论文摘要：

须弥红豆杉复合群（Taxus wallichiana complex）是古老的第三纪孑遗植物，零星分布于我国秦岭以南的大部分省区的山地林中。本研究中，我们利用cpDNA片段、核基因ITS和微卫星标记，对须弥红豆杉复合群开展谱系地理学研究。其主要结论如下：

1. cpDNA片段的谱系地理结构

基于两个叶绿体片段，共得到11种叶绿体单倍型。结果表明，须弥红豆杉复合群具有较高的遗传多样性和显著的遗传分化。44个居群具有明显的地理结构，可以被分成5个组，即华南组、大巴组、峨眉组、云南组和秦岭组。不同组间具有极高的遗传分化，而组内居群间遗传分化不明显。利用分子钟方法对5个分支分歧时间的估算表明，它们在上新世时期就已分化形成。

2. 基于核糖体ITS序列的谱系地理结构

基于ITS结果，鉴定出38种ITS单倍型。遗传分析表明，须弥红豆杉复合群在物种和居群水平上均具有较高的遗传多样性水平。这些居群分为个4组，即华南组、大巴/峨眉组、云南组和秦岭组。几个谱系分支在第四纪冰期前就已形成，冰期时在各自独立的避难所幸存下来；一些谱系在冰期发生融合和杂交（如大巴和峨眉谱系在四川盆地以西），一些谱系在间冰期扩散过程中形成一些融合区（如秦岭谱系与大巴谱系在川西北地区的松潘一带），现在谱系地理格局可能是经冰期-间冰期多次反复作用的结果。

3. SSR标记的居群遗传学分析

利用8个微卫星位点对复合群进行了检测与分析，发现须弥红豆杉复合群具有较低的遗传多样性和较高的遗传分化，遗传分化主要存在于不同组间。分组分析结果与ITS相同，44个居群划分为4个组。根据SSR聚类分析结果，我们推断须弥红豆杉复合群不同谱系具有各自的避难所，某些谱系（如秦岭谱系和华南谱系）可能在冰期存在多个避难所，其现代分布区的格局的形成受到了青藏高原的隆升和第四纪冰期的影响。

Abstract：The Taxus wallichiana complex represents an old relict conifer lineage that survived through the Tertiary. It is currently distributed in the mountain forests in South and Southwest China south of the Qinling Mountains. In the present study, we explored phylogeography of the complex by using two chloroplast DNA regions, one nuclear ribosomal DNA spacer region and eight microsatellite (SSR) loci. The main conclusions can be summarized as follows:

1. Phylogeographic pattern based on chloroplast haplotypes

There were 11 cpDNA haplotypes identified in the T. wallichiana complex The complex showed a high level of genetic diversity and obvious genetic differentiation. The 44 sampled populations showed obvious genetic structure, which could be divided into five groups, namely the Huanan group, the Daba group, the Emei group, the Yunnan group and the Qinling group. There was extremely high genetic differentiation among groups, but not significant within group. The divergence times of the five lineages, estimated using average mutation rates of trnL-trnF, fell in the Pliocene. 

2. Phylogeographic patterns based on ITS sequences

These included 38 unique ‘haplotypes’ based on ITS data. Their analysis showed that the T. wallichiana complex possessed a high genetic diversity. These populations could be divided into four groups, namely the Huanan group, the Daba/Emei group, the Yunnan group and the Qinling group. Based on all results, it appears that the major lineages constituting the T. wallichiana complex have arisen before Quaternary glaciation cycles, and may have survived isolated in different refugia. During interglacial periods some lineages appear to have come in contact and hybridizedbut other lineages merged forming populations with mixed haplotypes without signs of hybridization. The present-day phylogeographical distribution pattern of the T. wallichiana complex might thus be the result of repeated expansion / contractions of populations during interglacial / glacial cycles.

3. Population genetic analysis using microsatellite (SSR) markers

Eight SSR loci were used for population genetic analysis on the T. wallichiana complex. A lower level of genetic diversity at the population level and high genetic differentiation among population was detected. The results of structure analysis were similar to those on the ITS data, dividing the populations into four groups (lineages). According to the results here, it was deduced that each of the 4 lineages of the T. wallichiana complex may possessed respective glacial refugia, and some lineages (such as the Qinling and Huanan lineage) might have survived in multiple refugia in the Quaternay glaciations. The present distribution pattern of this complex was likely influenced by the uplift of the QTP and Quaternary glaciation.