Glossary#
- Anopheles gambiae species complex#
A cryptic species complex comprising at least seven morphologically indistinguishable species of mosquitoes in the genus Anopheles. Includes the major malaria vector species Anopheles gambiae, Anopheles coluzzii and Anopheles arabiensis.
- cohort#
A group of mosquito specimens which are analysed together. For the selection atlas, mosquito specimens are grouped into cohorts by taxon, level 2 administrative divisions, and year quarter. For example, the cohort labelled “Burkina Faso / Houet / coluzzii / 2012 / Q3” includes Anopheles coluzzii mosquitoes collected from Houet Province, Burkina Faso, during the third quarter of 2012.
- copy number variation#
- CNV#
A genetic mutation where multiple additional copies of a particular DNA sequence are present in some individuals in a population. If a CNV spans one or more protein-coding genes then expression of those genes may be increased as a result. If the protein product interacts with insecticides in some way, then increased expression may alter insecticide susceptibility. For example, CNVs affecting cytochrome P450 genes which metabolise pyrethroid insecticides may cause resistance to pyrethroids.
- G123#
A statistical method for performing genome-wide selection scans using unphased SNP data and multi-locus genotype (diplotype) frequencies. See also Harris et al. (2018).
- gene#
A gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. Most genes are protein-coding, meaning that the RNA is then translated into an amino acid sequence to synthesize a protein.
- genome#
- reference genome#
A genome is all the genetic information of an organism. In the case of Anopheles mosquitoes, the nuclear genome comprises DNA sequences organised into three chromosomes, named Chromosome 2 (a.k.a. 2RL), Chromosome 3 (a.k.a. 3RL) and Chromosome X. A reference genome is a specific set of nucleotide sequences representing a particular species. All analyses reported in the selection atlas are based on the AgamP4 reference genome, also known as “PEST”. Note that in the AgamP4 reference genome, Chromosome 2 is divided into two arms named 2R and 2L, and similarly Chromosome 3 is divided into arms 3R and 3L. To simplify analyses, we have concatenated these arms together to create sequences representing entire chromosomes (2RL and 3RL).
- genome region#
A section of a chromosome with a defined start and end position relative to the reference genome coordinate system.
- genome-wide selection scan#
- GWSS#
A statistical analysis of genetic variation data derived from a given cohort of mosquitoes, which aims to detect patterns indicating that a specific genome region has experienced recent positive selection within the population from which that cohort was sampled. There are several different statistical methods available to perform genome-wide selection scans, such as H12, G123 and IHS.
- H12#
A statistical method for performing genome-wide selection scans using data on haplotype frequencies. See also Garud et al. (2015).
- haplotype#
A physical grouping of genetic variants that have been inherited together.
- integrated haplotype score#
- IHS#
A statistical method for performing genome-wide selection scans using data on the length of shared haplotypes. See also Voight et al. (2006).
- insecticide resistance#
- IR#
A situation where a population of mosquitoes becomes less susceptible to an insecticide which is being or has been used to control it. In the case of Anopheles mosquitoes, this can become a matter of public health concern when mosquitoes are less susceptible to insecticides used for vector control.
- MalariaGEN Python API#
An open source software library for accessing and analysing data from the Malaria Genomic Epidemiology Network (MalariaGEN).
- Malaria Vector Genome Observatory#
A collaborative project to sequence the genomes of thousands of Anopheles mosquitoes and use those data to benefit malaria vector surveillance and improve vector control.
- malaria vector#
A malaria vector is a mosquito species which transmits malaria.
- selection#
- recent positive selection#
Selection here refers to the evolution of a mosquito population by natural selection, where genetic variants change in frequency because they provide a survival or other reproductive advantage. The selection atlas focuses on recent positive selection, which is a type of selection where genetic variants increase rapidly in frequency because they provide a strong survival advantage, and this change has occurred within the recent past. For example, the use of insecticide-treated bednets has caused recent positive selection for genetic variants which confer insecticide resistance in Anopheles mosquito populations.
- selection signal#
A selection signal is a region of the genome where there is strong statistical evidence for recent positive selection, inferred from the results of a genome-wide selection scan.
- single nucleotide polymorphism#
- SNP#
A genetic mutation where a single nucleotide in a DNA sequence is replaced by a different nucleotide.
- vector control#
A set of methods used to limit the spread of disease-carrying animals, such as as Anopheles mosquitoes. For example, insecticide-treated bednets (ITNs) and indoor residual spraying of insecticides (IRS) are two widely used methods of malaria vector control in Africa.