Data from: Extensive introgression in a malaria vector species complex revealed by phylogenomics

Introgressive hybridization is now recognized as a widespread phenomenon, but its role in evolution remains contested. Here we use newly available reference genome assemblies to investigate phylogenetic relationships and introgression in a medically important group of Afrotropical mosquito sibling species. We have identified the correct species branching order to resolve a contentious phylogeny, and show that lineages leading to the principal vectors of human malaria were among the first to split. Pervasive autosomal introgression between these malaria vectors means that only a small fraction of the genome, mainly on the X chromosome, has not crossed species boundaries. Our results suggest that traits enhancing vectorial capacity may be gained through interspecific gene flow, including between non-sister species.,Mitochondrial genome alignment of the field individuals in the An. gambiae complexFasta alignment of the mitochondrial genome (14,843 bps) assembled from 75 individual mosquitoes from the Anopheles gambiae species complex (Cf SOM, section S2.2.4). It includes 73 individuals from each of the six ingroup species and the two outgroups, An. christyi and An. epiroticus, and the reference mtDNA genome (GeneBank Accession NC_002084).mtDNA_all_copy_N75_CUT14845_ID4GBK.fasVCF files of field individual samples from the AGC complexThis is a tar archive including the VCF files (one per chromosome arm) for the 69 individual mosquito samples sequenced at low-depth that passed QC filters, plus 2 outgroups (see SOM, section 2.2).VCFfile4DRYAD.tar.gzMAF TBA genome alignment of reference assemblies from the An gambiae complexWhole genome alignment of the of the reference assemblies from the members of the Anopheles gambiae species complex (AGC). The reference assemblies are mostly derived from colonized anopheline mosquitoes. This multiple genome alignment, in MAF format, include the new reference assemblies from six genomes of the AGC, plus the assemblies of An. gambiae PEST, An. gambiae Pimperena S, An. coluzzii, and two outgroup Pyretophorus species (An. christyi and An epiroticus). MAF for each chromosome arm are provided. See the SOM, section S1 for a full description of the methodology.AgamP3-C9-7chr.tba.unmasked.mafs.tar.gzMAF genome alignment from HD field samples of An gambiae complexMultiple whole genome alignments of the field individual samples from the members of the Anopheles gambiae species complex (AGC) sequenced at high depth. This multiple genome alignment, in MAF format, include the haploid genome of one individual sequenced at high depth in each six genomes of the AGC. The An gambiae PEST reference assembly and two outgroup Pyretophorus species (An christyi and An epiroticus) are also included. MAF for each chromosome arm are provided. See the SOM, section S2.1 and S3.1 for a full description of the methodology.MAF_HD_V4_TBA.C9.DRYAD.tar.gz