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Wadford DA, Baumrind N, Baylis EF, Bell JM, Bouchard EL, Crumpler M, Foote EM, Gilliam S, Glaser CA, Hacker JK, Ledin K, Messenger SL, Morales C, Smith EA, Sevinsky JR, Corbett-Detig RB, DeRisi J, Jacobson K. Implementation of California COVIDNet - a multi-sector collaboration for statewide SARS-CoV-2 genomic surveillance. Front Public Health 2023; 11:1249614. [PMID: 37937074 PMCID: PMC10627185 DOI: 10.3389/fpubh.2023.1249614] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/27/2023] [Indexed: 11/09/2023] Open
Abstract
Introduction The SARS-CoV-2 pandemic represented a formidable scientific and technological challenge to public health due to its rapid spread and evolution. To meet these challenges and to characterize the virus over time, the State of California established the California SARS-CoV-2 Whole Genome Sequencing (WGS) Initiative, or "California COVIDNet". This initiative constituted an unprecedented multi-sector collaborative effort to achieve large-scale genomic surveillance of SARS-CoV-2 across California to monitor the spread of variants within the state, to detect new and emerging variants, and to characterize outbreaks in congregate, workplace, and other settings. Methods California COVIDNet consists of 50 laboratory partners that include public health laboratories, private clinical diagnostic laboratories, and academic sequencing facilities as well as expert advisors, scientists, consultants, and contractors. Data management, sample sourcing and processing, and computational infrastructure were major challenges that had to be resolved in the midst of the pandemic chaos in order to conduct SARS-CoV-2 genomic surveillance. Data management, storage, and analytics needs were addressed with both conventional database applications and newer cloud-based data solutions, which also fulfilled computational requirements. Results Representative and randomly selected samples were sourced from state-sponsored community testing sites. Since March of 2021, California COVIDNet partners have contributed more than 450,000 SARS-CoV-2 genomes sequenced from remnant samples from both molecular and antigen tests. Combined with genomes from CDC-contracted WGS labs, there are currently nearly 800,000 genomes from all 61 local health jurisdictions (LHJs) in California in the COVIDNet sequence database. More than 5% of all reported positive tests in the state have been sequenced, with similar rates of sequencing across 5 major geographic regions in the state. Discussion Implementation of California COVIDNet revealed challenges and limitations in the public health system. These were overcome by engaging in novel partnerships that established a successful genomic surveillance program which provided valuable data to inform the COVID-19 public health response in California. Significantly, California COVIDNet has provided a foundational data framework and computational infrastructure needed to respond to future public health crises.
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Affiliation(s)
- Debra A. Wadford
- California Department of Public Health, Richmond, CA, United States
| | - Nikki Baumrind
- California Department of Public Health, Richmond, CA, United States
| | | | - John M. Bell
- California Department of Public Health, Richmond, CA, United States
| | | | - Megan Crumpler
- Orange County Public Health Laboratory, Santa Ana, CA, United States
| | - Eric M. Foote
- California Department of Public Health, Richmond, CA, United States
| | - Sabrina Gilliam
- California Department of Public Health, Richmond, CA, United States
| | - Carol A. Glaser
- California Department of Public Health, Richmond, CA, United States
| | - Jill K. Hacker
- California Department of Public Health, Richmond, CA, United States
| | - Katya Ledin
- California Department of Public Health, Richmond, CA, United States
| | | | | | | | | | | | - Joseph DeRisi
- University of California, San Francisco, San Francisco, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
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Lindsey NP, Messenger SL, Hacker JK, Salas ML, Scott-Waldron C, Haydel D, Rider E, Simonson S, Brown CM, Patel P, Smole SC, Neitzel DF, Schiffman EK, Palm J, Strain AK, Vetter SM, Nefzger B, Fischer M, Rabe IB. Expanded Molecular Testing on Patients with Suspected West Nile Virus Disease. Vector Borne Zoonotic Dis 2019; 19:690-693. [PMID: 31081745 DOI: 10.1089/vbz.2018.2412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Most diagnostic testing for West Nile virus (WNV) disease is accomplished using serologic testing, which is subject to cross-reactivity, may require cumbersome confirmatory testing, and may fail to detect infection in specimens collected early in the course of illness. The objective of this project was to determine whether a combination of molecular and serologic testing would increase detection of WNV disease cases in acute serum samples. A total of 380 serum specimens collected ≤7 days after onset of symptoms and submitted to four state public health laboratories for WNV diagnostic testing in 2014 and 2015 were tested. WNV immunoglobulin M (IgM) antibody and RT-PCR tests were performed on specimens collected ≤3 days after symptom onset. WNV IgM antibody testing was performed on specimens collected 4-7 days after onset and RT-PCR was performed on IgM-positive specimens. A patient was considered to have laboratory evidence of WNV infection if they had detectable WNV IgM antibodies or WNV RNA in the submitted serum specimen. Of specimens collected ≤3 days after symptom onset, 19/158 (12%) had laboratory evidence of WNV infection, including 16 positive for only WNV IgM antibodies, 1 positive for only WNV RNA, and 2 positive for both. Of specimens collected 4-7 days after onset, 21/222 (9%) were positive for WNV IgM antibodies; none had detectable WNV RNA. These findings suggest that routinely performing WNV RT-PCR on acute serum specimens submitted for WNV diagnostic testing is unlikely to identify a substantial number of additional cases beyond IgM antibody testing alone.
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Affiliation(s)
- Nicole P Lindsey
- Arboviral Diseases Branch, Centers for Disease Control and Prevention, Fort Collins, Colorado
| | - Sharon L Messenger
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California
| | - Jill K Hacker
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California
| | - Maria L Salas
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California
| | | | | | - Errin Rider
- Louisiana Office of Public Health, Baton Rouge, Louisiana
| | - Sean Simonson
- Louisiana Office of Public Health, Baton Rouge, Louisiana
| | - Catherine M Brown
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts
| | - Pinal Patel
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts
| | - Sandra C Smole
- Massachusetts Department of Public Health, Jamaica Plain, Massachusetts
| | | | | | - Jennifer Palm
- Minnesota Department of Health, Saint Paul, Minnesota
| | - Anna K Strain
- Minnesota Department of Health, Saint Paul, Minnesota
| | - Sara M Vetter
- Minnesota Department of Health, Saint Paul, Minnesota
| | - Brian Nefzger
- Minnesota Department of Health, Saint Paul, Minnesota
| | - Marc Fischer
- Arboviral Diseases Branch, Centers for Disease Control and Prevention, Fort Collins, Colorado
| | - Ingrid B Rabe
- Arboviral Diseases Branch, Centers for Disease Control and Prevention, Fort Collins, Colorado
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Naccache SN, Federman S, Veeraraghavan N, Zaharia M, Lee D, Samayoa E, Bouquet J, Greninger AL, Luk KC, Enge B, Wadford DA, Messenger SL, Genrich GL, Pellegrino K, Grard G, Leroy E, Schneider BS, Fair JN, Martínez MA, Isa P, Crump JA, DeRisi JL, Sittler T, Hackett J, Miller S, Chiu CY. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res 2014; 24:1180-92. [PMID: 24899342 PMCID: PMC4079973 DOI: 10.1101/gr.171934.113] [Citation(s) in RCA: 311] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Unbiased next-generation sequencing (NGS) approaches enable comprehensive pathogen detection in the clinical microbiology laboratory and have numerous applications for public health surveillance, outbreak investigation, and the diagnosis of infectious diseases. However, practical deployment of the technology is hindered by the bioinformatics challenge of analyzing results accurately and in a clinically relevant timeframe. Here we describe SURPI (“sequence-based ultrarapid pathogen identification”), a computational pipeline for pathogen identification from complex metagenomic NGS data generated from clinical samples, and demonstrate use of the pipeline in the analysis of 237 clinical samples comprising more than 1.1 billion sequences. Deployable on both cloud-based and standalone servers, SURPI leverages two state-of-the-art aligners for accelerated analyses, SNAP and RAPSearch, which are as accurate as existing bioinformatics tools but orders of magnitude faster in performance. In fast mode, SURPI detects viruses and bacteria by scanning data sets of 7–500 million reads in 11 min to 5 h, while in comprehensive mode, all known microorganisms are identified, followed by de novo assembly and protein homology searches for divergent viruses in 50 min to 16 h. SURPI has also directly contributed to real-time microbial diagnosis in acutely ill patients, underscoring its potential key role in the development of unbiased NGS-based clinical assays in infectious diseases that demand rapid turnaround times.
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Affiliation(s)
- Samia N Naccache
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA
| | - Scot Federman
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA
| | - Narayanan Veeraraghavan
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA
| | - Matei Zaharia
- Department of Computer Science, University of California, Berkeley, California 94720, USA
| | - Deanna Lee
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA
| | - Erik Samayoa
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA
| | - Jerome Bouquet
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA
| | | | - Ka-Cheung Luk
- Abbott Diagnostics, Abbott Park, Illinois 60064, USA
| | - Barryett Enge
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California 94804, USA
| | - Debra A Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California 94804, USA
| | - Sharon L Messenger
- Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, California 94804, USA
| | - Gillian L Genrich
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA
| | - Kristen Pellegrino
- Department of Family and Community Medicine, UCSF, San Francisco, California 94143, USA
| | - Gilda Grard
- Viral Emergent Diseases Unit, Centre International de Recherches Médicales de Franceville, Franceville, BP 769, Gabon
| | - Eric Leroy
- Viral Emergent Diseases Unit, Centre International de Recherches Médicales de Franceville, Franceville, BP 769, Gabon
| | | | - Joseph N Fair
- Metabiota, Inc., San Francisco, California 94104, USA
| | - Miguel A Martínez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62260, Mexico
| | - Pavel Isa
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62260, Mexico
| | - John A Crump
- Division of Infectious Diseases and International Health and the Duke Global Health Institute, Duke University Medical Center, Durham, North Carolina 27708, USA; Kilimanjaro Christian Medical Centre, Moshi, Kilimanjaro, 7393, Tanzania; Centre for International Health, University of Otago, Dunedin, 9054, New Zealand
| | - Joseph L DeRisi
- Department of Biochemistry, UCSF, San Francisco, California 94107, USA
| | - Taylor Sittler
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA
| | - John Hackett
- Abbott Diagnostics, Abbott Park, Illinois 60064, USA
| | - Steve Miller
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, UCSF, San Francisco, California 94107, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94107, USA; Department of Medicine, Division of Infectious Diseases, UCSF, San Francisco, California 94143, USA
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Fritz CL, Kriner P, Garcia D, Padgett KA, Espinosa A, Chase R, Hu R, Messenger SL. Tick infestation and spotted-fever group Rickettsia in shelter dogs, California, 2009. Zoonoses Public Health 2011; 59:4-7. [PMID: 21824367 DOI: 10.1111/j.1863-2378.2011.01414.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In response to an outbreak of Rocky Mountain spotted fever (RMSF) in Baja California in early 2009, dogs at two shelters in neighbouring Imperial County, California, were evaluated for ectoparasites. Brown dog ticks (Rhipicephalus sanguineus), a recognized vector for RMSF, were found on 35 (30%) of 116 dogs but all ticks tested negative for Rickettsia rickettsii by PCR.
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Affiliation(s)
- C L Fritz
- Division of Communicable Disease Control, Center for Infectious Diseases, California Department of Public Health, Sacramento, CA 95899-7377, USA.
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Abstract
A novel rabies virus was identified after death in a man who had immigrated from Oaxaca, Mexico, to California, USA. Despite the patient’s history of exposure to domestic and wild carnivores, molecular and phylogenetic characterizations suggested that the virus originated from insectivorous bats. Enhanced surveillance is needed to elucidate likely reservoirs.
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Abstract
Most human rabies deaths in the United States can be attributed to unrecognized exposures to rabies viruses associated with bats, particularly those associated with two infrequently encountered bat species (Lasionycteris noctivagans and Pipistrellus subflavus). These human rabies cases tend to cluster in the southeastern and northwestern United States. In these regions, most rabies deaths associated with bats in nonhuman terrestrial mammals are also associated with virus variants specific to these two bat species rather than more common bat species; outside of these regions, more common bat rabies viruses contribute to most transmissions. The preponderance of rabies deaths connected with the two uncommon L. noctivagans and P. subflavus bat rabies viruses is best explained by their evolution of increased viral infectivity.
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Affiliation(s)
| | - Jean S. Smith
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Pamela A. Yager
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Hoffmaster AR, Meyer RF, Bowen MD, Marston CK, Weyant RS, Thurman K, Messenger SL, Minor EE, Winchell JM, Rassmussen MV, Newton BR, Parker JT, Morrill WE, McKinney N, Barnett GA, Sejvar JJ, Jernigan JA, Perkins BA, Popovic T. Evaluation and validation of a real-time polymerase chain reaction assay for rapid identification of Bacillus anthracis. Emerg Infect Dis 2002; 8:1178-82. [PMID: 12396935 PMCID: PMC2730313 DOI: 10.3201/eid0810.020393] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Messenger SL, Smith JS, Rupprecht CE. Emerging epidemiology of bat-associated cryptic cases of rabies in humans in the United States. Clin Infect Dis 2002; 35:738-47. [PMID: 12203172 DOI: 10.1086/342387] [Citation(s) in RCA: 162] [Impact Index Per Article: 7.4] [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: 11/05/2001] [Revised: 05/30/2002] [Indexed: 11/03/2022] Open
Abstract
In the United States, during the past half-century, the number of humans to die of rabies dramatically decreased to an average of 1-2 per year. Although the number of deaths is low, most deaths occur because individuals are unaware that they had been exposed to and infected with rabies virus, and, therefore, they do not seek effective postexposure treatment. Molecular epidemiological studies have linked most of these cryptic rabies exposures to rabies virus variants associated with insectivorous bats. In particular, virus variants associated with 2 relatively reclusive species, the silver-haired bat (Lasionycteris noctivagans) and the eastern pipistrelle (Pipistrellus subflavus), are the unexpected culprits of most cryptic cases of rabies in humans.
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Affiliation(s)
- Sharon L Messenger
- Viral and Rickettsial Zoonoses Branch, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA.
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Whitfield SG, Fekadu M, Shaddock JH, Niezgoda M, Warner CK, Messenger SL. A comparative study of the fluorescent antibody test for rabies diagnosis in fresh and formalin-fixed brain tissue specimens. J Virol Methods 2001; 95:145-51. [PMID: 11377721 DOI: 10.1016/s0166-0934(01)00304-4] [Citation(s) in RCA: 27] [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: 11/21/2022]
Abstract
Many diagnostic methods have been used to detect rabies virus antigen. The preferred method for routine diagnosis of rabies in fresh or frozen brain tissues is the fluorescent antibody test (FAT). In this study, the FAT was used to evaluate the rabies status of fresh/frozen brain specimens from more than 800 rabies-suspected cases, in more than 14 different species of animals. A comparable brain specimen from each case was fixed in 10% buffered formalin and examined by the FAT. The evaluation of rabies status between fresh and formalin-fixed tissues was in agreement in more than 99.8% of the cases. When fresh tissue is not available for testing, these results validate the use of this procedure for routine diagnosis of rabies in formalin-fixed brain tissues.
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Affiliation(s)
- S G Whitfield
- Rabies Section, Viral and Rickettsial Zoonoses Branch, Division of Viral and Rickettsial Diseases, National Center of Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30333, USA.
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Marshall FA, Messenger SL, Wyborn NR, Guest JR, Wing H, Busby SJ, Green J. A novel promoter architecture for microaerobic activation by the anaerobic transcription factor FNR. Mol Microbiol 2001; 39:747-53. [PMID: 11169114 DOI: 10.1046/j.1365-2958.2001.02262.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [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: 11/20/2022]
Abstract
The yfiD gene of Escherichia coli has an unusual promoter architecture in which an FNR dimer located at -93.5 inhibits transcription activation mediated by another FNR dimer bound at the typical class II position (-40.5). In vitro transcription from the yfiD promoter indicated that FNR alone can downregulate yfiD expression. Analysis of yfiD::lac reporters showed that five turns of the DNA helix between FNR sites was optimal for downregulation. FNR heterodimers, in which one subunit carried a defective repression surface, revealed that the upstream subunit of the -40.5 dimer and the downstream subunit of the -93.5 dimer were most important for downregulating yfiD expression. Deletion of the C-terminal domain of the alpha-subunit of RNA polymerase (RNAP) did not affect FNR-mediated repression, suggesting that repression is mediated through FNR-FNR and not FNR-RNAP interactions. Maximum yfiD::lac expression was observed in cultures exposed to 10 microM oxygen. More or less oxygen reduced expression dramatically. This pattern of response was dependent on the combination of a high-affinity site at the activating class II position and a lower affinity site at the upstream position.
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Affiliation(s)
- F A Marshall
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
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Abstract
The evolution of virulence was studied in a virus subjected to alternating episodes of vertical and horizontal transmission. Bacteriophage f1 was used as the parasite because it establishes a debilitating but non-fatal infection that can be transmitted vertically (from a host to its progeny) as well as horizontally (infection of new hosts). Horizontal transmission was required of all phage at specific intervals, but was prevented otherwise. Each episode of horizontal transmission was followed by an interval of obligate vertical transmission, followed by an interval of obligate horizontal transmission etc. The duration of vertical transmission was eight times longer per episode in one treatment than in the other, thus varying the relative intensity of selection against virulence while maintaining selection for some level of virus production. Viral lines with the higher enforced rate of infectious transmission evolved higher virulence and higher rates of virus production. These results support the trade-off model for the evolution of virulence.
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Affiliation(s)
- S L Messenger
- Department of Zoology, University of Texas, Austin 78712, USA
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Abstract
Recent phylogenetic analyses of cetacean relationships based on DNA sequence data have challenged the traditional view that baleen whales (Mysticeti) and toothed whales (Odontoceti) are each monophyletic, arguing instead that baleen whales are the sister group of the odontocete family Physeteridae (sperm whales). We reexamined this issue in light of a morphological data set composed of 207 characters and molecular data sets of published 12S, 16S, and cytochrome b mitochondrial DNA sequences. We reach four primary conclusions: (1) Our morphological data set strongly supports the traditional view of odontocete monophyly; (2) the unrooted molecular and morphological trees are very similar, and most of the conflict results from alternative rooting positions; (3) the rooting position of the molecular tree is sensitive to choice of artiodactyls outgroup taxa and the treatment of two small but ambiguously aligned regions of the 12S and 16S sequences, whereas the morphological root is strongly supported; and (4) combined analyses of the morphological and molecular data provide a well-supported phylogenetic estimate consistent with that based on the morphological data alone (and the traditional view of toothed-whale monophyly) but with increased bootstrap support at nearly every node of the tree.
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Affiliation(s)
- S L Messenger
- Department of Zoology, University of Texas at Austin, Austin, Texas 78712-1064, USA
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