 12554452 DOI: 10.1080/10635150290102564] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
We used simulations to compare the relative power of eight statistical tests to detect imbalance in phylogenies that is too great to be ascribed to an equal-rates Markov null model. Three of these tests have never had their power assessed before. Our simulations are the first to assess performance under scenarios in which the speciation rates of various lineages can evolve independently. In one of the scenarios explored, rates depend upon the value of an evolving trait, whereas in the other the probability that a species will speciate declines with the time since it last did so. The results indicate that the relative performance of the methods depends upon how the imbalance is generated. Different types of processes lead to different imbalance signatures, i.e., different patterns of imbalance at different depths in the phylogeny, and the measures of tree shape differ in the depth of phylogeny at which they are most sensitive. Relative performance is also affected by tree size but does not appear to depend greatly upon the degree of speciation rate variation among lineages. Two of the indices (Colless's index I(c) and Shao and Sokal's Nmacr;) show reasonable performance throughout, but another (Shao and Sokal's B(2)) is never indicated to be a preferred method. Two tests that do not require completely resolved phylogenies, mean I' and mean I'(10), have reasonable power.
Collapse
|
19
|
Abstract
Two lines of evidence indicate that the degree of symmetry in phylogenetic topologies differs at different hierarchical levels. First, in a set of 61 phylogenies with superspecific taxa as their terminals, trees were on average more unbalanced (asymmetric) when the species richness of terminals was considered than when it was not. Second, nodes with a given number of higher taxa descended from them were on average more unbalanced than were nodes with the same number of species as descendants. There are several possible reasons--some biological, some artifactual--for the differences. Whatever the reason, these results caution against treating species-level and higher level phylogenies as equivalent when considering tree shape. The imbalance measure adopted here permits the use of trees that contain polytomies, facilitating a larger sample than has been achieved previously.
Collapse
Affiliation(s)
- Andy Purvis
- Department of Biological Sciences, Imperial College, Silwood Park, Ascot SL5 7PY, UK
| | | |
Collapse
|
20
|
Abstract
Measurement of the degree of asymmetry in phylogenetic trees is important because a tree's shape reflects the process by which it has grown. For example, highly asymmetric trees are evidence that species have had different potential for diversification. Of the tree shape measures in the literature, that proposed by Fusco & Cronk (J. theor. Biol.175, 235-243) appears to be particularly useful, because it does not require fully-resolved trees whose terminals are of equal taxonomic rank. The value of the asymmetry or imbalance at a node is intended to be independent of the number of species ultimately descended from the node. In this paper, however, we point out that the value does depend upon species number. We propose two modifications that remove the dependency and so increase the measure's usefulness. We illustrate the use of the modified measures, which are implemented in a freely-available program, MESA.
Collapse
Affiliation(s)
- Andy Purvis
- Department of Biological Sciences, Imperial College, Silwood Park, Ascot, Berkshire, SL5 7PY, UK.
| | | | | |
Collapse
|
21
|
|
22
|
Abstract
The hierarchical nature of phylogenies means that random extinction of species affects a smaller fraction of higher taxa, and so the total amount of evolutionary history lost may be comparatively slight. However, current extinction risk is not phylogenetically random. We show the potentially severe implications of the clumped nature of threat for the loss of biodiversity. An additional 120 avian and mammalian genera are at risk compared with the number predicted under random extinction. We estimate that the prospective extra loss of mammalian evolutionary history alone would be equivalent to losing a monotypic phylum.
Collapse
Affiliation(s)
- A Purvis
- Department of Biology, Imperial College, Silwood Park, Ascot SL5 7PY, UK.
| | | | | | | |
Collapse
|
23
|
Winzor DJ, Agapow PM, Jackson CM. Preferential ligand binding to multi-state acceptor systems: comparisons of the calcium-binding and dimerization characteristics of prothrombin and fragment 1. J Theor Biol 1991; 153:385-99. [PMID: 1665891 DOI: 10.1016/s0022-5193(05)80577-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Consideration is given to the interactions of a ligand with self-associating acceptor systems for which preferential binding is an ambiguous term in that ligand-mediated self-association does not necessarily imply a greater binding constant for polymeric acceptor--even in instances where binding sites are preserved in the self-association process. This dilemma is shown to arise in situations involving the binding of ligand to monomeric and polymeric forms of an acceptor that also coexist in equilibrium with inactive isomeric states. For example, the ten-fold increase in the measured dimerization constant for prothrombin Fragment 1 in the presence of a saturating concentration of Ca2+ ion may well reflect the existence of a 12% greater binding constant for the interaction of metal ion with dimeric acceptor. However, that result, as well as the detailed form of the sigmoidal binding curve, are also reasonably described by another extreme model in which the monomeric and dimeric forms of the acceptor possess equal affinities for Ca2+ ion. Likewise, the fact that the same experimental dimerization constant applies to prothrombin and its Ca(2+)-saturated complex does not preclude the possibility that the active form of dimeric zymogen exhibits a 12% greater affinity for metal ion. Numerical simulations have established that characterization of the dimerization behaviour as a function of free ligand concentration should allow greater discrimination between such models of the interplay between calcium binding and self-association of prothrombin and Fragment 1. Finally, by illustrating the likelihood that the disparity in self-association behaviour of prothrombin and Fragment 1 merely reflects minor differences in the relative magnitudes of isomerization constants and/or binding constants for monomeric and dimeric states of the two acceptors, the present investigation serves to allay concern about the validity of employing the proteolytic fragment as a model of the intact zymogen.
Collapse
Affiliation(s)
- D J Winzor
- Department of Biochemistry, University of Queensland, Brisbane, Australia
| | | | | |
Collapse
|
24
|
Abstract
A simple procedure for assessing the extent of electrostatic effects on protein dimerization is described and illustrated by application to published results on the ionic strength dependence of the dimerization constant for alpha-chymotrypsin at pH 4 (Aune, K.C., Goldsmith, L.C. and Timasheff, S.N. (1971) Biochemistry 10, 1617-1622). From the analysis it is concluded that the inverse dependence of alpha-chymotrypsin dimerization upon ionic strength is predominantly a general electrostatic effect, rather than a consequence of repulsion between two specific charged residues on the adjacent monomers comprising dimer.
Collapse
Affiliation(s)
- P M Agapow
- Department of Biochemistry, University of Queensland, St. Lucia, Australia
| | | |
Collapse
|