Data from: Effects of inversions on within- and between-species recombination and divergence

Chromosomal inversions disrupt recombination in heterozygotes by both reducing crossing over within inverted regions and increasing it elsewhere in the genome. The reduction of recombination in inverted regions facilitates the maintenance of hybridizing species, as outlined by various models of chromosomal speciation. We present a comprehensive comparison of the effects of inversions on recombination rates and on nucleotide divergence. Within an inversion differentiating Drosophila pseudoobscura and D. persimilis, we detected one double-recombinant among 9739 progeny from F1 hybrids screened, consistent with published double crossover frequencies observed within species. Despite similar rates of exchange within and between species, we found no sequence-based evidence of ongoing gene exchange between species within this inversion, but significant exchange was inferred within species. We also observed greater differentiation at regions near inversion breakpoints between species vs. within species. Moreover, we observed strong ‘interchromosomal effect’ (higher recombination in inversion heterozygotes between species) with up to 9-fold higher recombination rates along collinear segments of chromosome two in hybrids. Further, we observed that regions most susceptible to changes in recombination rates corresponded to regions with lower recombination rates in homokaryotypes. Finally, we showed that interspecies nucleotide divergence is lower in regions with greater increases in recombination rate, potentially resulting from greater interspecies exchange. Overall, we have identified several similarities and differences between inversions segregating within vs. between species in their effects on recombination and divergence. We conclude that these differences are most likely due to lower frequency of heterokaryotypes and to fitness consequences from the accumulation of various incompatibilities between species. Additionally, we have identified possible effects of inversions on interspecies gene exchange that had not been considered previously.染色体倒位（chromosomal inversions）可通过双重途径干扰杂合子（heterozygotes）中的重组：既降低倒位区域内的交换（crossing over）水平，又提升基因组其他区域的重组频率。倒位区域内重组水平的降低，有助于杂交物种的维持，这一结论已被多种染色体物种形成（chromosomal speciation）模型所证实。 我们对倒位对重组率（recombination rates）与核苷酸歧异度（nucleotide divergence）的影响开展了全面比较。在区分拟暗果蝇（Drosophila pseudoobscura）和拟果蝇（D. persimilis）的某一倒位区域中，我们在筛选得到的9739份F1杂种（F1 hybrids）后代中检测到1例双重重组体（double-recombinant），这与已发表的种内双交换（double crossover）频率观测结果相符。 尽管种内与种间的交换速率相似，但我们未在该倒位区域内发现支持物种间持续发生基因交流（gene exchange）的基于序列的证据（sequence-based evidence），但却推断出物种内存在显著的基因交流。此外，我们观察到：物种间倒位断裂点（inversion breakpoints）附近区域的分化程度，高于物种内的对应区域。 进一步研究发现，杂种中存在显著的‘染色体间效应’（interchromosomal effect）：即倒位杂合子的种间重组水平更高，其中2号染色体共线性区段（collinear segments）的重组率最高可达同核型个体的9倍。同时，重组率变化最显著的区域，恰好是同核型（homokaryotypes）个体中原本重组率较低的区域。 最后，我们证实：重组率提升幅度更大的区域，其种间核苷酸歧异度更低，这一现象可能源于更高的种间基因交流频率。总体而言，我们明确了物种内与物种间分离的倒位，在对重组与歧异度的影响上存在若干异同点。我们认为，这些差异最可能源于两方面：一是异核型个体的出现频率更低，二是物种间多种生殖不相容性（incompatibilities）的积累所带来的适合度（fitness）后果。此外，我们还发现了此前未被关注的、倒位对种间基因交流的潜在影响。