Biology subjects

Carvajal, T. M.

Publications and source records attributed to Carvajal, T. M..

6 recordsLinked to original sources

bioRxiv2026

Detection of Japanese Encephalitis Virus in Mosquitoes Collected from Selected Areas of Laguna, Philippines Using an Optimized One-Step RT-PCR Protocol

Japanese encephalitis virus is a leading cause of encephalitis in humans and agricultural animals across Southern and Eastern Asia. It is primarily transmitted by mosquitoes of the Culex genus, notably Culex tritaeniorhynchus. In the Philippines, JEV is reported to account for 7% to 18% of clinical cases of meningitis and encephalitis. Therefore, updated and comprehensive data on circulating JEV strains in the country are crucial for developing effective mitigation strategies. This study aimed to optimize an assay for JEV detection using one-step reverse transcription polymerase chain reaction (RT-PCR). Additionally, the presence of JEV in mosquitoes collected from eleven cities and municipalities in Laguna was assessed, and the mosquito carriers were identified based on morphological characteristics. Results demonstrated that the optimized one-step RT-PCR assay successfully detected JEV at various dilutions, with a limit of detection (LoD) of 0.115 ng/L. The assay exhibited 100% specificity, with no amplification observed for any viruses other than JEV. Sequence analysis of the positive control, JEV SA14-14-2 RNA, revealed 96.96% to 98.41% similarity to JEV reference sequences in the NCBI database. Among the 5,522 female mosquitoes collected, Culex tritaeniorhynchus and Culex gelidus were the most prevalent species. The highest mosquito species diversity and the most even distribution were found in the three barangays of Paete, but Siniloan, Laguna had the highest vector density for the three Culex species, Culex tritaeniorhynchus, Culex gelidus, and Culex fuscocephala. RT-PCR analysis of 189 pooled mosquito samples revealed no detectable JEV genetic material. This study is likely the first investigation of JEV presence in mosquito samples from Laguna, Philippines. These findings contribute to proactive JEV surveillance, enhancing our understanding of the virus's presence and distribution. The results underscore the importance of targeted prevention and control measures to mitigate JEV transmission in high-risk areas.

molecular biology↗

bioRxiv2023

Fine-scale adaptive divergence of Aedes aegypti in heterogeneous landscapes and among climatic conditions in Metropolitan Manila, Philippines

The adaptive divergence of Aedes aegypti populations to heterogeneous environments may be a driving force behind the recent expansion of their habitat distribution and outbreaks of dengue disease in urbanized areas. In this study, we investigated the population genomics of Ae. aegypti at a regional scale in Metropolitan Manila, Philippines using double digestion restriction-site association DNA sequencing (ddRAD-Seq). Specifically, we used a Pool-Seq approach to generate a high number of single nucleotide polymorphisms (SNPs), which were used to determine local adaptation and population structure. We detected 65,473 SNPs in 217 Ae. aegypti individuals from 14 populations with 76 non-neutral SNP loci. Additionally, 57 of these non-neutral SNP loci were associated with 8 landscape variables (e.g., open space, forest, etc) and 4 climate variables (e.g., air temperature, humidity, etc). Furthermore, the percentage of the area of landscape variables, such as forest, parks and recreation, air temperature, man-made building, and open space per local population was frequently associated with non-neutral SNP loci. Most non-neutral SNP loci formed four clusters that were in linkage disequilibrium with each other in physical proximity on the chromosome and were associated with a common environmental variable. Male and female populations exhibited contrasting spatial divergence, i.e., males exhibited greater divergence, likely reflecting their different dispersal abilities. In comparative analysis of the same Ae. aegypti individuals, the pairwise FST values of 11 microsatellite markers were lower than those of neutral SNP loci, indicating that the neutral SNP loci generated via ddRAD-Seq were more sensitive in terms of detecting genetic differences between populations at fine-spatial scales. Overall, this study demonstrates the utility of ddRAD-Seq for examining genetic differences in Ae. aegypti populations, and our data on mosquito dispersal at a regional spatial scale could inform vector control programs. Author SummaryThe population expansion of dengue vector, Aedes aegypti mosquitoes is one of the factors that may promote the outbreak of the diseases. Understanding the population genomics of Ae.aegypti may contribute to better knowledge about mosquito expansion and how they can adapt to the change in environment. In this study, we used pool-based ddRAD-Seq (Double Digest Restriction site Association DNA Sequencing) to generate SNPs that occur between the Ae.aegypti populations in Metropolitan Manila, Philippines. We found that non-neutral SNP loci are frequently associated with landscape variables compared to climatic variables. Landscape variables such as forest, park and recreation, air temperature, man-made building and open space are more frequently associated with non-neutral SNPs loci. Those landscape variables may relate to the mosquitos fitness, therefore, induce the adaptive divergence within Ae.aegypti population. We also found male and female populations are exhibiting a contrast spatial divergence by using neutral SNP loci. In addition, neutral SNPs loci showed higher resolution in population structuring than microsatellite markers using the same individuals.

genomics↗

bioRxiv2020

Wing Geometry and Genetic Analyses Reveal Contrasting Spatial Structures between Male and Female Aedes aegypti Populations in Metropolitan Manila, Philippines

BackgroundMany important arboviral diseases (e.g. dengue, chikungunya) are transmitted by the bite of a female mosquito vector, Aedes aegypti. Hence, the population genetic structure of the mosquito has been studied in order to understand its role as an efficient vector. Several studies utilized an integrative approach; to combine genetic and phenotypic data to determine the population structure of Ae. aegypti but these studies have only focused on female populations. To address this particular gap, our study compared the population variability and structuring between male and female Ae. aegypti populations using phenotypic (wing geometry) and genetic (microsatellites) data from a highly-urbanized and dengue-endemic region of the Philippines, Metropolitan Manila. MethodsFive mosquito populations comprised of female (n = 137) and male (n = 49) adult Ae. aegypti mosquitoes were used in this study. All mosquito individuals underwent geometric morphometric (26 landmarks), and genetic (11 microsatellite loci) analyses. ResultsResults revealed that FST estimates (genetic) were 0.055 and 0.009 while QST estimates (phenotypic) were 0.318 and 0.309 in in male and female populations, respectively. Wing shape variation plots showed that male populations were distinctly separated from each other while female populations overlapped. Similarly, discriminant analysis of principal components using genetic data revealed that male populations were also distinctly separated from each other while female populations showed near-overlapping populations. Genetic and phenetic dendrograms showed the formation of two groups in male populations but no groups in female populations. Further analysis indicated a significant correlation (r = 0.68, p = 0.02) between the genetic and phenetic distances of male populations. Bayesian analysis using genetic data also detected multiple clusters in male (K = 3) and female (K = 2) populations, while no clusters were detected using the phenotypic data from both sexes. ConclusionsOur results revealed contrasting phenotypic and genetic patterns between male and female Ae. aegypti, indicating that male populations were more spatially structured than female populations. Although genetic markers demonstrated higher sensitivity in detecting population structures than phenotypic markers, correlating patterns of population structure were still observed between the two markers.

zoology↗

bioRxiv2020

The influence of roads on the fine-scale population genetic structure of the dengue vector Aedes aegypti (Linnaeus)

Dengue is endemic in tropical and subtropical countries and is transmitted mainly by Aedes aegypti. Mosquito movement can be affected by human-made structures such as roads that can act as a barrier. Roads can influence the population genetic structure of Ae. aegypti. We investigated the genetic structure and gene flow of Ae. aegypti as influenced by a primary road, Espana Boulevard (EB) with 2000-meter-long stretch and 24-meters-wide in a very fine spatial scale. We hypothesized that Ae. aegypti populations separated by EB will be different due to the limited gene flow as caused by the barrier effect of the road. A total of 376 adults and larval Ae. aegypti were collected from June to September 2017 in 21 sites across EB. North (N1-N11) and South (S1-S10) comprised of 211 and 165 individuals, respectively. All mosquitoes were genotyped at 11 microsatellite loci. AMOVA FST indicated significant genetic differentiation across the road. The constructed UPGMA dendrogram found 4 genetic groups revealing the clear separation between North and South sites across the road. On the other hand, Bayesian cluster analysis showed four genetic clusters (K = 4) wherein each individual samples have no distinct genetic cluster thus genetic admixture. Moreover, significant positive spatial autocorrelation was observed at 100 - 200 m distance class, suggesting dispersal potential of the adult mosquitoes within a 200 m spatial scale. Our results suggest that human-made landscape features such as primary roads are potential barriers to mosquito movement thereby limiting its gene flow across the road. This information is valuable in designing an effective mosquito control program in a very fine spatial scale. Author SummaryDengue, a mosquito-borne viral infection is a serious health problem in tropical and subtropical countries such as Philippines. Most dengue prevention programs aim to eradicate its mosquito vector, Aedes aegypti. A successful population control program is reliant in understanding the mosquito behavior and ecology including how human-made structures such as roads influence its expansion and movement. Previous studies have discovered the barrier effect of roads in the movement of mosquitoes. In this study, we examined the influence of roads in the population genetic structure of Ae. aegypti in a fine spatial scale using 11 microsatellite markers. We found significant genetic differentiation of mosquito populations across the road. Our results suggest limited gene flow across the road and supports our hypothesis that roads are potential barriers to mosquito dispersal. This information can be used in designing an effective mosquito population control zones in perceived barrier to mosquito dispersal such as roads.

molecular biology↗

bioRxiv2020

Dengue Disease Dynamics are Modulated by the Combined Influence of Precipitation and Landscapes: A Machine Learning-based Approach

BackgroundDengue is an endemic vector-borne disease influenced by environmental factors such as landscape and climate. Previous studies separately assessed the effects of landscape and climate factors on mosquito occurrence and dengue incidence. However, both factors interact in time and space to affect mosquito development and dengue disease transmission. For example, eggs laid in a suitable environment can hatch after being submerged in rain or flood water. ObjectivesThis study aimed to investigate the combined influences of landscape and climate factors on mosquito occurrence and dengue incidence. MethodsEntomological, epidemiological, and landscape data from the rainy season (July-December) were obtained from respective government agencies in Metro Manila, Philippines, from 2012 to 2014. Temperature, precipitation, and vegetation data were obtained through remote sensing. A random forest algorithm was used to select the landscape and climate variables. Afterwards, using the identified key variables, a model-based (MOB) recursive partitioning was implemented to test the combinatory influences of landscape and climate factors on the ovitrap index and dengue incidence. ResultsThe MOB recursive partitioning for the ovitrap index indicated that mosquito occurrence was higher in high residential density areas, where industrial areas also exist and are well connected with roads. Precipitation was another key covariate modulating the effects of landscape factors, possibly by expanding breeding sites and activating mosquito reproduction. Moreover, the MOB recursive partitioning indicated that precipitation was the main predictor of dengue incidence, with a stronger effect in high residential density and commercial areas. DiscussionPrecipitation with floods has epidemiologically important implications by damaging shelters and causing population displacement, thus increasing exposure to dengue vectors. Our findings suggest that the intensification of vector control during the rainy season can be prioritized in residential and commercial areas to better control dengue disease dynamics.

ecology↗

bioRxiv2018

Detection of adaptive divergence in populations of the stream mayfly Ephemera strigata with machine learning

Adaptive divergence is a key mechanism shaping the genetic variation of natural populations. A central question linking ecology with evolutionary biology concerns the role of environmental heterogeneity in determining adaptive divergence among local populations within a species. In this study, we examined adaptive the divergence among populations of the stream mayfly Ephemera strigata in the Natori River Basin in northeastern Japan. We used a genome scanning approach to detect candidate loci under selection and then applied a machine learning method (i.e. Random Forest) and traditional distance-based redundancy analysis (dbRDA) to examine relationships between environmental factors and adaptive divergence at non-neutral loci. We also assessed spatial autocorrelation at neutral loci to quantify the dispersal ability of E. strigata. Our main findings were as follows: 1) random forest shows a higher resolution than traditional statistical analysis for detecting adaptive divergence; 2) separating markers into neutral and non-neutral loci provides insights into genetic diversity, local adaptation and dispersal ability and 3) E. strigata shows altitudinal adaptive divergence among the populations in the Natori River Basin.

evolutionary biology↗