- Genome-wide divergence among invasive populations of Aedes aegypti in California. - Background: In the summer of 2013, Aedes aegypti Linnaeus was first detected in three cities in central California (Clovis, Madera and Menlo Park). - Results: Here we report the first population genomics analyses of Ae. - one that includes all sample sites in the southern part of the state (South of Tehachapi mountain range) plus the town of Exeter in central California and two additional clusters in central California.. - One of these has been lost in the Clovis populations, possibly by a founder effect. - Our observations support recent introductions of Ae. - One central question concerning the populations dynamics of Ae. - introductions from other sites in the U.S. - California had no known established local populations of Ae. - aegypti prior to the summer of 2013 when it was detected in three cities in central California: Clovis, Ma- dera and Menlo Park [4–6]. - In the spring and summer of the following year, this mosquito was again found in the same three California locations and for the first time in additional communities in central California and fur- ther south in San Diego County (Fig. - 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. - The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.. - Full list of author information is available at the end of the article Lee et al. - aegypti has now become established and is spreading through large parts of the state (Fig. - Population genomics studies are especially critical to the development of control strategies based on genetic ma- nipulation of vectors, which is a matter of growing interest.. - Modelling, planning and monitoring activities associated with control programs require affordable and rapid assays to distinguish vector sub-populations within a species and a deep understanding of the processes that shape their gen- etic structure. - We sequenced the genomes of 46 specimens of Ae.. - Populations from the restricted area around Clovis and Sanger in central CA form the GC3 cluster. - Overall, the distribution of the three Ae. - aegypti have a nearly parapa- tric distribution with the three groups potentially con- verging in the Central Valley. - 3) indicate additional population subdivisions further divid- ing Mission Viejo, Garden Grove, Exeter and Vero Beach samples from the rest of GC2 (Fig. - This may seem slightly different from pub- lished SNPchip data [3] but is consistent with the microsatellite-based genetic clustering reported in the same study.. - 1 History of the recent Ae. - The respective year of the first detection of the species in each site is displayed on the map. - Nu- cleotide diversity (π) is highly variable but lowest in the. - These regions correspond to the location of the centromeres (coordinates obtained from personal communications with M. - Sharakhova at Virginia Polytechnic Institute) and include a relatively high density of repeated and difficult to sequence regions which are excluded from the SNP set analyzed. - 2 Geographic origin of Ae. - 3 Genetic Clusters of Ae. - Principal Component Analysis based on the SNP data. - Lee et al. - As a peculiarity, the South African populations have noticeably higher nucleotide diver- sity in a region around 160–170 Mbp of Chromo- some 1 compared to samples from the southern CA GC1.. - 4 Genome-wide comparison of Ae. - Overall F ST ± estimated standard error between groups is given in the title of each pane. - a: GC1 (Southern California, N = 18) vs GC2 (Central California – Menlo Park, Madera and Fresno, N = 9). - b: GC1 (Southern California, N = 18) vs GC3 (Central California – Clovis, N = 7). - The F ST distance between one sample from the town of Sanger (sample Ae17CON058) to GC2 and GC3 clusters were equivalent (Additional file 2: Table S2) and its place- ment in the PCA (Fig. - This is due to the very large number of SNPs (i.e. - The 4.65 million loci used in our analysis is well in excess of the number of loci re- quired for an accurate assessment of F ST . - Samples from Florida and South Africa are distributed among the two major lineages suggesting that these lineages might be present throughout the global range of Ae. - These cor- respond roughly to geographic regions in the state (Figs. - However, their ge- nealogy differs from the nuclear genome genealogy. - This is comparable to a previous study using ND4 sequence analysis of Ae. - aegypti populations and is likely due to the saltatory nature of dispersal in this species.. - Our BLAST results comparing AaegL1-based SNP sequences to the AaegL5 assembly revealed numerous and significant differences,. - Due to these problems a direct comparison of SNP genotype calls using the published SNP chip data with those generated from genome sequence data is deemed inappropriate and we highly recommend taking this into account when applying SNP chip analyses in the future.. - Microsatellite data from [3, 4] indicated that San Mateo (=Menlo Park), Madera and Fresno samples were genetically similar to samples from the southeastern USA which includes samples from Louisiana, Georgia and Florida. - Pless et al. - Labelling refers to the Principal Component Analysis and resulting genetic clusters (GCs). - Contrary to the microsatellite data, the SNP chip data from the same study [3] groups the Exeter population apart from all other CA populations including those in central CA, consistent with our genome-wide SNP data.. - Unfortunately, their SNP chip data clustering results did not include samples from the southeast USA preventing direct comparison with their SNP clustering result. - This, however, could support the view that the Exeter popula- tion, introduced in 2014 is distinct from all other CA populations and that it was introduced independently, rather than resulting from local spread of Ae. - PCA analyses of the SNP chip data separated Clovis (GC3) from the GC2 cluster with some overlap [3]. - Our data together with previous reports strongly support multiple introductions of Ae. - probably in 2013 (iii) southern CA, probably in 2014 (iv) Exeter, probably in 2014 intro- duced from someplace in the southeast USA like Florida.. - The years are based on reports from the California vec- tor control districts. - This scenario is also in line with most of the results published based on microsatellites and SNP chip data [3]. - From our data the exact origin of the introductions remains uncertain with only the Exeter population showing signs of presumable derivation from the southeast USA.. - The degree of genetic differentiation found in the Clovis population between the years 2013 and 2016 (Fig. - The only other longitudinal investigation of a CA population of Ae. - Investigating samples from different origins using the same NGS platform may pro- vide a clearer description of Ae. - In addition, investigation describing genomic changes over time may provide information on local adaptation and potentially will be useful for the control of the species in California.. - Our mitogenome analysis suggests that founding popula- tions were polymorphic for two mitochondrial lineages with one or the other lost in the various extant popula- tions. - These observations support recent multiple intro- ductions of Ae. - This is the first paper that utilizes the whole genome sequences of Aedes aegypti field isolates. - Raw reads were trimmed using Trimmomatic [26] ver- sion 0.36 and mapped to the AaegL5 reference genome [27] using BWA-MEM [28] version 0.7.15. - The repeat regions are “soft-masked” in the AaegL5 reference genome and SNPs in these regions were excluded from analysis. - The presence of mitochondrial pseudogenes in the nu- clear genomes of Ae. - [14] and mapped raw reads to the mitochondrial reference genome prior to mapping unmapped reads to the nuclear genome.. - Variants in the mitochondrial genome were called with Freebayes as described for the nuclear genome, but set to single ploidy. - Use of properly paired reads for variant calling reduced errors generated by failing to recognize mitochon- drial pseudogenes present in the nuclear genome. - The Vcf2fasta program [36] was used to extract mitogenome se- quences from the VCF file to FASTA format. - were obtained from GenBank and added to the alignment.. - Genome-wide comparison of Ae. - Comparison of Evans et al. - Bradley Main for his comments to the manuscript. - Michael Hearst, District Manager), Community Health Division of the Department of Environmental Health (Ms.. - Danny Governer and SANParks for permitting collection from Shingwedzi in the Kruger National Park. - We acknowledge funding support from the UC Davis Bridge Funding Program, UC Davis School of Veterinary Medicine Vector-borne Disease Pilot Grant Program, DARPA Safe Gene Program (HR and the Pacific Southwest Regional Center of Excellence for Vector-Borne Diseases funded by the U.S. - YL and MJH received salary support from the UC Davis Bridge Funding Program. - YL received research supply support from the UC Davis School of Veterinary Medicine Vector-Borne Disease Pilot Program. - HS received salary support from the Pacific Southwest Regional Center of Excellence for Vector-Borne Diseases. - All authors contributed to the writing and editing of this manuscript.. - Dispersal of Aedes aegypti and Aedes albopictus (Diptera:. - Culicidae) in an urban endemic dengue area in the state of Rio de Janeiro, Brazil. - Dispersal of the dengue vector Aedes aegypti within and between rural communities. - Multiple introductions of the dengue vector, Aedes aegypti, into California. - Origin of the dengue fever mosquito, Aedes aegypti, in California. - The genetic basis of host preference and resting behavior in the major African malaria vector, Anopheles arabiensis.. - Dual African origins of global Aedes aegypti s.L. - Complete mitogenome sequence of Aedes (Stegomyia) aegypti derived from field isolates from California and South Africa. - Phylogeography of Aedes aegypti (yellow fever mosquito) in South Florida: mtDNA evidence for human-aided dispersal. - Mutation rates and intraspecific divergence of the mitochondrial genome of Pristionchus pacificus. - Diversity, differentiation, and linkage disequilibrium: prospects for association mapping in the malaria vector Anopheles arabiensis. - A multipurpose high throughput SNP Chip for the dengue and yellow fever mosquito, Aedes aegypti. - Improved reference genome of Aedes aegypti informs arbovirus vector control. - Mitochondrial pseudogenes in the nuclear genome of Aedes aegypti mosquitoes: implications for past and future population genetic studies. - Complete sequences of mitochondria genomes of Aedes aegypti and Culex quinquefasciatus and comparative analysis of mitochondrial DNA fragments inserted in the nuclear genomes
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