Supplementary Material

SUPPLEMENTARY 1., 2. Plant material and GenBank accessions for nuclear and chloroplast sequences respectively.
SUPPLEMENTARY 3. Material and methods for sequencing the plant material with a description of all primers designed for this study
SUPPLEMENTARY 4. Illustration of the clone filtering procedure for identifying putative PCR-recombinant sequences and cross taxon contamination. All clones for the octoploid F. mirabilis (specimen 13673) were used to construct a neighborNet (uncorrected p-distances) in SplitsTree4. From ploidal level, four distinct sequences are expected. Each group highlighted in green was composed of several nearly identical sequences and was retained for phylogenetic analysis. Red sequences, connected to the main frame of the network with zero-length terminal edges, were considered to be putative PCR recombinants and were therefore discarded. A sufficient number of clones was not recovered for the blue group, which was further investigated with clade specific primers.
SUPPLEMENTARY 5. Description of the phylogenetic analyses deployed for inferring gene trees.
SUPPLEMENTARY 6. Details of the BEAST analysis dating the Dicentra-Corydalis split.
SUPPLEMENTARY 7. Description and results of the simulation that assessed the performance of the coalescent stochasticity test.
SUPPLEMENTARY 8. Table that reports the result of the coalescent stochasticity test for the sets of sequences derived from the individual small Ne and large Ne analyses of coalescent stochasticity tests. Here, all the sequences in a set are analyzed together and the inference Ne is increased until the full set passes the coalescent stochasticity test.
SUPPLEMENTARY 9. Tanglegram inferred with RAxML from sequences of the primary set. Nuclear (a) and chloroplast (b) topologies correspondences were visualized in Dendroscope 3 (Huson and Scornavacca 2012).
SUPPLEMENTARY 10. Genome tree inferred with BEAST. The maximum clade credibility chronogram was built from all nuclear homoeologues (except sequences from F. bastardii), together with chloroplast haplotypes from the primary set plus those that passed the substitution model error test. PP ≥ 0.70 are indicated below branches. Icons indicate the chloroplast sequences that were added to the analysis at the different steps of genome tree reconstruction.

SUPPLEMENTARY 1.、2. 分别对应核序列与叶绿体序列的植物材料及基因银行（GenBank）登录号。
SUPPLEMENTARY 3. 本研究中用于植物材料测序的实验方法，以及本研究设计的所有引物（primer）的详细说明。
SUPPLEMENTARY 4. 用于鉴定疑似PCR重组体序列与跨类群污染的克隆筛选流程示意图。本研究使用八倍体美丽草莓（Fragaria mirabilis，标本编号13673）的全部克隆序列，在SplitsTree4软件中构建邻域网（neighborNet，基于未校正p距离）。根据倍性水平，预期可获得4种不同的序列。每组以绿色高亮的序列均由多条高度相似的序列组成，被保留用于系统发育分析。红色序列通过零长度末端边连接至网络主框架，被判定为疑似PCR重组体，因此予以剔除。蓝色组未获得足够数量的克隆序列，后续将使用类群特异性引物开展进一步研究。
SUPPLEMENTARY 5. 用于推断基因树的系统发育分析方法说明。
SUPPLEMENTARY 6. 用于定年荷包牡丹属（Dicentra）-紫堇属（Corydalis）分化时间的BEAST分析细节。
SUPPLEMENTARY 7. 用于评估溯合随机性检验（coalescent stochasticity test）性能的模拟实验说明与结果。
SUPPLEMENTARY 8. 针对溯合随机性检验的结果统计表：该统计针对分别基于小有效种群规模（effective population size，Ne）与大有效种群规模（Ne）的溯合随机性检验得到的序列集。此处将序列集中的全部序列一同进行分析，并逐步增大推断有效种群规模，直至全序列集通过溯合随机性检验。
SUPPLEMENTARY 9. 基于原始序列集，通过RAxML软件构建的缠结树（tanglegram）。本研究将核序列拓扑结构（a）与叶绿体序列拓扑结构（b）的对应关系在Dendroscope 3软件中进行可视化（Huson与Scornavacca，2012）。
SUPPLEMENTARY 10. 通过BEAST软件推断的基因组树。该最大类群置信度年代树（maximum clade credibility chronogram）由所有核部分同源序列（homoeologue，剔除Fragaria bastardii的序列），结合原始序列集的叶绿体单倍型（chloroplast haplotypes）以及通过替换模型误差检验（substitution model error test）的叶绿体序列共同构建。分支下方标注了后验概率（Posterior Probability，PP）≥0.70的节点。图标用于标注在基因组树重建的不同步骤中加入分析的叶绿体序列。