Climate adaptation and genetic differentiation in the mosquito species Culex tarsalis

The increasing prevalence of vector-borne diseases around the world highlights the pressing need for an in-depth exploration of the genetic and environmental factors that shape the adaptability and widespread distribution of mosquito populations. This research focuses on Culex tarsalis, a principal vector for various viral diseases including West Nile Virus (WNV). Through the development of a new reference genome and the examination of Restriction-Site Associated DNA sequencing (RAD-seq) data from over 300 individuals and 28 locations, we demonstrate that variables such as temperature, evaporation rates, and the density of vegetation significantly impact the genetic makeup of Cx. tarsalis populations. Among the alleles most strongly associated with environmental factors is a nonsynonymous mutation in a key gene related to circadian rhythms.  These results offer new insights into the mechanisms of spread and adaptation in a key North American vector species, which is poised to become a g..., Sample Collection
Individual mosquitoes were trapped and collected from 28 different locations across the United States and Canada as part of the North American Mosquito Project (NAMP).  All samples used in this study were collected in 2012 between the months of April and October.
Genome Sequencing, Assembly, and Annotation
An F4  population was used to generate the reference genome assembly, and high molecular weight DNA was extracted and sequenced on a Pacific Biosciences (PacBio) RS II (University of Delaware). Thirty-five SMRTcells were generated. The resulting reads provided 76X coverage of the ~790Mb Cx. tarsalis genome, and were assembled with MECAT Gene annotation was completed by MAKER using EST and protein data from the Culex quinquefasciatus and Aedes aegypti mosquitoes. Sequences were downloaded from the NCBI Taxonomy database and both Trinotate and InterProScan were used for functional annotation of the MAKER predicted genes.  The annotated assembly was assessed for complet..., , # Culex tarsalis dataset

[https://doi.org/10.5061/dryad.51c59zwh3](https://doi.org/10.5061/dryad.51c59zwh3)

## Description of the data and file structure

The data were stored in 5 different files.

1. bi_20missing_filtSNP_maf_005.recode.vcf is the filtered .vcf file used in the paper analysis. 
2. land_monthly_climate_2009_2012_partial_canada.nc is the file used to extract climate variable information for the samples based on the latitude and longitude.
3. *The Culex-tarsalis-v1.0.a1-merged-2019-08-30-4-45-01.gff3 for annotating SNPs to the gene.*
4. Culex-tarsalis-v1.0.a1.5d6405151b078-interproscan.tab file for annotating the protein function. 
5.  Ctarsalis_sample_w_GPS_climate_average_new_filtered_id_region.csv file contains the samples information such as location, environmental variables information.

## Code/Software

The code uses the data above are presented in github: [https://github.com/Afei99357/Culex_Tarsalis_GWAS_manuscript.git](https://github.com/Afei99357/Culex_Tarsali...