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Neal A, Sassi J, Vardo-Zalik A. Drought correlates with reduced infection complexity and possibly prevalence in a decades-long study of the lizard malaria parasite Plasmodium mexicanum. PeerJ 2023; 11:e14908. [PMID: 36860770 PMCID: PMC9969858 DOI: 10.7717/peerj.14908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 01/25/2023] [Indexed: 03/03/2023] Open
Abstract
Microparasites often exist as a collection of genetic 'clones' within a single host (termed multi-clonal, or complex, infections). Malaria parasites are no exception, with complex infections playing key roles in parasite ecology. Even so, we know little about what factors govern the distribution and abundance of complex infections in natural settings. Utilizing a natural dataset that spans more than 20 years, we examined the effects of drought conditions on infection complexity and prevalence in the lizard malaria parasite Plasmodium mexicanum and its vertebrate host, the western fence lizard, Sceloporus occidentalis. We analyzed data for 14,011 lizards sampled from ten sites over 34 years with an average infection rate of 16.2%. Infection complexity was assessed for 546 infected lizards sampled during the most recent 20 years. Our data illustrate significant, negative effects of drought-like conditions on infection complexity, with infection complexity expected to increase by a factor of 2.27 from the lowest to highest rainfall years. The relationship between rainfall and parasite prevalence is somewhat more ambiguous; when prevalence is modeled over the full range in years, a 50% increase in prevalence is predicted between the lowest and highest rainfall years, but this trend is not apparent or is reversed when data are analyzed over a shorter timeframe. To our knowledge, this is the first reported evidence for drought affecting the abundance of multi-clonal infections in malaria parasites. It is not yet clear what mechanism might connect drought with infection complexity, but the correlation we observed suggests that additional research on how drought influences parasite features like infection complexity, transmission rates and within-host competition may be worthwhile.
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Affiliation(s)
- Allison Neal
- Norwich University, Northfield, VT, United States
| | - Joshua Sassi
- Norwich University, Northfield, VT, United States
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Neal AT. Distribution of clones among hosts for the lizard malaria parasite Plasmodium mexicanum. PeerJ 2021; 9:e12448. [PMID: 34760403 PMCID: PMC8570175 DOI: 10.7717/peerj.12448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 10/18/2021] [Indexed: 11/26/2022] Open
Abstract
Background Malaria parasites reproduce asexually, leading to the production of large numbers of genetically identical parasites, here termed a clonal line or clone. Infected hosts may harbor one or more clones, and the number of clones in a host is termed multiplicity of infection (MOI). Understanding the distribution of parasite clones among hosts can shed light on the processes shaping this distribution and is important for modeling MOI. Here, I determine whether the distribution of clones of the lizard malaria parasite Plasmodium mexicanum differ significantly from statistical distributions commonly used to model MOI and logical extensions of these models. Methods The number of clones per infection was assessed using four microsatellite loci with the maximum number of alleles at any one locus used as a simple estimate of MOI for each infection. I fit statistical models (Poisson, negative binomial, zero-inflated models) to data from four individual sites to determine a best fit model. I also simulated the number of alleles per locus using an unbiased estimate of MOI to determine whether the simple (but potentially biased) method I used to estimate MOI influenced model fit. Results The distribution of clones among hosts at individual sites differed significantly from traditional Poisson and negative binomial distributions, but not from zero-inflated modifications of these distributions. A consistent excess of two-clone infections and shortage of one-clone infections relative to all fit distributions was also observed. Any bias introduced by the simple method for estimating of MOI did not appear to qualitatively alter the results. Conclusions The statistical distributions used to model MOI are typically zero-truncated; truncating the Poisson or zero-inflated Poisson yield the same distribution, so the reasonable fit of the zero-inflated Poisson to the data suggests that the use of the zero-truncated Poisson in modeling is adequate. The improved fit of zero-inflated distributions relative to standard distributions may suggest that only a portion of the host population is located in areas suitable for transmission even at small sites (<1 ha). Collective transmission of clones and premunition may also contribute to deviations from standard distributions.
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Affiliation(s)
- Allison T Neal
- Department of Biology, Norwich University, Northfield, VT, United States of America
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Genetic Variations of the Parasitic Dinoflagellate Hematodinium Infecting Cultured Marine Crustaceans in China. Protist 2016; 167:597-609. [DOI: 10.1016/j.protis.2016.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 09/09/2016] [Accepted: 10/08/2016] [Indexed: 12/24/2022]
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de Souza AM, de Araújo FCF, Fontes CJF, Carvalho LH, de Brito CFA, de Sousa TN. Multiple-clone infections of Plasmodium vivax: definition of a panel of markers for molecular epidemiology. Malar J 2015; 14:330. [PMID: 26303668 PMCID: PMC4548710 DOI: 10.1186/s12936-015-0846-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 08/11/2015] [Indexed: 11/10/2022] Open
Abstract
Background Plasmodium vivax infections commonly contain multiple genetically distinct parasite clones. The detection of multiple-clone infections depends on several factors, such as the accuracy of the genotyping method, and the type and number of the molecular markers analysed. Characterizing the multiplicity of infection has broad implications that range from population genetic studies of the parasite to malaria treatment and control. This study compared and evaluated the efficiency of neutral and non-neutral markers that are widely used in studies of molecular epidemiology to detect the multiplicity of P. vivax infection. Methods The performance of six markers was evaluated using 11 mixtures of DNA with well-defined proportions of two different parasite genotypes for each marker. These mixtures were generated by mixing cloned PCR products or patient-derived genomic DNA. In addition, 51 samples of natural infections from the Brazil were genotyped for all markers. The PCR-capillary electrophoresis-based method was used to permit direct comparisons among the markers. The criteria for differentiating minor peaks from artifacts were also evaluated. Results The analysis of DNA mixtures showed that the tandem repeat MN21 and the polymorphic blocks 2 (msp1B2) and 10 (msp1B10) of merozoite surface protein-1 allowed for the estimation of the expected ratio of both alleles in the majority of preparations. Nevertheless, msp1B2 was not able to detect the majority of multiple-clone infections in field samples; it identified only 6 % of these infections. The merozoite surface protein-3 alpha and microsatellites (PvMS6 and PvMS7) did not accurately estimate the relative clonal proportions in artificial mixtures, but the microsatellites performed well in detecting natural multiple-clone infections. Notably, the use of a less stringent criterion to score rare alleles significantly increased the sensitivity of the detection of multi-clonal infections. Conclusions Depending on the type of marker used, a considerable amplification bias was observed, which may have serious implications for the characterization of the complexity of a P. vivax infection. Based on the performance of markers in artificial mixtures of DNA and natural infections, a minimum panel of four genetic markers (PvMS6, PvMS7, MN21, and msp1B10) was defined, and these markers are highly informative regarding the genetic variability of P. vivax populations. Electronic supplementary material The online version of this article (doi:10.1186/s12936-015-0846-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aracele M de Souza
- Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil.
| | - Flávia C F de Araújo
- Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil.
| | - Cor J F Fontes
- Hospital Julio Muller, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil.
| | - Luzia H Carvalho
- Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil.
| | - Cristiana F A de Brito
- Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil.
| | - Taís N de Sousa
- Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil.
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Juliano JJ, Barnett E, Parobek CM, Taylor SM, Meshnick SR, Stone S, Chang E, Fong S, Huang L. Use of Oropharyngeal Washes to Diagnose and Genotype Pneumocystis jirovecii. Open Forum Infect Dis 2015; 2:ofv080. [PMID: 26180832 PMCID: PMC4498285 DOI: 10.1093/ofid/ofv080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 06/01/2015] [Indexed: 11/13/2022] Open
Abstract
Pneumocystis jirovecii is a symbiotic respiratory fungus that presents in 2 clinical forms: pneumonia in immunocompromised patients or colonization, defined by the presence of the organism without associated clinical symptoms. Currently, diagnosis requires invasive bronchoscopy, which may not be available in some settings and is inappropriate for detecting colonization in healthy individuals. Noninvasive diagnostic techniques and molecular strain typing tools that can be used on these samples are critical for conducting studies to better understand transmission. We evaluated 2 real-time polymerase chain reaction (PCR) assays targeting dihydropteroate synthase and the major surface glycoprotein for detection in 77 oropharyngeal washes (OPWs) from 43 symptomatic human immunodeficiency virus-infected patients who underwent bronchoscopy. We also evaluated the ability of a new microsatellite (MS) genotyping panel to strain type infections from these samples. Each PCR used individually provided a high sensitivity (>80%) for detection of pneumonia but a modest specificity (<70%). When used in combination, specificity was increased to 100% with a drop in sensitivity (74%). Concentration of organisms by PCR in the OPW tended to be lower in colonized individuals compared with those with pneumonia, but differences in concentration could not clearly define colonization in symptomatic individuals. Oropharyngeal wash samples were genotyped using 6 MSs with ≥4 alleles successfully genotyped in the majority of colonized patients and ≥5 alleles in patients with pneumonia. The MS profile was consistent over time within patients with serial OPWs analyzed. Microsatellite genotyping on noninvasive samples may aid in studying the molecular epidemiology of this pathogen without requiring invasive diagnostic techniques.
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Affiliation(s)
- Jonathan J Juliano
- Division of Infectious Diseases ; Curriculum in Genetics and Molecular Biology , University of North Carolina School of Medicine ; Department of Epidemiology , Gillings School of Global Public Health, University of North Carolina , Chapel Hill
| | | | - Christian M Parobek
- Division of Infectious Diseases ; Curriculum in Genetics and Molecular Biology , University of North Carolina School of Medicine
| | - Steve M Taylor
- Department of Epidemiology , Gillings School of Global Public Health, University of North Carolina , Chapel Hill ; Division of Infectious Diseases and International Health , Duke University Medical Center , Durham
| | - Steven R Meshnick
- Department of Epidemiology , Gillings School of Global Public Health, University of North Carolina , Chapel Hill
| | | | | | | | - Laurence Huang
- HIV/AIDS Division ; Division of Pulmonary and Critical Care Medicine , San Francisco General Hospital, University of California
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Dynamics of clonal diversity in natural infections of the malaria parasite Plasmodium mexicanum in its free-ranging lizard host. Parasitol Res 2014; 113:2059-67. [PMID: 24647987 DOI: 10.1007/s00436-014-3854-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 03/05/2014] [Indexed: 10/25/2022]
Abstract
Within mixed-genotype infections of malaria parasites (Plasmodium), the number of genetic clones present is associated with variation in important life history traits of the infection, including virulence. Although the number of clones present is important, how the proportion of those clones varies over time is poorly known. Clonal proportions of the lizard malaria parasite, Plasmodium mexicanum, were assessed in naturally infected free-ranging lizards followed in a mark-recapture program over as long as two warm seasons, the typical life span of the lizard. Clonal proportions were determined by amplifying two microsatellite markers, a method previously verified for accuracy. Most blood samples had been stored for over a decade, so a verification test determined that these samples had not degraded. Although the environment experienced by the parasite (its host) varies over the seasons and transmission occurs over the entire warm season, 68% of infections were stable over time, harboring a single clone (37% of infections) or multiple clones changing only 1-12% maximum comparing any two samples (31% of infections). The maximum change seen in any infection (comparing any two sample periods) was only 30%. A new clone entered three infections (only once successfully), and a clone was lost in only three infections. These results mirror those seen for a previous study of experimentally induced infections that showed little change in relative proportions over time. The results of this study, the first look at how clonal proportions vary over time for any malaria parasite of a nonhuman vertebrate host for natural infections, were surprising because experimental studies show clones of P. mexicanum appear to interact, yet relative proportions of clones typically remain constant over time.
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Neal AT, Schall JJ. TESTING SEX RATIO THEORY WITH THE MALARIA PARASITEPLASMODIUM MEXICANUMIN NATURAL AND EXPERIMENTAL INFECTIONS. Evolution 2014; 68:1071-81. [DOI: 10.1111/evo.12334] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 12/05/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Allison T. Neal
- Department of Biology; University of Vermont; Burlington Vermont 05405
| | - Jos. J. Schall
- Department of Biology; University of Vermont; Burlington Vermont 05405
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Hicks ND, Schall JJ. Establishment efficiency among clones of the malaria parasite, Plasmodium mexicanum, for mixed-clone infections in its natural lizard host. J Parasitol 2013; 99:1050-5. [PMID: 23841469 DOI: 10.1645/12-72.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Within genetically diverse infections of malaria parasites ( Plasmodium spp.), the relative proportions of genetic clones in the vertebrate host's blood can influence clonal competition, transmission success, gametocyte sex ratio, and virulence. Clonal proportions depend on establishment success of each clone when they enter a new host and on subsequent differences in rates of asexual replication and clearance. Both of these life history traits could be influenced by clone genotype. To assess genetic (clonal) influences on both establishment success and later changes in relative proportion for the lizard malaria parasite Plasmodium mexicanum , 7 naturally infected fence lizards harboring a single clone of P. mexicanum served as donors to initiate replicate experimental infections containing each of the clones and combinations of 2 clones. Measured were relative establishment success of each clone, change in relative proportions over time, and rate of increase of parasite density and total parasitemia. Relative clonal proportions were determined using microsatellite markers. Rates of increase in the parasitemia and degree of change in relative proportions were not correlated, so both rapidly and slowly growing infections could show either little or substantial change in clonal proportions over time. There was a significant clone effect on establishment efficiency but not on later changes in relative proportions. These results argue for a combination of genetic and environmental (host) effects on the success of P. mexicanum clones in genetically complex infections. The maintenance of genetic variation for establishment success, but not subsequent replication rate or shifts in relative proportion, suggests trade-offs between these traits during life history evolution of malaria parasites.
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Affiliation(s)
- Nathan D Hicks
- Department of Biology, University of Vermont, Burlington, Vermont 05405
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Microsatellite loci over a thirty-three year period for a malaria parasite (Plasmodium mexicanum): bottleneck in effective population size and effect on allele frequencies. Parasitology 2012; 140:21-8. [PMID: 22948096 DOI: 10.1017/s0031182012001217] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Changes in population allele frequencies may be driven by several forces, including selection and drift, and are revealed only by sampling over many generations. Such studies, however, are rare for protist parasites. Microsatellite allele frequencies for 4 loci were followed in a population of Plasmodium mexicanum, a malaria parasite of lizards in California USA at 1 site from 1978 to 2010. Rapid turnover of the lizards indicates the parasite was studied for a minimum of 33 transmission cycles and possibly twice that number. Sample sizes ranged from 841 to 956 scored parasite clones per locus. DNA was extracted from frozen dried blood and blood removed from stained blood smears from the earliest years, and a verification study demonstrated DNA from the blood smears provided valid genetic data. Parasite prevalence and effective population size (Ne) dropped after 2000, remaining lower for the next decade. For 2 loci, allele frequencies appeared stable for the first 2 decades of the study, but changed more rapidly after the decline in prevalence. Allele frequencies changed more gradually for the other 2 loci. Genetic drift could account for changes in allele frequencies, especially after the drop in prevalence and Ne, but the force of selection could also have driven the observed patterns.
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Prevalence, diversity, and interaction patterns of avian haemosporidians in a four-year study of blackcaps in a migratory divide. Parasitology 2011; 138:824-35. [PMID: 21518466 DOI: 10.1017/s0031182011000515] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Migratory birds contribute to the movement of avian parasites between distant locations, thereby influencing parasite distribution and ecology. Here we analyse the prevalence, diversity and interaction patterns of Haemosporida parasites infecting Blackcap (Sylvia atricapilla) populations in a recently established migratory divide of southwestern Germany across 4 years. We hypothesize that the temporal and spatial isolation provided by 2 sympatric Blackcap breeding populations (migratory divide) might modify ecological interactions and thus create differences in the structure of the parasite community according to migratory route. We used a fragment of the mitochondrial DNA cytochrome b gene to determine haemosporidian haplotypes. We detected an overall infection prevalence of 70.3% (348 out of 495 blackcaps sampled from 2006 to 2009), and prevalence rates were significantly different among years and seasons. We observed a total of 27 parasite haplotypes infecting blackcaps, from them 6 new rare Haemoproteus haplotypes were found in 2 mixed infections. H. parabelopolskyi haplotypes SYAT01 (35.7%) and SYAT02 (20.8%) comprised most of the infections. An association analysis suggests that SYAT01 and SYAT02 are interacting negatively, implying that they are either competing directly for host resources, or indirectly by eliciting a cross-immune response. Molecular data show no clear difference between the parasite communities infecting blackcaps with different migratory routes, despite some temporal and spatial isolation between the two sympatric blackcap populations.
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Ford AF, Schall JJ. Relative clonal proportions over time in mixed-genotype infections of the lizard malaria parasite Plasmodium mexicanum. Int J Parasitol 2011; 41:731-8. [PMID: 21396372 DOI: 10.1016/j.ijpara.2011.01.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Revised: 01/20/2011] [Accepted: 01/25/2011] [Indexed: 11/15/2022]
Abstract
Vertebrate hosts of malaria parasites (Plasmodium) often harbour two or more genetically distinct clones of a single species, and interaction among these co-existing clones can play an important role in Plasmodium biology. However, how relative clonal proportions vary over time in a host is still poorly known. Experimental mixed-clone infections of the lizard malaria parasite, Plasmodium mexicanum, were followed in its natural host, the western fence lizard using microsatellite markers to determine the relative proportions of two to five co-existing clones over time (2-3 months). Results for two markers, and two PCR primer pairs for one of those, matched very closely, supporting the efficacy of the method. Of the 54 infections, 67% displayed stable relative clonal proportions, with the others showing a shift in proportions, usually with one clone outpacing the others. Infections with rapidly increasing or slowly increasing parasitemia were stable, showing that all clones within these infections reproduced at the same rapid or slow rate. Replicate infections containing the same clones did not always reveal the same growth rate, final parasitemia or dominant clone; thus there was no clone effect for these life history measures. The rate of increase in parasitemia was not associated with stable versus unstable relative proportions, but infections with four to five clones were more likely to be unstable than those with two to three clones. This rare look into events in genetically complex Plasmodium infections suggests that parasite clones may be interacting in complex and unexpected ways.
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Affiliation(s)
- Alice Flynn Ford
- Department of Biology, University of Vermont, Burlington, VT 05405, USA
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Vardo-Zalik AM. Clonal diversity of a malaria parasite, Plasmodium mexicanum, and its transmission success from its vertebrate-to-insect host. Int J Parasitol 2009; 39:1573-9. [PMID: 19523471 DOI: 10.1016/j.ijpara.2009.05.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 05/13/2009] [Accepted: 05/15/2009] [Indexed: 11/18/2022]
Abstract
Infections of the lizard malaria parasite Plasmodium mexicanum are often genetically complex within their fence lizard host (Sceloporus occidentalis) harbouring two or more clones of parasite. The role of clonal diversity in transmission success was studied for P. mexicanum by feeding its sandfly vectors (Lutzomyia vexator and Lutzomyia stewarti) on experimentally infected lizards. Experimental infections consisted of one, two, three or more clones, assessed using three microsatellite markers. After 5days, vectors were dissected to assess infection status, oocyst burden and genetic composition of the oocysts. A high proportion (92%) of sandflies became infected and carried high oocyst burdens (mean of 56 oocysts) with no influence of clonal diversity on these two measures of transmission success. Gametocytemia was positively correlated with transmission success and the more common vector (L. vexator) developed more oocysts on midguts. A high proportion ( approximately 74%) of all alleles detected in the lizard blood was found in infected vectors. The relative proportion of clones within mixed infections, determined by peak heights on pherograms produced by the genetic analyser instrument, was very similar for the lizard's blood and infections in the vectors. These results demonstrate that P. mexicanum achieves high transmission success, with most clones making the transition from vertebrate-to-insect host, and thus explains in part the high genetic diversity of the parasite among all hosts at the study site.
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Affiliation(s)
- A M Vardo-Zalik
- Program in Public Health, College of Health Sciences, University of California at Irvine, Room 3501 Hewitt Hall, Irvine, CA 92697-4050, USA.
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