DOI: 10.5061/dryad.t201q
title: Data from: Unconstrained evolution in short introns?—An analysis of genome-wide polymorphism and divergence data from Drosophila

description: An unconstrained reference sequence facilitates the detection of
 selection. In Drosophila, sequence variation in short introns seems to be
 least influenced by selection and dominated by mutation and drift. Here,
 we test this with genome-wide sequences using an African population
 (Malawi) of D. melanogaster and data from the related outgroup species D.
 simulans, D. sechellia, D. erecta, and D. yakuba. The distribution of
 mutations deviates from equilibrium and the content of A and T (AT)
 nucleotides shows an excess of variance among introns. We explain this by
 a complex mutational pattern: a shift in mutational bias towards AT,
 leading to a slight non-equilibrium in base composition, and
 context-dependent mutation rates, with GC-sites mutating most frequently
 in AT-rich introns. By comparing the corresponding allele frequency
 spectra of AT-rich versus GC-rich introns, we can rule out the influence
 of directional selection or biased gene conversion (BGC) on the mutational
 pattern. Compared to neutral equilibrium expectations, polymorphism
 spectra show an excess of low frequency and a paucity of intermediate
 frequency variants, irrespective of the direction of mutation. Combining
 the information from different outgroups with the polymorphism data and
 using a generalized linear model, we find evidence for shared ancestral
 polymorphism between D. melanogaster and D. simulans/D. sechellia, arguing
 against a bottleneck in D. melanogaster. Generally, we find that short
 introns can be used as a neutral reference on a genome-wide level, if the
 spatially and temporally varying mutational pattern is accounted for.
description: Short intron sequence
 alignment of the 2L chromosome armWe analyzed whole-genome
 data (Langley C. et al., accepted 2012) of D. melanogaster (Release 1.0)
 from a sample of six inbred Malawi isofemale lines from the 50 genomes
 Drosophila Population Genomics Project (DPGP) (http://www.dpgp.org/ ). We
 downloaded (http://genome.ucsc.edu/ ) aligned single sequences of D.
 simulans, D. sechellia, D. erecta and D. yakuba (Release 5) (Begun et al.,
 2007; Clark et al., 2007) and combined them with the six D. melanogaster
 sequences into a multiple alignment for all autosomes. We used position 8
 to 30 in short introns (less than 66 bp) as these are thought to be the
 least constrained sites in the Drosophila genome (Halligan and Keightley,
 2006; Parsch et al., 2010). We used the D. melanogaster Flybase annotation
 (release 5.31) to identify these sites. Introns, which overlapped with
 coding regions were excluded from the analyses. Python scripts were
 written to concatenate all 23 considered positions per short intron into
 one alignment file for each chromosome arm.alignment_2LShort intron sequence alignment of the 2R chromosome armWe analyzed whole-genome data (Langley C. et al., accepted 2012) of D. melanogaster (Release 1.0) from a sample of six inbred Malawi isofemale lines from the 50 genomes Drosophila Population Genomics Project (DPGP) (http://www.dpgp.org/ ). We downloaded (http://genome.ucsc.edu/ ) aligned single sequences of D. simulans, D. sechellia, D. erecta and D. yakuba (Release 5) (Begun et al., 2007; Clark et al., 2007) and combined them with the six D. melanogaster sequences into a multiple alignment for all autosomes. We used position 8 to 30 in short introns (less than 66 bp) as these are thought to be the least constrained sites in the Drosophila genome (Halligan and Keightley, 2006; Parsch et al., 2010). We used the D. melanogaster Flybase annotation (release 5.31) to identify these sites. Introns, which overlapped with coding regions were excluded from the analyses. Python scripts were written to concatenate all 23 considered positions per short intron into one alignment file for each chromosome arm.alignment_2RShort intron sequence alignment of the 3L chromosome armWe analyzed whole-genome data (Langley C. et al., accepted 2012) of D. melanogaster (Release 1.0) from a sample of six inbred Malawi isofemale lines from the 50 genomes Drosophila Population Genomics Project (DPGP) (http://www.dpgp.org/ ). We downloaded (http://genome.ucsc.edu/ ) aligned single sequences of D. simulans, D. sechellia, D. erecta and D. yakuba (Release 5) (Begun et al., 2007; Clark et al., 2007) and combined them with the five D. melanogaster sequences into a multiple alignment for all autosomes. We used position 8 to 30 in short introns (less than 66 bp) as these are thought to be the least constrained sites in the Drosophila genome (Halligan and Keightley, 2006; Parsch et al., 2010). We used the D. melanogaster Flybase annotation (release 5.31) to identify these sites. Introns, which overlapped with coding regions were excluded from the analyses. Python scripts were written to concatenate all 23 considered positions per short intron into one alignment file for each chromosome arm.alignment_3LShort intron sequence alignment of the 3R chromosome armWe analyzed whole-genome data (Langley C. et al., accepted 2012) of D. melanogaster (Release 1.0) from a sample of six inbred Malawi isofemale lines from the 50 genomes Drosophila Population Genomics Project (DPGP) (http://www.dpgp.org/ ). We downloaded (http://genome.ucsc.edu/ ) aligned single sequences of D. simulans, D. sechellia, D. erecta and D. yakuba (Release 5) (Begun et al., 2007; Clark et al., 2007) and combined them with the five D. melanogaster sequences into a multiple alignment for all autosomes. We used position 8 to 30 in short introns (less than 66 bp) as these are thought to be the least constrained sites in the Drosophila genome (Halligan and Keightley, 2006; Parsch et al., 2010). We used the D. melanogaster Flybase annotation (release 5.31) to identify these sites. Introns, which overlapped with coding regions were excluded from the analyses. Python scripts were written to concatenate all 23 considered positions per short intron into one alignment file for each chromosome arm.alignment_3R