Data from: Evidence for complex selection on four-fold degenerate sites in Drosophila melanogaster

 

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Title Sequence alignment of fourfold degenerate sites of the 2L chromosome arm
Downloaded 45 times
Description We analyzed genome-wide fourfold degenerate sites from an African (Malawi) D. melanogaster population (Release 1.0), provided by the Drosophila Population Genomics Project (http://www.dpgp.org/; Langley et al., 2012). To obtain outgroup sequences, we downloaded (http://genome.ucsc.edu/ ) aligned single genome-wide sequences of D. simulans, D. sechellia, D. erecta and D. yakuba (Begun et al., 2007; Clark et al., 2007) (Release 5), and combined them with the D. melanogaster sequences for all autosomes. We wrote Python and R scripts to extract the data according to the annotation of the D. melanogaster genome reference file (Release 5.31) from Flybase and to perform the analyses. We compared the data of fourfold degenerate sites to short introns (bases 8 to 30 of introns < 66 bp) from the same dataset (doi:10.5061/dryad.t201q). A detailed description of short introns can be seen in Clemente and Vogl (2012).
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Title Sequence alignment of fourfold degenerate sites of the 2R chromosome arm
Downloaded 34 times
Description We analyzed genome-wide fourfold degenerate sites from an African (Malawi) D. melanogaster population (Release 1.0), provided by the Drosophila Population Genomics Project (http://www.dpgp.org/; Langley et al., 2012). To obtain outgroup sequences, we downloaded (http://genome.ucsc.edu/ ) aligned single genome-wide sequences of D. simulans, D. sechellia, D. erecta and D. yakuba (Begun et al., 2007; Clark et al., 2007) (Release 5), and combined them with the D. melanogaster sequences for all autosomes. We wrote Python and R scripts to extract the data according to the annotation of the D. melanogaster genome reference file (Release 5.31) from Flybase and to perform the analyses. We compared the data of fourfold degenerate sites to short introns (bases 8 to 30 of introns < 66 bp) from the same dataset (doi:10.5061/dryad.t201q). A detailed description of short introns can be seen in Clemente and Vogl (2012).
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Title Sequence alignment of fourfold degenerate sites of the 3L chromosome arm
Downloaded 41 times
Description We analyzed genome-wide fourfold degenerate sites from an African (Malawi) D. melanogaster population (Release 1.0), provided by the Drosophila Population Genomics Project (http://www.dpgp.org/; Langley et al., 2012). To obtain outgroup sequences, we downloaded (http://genome.ucsc.edu/ ) aligned single genome-wide sequences of D. simulans, D. sechellia, D. erecta and D. yakuba (Begun et al., 2007; Clark et al., 2007) (Release 5), and combined them with the D. melanogaster sequences for all autosomes. We wrote Python and R scripts to extract the data according to the annotation of the D. melanogaster genome reference file (Release 5.31) from Flybase and to perform the analyses. We compared the data of fourfold degenerate sites to short introns (bases 8 to 30 of introns < 66 bp) from the same dataset (doi:10.5061/dryad.t201q). A detailed description of short introns can be seen in Clemente and Vogl (2012).
Download alignment_3L (6.251 Mb)
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Title Sequence alignment of fourfold degenerate sites of the 3R chromosome arm
Downloaded 42 times
Description We analyzed genome-wide fourfold degenerate sites from an African (Malawi) D. melanogaster population (Release 1.0), provided by the Drosophila Population Genomics Project (http://www.dpgp.org/; Langley et al., 2012). To obtain outgroup sequences, we downloaded (http://genome.ucsc.edu/ ) aligned single genome-wide sequences of D. simulans, D. sechellia, D. erecta and D. yakuba (Begun et al., 2007; Clark et al., 2007) (Release 5), and combined them with the D. melanogaster sequences for all autosomes. We wrote Python and R scripts to extract the data according to the annotation of the D. melanogaster genome reference file (Release 5.31) from Flybase and to perform the analyses. We compared the data of fourfold degenerate sites to short introns (bases 8 to 30 of introns < 66 bp) from the same dataset (doi:10.5061/dryad.t201q). A detailed description of short introns can be seen in Clemente and Vogl (2012).
Download alignment_3R (7.893 Mb)
Details View File Details

When using this data, please cite the original publication:

Clemente F, Vogl C (2012) Evidence for complex selection on four-fold degenerate sites in Drosophila melanogaster. Journal of Evolutionary Biology 25(12): 2582–2595. http://dx.doi.org/10.1111/jeb.12003

Additionally, please cite the Dryad data package:

Clemente F, Vogl C (2012) Data from: Evidence for complex selection on four-fold degenerate sites in Drosophila melanogaster. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.1pd2j
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