Genomic impacts of chromosomal inversions in parapatric Drosophila species - PubMed (original) (raw)

Comparative Study

Genomic impacts of chromosomal inversions in parapatric Drosophila species

Suzanne E McGaugh et al. Philos Trans R Soc Lond B Biol Sci. 2012.

Abstract

Chromosomal inversions impact genetic variation and facilitate speciation in part by reducing recombination in heterokaryotypes. We generated multiple whole-genome shotgun sequences of the parapatric species pair Drosophila pseudoobscura and Drosophila persimilis and their sympatric outgroup (Drosophila miranda) and compared the average pairwise differences for neutral sites within, just outside and far outside of the three large inversions. Divergence between D. pseudoobscura and D. persimilis is high inside the inversions and in the suppressed recombination regions extending 2.5 Mb outside of inversions, but significantly lower in collinear regions further from the inversions. We observe little evidence of decreased divergence predicted to exist in the centre of inversions, suggesting that gene flow through double crossovers or gene conversion is limited within the inversion, or selection is acting within the inversion to maintain divergence in the face of gene flow. In combination with past studies, we provide evidence that inversions in this system maintain areas of high divergence in the face of hybridization, and have done so for a substantial period of time. The left arm of the X chromosome and chromosome 2 inversions appear to have arisen in the lineage leading to D. persimilis approximately 2 Ma, near the time of the split of D. persimilis-D. pseudoobscura-D. miranda, but likely fixed within D. persimilis much more recently, as diversity within D. persimilis is substantially reduced inside and near these two inversions. We also hypothesize that the inversions in D. persimilis may provide an empirical example of the 'mixed geographical mode' theory of inversion origin and fixation, whereby allopatry and secondary contact both play a role.

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Figures

Figure 1.

Figure 1.

Sliding window analysis of the fraction of bases in intergenic regions differentiating two genome sequences along a 200 kbp interval, iterated every 50 kbp for chromosome 2. Average pairwise differences were used for comparisons where a total of more than two genome sequences were available. Eleven Drosophila pseudoobscura genomes, three Drosophila persimilis and three Drosophila miranda were used in generating the graphs. Dashed lines represent the boundaries of the inversions and dotted lines are the boundaries of recombination suppression as defined in Stevison et al. [6]. Chromosomes are presented from telomere to centromere. Orange, D. persimilis_–_D. persimilis; pink, D. pseudoobscura_–_D. pseudoobscura; green, D. pseuodoobscura_–_D. persimilis; blue, D. miranda_–_D. seudoobscura; grey, D. miranda_–_D. persimilis.

Figure 2.

Figure 2.

Sliding window analysis of the fraction of bases in intergenic regions differentiating two genome sequences along a 200 kbp interval, iterated every 50 kbp for the XL chromosome arm. All legends and data used same as in figure 1.

Figure 3.

Figure 3.

Sliding window analysis of the fraction of bases in intergenic regions differentiating two genome sequences along a 200 kbp interval, iterated every 50 kbp for the XR chromosome arm. All legends and data used same as in figure 1, except that one resequenced line of Drosophila persimilis was not included.

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