A two-phase approach for detecting recombination in nucleotide sequences

Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombinationdetecting approaches can vary, depending on evolutionary events that take place after recombination. We recently evaluated the effects of postrecombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach in delineating breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results.Comment: 5 pages, 3 figures. Chan CX, Beiko RG and Ragan MA (2007). A two-phase approach for detecting recombination in nucleotide sequences. In Hazelhurst S and Ramsay M (Eds) Proceedings of the First Southern African Bioinformatics Workshop, 28-30 January, Johannesburg, 9-1

A two-phase strategy for detecting recombination in nucleotide sequences

Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombination-detecting approaches can vary, depending on evolutionary events that take place after recombination. We previously evaluated the effects of post-recombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach to delineate breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results

The evolution of TEP1, an exceptionally polymorphic immunity gene in Anopheles gambiae

<p>Abstract</p> <p>Background</p> <p>Host-parasite coevolution can result in balancing selection, which maintains genetic variation in the susceptibility of hosts to parasites. It has been suggested that variation in a thioester-containing protein called <it>TEP1 </it>(AGAP010815) may alter the ability of <it>Anopheles </it>mosquitoes to transmit <it>Plasmodium </it>parasites, and high divergence between alleles of this gene suggests the possible action of long-term balancing selection. We studied whether <it>TEP1 </it>is a case of an ancient balanced polymorphism in an animal immune system.</p> <p>Results</p> <p>We found evidence that the high divergence between <it>TEP1 </it>alleles is the product of genetic exchange between <it>TEP1 </it>and other TEP loci, i.e. gene conversion. Additionally, some <it>TEP1 </it>alleles showed unexpectedly low variability.</p> <p>Conclusion</p> <p>The <it>TEP1 </it>gene appears to be a chimera produced from at least two other <it>TEP </it>loci, and the divergence between <it>TEP1 </it>alleles is probably not caused by long-term balancing selection, but is instead due to two independent gene conversion events from one of these other genes. Nevertheless, <it>TEP1 </it>still shows evidence of natural selection, in particular there appears to have been recent changes in the frequency of alleles that has diminished polymorphism within each allelic class. Although the selective force driving this dynamic was not identified, given that susceptibility to <it>Plasmodium </it>parasites is known to be associated with allelic variation in <it>TEP1</it>, these changes in allele frequencies could alter the vectoring capacity of populations.</p

Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli

BACKGROUND: Comparisons of complete bacterial genomes reveal evidence of lateral transfer of DNA across otherwise clonally diverging lineages. Some lateral transfer events result in acquisition of novel genomic segments and are easily detected through genome comparison. Other more subtle lateral transfers involve homologous recombination events that result in substitution of alleles within conserved genomic regions. This type of event is observed infrequently among distantly related organisms. It is reported to be more common within species, but the frequency has been difficult to quantify since the sequences under comparison tend to have relatively few polymorphic sites. RESULTS: Here we report a genome-wide assessment of homologous recombination among a collection of six complete Escherichia coli and Shigella flexneri genome sequences. We construct a whole-genome multiple alignment and identify clusters of polymorphic sites that exhibit atypical patterns of nucleotide substitution using a random walk-based method. The analysis reveals one large segment (approximately 100 kb) and 186 smaller clusters of single base pair differences that suggest lateral exchange between lineages. These clusters include portions of 10% of the 3,100 genes conserved in six genomes. Statistical analysis of the functional roles of these genes reveals that several classes of genes are over-represented, including those involved in recombination, transport and motility. CONCLUSION: We demonstrate that intraspecific recombination in E. coli is much more common than previously appreciated and may show a bias for certain types of genes. The described method provides high-specificity, conservative inference of past recombination events

Detecting recombination in evolving nucleotide sequences

BACKGROUND: Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. These recombination events can be obscured by subsequent residue substitutions, which consequently complicate their detection. While there are many algorithms for the identification of recombination events, little is known about the effects of subsequent substitutions on the accuracy of available recombination-detection approaches. RESULTS: We assessed the effect of subsequent substitutions on the detection of simulated recombination events within sets of four nucleotide sequences under a homogeneous evolutionary model. The amount of subsequent substitutions per site, prior evolutionary history of the sequences, and reciprocality or non-reciprocality of the recombination event all affected the accuracy of the recombination-detecting programs examined. Bayesian phylogenetic-based approaches showed high accuracy in detecting evidence of recombination event and in identifying recombination breakpoints. These approaches were less sensitive to parameter settings than other methods we tested, making them easier to apply to various data sets in a consistent manner. CONCLUSION: Post-recombination substitutions tend to diminish the predictive accuracy of recombination-detecting programs. The best method for detecting recombined regions is not necessarily the most accurate in identifying recombination breakpoints. For difficult detection problems involving highly divergent sequences or large data sets, different types of approach can be run in succession to increase efficiency, and can potentially yield better predictive accuracy than any single method used in isolation

Determinants of Fine-Scale Heterogeneity in Mosquito-Borne Virus Systems

ABSTRACT Arthropod-borne viruses (arboviruses) are the etiological agents of much morbidity and mortality, especially in low- and middle-income countries. Many of these viruses are spread and maintained by mosquitoes, particularly the urban mosquito Aedes aegypti. Zika virus (ZIKV) is responsible for one of the largest vector-borne disease outbreaks in the past decade, affecting millions in Central and South America including a wave of microcephaly among newborns. Mayaro virus (MAYV) is a mosquito-borne virus endemic to South America and is predicted to become an emergent public health threat. Describing the vector-virus transmission systems are critical for understanding the potential spread of these viruses. Traditionally, laboratory vector competence measures are used to evaluate the ability of a species of mosquito to take up and subsequently transmit an arbovirus by exposing mosquitoes to virus and terminally sampling for the presence of virus in the saliva or peripheral tissues at predetermined time points. However, traditional measures do not assess critical vector-virus interactions that will ultimately impact transmission potential, as these measures focus solely on rates of infectious mosquitoes. My overarching hypothesis is that there are undescribed sources of fine-scale heterogeneity within the vector-virus transmission system that will alter transmission potential. To test this hypothesis, I 1) investigated the impact of the age structure of the mosquito population on the transmission potential of ZIKV by Aedes aegypti, 2) developed a novel method for the quantification of observed heterogeneity among individual mosquitoes, and 3) characterized genotypic diversity among strains of MAYV and the potential impacts on vector competence measurements

Relación entre factores bióticos y abióticos en los cultivos de guayaba con la infestación de picudo (conotrachelus psidii, coleóptera: curculionidae) en Puente Nacional (Santander, Colombia)

Los insectos que son “plagas” causan daño a los sistemas naturales y aquellos que son manejados por el hombre y durante mucho tiempo se ha demostrado que las plagas generan resistencia a los pesticidas y se ha generado un problema ambiental con el mal uso de dichos productos. Los cultivos de guayaba en el país actualmente son atacados por picudo lo que genera grandes pérdidas económicas. En la actualidad los programas agrícolas están dirigidos a controlar las plagas juntando conocimientos biológicos, culturales y químicos, pues estas prácticas son de bajo costo y no degradan el medio ambiente. El objetivo de la presente investigación fue conocer y analizar algunos de los factores bióticos y abióticos que afectan la infestación de picudo a cultivos de guayaba; adicional a esto se estudió el crecimiento en diámetro polar y ecuatorial de frutos sanos e infestados a través del tiempo de desarrollo. Se analizó el crecimiento de 508 frutos en cuatro meses y la edad más vulnerable a la infestación; adicional a esto registros de daño en flores y botones florales. Para establecer las relaciones entre factores bióticos y abióticos con la infestación se tuvieron en cuentas las siguientes variables: altitud de la finca, altura de las plantas, cobertura de las plantas, distancia de siembra, aplicación de insecticidas y aplicación de fertilizantes. Los botones presentaron daño ocasionado por consumo y un desarrollo de tipo exponencial en 30 días de crecimiento. El crecimiento de los frutos sanos e infectados tardo en promedio 120 días y el diámetro ecuatorial y polar presento un crecimiento ajustado a la curva de Gompertz, dividida en tres etapas que se caracterizaron por la velocidad de crecimiento. La región estudiada presenta un porcentaje de infestación del 60% donde los cultivos no tecnificados alrededor de los cultivos pueden estar explicando cerca del 61% de la infestación, factores abióticos como temperatura, humedad y precipitación o factores biológicos como otras plagas pueden estar determinando el restante porcentaje de infestación. Las fincas estudiadas presentaron perdidas de aproximadamente de 3 toneladas de fruta por la infestación de picudo. Finalmente se concluye que las hembras de picudo solo ovipositan en los frutos y con preferencia en las primeras edades del desarrollo, dentro de los factores que se estudiaron y que explican la infestación son los cultivos de guayaba no tecnificados alrededor de los cultivos tecnificados.Abstract. The insect "pests "cause damage to natural systems and culture has long been demonstrated that pests develop resistance to pesticides and has generated an environmental problem. Guava crops in the country are attacked by the weevil causing economic losses. At present farm programs are aimed at controlling pests with biological, cultural and chemical knowledge , as these practices are inexpensive and do not degrade the environment. The objective of this research was to analyze some of the biotic and abiotic factors affecting infestation of crops guava weevil, en Puente Nacional (Santander), in addition to this growth was studied in polar and equatorial diameter of healthy fruit infested through the development time. Additional records of this damage flowers and flower buds, the growth of 480 fruits in four months and the most vulnerable to infestation age were analyzed. To establish the relationships between biotic and abiotic factors with infestation took into account the following variables: altitude of the farm, plant height, coverage, planting distance, application of insecticides and fertilizer application. The buttons had damage caused by consumption and exponential growth in 30 days. The growth of healthy and infected fruits slow on average 120 days and the polar and equatorial diameter presented a growth adjusted Gompertz curve, divided into three stages which are characterized by the growth rate. The study region has a percentage of 60% infestation where wild guava trees around crops can be explaining about 61% of the infestation, abiotic factors such as temperature, humidity and precipitation o biotic factors as others pests can be given the remainder of infestation. Farms studied had lost about 3 tons of fruit for weevil infestation. The conclude that female weevils oviposit only in fruit and preferably in the early ages, one of the factors which may explain the infestation is wild guava trees around crops.Maestrí