Honorio NA, Silva Wda C, Leite PJ, Goncalves JM, Lounibos LP, Lourenco-de-Oliveira R. Dispersal of Aedes aegypti and Aedes albopictus (Diptera: Culicidae) in an urban endemic dengue area in the state of Rio de Janeiro, Brazil. Mem Inst Oswaldo Cruz. 2003;98(2):191–8.
Article
Google Scholar
Harrington LC, Scott TW, Lerdthusnee K, Coleman RC, Costero A, Clark GG, Jones JJ, Kitthawee S, Kittayapong P, Sithiprasasna R, et al. Dispersal of the dengue vector Aedes aegypti within and between rural communities. Am J Trop Med Hyg. 2005;72(2):209–20.
Article
Google Scholar
Pless E, Gloria-Soria A, Evans BR, Kramer V, Bolling BG, Tabachnick WJ, Powell JR. Multiple introductions of the dengue vector, Aedes aegypti, into California. PLoS Negl Trop Dis. 2017;11(8):e0005718.
Article
Google Scholar
Gloria-Soria A, Brown JE, Kramer V, Hardstone Yoshimizu M, Powell JR. Origin of the dengue fever mosquito, Aedes aegypti, in California. PLoS Negl Trop Dis. 2014;8(7):e3029.
Article
Google Scholar
Cornel AJ, Holeman J, Nieman CC, Lee Y, Smith C, Amorino M, Brisco KK, Barrera R, Lanzaro GC. Mulligan iii FS: surveillance, insecticide resistance and control of an invasive Aedes aegypti (Diptera: Culicidae) population in California. F1000Res. 2016;5:194.
Article
Google Scholar
Jewell D. Grodhaus G. In: Commerce and the Spread of Pests and Disease Vectors edited by Laird M. New York: Praeger Publishers; 1984. p. 103–7.
Google Scholar
Main BJ, Lee Y, Collier TC, Norris LC, Brisco K, Fofana A, Cornel AJ, Lanzaro GC. Complex genome evolution in Anopheles coluzzii associated with increased insecticide usage in Mali. Mol Ecol. 2015;24(20):5145–57.
Article
CAS
Google Scholar
Main BJ, Lee Y, Ferguson HM, Kreppel KS, Kihonda A, Govella NJ, Collier TC, Cornel AJ, Eskin E, Kang EY, et al. The genetic basis of host preference and resting behavior in the major African malaria vector, Anopheles arabiensis. PLoS Genet. 2016;12(9):e1006303.
Article
Google Scholar
Vicente JL, Clarkson CS, Caputo B, Gomes B, Pombi M, Sousa CA, Antao T, Dinis J, Botta G, Mancini E, et al. Massive introgression drives species radiation at the range limit of Anopheles gambiae. Sci Rep. 2017;7:46451.
Article
CAS
Google Scholar
Norris LC, Main BJ, Lee Y, Collier TC, Fofana A, Cornel AJ, Lanzaro GC. Adaptive introgression in an African malaria mosquito coincident with the increased usage of insecticide-treated bed nets. Proc Natl Acad Sci U S A. 2015;112(3):815–20.
Article
CAS
Google Scholar
Hanemaaijer MJ, Collier TC, Chang A, Shott CC, Houston PD, Schmidt H, Main BJ, Cornel AJ, Lee Y, Lanzaro GC. The fate of genes that cross species boundaries after a major hybridization event in a natural mosquito population. Mol Ecol. 2018; In press.
Nazareno AG, Bemmels JB, Dick CW, Lohmann LG. Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species. Mol Ecol Resour. 2017;17(6):1136–47.
Article
CAS
Google Scholar
Moore M, Sylla M, Goss L, Burugu MW, Sang R, Kamau LW, Kenya EU, Bosio C, Munoz Mde L, Sharakova M, et al. Dual African origins of global Aedes aegypti s.L. populations revealed by mitochondrial DNA. PLoS Negl Trop Dis. 2013;7(4):e2175.
Article
CAS
Google Scholar
Schmidt H, Hanemaaijer MJ, Cornel AJ, Lanzaro GC, Braack L, Lee Y. Complete mitogenome sequence of Aedes (Stegomyia) aegypti derived from field isolates from California and South Africa. Mitochondrial DNA Part B. 2018. https://doi.org/10.1080/23802359.2018.1495117.
Damal K, Murrell EG, Juliano SA, Conn JE, Loew SS. Phylogeography of Aedes aegypti (yellow fever mosquito) in South Florida: mtDNA evidence for human-aided dispersal. Am J Trop Med Hyg. 2013;89(3):482–8.
Article
Google Scholar
Lynch M. The origins of genome architecture. Sunderland, mass: Sinauer Associates; 2007.
Havird JC, Sloan DB. The roles of mutation, selection, and expression in determining relative rates of evolution in mitochondrial versus nuclear genomes. Mol Biol Evol. 2016;33(12):3042–53.
Article
CAS
Google Scholar
Molnar RI, Bartelmes G, Dinkelacker I, Witte H, Sommer RJ. Mutation rates and intraspecific divergence of the mitochondrial genome of Pristionchus pacificus. Mol Biol Evol. 2011;28(8):2317–26.
Article
CAS
Google Scholar
Marsden CD, Lee Y, Kreppel K, Weakley A, Cornel A, Ferguson HM, Eskin E, Lanzaro GC. Diversity, differentiation, and linkage disequilibrium: prospects for association mapping in the malaria vector Anopheles arabiensis. G3 (Bethesda). 2014;4(1):121–31.
Article
Google Scholar
Evans BR, Gloria-Soria A, Hou L, McBride C, Bonizzoni M, Zhao H, Powell JR. A multipurpose high throughput SNP Chip for the dengue and yellow fever mosquito, Aedes aegypti. G3 (Bethesda). 2015.
Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K, Grabherr M, et al. Genome sequence of Aedes aegypti, a major arbovirus vector. Science. 2007;316(5832):1718–23.
Article
CAS
Google Scholar
Bernhardt SA, Blair C, Sylla M, Bosio C. Black WCt: evidence of multiple chromosomal inversions in Aedes aegypti formosus from Senegal. Insect Mol Biol. 2009;18(5):557–69.
Article
CAS
Google Scholar
Ayala D, Ullastres A, Gonzalez J. Adaptation through chromosomal inversions in Anopheles. Front Genet. 2014;5:129.
Article
Google Scholar
Nieman CC, Yamasaki Y, Collier TC, Lee Y. A DNA extraction protocol for improved DNA yield from individual mosquitoes. F1000Res. 2015;4:1314.
Article
Google Scholar
Yamasaki YK, Nieman CC, Chang AN, Collier TC, Main BJ, Lee Y. Improved tools for genomic DNA library construction of small insects. F1000Res. 2016;5:211.
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014.
Matthews BJ, Dudchenko O, Kingan SB, Koren S, Antoshechkin I, Crawford JE, Glassford WJ, Herre M, Redmond SN, Rose NH, et al. Improved reference genome of Aedes aegypti informs arbovirus vector control. Nature. 2018;563(7732):501–7.
Article
CAS
Google Scholar
Li H: Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. In.: Cornell University Library; 2013: arXiv:1303.3997v1302.
Okonechnikov K, Conesa A, Garcia-Alcalde F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics. 2016;32(2):292–4.
CAS
PubMed
Google Scholar
Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing; 2012. p. arXiv preprint.
Google Scholar
Crawford JE, Lazzaro BP. Assessing the accuracy and power of population genetic inference from low-pass next-generation sequencing data. Front Genet. 2012;3:66.
Article
Google Scholar
Felsenstein J. PHYLIP - phylogeny inference package (version 3.2). Cladistics. 1989;5:164–6.
Google Scholar
Hudson RR, Slatkin M, Maddison WP. Estimation of levels of gene flow from DNA sequence data. Genetics. 1992;132(2):583–9.
CAS
PubMed
PubMed Central
Google Scholar
Miles A, Harding N: scikit-allel - Explore and analyse genetic variation. In., 1.2.0 edn. https://github.com/cggh/scikit-allel: GitHub; 2018.
Hlaing T, Tun-Lin W, Somboon P, Socheat D, Setha T, Min S, Chang MS, Walton C. Mitochondrial pseudogenes in the nuclear genome of Aedes aegypti mosquitoes: implications for past and future population genetic studies. BMC Genet. 2009;10:11.
Article
Google Scholar
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, et al. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156–8.
Article
CAS
Google Scholar
Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33(7):1870–4.
Article
CAS
Google Scholar
Behura SK, Lobo NF, Haas B, deBruyn B, Lovin DD, Shumway MF, Puiu D, Romero-Severson J, Nene V, Severson DW. Complete sequences of mitochondria genomes of Aedes aegypti and Culex quinquefasciatus and comparative analysis of mitochondrial DNA fragments inserted in the nuclear genomes. Insect Biochem Mol Biol. 2011;41(10):770–7.
Article
CAS
Google Scholar
UC Davis PopI OpenProjects- AedesGenomes [https://popi.ucdavis.edu/PopulationData/OpenProjects/AedesGenomes/].
CalSurv: California Surveilliance Gateway Maps. In.: California Vectorborne Disease Surveillance System; 2007.
Patterson T: CleanTOPO2: Edited SRTM30 Plus World Elevation Data. In. Online (author communicated that his data is published in public domain and free to use). ; 2008.