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）会通过两种方式干扰杂合子（heterozygotes）中的重组：一是降低倒位区域（inverted regions）内的交换事件，二是提升基因组其他区域的重组水平。正如多种染色体物种形成模型所阐述的那样，倒位区域内重组水平的降低，有助于杂交物种的稳定维持。本研究对倒位对重组率（recombination rates）以及核苷酸分歧（nucleotide divergence）的影响进行了全面比较分析。在区分拟暗果蝇（Drosophila pseudoobscura）和近拟暗果蝇（Drosophila persimilis）的倒位区域中，我们在筛选得到的9739份F1杂种（F1 hybrids）后代里检测到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近，但我们未在该倒位区域内发现基于序列的种间持续基因交流证据，不过种内却存在显著的基因交流推断结果。同时我们还观察到，相较于种内，物种间在倒位断点（inversion breakpoints）附近区域的分化程度更高。此外，我们还观测到显著的“染色体间效应（interchromosomal effect）”：即物种间倒位杂合子的重组水平更高，杂种的第二条染色体共线性区段（collinear segments）的重组率最高可达原水平的9倍。进一步研究发现，最易受重组率变化影响的区域，正是同核型（homokaryotypes）个体中重组率本就较低的区域。最后，我们证实重组率提升幅度越大的区域，其种间核苷酸分歧程度越低，这一现象可能源于更强的种间基因交流。总体而言，我们明确了在对重组与分化的影响方面，种内分离的倒位与种间分离的倒位之间存在若干异同点。我们推断，这些差异最可能源于异核型个体的较低出现频率，以及物种间多种不相容性积累所带来的适合度（fitness）后果。此外，我们还发现了倒位对种间基因交流的潜在影响，这是此前尚未被关注到的。