Data from: Understanding the spectacular failure of DNA barcoding in willows (Salix): Does this result from a trans-specific selective sweep?

AbstractWillows (Salix: Salicaceae) form a major ecological component of Holarctic floras, and consequently are an obvious target for a DNA-based identification system. We surveyed two to seven plastid genome regions (~3.8 kb; ~3% of the genome) from 71 Salix species across all five subgenera, to assess their performance as DNA barcode markers. Although Salix has a relatively high level of interspecific hybridization, this may not sufficiently explain the near complete failure of barcoding that we observed: only one species had a unique barcode. We recovered 39 unique haplotypes, from more than 500 specimens, that could be partitioned into six major haplotype groups. A unique variant of group I (haplotype 1*) was shared by 53 species in three of five Salix subgenera. This unusual pattern of haplotype sharing across infrageneric taxa is suggestive of either a massive non-random coalescence failure (incomplete lineage sorting), or of repeated plastid capture events, possibly including a historical selective sweep of haplotype 1* across taxonomic sections. The former is unlikely as molecular dating indicates that haplotype 1* originated recently, and is nested in the oldest major haplotype group in the genus. Further, we detected significant non-neutrality in the frequency spectrum of mutations in group I, but not outside group I, and demonstrated a striking absence of geographic structure to the haplotype distributions in this group. The most likely explanation for the patterns we observed involves recent repeated plastid capture events, aided by widespread hybridization and long-range seed dispersal, but primarily propelled by one or more trans-species selective sweeps., Usage notesbold salix samplesspecies, specimen, location listsSALIX_matKmatK sequence alignmentSALIX_rbcLrbcL sequence alignmentSALIX_rpoBrpoB sequence alignmentSALIX_rpoC1rpoC1 sequence alignmentSALIX_trnHtrnH-psbA sequence alignmentSALIX_psbKpsbK-psbI sequence alignmentSALIX_atpFatpF-atpH sequence alignmentSALIX_COICOI sequence alignment

【摘要】柳属（Salix，杨柳科Salicaceae）是全北极植物区系（Holarctic flora）中重要的生态组成类群，因此成为DNA鉴定系统的理想研究对象。本研究从隶属于该属全部5个亚属的71个柳属物种中，选取2至7个质体基因组（plastid genome）区域（总长约3.8 kb，约占全基因组的3%）进行测序，以评估其作为DNA条形码标记（DNA barcode marker）的效能。尽管柳属存在较高水平的种间杂交（interspecific hybridization），但这不足以解释我们观测到的DNA条形码鉴定近乎完全失效的现象：本研究中仅1个物种拥有独特的DNA条形码。我们从500余份标本中成功获取了39个独特单倍型（haplotype），可划分为6个主要单倍型类群。类群I的一个独特变异型（单倍型1*）被5个亚属中的3个亚属的53个物种所共有。这种属下类群间单倍型共享的异常模式，提示存在两种可能性：一是大规模的非随机溯祖失败（coalescence failure），即谱系不完全分选（incomplete lineage sorting）；二是反复发生的质体捕获事件（plastid capture event），其中可能包含一次跨分类组的单倍型1*历史性选择性清除（selective sweep）。由于分子定年（molecular dating）结果显示单倍型1*起源较晚，且嵌套于该属最古老的主要单倍型类群中，因此第一种可能性较低。此外，我们在类群I中检测到突变频率谱（frequency spectrum of mutations）存在显著的非中性选择信号，而在类群I之外未发现该现象；同时该类群的单倍型分布完全不存在地理结构（geographic structure）。我们所观测到的上述模式最合理的解释为：近期反复发生的质体捕获事件，辅以广泛的种间杂交和长距离种子传播（seed dispersal），但核心驱动力为一次或多次跨物种选择性清除（trans-species selective sweep）。

【使用说明】
- 标注说明：需加粗标注的内容包括柳属样本、物种、标本、地点列表
- 序列比对文件：
1. SALIX_matK：matK序列比对
2. SALIX_rbcL：rbcL序列比对
3. SALIX_rpoB：rpoB序列比对
4. SALIX_rpoC1：rpoC1序列比对
5. SALIX_trnH：trnH-psbA序列比对
6. SALIX_psbK：psbK-psbI序列比对
7. SALIX_atpF：atpF-atpH序列比对
8. SALIX_COI：COI序列比对