DIS genotype data

Divergence Island SNP genotype data for each individual isolates from four sites (Kondi, Foumbot, Tiko and Abu)

Chromosome Inversions, Genomic Differentiation and Speciation in the African Malaria Mosquito <em>Anopheles gambiae</em>

<div><p>The African malaria vector, <i>Anopheles gambiae</i>, is characterized by multiple polymorphic chromosomal inversions and has become widely studied as a system for exploring models of speciation. Near complete reproductive isolation between different inversion types, known as chromosomal forms, has led to the suggestion that <i>A. gambiae</i> is in early stages of speciation, with divergence evolving in the face of considerable gene flow. We compared the standard chromosomal arrangement (<i>Savanna</i> form) with genomes homozygous for <i>j</i>, <i>b</i>, <i>c</i>, and <i>u</i> inversions (<i>Bamako</i> form) in order to identify regions of genomic divergence with respect to inversion polymorphism. We found levels of divergence between the two sub-taxa within some of these inversions (2R<i>j</i> and 2R<i>b</i>), but at a level lower than expected and confined near the inversion breakpoints, consistent with a gene flux model. Unexpectedly, we found that the majority of diverged regions were located on the X chromosome, which contained half of all significantly diverged regions, with much of this divergence located within exons. This is surprising given that the <i>Bamako</i> and <i>Savanna</i> chromosomal forms are both within the S molecular form that is defined by a locus near centromere of X chromosome. Two X-linked genes (a heat shock protein and P450 encoding genes) involved in reproductive isolation between the M and S molecular forms of <i>A. gambiae</i> were also significantly diverged between the two chromosomal forms. These results suggest that genes mediating reproductive isolation are likely located on the X chromosome, as is thought to be the case for the M and S molecular forms. We conclude that genes located on the sex chromosome may be the major force driving speciation between these chromosomal forms of <i>A. gambiae</i>.</p> </div

Distribution of divergence on each chromosome.

<p>Fraction of significant probes, denoted “hit density”, using a 200 kbp windows across the X, 2R and 2L chromosomes is indicated by the solid red line. Smooth gray lines indicate the fraction of significant probes in 1 Mbp windows. Positions of inversions (<i>j</i>,<i>b</i>,<i>c</i>,<i>u</i> and <i>a</i>) are depicted as rectangles, with shading indicating the approximate location of inversion breakpoints. Centromere positions are marked as green dots on the X axis. The log-ratio of significant probes is marked with blue dots, log ratios above zero are probes with higher signal intensity in the <i>Bamako</i> relative to <i>Savanna</i> forms, below zero weaker signal intensity. Log-ratio of 1 indicates a two fold increase in hybridization signal intensities in <i>Bamako</i> forms relative to <i>Savanna</i> forms. Log-ratio of −1 indicates a two fold increase in signal intensities in <i>Savanna</i> forms compared to <i>Bamako</i> forms.</p

Genetic information for mosquito samples used for microarray hybridization.

<p>Sample IDs represent a concatenation of collection site, collection date and tube index number, and correspond to identification numbers stored on the publically available online database, <i>PopI</i> at: <a href="https://grassi2.ucdavis.edu/" target="_blank">https://grassi2.ucdavis.edu/</a>. In addition, photomicrographic images of polytene chromosome preparations used to determine karyotypes for all specimens, except the two samples from Yorobougoula, are available on <i>PopI</i>.</p

Divergence in coding sequences contained in chromosome inversions.

<p>Significantly greater proportions of significant features (SFs) in exons or non-coding regions are marked in bold.</p

Evidence for gene duplications.

<p><b>A:</b> Duplication of gene AGAP002773 on chromosome 2R, located in a hotspot near the 5′ end of inversion 2R<i>b</i>; <b>B:</b> AGAP009502 located at the 1st hotspot of divergence on the right arm of chromosome 3 (at around 35 Mbp position); and <b>C:</b> AGAP009669 located in the 2nd hotspot of divergence on the right arm of chromosome 3 (at around 38 Mbp position). Black bars indicate log-ratios of a SF. Gray bars indicate log ratios of a non-significant probe. Gray boxes and black lines at the top of each graph represent exons and introns respectively. The log-ratio data in the introns of AGAP002273 and upstream of AGAP009669 appear to be missing because genome sequence is unavailable for these regions and consequently no probe was designed for these regions.</p

Distribution and characterization of genomic divergence.

<p><b>A:</b> Proportion (%) of significantly differentiated regions (SDRs) expressed as a percentage of the total chromosome segment size are shown in light colored bars. Proportions of SDRs in exons as a percentage of the total exon size per segment are shown in dark colored bars. The X3M segment includes the 3 Mbp region proximal to the centromere. The X includes the X chromosome minus the X3M region. <b>B:</b> Proportion (%) of total SDR size categorized by chromosome segment. <b>C:</b> Proportion (%) of total SDR size categorized by the role of the nearest gene. An SDR is classified as 'intergenic' if there is no gene located within 250 bp from either end of that SDR.</p

A. coluzzii variant file

This file contains variants from all A. coluzzii individuals described in this study (plus a few others). See the README for the list of individual sample ID's from pre- and post-2006 samples that can be used with VCFtools to recreate the figures

SRP063464

Illumina sequencing data for pre- and post-2006 A. coluzzii individuals from Selenkenyi, Mali

Total size of significantly differentiated regions (SDRs) in base pairs along different chromosome segments.

*<p>Total proportion of significantly differentiated regions in relation to the total <i>A. gambiae</i> genome size ( = 273 Mbp) **The remaining genes 827 ( = 13,254–12,427) belong to UNKN segment, a large segment that has not mapped to chromosome.</p