- heterogeneity within the genome of the malaria vector Anopheles gambiae. - A recently separated species of the complex, An. - Most notably, the frequencies of the largest and most geo- graphically distributed inversions in the second chromo- some of An. - The goal of this dimen- sionality reduction is to preserve as much of the high dimensional population structure information in the low dimensional representation as possible. - 0.2) in most of the outer clusters (Fig. - In the An. - [36], a 15 Mb region of the. - Below is a schematic representation of the A. - coluzzii, contribute to the clustering in the t- SNE of genes that may be relevant to speciation (“spe- cies divergence cluster”, Fig. - Genes with high Species F ST are located on the right-hand side of the plot (F ST >. - Thus, the t-SNE provides a visual indication of the gen- omic extent of “islands of speciation”. - These genes are largely located either on the centromeric half of the X chromosome or close to the 3R centromere. - b Enlargement of the ‘ speciation cluster ’ showing neighboring genes (AGAP001073, AGAP001082, AGAP001083, AGAP001084) of the main diagnostic markers of A. - d Table containing the distribution of genes through chromosome arms in the ‘ speciation cluster. - e Scatter plot of the same 11,318 genes of A. - These two inversions in the second chromosome of An. - In the dataset studied here, 75% of the individuals are homo- karyotypes, including 43% 2La-standard. - The 2La-2 cluster (or in some cases, just the subset of its 15 most distal genes) is present in all 30 replicate plots (S1 Fig) and is discussed in the selective sweeps section.. - In the present study, 62% of the individuals are homokaryo- types for 2Rb-standard. - Black arrows indicate key genes referenced in the text. - The clustering of genes in the t- SNE largely follows the pattern of inversions and their overlaps. - Not all documented inversions will cause a clear clus- tering of genes in the t-SNE. - Two of the largest non-inversion clusters are 2R-vii. - a Five clusters are found in the 2L chromosome (2L-i – 2L-v). - b Seven clusters are found in the 2R chromosome (2Ri - 2Rvii). - Genes close to telomeres are not locally constrained in the t-SNE plot to the degree seen for genes in inversions and centromeres regions. - Another genetic factor that strongly influences popula- tion structure and therefore the layout of genes in the t- SNE is positive selection. - This region of strong selection was also identified in the original analysis of the Ag1000G dataset [22]. - The genes GSTE2 (AGAP009194), GSTE3 (AGAP009197) and GSTE4 (AGAP009193) are also lo- cated in this genomic region but fall in the center of the t-SNE due to low numbers of SNPs that pass the quality criteria. - This gene is located in the centromere-proximal region of the left arm of chromosome 2 and it belongs to cluster 2L-ii in the t-SNE (Fig. - Thus, visual interpretation of the t- SNE would not highlight this locus as a potential se- lective sweep. - 7b) overlap in an area of the t-SNE that we henceforth refer to as the “Guinea-Bissau cluster” (Fig. - Gene function enrichment in the t-SNE. - A systematic analysis was performed to detect over- representation of gene functions in sub-regions of the t- SNE. - However, the majority of the genes closely neighbouring the tandem array are found in other distinct clusters in the t-SNE, particularly the main 2Rc cluster. - So, the cholesterol transport genes appear to be in the “Guinea-Bissau cluster” by exception rather than by default. - a t-SNE plot highlighting genes in the “ Guinea Bissau cluster. - The goal of dimensionality reduction is to preserve as much information of the high-dimensional data set in the low-dimensional representation. - Each point in the t-SNE plot then represents one gene and genes close together in the plot indicate population structure similarity. - DBScan is a density-based spatial algorithm used to find clusters of genes in the t-SNE [80] in R. - The genes in the t-SNE were partitioned using K-means clustering on the 2D plot coordinates at different levels of granularity. - org/10.1186/s y.. - Ranked distribution of the number of unique nearest neighbors for each gene.. - Genes with low values reflect higher consistency of the local neighborhood in the t-SNE plot. - Genes with low values reflect higher consistency of global arrangement in the t-SNE plot. - Representation of the most signifi- cant gene function over-representation clusters. - Number of SNPs, genomic location and coordinates for each gene in the t-SNE plot.. - Measure of consistency of the t-SNE plot.. - Fst values for each gene in the t-SNE plot.. - We are grateful to Mara Lawniczak for sharing preliminary data in the early stages of the project. - A Polytene chromosome analysis of the Anopheles gambiae species complex. - Anopheles coluzzii and Anopheles amharicus, new members of the Anopheles gambiae complex. - https://doi.. - Chromosomal differentiation and adaptation to human environments in the Anopheles gambiae complex. - https://doi.org . - Ecological genetic studies in the chromosomal form Mopti of Anopheles gambiae s.str. - Systems genetic analysis of inversion polymorphisms in the malaria mosquito Anopheles gambiae. - https://doi.org/10.1073/pnas . - https://doi.org/10.1534/genetics . - Population structure, speciation, and introgression in the Anopheles gambiae complex.. - doi.org . - Adaptation to aridity in the malaria mosquito Anopheles gambiae: chromosomal inversion. - The Genome Sequence of the Malaria Mosquito Anopheles gambiae.. - https://doi.org/10.1111/. - https://doi.org/10.1371/. - https://doi.org/10.1038/. - https://doi.org/10.1371/journal.pone.. - Genetic diversity of the African malaria vector Anopheles gambiae. - https://doi.org/10.1111/j.1365-294X x.. - https://doi.org/10.1093/nar/gku1117.. - Chromosome inversions, genomic differentiation and speciation in the African malaria mosquito Anopheles gambiae. - Spatiotemporal dynamics of gene flow and hybrid fitness between the M and S forms of the malaria mosquito, Anopheles gambiae. - Dissecting functional components of reproductive isolation among closely related sympatric species of the Anopheles gambiae complex. - https://doi.org/10.1038/ncomms5248.. - https://doi.org/10.1073/. - https://doi.org/10.1093/gbe/evs095.. - Simultaneous identification of species and molecular forms of the Anopheles gambiae complex by PCR- RFLP. - https://doi.org/10.1046/j x.. - Identification of single specimens of the Anopheles gambiae complex by the polymerase chain reaction. - https://doi.org/10.4269/ajtmh . - A comprehensive gene expression atlas of sex- and tissue-specificity in the malaria vector, Anopheles gambiae. - Proteomics reveals novel components of the Anopheles gambiae eggshell. - Genetic structure of a local population of the Anopheles gambiae complex in Burkina Faso. - https://doi.org/10.1186/s . - doi.org/10.1534/genetics . - https://doi.org/10.1101/. - Detecting recent positive selection in the human genome from haplotype structure. - https://doi.org/10.1073/pnas.. - https://doi.org/10.1111/j x.. - CYP6 P450 enzymes and ACE-1 duplication produce extreme and multiple insecticide resistance in the malaria mosquito Anopheles gambiae.. - Insecticide resistance mechanisms associated with different environments in the malaria vector Anopheles gambiae: a case study in Tanzania. - Molecular characterization of pyrethroid knockdown resistance (kdr) in the major malaria vector Anopheles gambiae s.s. - https://doi.org/10.1016/j.. - https://doi.org/10.1038/srep4 6451.. - The roles of two clip domain serine proteases in innate immune responses of the malaria vector Anopheles gambiae. - https://doi.org/10.1074/jbc.. - https://doi.org/10.1371/journal.. - doi.org/10.1093/bioinformatics/btr330.. - https://doi.org/10.1 093/bioinformatics/bts606.. - org/10.1111/j x.
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