DOI: 10.5061/dryad.m905qfv76
title: Data from: Effective population size of Culex quinquefasciatus under insecticide-based vector management and following Hurricane Harvey in Harris County, Texas

description: Culex quinquefasciatus is mosquito species of significant public health
 importance due to its ability to transmit multiple pathogens that can
 cause mosquito-borne diseases, such as West Nile fever and St. Louis
 encephalitis. In Harris County, Texas, Cx. quinquefasciatus is a common
 vector species and is subjected to insecticide-based management by the
 Harris County Public Health Department. However, insecticide resistance in
 mosquitoes has increased rapidly worldwide and raises concerns about
 maintaining the effectiveness of vector control approaches. This concern
 is highly relevant in Texas, with its humid subtropical climate along the
 Gulf Coast that provides suitable habitat for Cx. quinquefasciatus and
 other mosquito species that are known disease vectors. Therefore, there is
 an urgent and ongoing need to monitor the effectiveness of current vector
 control programs. In this study, we evaluated the impact of vector control
 approaches by estimating the effective population size of Cx.
 quinquefasciatus in Harris County. We applied Approximate Bayesian
 Computation to microsatellite data to estimate effective population size.
 We collected Cx. quinquefasciatus samples from two mosquito
 control operation areas, 415 and 802, during routine vector monitoring in
 2016 and 2017. No county mosquito control operations were applied at area
 415 in 2016 and 2017, whereas extensive adulticide spraying operations
 were in effect at area 802 during the summer of 2016. We collected data
 for eighteen microsatellite markers for 713 and 723 mosquitoes at eight
 timepoints from 2016 to 2017 in areas 415 and 802, respectively. We also
 investigated the impact of Hurricane Harvey's landfall in the Houston
 area in August of 2017 on Cx. quinquefasciatus population fluctuation.
 Although we did not detect significant effects of vector control
 interventions, we found considerable influences of the winter season and a
 major hurricane on the effective population size of Cx. quinquefasciatus.
 The fluctuations in effective population size in both areas showed a
 significant seasonal pattern. Additionally, the significant population
 expansion following Hurricane Harvey in 2017 supports the necessity for
 post-hurricane vector-control interventions.
description: <em><strong>Mosquito
 collection</strong></em> Adult
 <em>Cx. quinquefasciatus </em>are routinely collected by
 Harris County Public Health (HCPH) personnel from Houston, Texas, United
 States. The samples used in this study were collected four times per year
 in 2016 and 2017 from two operational areas, 415 and 802. Samples from a
 single time point were collected within a one week time frame. Mosquitoes
 were stored at −80 ℃ until processing. There were no mosquito control
 operations by HCPH in area 415 during 2016 and 2017. In contrast, 26
 malathion spraying operations were performed on ten separate dates, and
 ten permethrin spraying operations were performed on five separate dates
 during the summer of 2016 at area 802. Neither site was subjected to
 adulticidal spraying in 2017. From area 415, mosquito samples collected in
 weeks 14, 23, 38, and 46 in 2016 and in weeks 2, 20, 32, and 42 in 2017
 were included in this study. From area 802, mosquito samples collected in
 weeks 14, 23, 39, and 48 in 2016 and in weeks 12, 20, 31, and 42 in 2017
 were included. <em><strong>DNA
 extraction</strong></em> For each timepoint
 and location, 95 individuals were included. Total DNA was extracted and
 purified from each individual mosquito. The whole mosquito body was
 homogenized using a Qiagen® TissueLyser (Qiagen, Germantown, Maryland).
 Mosquito tissues were individually transferred into a well of a 96-well
 plate, which included a negative control. DNA extraction and purification
 were performed on the BioSprint® 96 workstation (Qiagen, Hilden, Germany)
 following their standard protocol. The final DNA product was stored at 4
 ℃. <em><strong>Species
 diagnostic</strong></em> Morphological
 species identification was conducted by personnel from HCPH as the primary
 filtering for the field-collected adult <em>Cx.
 quinquefasciatus</em>. To confirm the result of morphological
 identification, species diagnostic polymerase chain reaction (PCR) was
 performed on each sample (Crabtree et al., 1995), using the
 <em>PQ10</em> and the <em>CP16</em> primers. Each
 20 µL reaction included 10 µL 2× Thermo Scientific™ PCR Master Mix (Thermo
 Fisher Scientific, Carlsbad, California), 10 ng <em>PQ10</em>
 primer, 10 ng <em>CP16</em> primer, 20 ng template DNA, and
 nuclease-free water. The PCR program was set up following protocol by
 Crabtree et al. (1995) and was performed on the Eppendorf™ Mastercycler
 X50a thermocycler (Eppendorf, Hamburg, Germany). PCR products were
 visualized on a 2% agarose gel. Those samples that failed to show a clear
 698-bp band were not used for microsatellite genotyping and data analysis
 in the following steps.
 <em><strong>Microsatellite
 Genotyping</strong></em> Eighteen
 microsatellite loci for <em>Cx. quinquefasciatus</em> (Fonseca
 et al., 2004, Smith et al., 2005, Edillo et al., 2007, Hickner et al.,
 2010) were amplified in multiplex PCR reactions. The forward primers were
 labeled using one of three fluorescent dyes, FAM, HEX and NED. Primers for
 six loci were multiplexed in a single reaction, with each primer in
 equimolar concentrations of 0.2 µM. Each 50 µL amplification reaction
 included 25 µL 2× QIAGEN® Multiplex PCR Master Mix, 5 µL 10× Primer Mix,
 20ng DNA and nuclease-free water (with 3mM MgCl<sub>2</sub> in
 final concentration). The thermoprofile for the multiplex PCR was: 2 min
 at 95 ℃, followed by 30 cycles performed for 30 sec at 95 ℃; 90 sec at 57
 ℃; and 30 sec at 72 ℃, and a final cycle for 30 min at 72 ℃. The PCR
 products were submitted to the DNA Analysis Facility on Science Hill at
 Yale University for fragment analyses. Genotyping was performed using
 Genemarker (Hulce et al., 2011).
 <em><strong>Data
 Analysis</strong></em> Microchecker version
 2.2.3 was used to check for microsatellite null alleles (Van Oosterhout et
 al., 2004). Loci CX4, CX10, and CX11 were not included in subsequent
 analyses, as null alleles were detected in these three loci. Due to low
 amplification efficiency, data of CX5 from area 802 was also not included
 in downstream analysis. Microsatellite genotyping data were converted to
 Genepop format with GenAlEx version 6.503 (Peakall and Smouse,
 2012). Data were loaded into DIYabc version 2.1.0
 (Cornuet et al., 2014). This software package implements approximate
 Bayesian computation inferences about population history (Cornuet et al.,
 2014). We tested four basic demographic scenarios in our study, which
 included variations of population size (bottleneck, expansion, decline, or
 constant)for two time periods. For each scenario, 2,000,000 simulated
 datasets were generated, with specific mutation models and prior
 distributions for parameters. The summary statistics of each simulated
 dataset were compared with those of the observed dataset. More
 specifically, we used three single-sample statistics, including the mean
 number of alleles, mean genetic diversity (Nei, 1987), mean allele size
 variance across loci, and three two-sample statistics, including the
 fixation index (F<sub>ST</sub>) (Weir and Cockerham, 1984),
 mean index of classification (Rannala and Mountain, 1997, Pascual et al.,
 2007), and Euclidean distance between every two samples (Goldstein et al.,
 1995). Through this process, the posterior probability of each scenario
 was calculated, and the most likely scenario was identified. The effective
 population size of <em>Cx. quinquefasciatus </em>from each
 site of the Houston area was obtained by estimating the posterior
 distribution for the most likely scenario. We set two
 weeks as the average generation time of <em>Cx.
 quinquefasciatus</em>, as the life cycle from egg to adult stage
 usually takes 10 to 14 days (Manimegalai and Sukanya, 2014). The minimum
 value for effective population size (N<sub>e</sub>) was set as
 0 and the maximum value for 1,000,000, except for the bottleneck scenario.
 The prior range for N<sub>e</sub> at earlier time points was
 between 0 and 1,000,000, while the prior range of Ne at the latter time
 points was between 0 and 200,000 for the bottleneck scenario. 
 We tested three time points from spring in 2016 to winter in 2017
 per area to find the effects of the winter season. Genotyping data from
 weeks 14 and 23 in 2016 and week 2 in 2017 were used for area 415, while
 genotyping data from weeks 14 and 23 in 2016 and week 12 in 2017 were used
 for analysis for area 802. First, we performed the parameter estimation
 with a prior normal distribution, where parameters had a mean value and a
 standard deviation within a range between extremum values (minimum and
 maximum). We also performed the parameter estimation with a uniform prior
 distribution to test if different prior distributions affect the choice of
 best demographic scenario. In this case, the prior distribution had
 minimum and maximum values but without the mean value and standard
 deviation. Next, we performed N<sub>e
 </sub>estimation from three time points from 2016 and three
 timepoints from 2017 at area 802 to evaluate the effects of Hurricane
 Harvey on the N<sub>e</sub> of the mosquito population. The
 mosquito samples were collected before and after Hurricane Harvey, which
 landed in the Houston area on August 27, 2017. For area 802, genotyping
 data from weeks 14, 23, and 48 in 2016 were used for pre-hurricane
 analysis in DIYabc, while genotyping data from weeks 12, 20, and 42 in
 2017 were used for post-hurricane analysis. In addition
 to DIYabc, we used NeEstimator version 2.1 (Do et al., 2014) to estimate
 the N<sub>e</sub> of <em>Cx. quinquefasciatus
 </em>from eight sampling time points in 2016 and 2017 at area 802 to
 further explore the impact of Hurricane Harvey on the
 N<sub>e</sub> of mosquito population in Harris County. The
 N<sub>e</sub> at each time point was estimated with the
 Linkage Disequilibrium (LD) method. The mating system was defined as
 random mating.
description: # Data from: Effective population size of Culex quinquefasciatus under
 insecticide-based vector management and following Hurricane Harvey in
 Harris County, Texas The microsatellite genotyping data for the two study
 populations are provided in an Excel file with four sheets, each labeled
 by year and area, corresponding to the years and areas studied in the
 paper. The data is formatted with two columns per locus. For inquiries
 regarding the data, please reach out to the corresponding author.