351
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Hope AG, Ho SYW, Malaney JL, Cook JA, Talbot SL. ACCOUNTING FOR RATE VARIATION AMONG LINEAGES IN COMPARATIVE DEMOGRAPHIC ANALYSES. Evolution 2014; 68:2689-700. [DOI: 10.1111/evo.12469] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Accepted: 05/22/2014] [Indexed: 01/16/2023]
Affiliation(s)
- Andrew G. Hope
- U.S. Geological Survey; Alaska Science Center; 4210 University Drive Anchorage Alaska 99508
| | - Simon Y. W. Ho
- School of Biological Sciences; Edgeworth David Building A11; The University of Sydney; Sydney New South Wales 2006 Australia
| | - Jason L. Malaney
- Department of Natural Resources and Environmental Science; University of Nevada-Reno; Reno Nevada 89557
| | - Joseph A. Cook
- Department of Biology; University of New Mexico; Museum of Southwestern Biology MSC03 2020; Albuquerque New Mexico 87131
| | - Sandra L. Talbot
- U.S. Geological Survey; Alaska Science Center; 4210 University Drive Anchorage Alaska 99508
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352
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Molak M, Suchard MA, Ho SYW, Beilman DW, Shapiro B. Empirical calibrated radiocarbon sampler: a tool for incorporating radiocarbon-date and calibration error into Bayesian phylogenetic analyses of ancient DNA. Mol Ecol Resour 2014; 15:81-6. [PMID: 24964386 DOI: 10.1111/1755-0998.12295] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 06/06/2014] [Accepted: 06/09/2014] [Indexed: 10/25/2022]
Abstract
Studies of DNA from ancient samples provide a valuable opportunity to gain insight into past evolutionary and demographic processes. Bayesian phylogenetic methods can estimate evolutionary rates and timescales from ancient DNA sequences, with the ages of the samples acting as calibrations for the molecular clock. Sample ages are often estimated using radiocarbon dating, but the associated measurement error is rarely taken into account. In addition, the total uncertainty quantified by converting radiocarbon dates to calendar dates is typically ignored. Here, we present a tool for incorporating both of these sources of uncertainty into Bayesian phylogenetic analyses of ancient DNA. This empirical calibrated radiocarbon sampler (ECRS) integrates the age uncertainty for each ancient sequence over the calibrated probability density function estimated for its radiocarbon date and associated error. We use the ECRS to analyse three ancient DNA data sets. Accounting for radiocarbon-dating and calibration error appeared to have little impact on estimates of evolutionary rates and related parameters for these data sets. However, analyses of other data sets, particularly those with few or only very old radiocarbon dates, might be more sensitive to using artificially precise sample ages and should benefit from use of the ECRS.
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Affiliation(s)
- Martyna Molak
- School of Biological Sciences, University of Sydney, Edgeworth David building A11, Science Road, 2006, Sydney, NSW, Australia; Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warsaw, Poland
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353
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Rodriguez-Rivera LD, Moreno Switt AI, Degoricija L, Fang R, Cummings CA, Furtado MR, Wiedmann M, den Bakker HC. Genomic characterization of Salmonella Cerro ST367, an emerging Salmonella subtype in cattle in the United States. BMC Genomics 2014; 15:427. [PMID: 24898914 PMCID: PMC4070546 DOI: 10.1186/1471-2164-15-427] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 05/21/2014] [Indexed: 11/20/2023] Open
Abstract
Background Within the last decade, Salmonella enterica subsp. enterica serovar Cerro (S. Cerro) has become one of the most common serovars isolated from cattle and dairy farm environments in the northeastern US. The fact that this serovar is commonly isolated from subclinically infected cattle and is rarely associated with human disease, despite its frequent isolation from cattle, has led to the hypothesis that this emerging serovar may be characterized by reduced virulence. We applied comparative and population genomic approaches to (i) characterize the evolution of this recently emerged serovar and to (ii) gain a better understanding of genomic features that could explain some of the unique epidemiological features associated with this serovar. Results In addition to generating a de novo draft genome for one Salmonella Cerro strain, we also generated whole genome sequence data for 26 additional S. Cerro isolates, including 16 from cattle operations in New York (NY) state, 2 from human clinical cases from NY in 2008, and 8 from diverse animal sources (7 from Washington state and 1 from Florida). All isolates sequenced in this study represent sequence type ST367. Population genomic analysis showed that isolates from the NY cattle operations form a well-supported clade within S. Cerro ST367 (designated here “NY bovine clade”), distinct from isolates from Washington state, Florida and the human clinical cases. A molecular clock analysis indicates that the most recent common ancestor of the NY bovine clade dates back to 1998, supporting the recent emergence of this clone. Comparative genomic analyses revealed several relevant genomic features of S. Cerro ST367, that may be responsible for reduced virulence of S. Cerro, including an insertion creating a premature stop codon in sopA. In addition, patterns of gene deletion in S. Cerro ST367 further support adaptation of this clone to a unique ecological or host related niche. Conclusions Our results indicate that the increase in prevalence of S. Cerro ST367 is caused by a highly clonal subpopulation and that S. Cerro ST367 is characterized by unique genomic deletions that may indicate adaptation to specific ecological niches and possibly reduced virulence in some hosts. Electronic supplementary material The online version of this article (doi: 10.1186/1471-2164-15-427) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Henk C den Bakker
- Department of Food Science, Stocking Hall, Cornell University, Ithaca, NY 14853, USA.
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354
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Groom SVC, Stevens MI, Schwarz MP. Parallel responses of bees to Pleistocene climate change in three isolated archipelagos of the southwestern Pacific. Proc Biol Sci 2014; 281:20133293. [PMID: 24807250 DOI: 10.1098/rspb.2013.3293] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The impacts of glacial cycles on the geographical distribution and size of populations have been explored for numerous terrestrial and marine taxa. However, most studies have focused on high latitudes, with only a few focused on the response of biota to the last glacial maximum (LGM) in equatorial regions. Here, we examine how population sizes of key bee fauna in the southwest Pacific archipelagos of Fiji, Vanuatu and Samoa have fluctuated over the Quaternary. We show that all three island faunas suffered massive population declines, roughly corresponding in time to the LGM, followed by rapid expansion post-LGM. Our data therefore suggest that Pleistocene climate change has had major impacts across a very broad tropical region. While other studies indicate widespread Holarctic effects of the LGM, our data suggest a much wider range of latitudes, extending to the tropics, where these climate change repercussions were important. As key pollinators, the inferred changes in these bee faunas may have been critical in the development of the diverse Pacific island flora. The magnitude of these responses indicates future climate change scenarios may have alarming consequences for Pacific island systems involving pollinator-dependent plant communities and agricultural crops.
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Affiliation(s)
- Scott V C Groom
- School of Biological Sciences, Flinders University, , GPO Box 2100, Adelaide, South Australia 5001, Australia, South Australian Museum, , GPO Box 234, Adelaide, South Australia 5000, Australia, School of Pharmacy and Medical Sciences, University of South Australia, , Adelaide, South Australia 5000, Australia
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355
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Nunes MRT, Palacios G, Faria NR, Sousa EC, Pantoja JA, Rodrigues SG, Carvalho VL, Medeiros DBA, Savji N, Baele G, Suchard MA, Lemey P, Vasconcelos PFC, Lipkin WI. Air travel is associated with intracontinental spread of dengue virus serotypes 1-3 in Brazil. PLoS Negl Trop Dis 2014; 8:e2769. [PMID: 24743730 PMCID: PMC3990485 DOI: 10.1371/journal.pntd.0002769] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 02/18/2014] [Indexed: 01/01/2023] Open
Abstract
Dengue virus and its four serotypes (DENV-1 to DENV-4) infect 390 million people and are implicated in at least 25,000 deaths annually, with the largest disease burden in tropical and subtropical regions. We investigated the spatial dynamics of DENV-1, DENV-2 and DENV-3 in Brazil by applying a statistical framework to complete genome sequences. For all three serotypes, we estimated that the introduction of new lineages occurred within 7 to 10-year intervals. New lineages were most likely to be imported from the Caribbean region to the North and Northeast regions of Brazil, and then to disperse at a rate of approximately 0.5 km/day. Joint statistical analysis of evolutionary, epidemiological and ecological data indicates that aerial transportation of humans and/or vector mosquitoes, rather than Aedes aegypti infestation rates or geographical distances, determine dengue virus spread in Brazil.
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Affiliation(s)
- Marcio R. T. Nunes
- Centro de Inovação Tecnológica, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Gustavo Palacios
- Center for Genomic Sciences, United States Army Medical Research Institute for Infectious Diseases, Frederick, Maryland, United States of America
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | | | | | - Jamilla A. Pantoja
- Centro de Inovação Tecnológica, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Sueli G. Rodrigues
- Departamento de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Valéria L. Carvalho
- Departamento de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Daniele B. A. Medeiros
- Departamento de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Nazir Savji
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Guy Baele
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Marc A. Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California – Los Angeles, Los Angeles, California, United States of America
- Department of Human Genetics, David Geffen School of Medicine, University of California – Los Angeles, Los Angeles, California, United States of America
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California - Los Angeles, Los Angeles, California, United States of America
| | - Philippe Lemey
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Pedro F. C. Vasconcelos
- Departamento de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua, Brazil
- Universidade do Estado do Pará, Belém, Pará, Brazil
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
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356
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Horn S, Prost S, Stiller M, Makowiecki D, Kuznetsova T, Benecke N, Pucher E, Hufthammer AK, Schouwenburg C, Shapiro B, Hofreiter M. Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe. Mol Ecol 2014; 23:1717-29. [DOI: 10.1111/mec.12691] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Susanne Horn
- Max Planck Institute for Evolutionary Anthropology; Deutscher Platz 6 Leipzig Germany
| | - Stefan Prost
- Department of Anatomy; Allan Wilson Centre for Molecular Ecology and Evolution; University of Otago; 270 Great King Street Dunedin 9054 New Zealand
- Department of Integrative Biology; University of California; 1005 Valley Life Sciences Bldg. #3140 Berkeley CA 94720-3140 USA
- Department of Biodiversity Informatics and Genetics; Swedish Museum of Natural History; Box 50007 10405 Stockholm Sweden
| | - Mathias Stiller
- Department of Ecology and Evolutionary Biology; University of California Santa Cruz; 1156 High Street Santa Cruz CA 95064 USA
| | - Daniel Makowiecki
- Institute of Archaeology; Nicolaus Copernicus University; Szosa Bydgoska 44/48 PL 87-100 Toruń Poland
| | - Tatiana Kuznetsova
- Department of Paleontology; Faculty of Geology; Moscow State University; Leninskie Gory 1 MSU Moscow 119991 Russia
| | - Norbert Benecke
- Scientific Department of the Head Office; German Archaeological Institute; Im Dol 2-6 (Haus I) D-14195 Berlin Germany
| | - Erich Pucher
- Department for Zooarchaeology; Natural History Museum Vienna; Burgring 7 A-1010 Vienna Austria
| | - Anne K. Hufthammer
- University Museum Bergen; University of Bergen; Post box 7800 5020 Bergen Norway
| | | | - Beth Shapiro
- Department of Ecology and Evolutionary Biology; University of California Santa Cruz; 1156 High Street Santa Cruz CA 95064 USA
| | - Michael Hofreiter
- Department of Biology; University of York; Wentworth Way; Heslington York YO31 7SG UK
- Evolutionary and Adaptive Genomics; Institute of Biochemistry and Biology; Faculty of Mathematics and Life Sciences; University of Potsdam; Karl-Liebknecht-Straße 24-25; 14476 Potsdam Germany
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357
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Bielejec F, Lemey P, Baele G, Rambaut A, Suchard MA. Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography. Syst Biol 2014; 63:493-504. [PMID: 24627184 PMCID: PMC4055869 DOI: 10.1093/sysbio/syu015] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Molecular phylogenetic and phylogeographic reconstructions generally assume time-homogeneous substitution processes. Motivated by computational convenience, this assumption sacrifices biological realism and offers little opportunity to uncover the temporal dynamics in evolutionary histories. Here, we propose an evolutionary approach that explicitly relaxes the time-homogeneity assumption by allowing the specification of different infinitesimal substitution rate matrices across different time intervals, called epochs, along the evolutionary history. We focus on an epoch model implementation in a Bayesian inference framework that offers great modeling flexibility in drawing inference about any discrete data type characterized as a continuous-time Markov chain, including phylogeographic traits. To alleviate the computational burden that the additional temporal heterogeneity imposes, we adopt a massively parallel approach that achieves both fine- and coarse-grain parallelization of the computations across branches that accommodate epoch transitions, making extensive use of graphics processing units. Through synthetic examples, we assess model performance in recovering evolutionary parameters from data generated according to different evolutionary scenarios that comprise different numbers of epochs for both nucleotide and codon substitution processes. We illustrate the usefulness of our inference framework in two different applications to empirical data sets: the selection dynamics on within-host HIV populations throughout infection and the seasonality of global influenza circulation. In both cases, our epoch model captures key features of temporal heterogeneity that remained difficult to test using ad hoc procedures. [Bayesian inference; BEAGLE; BEAST; Epoch Model; phylogeography; Phylogenetics.]
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Affiliation(s)
- Filip Bielejec
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium;
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom;Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Marc A Suchard
- Departments of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, 90095, USA;Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA
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358
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Kuzmina NA, Lemey P, Kuzmin IV, Mayes BC, Ellison JA, Orciari LA, Hightower D, Taylor ST, Rupprecht CE. The phylogeography and spatiotemporal spread of south-central skunk rabies virus. PLoS One 2013; 8:e82348. [PMID: 24312657 PMCID: PMC3849458 DOI: 10.1371/journal.pone.0082348] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 10/25/2013] [Indexed: 12/25/2022] Open
Abstract
The south-central skunk rabies virus (SCSK) is the most broadly distributed terrestrial viral lineage in North America. Skunk rabies has not been efficiently targeted by oral vaccination campaigns and represents a natural system of pathogen invasion, yielding insights to rabies emergence. In the present study we reconstructed spatiotemporal spread of SCSK in the whole territory of its circulation using a combination of Bayesian methods. The analysis based on 241 glycoprotein gene sequences demonstrated that SCSK is much more divergent phylogenetically than was appreciated previously. According to our analyses the SCSK originated in the territory of Texas ~170 years ago, and spread geographically during the following decades. The wavefront velocity in the northward direction was significantly greater than in the eastward and westward directions. Rivers (except the Mississippi River and Rio Grande River) did not constitute significant barriers for epizootic spread, in contrast to deserts and mountains. The mean dispersal rate of skunk rabies was lower than that of the raccoon and fox rabies. Viral lineages circulate in their areas with limited evidence of geographic spread during decades. However, spatiotemporal reconstruction shows that after a long period of stability the dispersal rate and wavefront velocity of SCSK are increasing. Our results indicate that there is a need to develop control measures for SCSK, and suggest how such measure can be implemented most efficiently. Our approach can be extrapolated to other rabies reservoirs and used as a tool for investigation of epizootic patterns and planning interventions towards disease elimination.
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Affiliation(s)
- Natalia A. Kuzmina
- Rabies Program, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
| | - Philippe Lemey
- Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Ivan V. Kuzmin
- Rabies Program, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Bonny C. Mayes
- Zoonosis Control Branch, Texas Department of State Health Services, Austin, Texas, United States of America
| | - James A. Ellison
- Rabies Program, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Lillian A. Orciari
- Rabies Program, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Dillon Hightower
- Rabies Program, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Steven T. Taylor
- Rabies Program, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Charles E. Rupprecht
- Rabies Program, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Department of Epidemiology and Public Health, Ross University School of Veterinary Medicine, Basseterre, St. Kitts, West Indies
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359
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Thalmann O, Shapiro B, Cui P, Schuenemann VJ, Sawyer SK, Greenfield DL, Germonpre MB, Sablin MV, Lopez-Giraldez F, Domingo-Roura X, Napierala H, Uerpmann HP, Loponte DM, Acosta AA, Giemsch L, Schmitz RW, Worthington B, Buikstra JE, Druzhkova A, Graphodatsky AS, Ovodov ND, Wahlberg N, Freedman AH, Schweizer RM, Koepfli KP, Leonard JA, Meyer M, Krause J, Paabo S, Green RE, Wayne RK. Complete Mitochondrial Genomes of Ancient Canids Suggest a European Origin of Domestic Dogs. Science 2013; 342:871-4. [DOI: 10.1126/science.1243650] [Citation(s) in RCA: 348] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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