Departament de Genètica, Microbiologia i Estadística and IRBio, Facultat de Biologia, Universitat de Barcelona, 08028, Barcelona, Spain.
Present Address: cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal.
BMC Evol Biol. 2018 Apr 24;18(1):60. doi: 10.1186/s12862-018-1178-1.
The role of chromosomal arrangements in adaptation is supported by the repeatable clinal variation in inversion frequencies across continents in colonizing species such as Drosophila subobscura. However, there is a lack of knowledge on the genetic variation in genes within inversions, possibly targets of climatic selection, across a geographic latitudinal gradient. In the present study we analysed four candidate loci for thermal adaptation, located close to the breakpoints, in two chromosomal arrangements of the sex (A) chromosome of Drosophila subobscura with different thermal preferences. Individual chromosomes with A (the inverted arrangement considered warm adapted) or A (the standard ancestral arrangement considered cold adapted) were sequenced across four European localities at varying latitudes, up to ~ 2500 Kms apart.
Importantly, we found very low differentiation for each specific arrangement across populations as well as no clinal patterns of genomic variation. This suggests wide gene exchange along the cline. Differentiation between the sex chromosome arrangements was significant in the two more proximal regions relative to the A orientation but not in the distal ones, independently of their location inside or outside the inversion. This can be possibly due to variation in the levels of gene flux and/or selection acting in these regions.
Gene flow appears to have homogenized the genetic content within-arrangement at a wide geographical scale, despite the expected diverse selective pressures in the specific natural environments of the different populations sampled. It is thus likely that the inversion frequency clines in this species are being maintained by local adaptation in face of gene flow. The differences between arrangements at non-coding regions might be associated with the previously observed differential gene expression in different thermal regimes. Higher resolution genomic scans for individual chromosomal arrangements performed over a large environmental gradient are needed to find the targets of selection and further elucidate the adaptive mechanisms maintaining chromosomal inversion polymorphisms.
染色体排列在适应中的作用得到了支持，即在殖民物种如 Drosophila subobscura 中，反转频率在大陆间呈可重复的渐变。然而，我们对于位于反转内部的基因的遗传变异知之甚少，这些基因可能是气候选择的目标，而这种变异在地理纬度梯度上是未知的。在本研究中，我们分析了四个候选热适应基因位点，它们位于 Drosophila subobscura 的性（A）染色体的两个染色体排列的断点附近，这两个排列具有不同的热偏好。具有 A（被认为是温暖适应的反转排列）或 A（被认为是寒冷适应的标准祖先排列）的个体染色体在四个不同纬度的欧洲地点进行了测序，这些地点之间的距离长达约 2500 公里。
重要的是，我们发现每个特定排列在种群之间的分化非常低，也没有基因组变异的渐变模式。这表明在整个渐变过程中有广泛的基因交换。在相对于 A 取向的两个更近端区域，性染色体排列之间的分化是显著的，但在远端区域则没有，无论它们位于反转内部还是外部。这可能是由于这些区域中基因流动和/或选择的水平变化。
尽管在不同取样的自然环境中存在不同的选择压力，但基因流动似乎已经在广泛的地理范围内使排列内的遗传内容同质化。因此，在面对基因流动时，该物种的反转频率渐变很可能是由局部适应维持的。在非编码区域中，排列之间的差异可能与之前在不同热环境中观察到的差异基因表达有关。需要对个体染色体排列进行更大环境梯度的更高分辨率基因组扫描，以找到选择的目标，并进一步阐明维持染色体倒位多态性的适应机制。
