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DeAngelis H, Scarpino SV, Althouse BM. Modeling the Effects of Priming With the Whole-Cell Bordetella Pertussis Vaccine-Reply. JAMA Pediatr 2016; 170:1229. [PMID: 27802485 DOI: 10.1001/jamapediatrics.2016.2819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
| | - Samuel V Scarpino
- Santa Fe Institute, Santa Fe, New Mexico3University of Vermont, Burlington
| | - Benjamin M Althouse
- New Mexico State University, Las Cruces2Santa Fe Institute, Santa Fe, New Mexico4Institute for Disease Modeling, Bellevue, Washington5University of Washington, Seattle
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DeAngelis H, Scarpino SV, Fitzpatrick MC, Galvani AP, Althouse BM. Epidemiological and Economic Effects of Priming With the Whole-Cell Bordetella pertussis Vaccine. JAMA Pediatr 2016; 170:459-65. [PMID: 27018830 PMCID: PMC6859645 DOI: 10.1001/jamapediatrics.2016.0047] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
IMPORTANCE Current acellular pertussis vaccines may not protect against transmission of Bordetella pertussis. OBJECTIVE To assess whether a priming dose of whole-cell pertussis (wP) vaccine is cost-effective at reducing pertussis infection in infants. DESIGN, SETTING, AND PARTICIPANTS Mathematical model of pertussis transmission fit to US incidence data in a simulation of the US population. In this simulation study conducted from June 2014 to May 2015, the population was divided into 9 age groups corresponding to the current pertussis vaccination schedule and fit to 2012 pertussis incidence. INTERVENTIONS Inclusion of a priming dose of wP vaccine into the current acellular pertussis vaccination schedule. MAIN OUTCOMES AND MEASURES Reductions in symptomatic pertussis incidence by age group, increases in wP vaccine-related adverse effects, and quality-adjusted life-years owing to changing vaccine schedule. RESULTS Switching to a wP-priming vaccination strategy could reduce whooping cough incidence by up to 95% (95% CI, 91-98), including 96% (95% CI, 92-98) fewer infections in neonates. Although there may be an increase in the number of vaccine adverse effects, we nonetheless estimate a 95% reduction in quality-adjusted life-years lost with a switch to the combined strategy and a cost reduction of 94% (95% CI, 91-97), saving more than $142 million annually. CONCLUSIONS AND RELEVANCE Our results suggest that an alternative vaccination schedule including 1 dose of wP vaccine may be highly cost-effective and ethically preferred until next-generation pertussis vaccines become available.
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Affiliation(s)
| | | | - Meagan C. Fitzpatrick
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, New Haven, Connecticut
| | - Alison P. Galvani
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, New Haven, Connecticut; Yale Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut
| | - Benjamin M. Althouse
- New Mexico State University, Las Cruces; Santa Fe Institute, Santa Fe, New Mexico
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Fitzpatrick MC, Wenzel NS, Scarpino SV, Althouse BM, Atkins KE, Galvani AP, Townsend JP. Cost-effectiveness of next-generation vaccines: The case of pertussis. Vaccine 2016; 34:3405-11. [PMID: 27087151 DOI: 10.1016/j.vaccine.2016.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 04/01/2016] [Accepted: 04/04/2016] [Indexed: 12/19/2022]
Abstract
Despite steady vaccination coverage rates, pertussis incidence in the United States has continued to rise. This public health challenge has motivated calls for the development of a new vaccine with greater efficacy and duration of protection. Any next-generation vaccine would likely come at a higher cost, and must provide sufficient health benefits beyond those provided by the current vaccine in order to be deemed cost-effective. Using an age-structured transmission model of pertussis, we quantified the health and economic benefits of a next-generation vaccine that would enhance either the efficacy or duration of protection of the childhood series, the duration of the adult booster, or a combination. We developed a metric, the maximum cost-effective price increase (MCPI), to compare the potential value of such improvements. The MCPI estimates the per-dose price increase that would maintain the cost-effectiveness of pertussis vaccination. We evaluated the MCPI across a range of potential single and combined improvements to the pertussis vaccine. As an upper bound, we found that a next-generation vaccine which could achieve perfect efficacy for the childhood series would permit an MCPI of $18 per dose (95% CI: $12-$31). Pertussis vaccine improvements that extend the duration of protection to an average of 75 years would allow for an MCPI of $22 per dose for the childhood series (CI: $10-$33) or $12 for the adult booster (CI: $4-$18). Despite the short duration of the adult booster, improvements to the childhood series could be more valuable than improvements to the adult booster. Combining improvements in both efficacy and duration, a childhood series with perfect efficacy and average duration of 75 years would permit an MCPI of $39 per dose, the highest of any scenario evaluated. Our results highlight the utility of the MCPI metric in evaluating potential vaccines or other interventions when prices are unknown.
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Affiliation(s)
- Meagan C Fitzpatrick
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, New Haven, CT, USA.
| | - Natasha S Wenzel
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, New Haven, CT, USA; Center for Inference and Dynamics of Infectious Disease, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Benjamin M Althouse
- Santa Fe Institute, Santa Fe, NM, USA; Institute for Disease Modeling, Bellevue, WA, USA; New Mexico State University, Las Cruces, NM, USA
| | - Katherine E Atkins
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Alison P Galvani
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, New Haven, CT, USA
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
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Shrestha M, Scarpino SV, Moore C. Message-passing approach for recurrent-state epidemic models on networks. Phys Rev E Stat Nonlin Soft Matter Phys 2015; 92:022821. [PMID: 26382468 DOI: 10.1103/physreve.92.022821] [Citation(s) in RCA: 15] [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] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Indexed: 05/25/2023]
Abstract
Epidemic processes are common out-of-equilibrium phenomena of broad interdisciplinary interest. Recently, dynamic message-passing (DMP) has been proposed as an efficient algorithm for simulating epidemic models on networks, and in particular for estimating the probability that a given node will become infectious at a particular time. To date, DMP has been applied exclusively to models with one-way state changes, as opposed to models like SIS and SIRS where nodes can return to previously inhabited states. Because many real-world epidemics can exhibit such recurrent dynamics, we propose a DMP algorithm for complex, recurrent epidemic models on networks. Our approach takes correlations between neighboring nodes into account while preventing causal signals from backtracking to their immediate source, and thus avoids "echo chamber effects" where a pair of adjacent nodes each amplify the probability that the other is infectious. We demonstrate that this approach well approximates results obtained from Monte Carlo simulation and that its accuracy is often superior to the pair approximation (which also takes second-order correlations into account). Moreover, our approach is more computationally efficient than the pair approximation, especially for complex epidemic models: the number of variables in our DMP approach grows as 2mk where m is the number of edges and k is the number of states, as opposed to mk^{2} for the pair approximation. We suspect that the resulting reduction in computational effort, as well as the conceptual simplicity of DMP, will make it a useful tool in epidemic modeling, especially for high-dimensional inference tasks.
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Affiliation(s)
- Munik Shrestha
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87131, USA and Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, New Mexico 87501, USA
| | - Samuel V Scarpino
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, New Mexico 87501, USA
| | - Cristopher Moore
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, New Mexico 87501, USA
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Abstract
BACKGROUND The recent increase in whooping cough incidence (primarily caused by Bordetella pertussis) presents a challenge to both public health practitioners and scientists trying to understand the mechanisms behind its resurgence. Three main hypotheses have been proposed to explain the resurgence: 1) waning of protective immunity from vaccination or natural infection over time, 2) evolution of B. pertussis to escape protective immunity, and 3) low vaccine coverage. Recent studies have suggested a fourth mechanism: asymptomatic transmission from individuals vaccinated with the currently used acellular B. pertussis vaccines. METHODS Using wavelet analyses of B. pertussis incidence in the United States (US) and United Kingdom (UK) and a phylodynamic analysis of 36 clinical B. pertussis isolates from the US, we find evidence in support of asymptomatic transmission of B. pertussis. Next, we examine the clinical, public health, and epidemiological consequences of asymptomatic B. pertussis transmission using a mathematical model. RESULTS We find that: 1) the timing of changes in age-specific attack rates observed in the US and UK are consistent with asymptomatic transmission; 2) the phylodynamic analysis of the US sequences indicates more genetic diversity in the overall bacterial population than would be suggested by the observed number of infections, a pattern expected with asymptomatic transmission; 3) asymptomatic infections can bias assessments of vaccine efficacy based on observations of B. pertussis-free weeks; 4) asymptomatic transmission can account for the observed increase in B. pertussis incidence; and 5) vaccinating individuals in close contact with infants too young to receive the vaccine ("cocooning" unvaccinated children) may be ineffective. CONCLUSIONS Although a clear role for the previously suggested mechanisms still exists, asymptomatic transmission is the most parsimonious explanation for many of the observations surrounding the resurgence of B. pertussis in the US and UK. These results have important implications for B. pertussis vaccination policy and present a complicated scenario for achieving herd immunity and B. pertussis eradication.
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Althouse BM, Scarpino SV, Meyers LA, Ayers JW, Bargsten M, Baumbach J, Brownstein JS, Castro L, Clapham H, Cummings DAT, Del Valle S, Eubank S, Fairchild G, Finelli L, Generous N, George D, Harper DR, Hébert-Dufresne L, Johansson MA, Konty K, Lipsitch M, Milinovich G, Miller JD, Nsoesie EO, Olson DR, Paul M, Polgreen PM, Priedhorsky R, Read JM, Rodríguez-Barraquer I, Smith DJ, Stefansen C, Swerdlow DL, Thompson D, Vespignani A, Wesolowski A. Enhancing disease surveillance with novel data streams: challenges and opportunities. EPJ Data Sci 2015; 4:17. [PMID: 27990325 PMCID: PMC5156315 DOI: 10.1140/epjds/s13688-015-0054-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Novel data streams (NDS), such as web search data or social media updates, hold promise for enhancing the capabilities of public health surveillance. In this paper, we outline a conceptual framework for integrating NDS into current public health surveillance. Our approach focuses on two key questions: What are the opportunities for using NDS and what are the minimal tests of validity and utility that must be applied when using NDS? Identifying these opportunities will necessitate the involvement of public health authorities and an appreciation of the diversity of objectives and scales across agencies at different levels (local, state, national, international). We present the case that clearly articulating surveillance objectives and systematically evaluating NDS and comparing the performance of NDS to existing surveillance data and alternative NDS data is critical and has not sufficiently been addressed in many applications of NDS currently in the literature.
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Affiliation(s)
| | | | - Lauren Ancel Meyers
- Santa Fe Institute, Santa Fe, NM USA
- The University of Texas at Austin, Austin, TX USA
| | | | | | | | - John S Brownstein
- Children’s Hospital Informatics Program, Boston Children’s Hospital, Boston, MA USA
- Department of Pediatrics, Harvard Medical School, Boston, MA USA
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC Canada
| | - Lauren Castro
- Defense Systems and Analysis Division, Los Alamos National Laboratory, Los Alamos, NM USA
| | - Hannah Clapham
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Derek AT Cummings
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Sara Del Valle
- Defense Systems and Analysis Division, Los Alamos National Laboratory, Los Alamos, NM USA
| | - Stephen Eubank
- Virginia BioInformatics Institute and Department of Population Health Sciences, Virginia Tech, Blacksburg, VA USA
| | - Geoffrey Fairchild
- Defense Systems and Analysis Division, Los Alamos National Laboratory, Los Alamos, NM USA
| | - Lyn Finelli
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Nicholas Generous
- Defense Systems and Analysis Division, Los Alamos National Laboratory, Los Alamos, NM USA
| | - Dylan George
- Biomedical Advanced Research and Development Authority (BARDA), Assistant Secretary for Preparedness and Response (ASPR), Department of Health and Human Services, Washington, DC USA
| | - David R Harper
- Chatham House, 10 St James’s Square, London, SW1Y 4LE UK
| | | | - Michael A Johansson
- Division of Vector-Borne Diseases, NCEZID, Centers for Disease Control and Prevention, San Juan, PR USA
| | - Kevin Konty
- Division of Epidemiology, New York City Department of Health and Mental Hygiene, New York, NY USA
| | - Marc Lipsitch
- Communicable Disease Dynamics, Harvard School of Public Health, Boston, MA USA
| | - Gabriel Milinovich
- School of Population Health, The University of Queensland, Brisbane, QLD Australia
| | - Joseph D Miller
- Division of Vector-Borne Diseases, NCEZID, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Elaine O Nsoesie
- Children’s Hospital Informatics Program, Boston Children’s Hospital, Boston, MA USA
- Department of Pediatrics, Harvard Medical School, Boston, MA USA
| | - Donald R Olson
- Division of Epidemiology, New York City Department of Health and Mental Hygiene, New York, NY USA
| | - Michael Paul
- Department of Computer Science, Johns Hopkins University, Baltimore, MD USA
| | | | - Reid Priedhorsky
- Defense Systems and Analysis Division, Los Alamos National Laboratory, Los Alamos, NM USA
| | - Jonathan M Read
- Department of Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Liverpool, CH64 7TE UK
- Health Protection Research Unit in Emerging and Zoonotic Infections, NIHR, Liverpool, L69 7BE UK
| | | | - Derek J Smith
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ UK
| | | | - David L Swerdlow
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA USA
| | | | - Alessandro Vespignani
- Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA
| | - Amy Wesolowski
- Communicable Disease Dynamics, Harvard School of Public Health, Boston, MA USA
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Scarpino SV, Iamarino A, Wells C, Yamin D, Ndeffo-Mbah M, Wenzel NS, Fox SJ, Nyenswah T, Altice FL, Galvani AP, Meyers LA, Townsend JP. Epidemiological and viral genomic sequence analysis of the 2014 ebola outbreak reveals clustered transmission. Clin Infect Dis 2014; 60:1079-82. [PMID: 25516185 DOI: 10.1093/cid/ciu1131] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [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: 01/09/2023] Open
Abstract
Using Ebolavirus genomic and epidemiological data, we conducted the first joint analysis in which both data types were used to fit dynamic transmission models for an ongoing outbreak. Our results indicate that transmission is clustered, highlighting a potential bias in medical demand forecasts, and provide the first empirical estimate of underreporting.
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Affiliation(s)
| | - Atila Iamarino
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, Brazil
| | - Chad Wells
- Yale Center for Infectious Disease Modeling and Analysis Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut
| | - Dan Yamin
- Yale Center for Infectious Disease Modeling and Analysis Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut
| | - Martial Ndeffo-Mbah
- Yale Center for Infectious Disease Modeling and Analysis Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut
| | | | - Spencer J Fox
- Department of Integrative Biology, The University of Texas at Austin
| | | | - Frederick L Altice
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut Section of Infectious Diseases, Yale University School of Medicine
| | - Alison P Galvani
- Yale Center for Infectious Disease Modeling and Analysis Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut Program in Computational Biology and Bioinformatics Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut
| | - Lauren Ancel Meyers
- Santa Fe Institute, New Mexico Department of Integrative Biology, The University of Texas at Austin
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut Program in Computational Biology and Bioinformatics Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut
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Halloran ME, Vespignani A, Bharti N, Feldstein LR, Alexander KA, Ferrari M, Shaman J, Drake JM, Porco T, Eisenberg JNS, Del Valle SY, Lofgren E, Scarpino SV, Eisenberg MC, Gao D, Hyman JM, Eubank S, Longini IM. Ebola: mobility data. Science 2014; 346:433. [PMID: 25342792 PMCID: PMC4408607 DOI: 10.1126/science.346.6208.433-a] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- M Elizabeth Halloran
- Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA 98109, USA. Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.
| | | | - Nita Bharti
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Leora R Feldstein
- Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA 98109, USA. Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - K A Alexander
- Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Matthew Ferrari
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Jeffrey Shaman
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - John M Drake
- Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
| | - Travis Porco
- Francis I. Proctor Foundation, University of California, San Francisco, CA 94143, USA
| | | | | | - Eric Lofgren
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | | | - Marisa C Eisenberg
- Department of Epidemiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daozhou Gao
- Francis I. Proctor Foundation, University of California, San Francisco, CA 94143, USA
| | - James M Hyman
- Department of Mathematics, Tulane University, New Orleans, LA 70118, USA
| | - Stephen Eubank
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. Department of Population Health Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Ira M Longini
- Department of Biostatistics, University of Florida, Gainesville, FL 32611, USA
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Abstract
Polyploidy, or whole genome duplication, has been an important feature of eukaryotic evolution. This is especially true in flowering plants, where all extant angiosperms have descended from polyploid species. Here we present a broad comparative analysis of the effect of polyploidy on flowering plant diversity. We examine the widely held hypothesis that polyploid flowering plants generate more diversity than their diploid counterparts, by fitting stochastic birth/death models to observed ploidal frequency data from 60 extant angiosperm genera. Our results suggest the opposite, that diploids speciate at higher rates than polyploids, through a combination of simple diploid speciation and tetraploidy. Importantly, the estimated diploid advantage stemmed primarily from a higher rate of polyploidization in diploids than polyploids. Our model is also able to account for the empirically observed correlation between polyploidy and species richness without assuming that polyploids have a speciation advantage over diploids.
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Affiliation(s)
- Samuel V Scarpino
- Department of Integrative Biology, University of Texas, Austin, Texas 78712
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Scarpino SV, Hunt PJ, Garcia-De-Leon FJ, Juenger TE, Schartl M, Kirkpatrick M. Evolution of a genetic incompatibility in the genus Xiphophorus. Mol Biol Evol 2013; 30:2302-10. [PMID: 23894140 DOI: 10.1093/molbev/mst127] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [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: 12/16/2022] Open
Abstract
Genetic incompatibilities are commonly observed between hybridizing species. Although this type of isolating mechanism has received considerable attention, we have few examples describing how genetic incompatibilities evolve. We investigated the evolution of two loci involved in a classic example of a Bateson-Dobzhansky-Muller (BDM) incompatibility in Xiphophorus, a genus of freshwater fishes from northern Central America. Hybrids develop a lethal melanoma due to the interaction of two loci, an oncogene and its repressor. We cloned and sequenced the putative repressor locus in 25 Xiphophorus species and an outgroup species, and determined the status of the oncogene in those species from the literature. Using phylogenetic analyses, we find evidence that a repeat region in the proximal promoter of the repressor is coevolving with the oncogene. The data support a hypothesis that departs from the standard BDM model: it appears the alleles that cause the incompatibilities have coevolved simultaneously within lineages, rather than in allopatric or temporal isolation.
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Otto SP, Pannell JR, Peichel CL, Ashman TL, Charlesworth D, Chippindale AK, Delph LF, Guerrero RF, Scarpino SV, McAllister BF. About PAR: the distinct evolutionary dynamics of the pseudoautosomal region. Trends Genet 2012; 27:358-67. [PMID: 21962971 DOI: 10.1016/j.tig.2011.05.001] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 05/03/2011] [Accepted: 05/04/2011] [Indexed: 01/05/2023]
Abstract
Sex chromosomes differ from other chromosomes in the striking divergence they often show in size, structure, and gene content. Not only do they possess genes controlling sex determination that are restricted to either the X or Y (or Z or W) chromosomes, but in many taxa they also include recombining regions. In these 'pseudoautosomal regions' (PARs), sequence homology is maintained by meiotic pairing and exchange in the heterogametic sex. PARs are unique genomic regions, exhibiting some features of autosomes, but they are also influenced by their partial sex linkage. Here we review the distribution and structure of PARs among animals and plants, the theoretical predictions concerning their evolutionary dynamics, the reasons for their persistence, and the diversity and content of genes that reside within them. It is now clear that the evolution of the PAR differs in important ways from that of genes in either the non-recombining regions of sex chromosomes or the autosomes.
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Affiliation(s)
- Sarah P Otto
- Department of Zoology, 6270 University Boulevard, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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Delph LF, Andicoechea J, Steven JC, Herlihy CR, Scarpino SV, Bell DL. Environment-dependent intralocus sexual conflict in a dioecious plant. New Phytol 2011; 192:542-552. [PMID: 21726233 DOI: 10.1111/j.1469-8137.2011.03811.x] [Citation(s) in RCA: 46] [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] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Intralocus sexual conflict is a form of conflict that does not involve direct interactions between males and females. It arises when selection on a shared trait with a common genetic basis differs between the sexes. Environmental factors, such as resource availability, may influence the expression and evolutionary outcome of such conflict. We quantified the genetic variance-covariance matrix, G, for both sexes of Silene latifolia for floral and leaf traits, as well as the between-sex matrix, B. We also quantified selection on the sexes via survival for 2 yr in four natural populations that varied in water availability. Environment-dependent intralocus sexual conflict exists for specific leaf area, a trait that is genetically correlated between the sexes. Males experienced significant negative selection, but only in populations with relatively limited water availability. Females experienced weakly positive or significant stabilizing selection on the same trait. Specific leaf area is genetically correlated with flower size and number, which are sexually dimorphic in this species. The extent of intralocus sexual conflict varied with the environment. Resolution of such conflict is likely to be confounded, given that specific leaf area is highly genetically integrated with other traits that are also divergent between the sexes.
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Affiliation(s)
- Lynda F Delph
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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63
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Pourbohloul B, Ahued A, Davoudi B, Meza R, Meyers LA, Skowronski DM, Villaseñor I, Galván F, Cravioto P, Earn DJD, Dushoff J, Fisman D, Edmunds WJ, Hupert N, Scarpino SV, Trujillo J, Lutzow M, Morales J, Contreras A, Chávez C, Patrick DM, Brunham RC. Initial human transmission dynamics of the pandemic (H1N1) 2009 virus in North America. Influenza Other Respir Viruses 2011; 3:215-22. [PMID: 19702583 PMCID: PMC3122129 DOI: 10.1111/j.1750-2659.2009.00100.x] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Background Between 5 and 25 April 2009, pandemic (H1N1) 2009 caused a substantial, severe outbreak in Mexico, and subsequently developed into the first global pandemic in 41 years. We determined the reproduction number of pandemic (H1N1) 2009 by analyzing the dynamics of the complete case series in Mexico City during this early period. Methods We analyzed three mutually exclusive datasets from Mexico City Distrito Federal which constituted all suspect cases from 15 March to 25 April: confirmed pandemic (H1N1) 2009 infections, non‐pandemic influenza A infections and patients who tested negative for influenza. We estimated the initial reproduction number from 497 suspect cases identified prior to 20 April, using a novel contact network methodology incorporating dates of symptom onset and hospitalization, variation in contact rates, extrinsic sociological factors, and uncertainties in underreporting and disease progression. We tested the robustness of this estimate using both the subset of laboratory‐confirmed pandemic (H1N1) 2009 infections and an extended case series through 25 April, adjusted for suspected ascertainment bias. Results The initial reproduction number (95% confidence interval range) for this novel virus is 1·51 (1·32–1·71) based on suspected cases and 1·43 (1·29–1·57) based on confirmed cases before 20 April. The longer time series (through 25 April) yielded a higher estimate of 2·04 (1·84–2·25), which reduced to 1·44 (1·38–1·51) after correction for ascertainment bias. Conclusions The estimated transmission characteristics of pandemic (H1N1) 2009 suggest that pharmaceutical and non‐pharmaceutical mitigation measures may appreciably limit its spread prior the development of an effective vaccine.
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Affiliation(s)
- Babak Pourbohloul
- Division of Mathematical Modeling, British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada.
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Caillaud D, Crofoot MC, Scarpino SV, Jansen PA, Garzon-Lopez CX, Winkelhagen AJS, Bohlman SA, Walsh PD. Modeling the spatial distribution and fruiting pattern of a key tree species in a neotropical forest: methodology and potential applications. PLoS One 2010; 5:e15002. [PMID: 21124927 PMCID: PMC2989912 DOI: 10.1371/journal.pone.0015002] [Citation(s) in RCA: 19] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 10/05/2010] [Indexed: 11/20/2022] Open
Abstract
Background The movement patterns of wild animals depend crucially on the spatial and temporal availability of resources in their habitat. To date, most attempts to model this relationship were forced to rely on simplified assumptions about the spatiotemporal distribution of food resources. Here we demonstrate how advances in statistics permit the combination of sparse ground sampling with remote sensing imagery to generate biological relevant, spatially and temporally explicit distributions of food resources. We illustrate our procedure by creating a detailed simulation model of fruit production patterns for Dipteryx oleifera, a keystone tree species, on Barro Colorado Island (BCI), Panama. Methodology and Principal Findings Aerial photographs providing GPS positions for large, canopy trees, the complete census of a 50-ha and 25-ha area, diameter at breast height data from haphazardly sampled trees and long-term phenology data from six trees were used to fit 1) a point process model of tree spatial distribution and 2) a generalized linear mixed-effect model of temporal variation of fruit production. The fitted parameters from these models are then used to create a stochastic simulation model which incorporates spatio-temporal variations of D. oleifera fruit availability on BCI. Conclusions and Significance We present a framework that can provide a statistical characterization of the habitat that can be included in agent-based models of animal movements. When environmental heterogeneity cannot be exhaustively mapped, this approach can be a powerful alternative. The results of our model on the spatio-temporal variation in D. oleifera fruit availability will be used to understand behavioral and movement patterns of several species on BCI.
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Affiliation(s)
- Damien Caillaud
- Section of Integrative Biology, University of Texas at Austin, Austin, Texas, USA.
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