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

Fontaine MC, Pease JB, Steele A, Waterhouse RM, Neafsey DE, Sharakhov IV, Jiang X, Hall AB, Catteruccia F, Kakani E, Mitchell SN, Wu Y, Smith HA, Love RR, Lawniczak MK, Slotman MA, Emrich SJ, Hahn MW, Besansky NJ

Date Published: December 3, 2014

DOI: http://dx.doi.org/10.5061/dryad.f4114

 

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Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Mitochondrial genome alignment of the field individuals in the An. gambiae complex
Downloaded 15 times
Description Fasta 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).
Download mtDNA_all_copy_N75_CUT14845_ID4GBK.fas (1.137 Mb)
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Title VCF files of field individual samples from the AGC complex
Downloaded 26 times
Description This 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).
Download VCFfile4DRYAD.tar.gz (1.645 Gb)
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Title MAF TBA genome alignment of reference assemblies from the An gambiae complex
Downloaded 18 times
Description Whole 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.
Download AgamP3-C9-7chr.tba.unmasked.mafs.tar.gz (244.1 Mb)
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Title MAF genome alignment from HD field samples of An gambiae complex
Downloaded 10 times
Description Multiple 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.
Download MAF_HD_V4_TBA.C9.DRYAD.tar.gz (277.1 Mb)
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When using this data, please cite the original publication:

Fontaine MC, Pease JB, Steele A, Waterhouse RM, Neafsey DE, Sharakhov IV, Jiang X, Hall AB, Catteruccia F, Kakani E, Mitchell SN, Wu Y, Smith HA, Love RR, Lawniczak MK, Slotman MA, Emrich SJ, Hahn MW, Besansky NJ (2015) Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science 347(6217). http://dx.doi.org/10.1126/science.1258524

Additionally, please cite the Dryad data package:

Fontaine MC, Pease JB, Steele A, Waterhouse RM, Neafsey DE, Sharakhov IV, Jiang X, Hall AB, Catteruccia F, Kakani E, Mitchell SN, Wu Y, Smith HA, Love RR, Lawniczak MK, Slotman MA, Emrich SJ, Hahn MW, Besansky NJ (2014) Data from: Extensive introgression in a malaria vector species complex revealed by phylogenomics. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.f4114
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