Data from: Altered gene expression and ecological divergence in sibling allopolyploids of Dactylorhiza (Orchidaceae)

Background: Hybridization and polyploidy are potent forces that have regularly stimulated plant evolution and adaptation. Dactylorhiza majalis s.s., D. traunsteineri s.l. and D. ebudensis are three allopolyploid species of a polyploid complex formed through unidirectional (and, in the first two cases, recurrent) hybridization between the widespread diploids D. fuchsii and D. incarnata. Differing considerably in geographical extent and ecological tolerance, the three allopolyploids together provide a useful system to explore genomic responses to allopolyploidization and reveal their role in adaptation to contrasting environments.
Results: Analyses of cDNA-AFLPs show a significant increase in the range of gene expression of these allopolyploid lineages, demonstrating higher potential for phenotypic plasticity than shown by either parent. Moreover, allopolyploid individuals express significantly more gene variants (including novel alleles) than their parents, providing clear evidence for an increase in biological complexity following allopolyploidization. Significantly more genetic mutations have accumulated in the older D. majalis compared with the younger D. traunsteineri since their respective formation.
Conclusions: Multiple origins of these tetraploids contribute to differential patterns of gene expression with a distinct geographic structure. However, several transcripts conserved within each allopolyploid taxon differ between taxa, indicating that habitat preferences shape similar expression patterns in these independently formed allopolyploids. Statistical signals separate several adaptive transcripts, related mainly to a combination of water availability and temperature that may play a role favouring the persistence of individuals in their native environments. In addition to stabilizing the allopolyploid genome, genetic and epigenetic alterations are key determinants of the adaptive success of the new polyploid species after recurrent allopolyploidization events, potentially triggering reproductive isolation between the resulting lineages.

背景：杂交与多倍化是推动植物演化与适应的核心动力，长期持续塑造着植物的进化历程。狭义掌裂兰（*Dactylorhiza majalis s.s.*）、广义特拉恩施泰因特兰（*Dactylorhiza traunsteineri s.l.*）与埃布丹掌裂兰（*Dactylorhiza ebudensis*）是由广布二倍体（diploid）宽叶掌裂兰（*Dactylorhiza fuchsii*）和淡紫掌裂兰（*Dactylorhiza incarnata*）通过单向杂交（前两类物种的杂交为反复发生）形成的多倍体复合体中的三个异源多倍体（allopolyploid）物种。这三个异源多倍体物种在地理分布范围与生态耐受特性上存在显著差异，共同构成了一套理想的研究体系，可用于解析异源多倍化（allopolyploidization）后的基因组响应机制，并揭示其在适应不同生境过程中发挥的作用。
结果：对cDNA扩增片段长度多态性（cDNA-AFLP）的分析显示，这些异源多倍体谱系的基因表达谱范围显著扩大，表现出相较于双亲更高的表型可塑性（phenotypic plasticity）潜力。此外，异源多倍体个体所表达的基因变异（包括新等位基因）数量显著多于双亲，为异源多倍化后生物复杂性的提升提供了明确证据。值得注意的是，自形成以来，起源更早的狭义掌裂兰相较于较年轻的广义特拉恩施泰因特兰积累了更多的遗传突变。
结论：这些四倍体（tetraploid）物种的多重起源事件，造就了具有显著地理结构特征的差异化基因表达模式。然而，每个异源多倍体类群内保守的若干转录本在不同类群间存在差异，这表明生境偏好塑造了这些独立起源的异源多倍体的相似表达模式。统计学分析信号筛选出了若干适应性转录本，这些转录本主要与水分有效性与温度的组合效应相关，可能有助于个体在原生境中持续存活。除了稳定异源多倍体基因组外，遗传与表观遗传修饰（epigenetic alteration）是反复异源多倍化事件后新多倍体物种适应成功的关键决定因素，还可能在衍生谱系间引发生殖隔离（reproductive isolation）。