Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an 710069, PR China.
Mol Phylogenet Evol. 2010 May;55(2):721-32. doi: 10.1016/j.ympev.2010.02.010. Epub 2010 Feb 19.
In this paper, we report the phylogeographic history of Clintoniaudensis Trautv. & Mey. (Liliaceae) inferred from two types of chloroplast DNA markers, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and DNA sequences. Eighty samples were collected from 20 natural populations, 19 located in China and one in Japan, across the entire range of the species in East Asia. High genetic diversity (h(T)(PCR-RFLP)=0.972, h(T)(sequencing)=0.874) and significant differentiation (N(ST)(PCR-RFLP)=0.893, N(ST)(sequencing)=0.988 and G(ST)(PCR-RFLP)=0.777, G(ST)(sequencing)=0.978) were detected at the species level. These findings are consistent with a scenario of clonal reproduction and locally restricted gene exchange. The level of diversity of tetraploid populations was slightly greater than that of diploid populations. Significant molecular variation was found between tetraploids and diploids. Tetraploids may be autopolyploids and may have formed repeatedly in different locations. At least three regions of origin could be recognized. Twenty-six distinct haplotypes were identified. Haplotype frequency distributions were strongly skewed, with most haplotypes (n=25) represented by only one sample each and thus restricted to a single population. Non-overlapping distributions of cpDNA haplotypes and strong genetic differentiation among populations and/or different ploid level were consistent with the findings of a nested clade analysis, which inferred long-distance colonization as the major process influencing the spatial haplotype distribution of this species. Nested clade analysis showed that the 26 haplotypes formed two 3-step, four 2-step and eleven 1-step clades, with twelve clades showing significant geographical associations. Higher N(ST) than G(ST) (P<0.05) suggested a distinct phylogeographical pattern. Based on mismatch distribution analysis and neutrality tests, we found no evidence of population expansion in the species. Our analyses indicate that the history of C.udensis involved both long-distance migration and the tectonic events of Mountains in East Asia.
本文报告了 Clintoniaudensis Trautv. & Mey.（百合科）的系统地理历史，该研究基于两种类型的叶绿体 DNA 标记，聚合酶链反应-限制性片段长度多态性（PCR-RFLP）和 DNA 序列。从东亚该物种的整个分布范围内的 20 个自然种群中采集了 80 个样本，其中 19 个位于中国，1 个位于日本。高遗传多样性（PCR-RFLP 下 h(T)=0.972，测序下 h(T)=0.874）和显著分化（PCR-RFLP 下 N(ST)=0.893，测序下 N(ST)=0.988 和 G(ST)(PCR-RFLP)=0.777，测序下 G(ST)=0.978）在种水平上被检测到。这些发现与克隆繁殖和局部限制基因交换的情况一致。四倍体种群的多样性水平略高于二倍体种群。在四倍体和二倍体之间发现了显著的分子变异。四倍体可能是同源多倍体，可能在不同的地点反复形成。可以识别出至少三个起源区域。鉴定出 26 个不同的单倍型。单倍型频率分布严重偏斜，大多数单倍型（n=25）仅由一个样本代表，因此仅局限于一个种群。叶绿体单倍型的非重叠分布和种群之间或不同倍性水平之间的强烈遗传分化与嵌套枝分析的结果一致，该分析推断长途殖民化是影响该物种空间单倍型分布的主要过程。嵌套枝分析表明，26 个单倍型形成了两个 3 步、四个 2 步和 11 个 1 步枝，其中 12 个枝表现出明显的地理相关性。N(ST)显著高于 G(ST)（P<0.05），表明存在明显的系统地理格局。基于不匹配分布分析和中性检验，我们没有发现该物种存在种群扩张的证据。我们的分析表明，C.udensis 的历史涉及长途迁徙和东亚山脉的构造事件。
