Data from: Deep sequencing of amplicons reveals widespread intraspecific hybridization and multiple origins of polyploidy in big sagebrush (Artemisia tridentata)

PREMISE OF THE STUDY: Hybridization has played an important role in the evolution and ecological adaptation in diploid and polyploid plants. Artemisia tridentata (Asteraceae) tetraploids are extremely widespread and of great ecological importance. These tetraploids are often taxonomically identified as A. tridentata ssp. wyomingensis, or as autotetraploids of diploid subspecies tridentata and vaseyana. Few details are available as to how these tetraploids are formed or how they are related to diploid subspecies. METHODS: We used amplicon sequencing to assess phylogenetic relationships among three recognized subspecies: tridentata, vaseyana and wyomingensis. DNA sequence data from putative genes were pyrosequenced and assembled from 329 samples. Nucleotide diversity and putative haplotypes were estimated from the high-read coverage. Phylogenies were constructed from Bayesian coalescence and neighbor-net network analyses. KEY RESULTS: Analyses support distinct diploid subspecies of tridentata and vaseyana in spite of known hybridization in ecotones. Nucleotide diversity estimates of populations compared to the total diversity indicate the relationships are predominately driven by a small proportion of the amplicons. Tetraploids, including subspecies wyomingenesis, are polyphyletic occurring within and between diploid subspecies groups. CONCLUSIONS: Artemisia tridentata is a species comprised of phylogenetically distinct diploid progenitors and a tetraploid complex with varying degrees of phylogenetic and morphological affinities to the diploid subspecies. These analyses suggest tetraploids are formed locally or regionally from diploid tridentata and vaseyana populations via autotetraploidy, followed by introgression between tetraploid groups. Understanding the phylogenetic versus ecological relationships of A. tridentata subspecies will have bearing on how to restore these desert ecosystems.

研究背景：杂交在二倍体和多倍体植物的演化与生态适应过程中发挥着关键作用。三齿蒿（Artemisia tridentata，菊科Asteraceae）的四倍体类群分布范围极广，生态重要性显著。该类四倍体通常被分类学鉴定为怀俄明三齿蒿亚种（A. tridentata ssp. wyomingensis），或是二倍体亚种tridentata与vaseyana的同源四倍体。目前针对这类四倍体的形成机制，以及其与二倍体亚种的亲缘关系，相关细节仍较为匮乏。
研究方法：本研究采用扩增子测序（amplicon sequencing）技术，解析三个已确认亚种（tridentata、vaseyana及wyomingensis）间的系统发育关系。从329份样本中获取候选基因的DNA序列数据，经焦磷酸测序（pyrosequencing）后完成序列组装。基于高测序覆盖度，估算种群的核苷酸多样性与候选单倍型。通过贝叶斯溯祖（Bayesian coalescence）分析与邻分网络（neighbor-net network）分析构建系统发育树。
主要结果：分析结果表明，尽管在生态交错带存在已知的杂交事件，但tridentata与vaseyana这两个二倍体亚种仍呈现显著的遗传分化。种群核苷酸多样性与总多样性的对比分析显示，整体亲缘关系主要由少数扩增子序列驱动。包括wyomingensis亚种在内的四倍体类群属于多系类群，其演化分支分散于二倍体亚种类群内部及不同二倍体类群之间。
研究结论：三齿蒿（Artemisia tridentata）是一个由系统发育分化显著的二倍体祖先类群，以及一个与二倍体亚种存在不同程度系统发育与形态亲缘关系的四倍体复合群所构成的物种。本研究结果提示，四倍体类群主要通过同源多倍化途径，在局部或区域范围内由tridentata与vaseyana二倍体种群形成，随后在四倍体类群间发生基因渐渗。阐明三齿蒿亚种间的系统发育与生态关系，将为此类荒漠生态系统的修复工作提供重要理论支撑。