澜沧江姬鼠（Apodemus ilex）为小型啮齿类动物，长期以来常被认为是中华姬鼠（A. draco）或长尾姬鼠（A. orestes）的同物异名，但近年基于线粒体Cyt b 的研究证明，该类群与中华姬鼠的遗传距离达到了种间水平，并被认为是一个独立种。本文提取、扩增并测定了来自云南14个地区42个产地156个澜沧江姬鼠的Cyt b 全序列，并将GenBank中的3条澜沧江姬鼠的Cyt b 全序列纳入分析，选取福建武夷山与四川峨眉山的2个中华姬鼠样品的Cyt b 全序列，以及台湾姬鼠、大耳姬鼠、高山姬鼠Cyt b 全序列作为外群，利用贝叶斯法和最大似然法构建系统发育树，并使用Network分析，分子变异分析（AMOVA）分析、错配分析（Mismatch analysis）与Fu`Fs检验等方法，探讨了这些地区澜沧江姬鼠的种群遗传结构，种群动态及生物地理格局。结果表明：云南地区过去被鉴定为中华姬鼠的样品均属于澜沧江姬鼠，澜沧江姬鼠与中华姬鼠间的遗传距离（K2P-ds+v）达到0.091，显著超过姬鼠属内种间差距（0.080），支持澜沧江姬鼠独立种的地位；该种不同地理种群可大致以澜沧江为界分为两大支系，且每个支系又各分为两个亚支系；进一步的AMOVA分析表明遗传变异主要来源于两大支系之间，而错配分析与Fu`Fs检验表明澜沧江姬鼠各地理种群及其两个支系都经历过多次扩张事件，这可能是和冰期与间冰期的轮回交替有关；分子系统树和中介网络图表明地理环境的隔离对于澜沧江姬鼠种群分化存在明显影响，其中澜沧江的阻隔作用最为显著。基于松散分子钟（Relax molecular clock）分析，中华姬鼠和澜沧江姬鼠的分歧时间大约在2.98 Ma（95％HPD: 4.32-1.88），而澜沧江姬鼠则在1.13 Ma（95％HPD: 1.95-0.65）分成两个支系。按照平均分歧时间来看，澜沧江姬鼠两个支系的的分歧事件发生在鄱阳冰期（1.2-0.9 Ma），两个支系内部进一步分化为两支的时间非常接近，分别为：Clade 1中为0.67 Ma （95％HPD: 1.17-0.34）和Clade 2 中为0.64 Ma (95％HPD: 1.17-0.36)，这种隔离种群各自产生分化的时间却非常接近，这提示其分化事件可能是受到古气候如冰期或间冰期的影响所产生。
其他摘要
As a small rodent, Apodemus ilex used to be regarded as a synonym of A. draco or A. orestes, whereas recent molecular study based on complete mtDNA cytochrome b (Cyt b) indicated that it is a separate species. We sequenced complete Cyt b from the 156 individuals of A. ilex from 14 areas, 42 locations in Yunnan. In addition, complete Cyt b sequences of all three published A. ilex was included in our study. We use two A. draco(from Kuatun, Fujian and Emeishan, Sichuan), and A. semotus, A. latronum, A. chevrieri download from Genbank as outgroup. Bayesian inference and Maximum likelihood were used to construct phylogenetic tree, and we analyzed genetic structure, history of population dynamics and pattern of biogeography of A. ilex using Network analysis、AMOVA analysis、Mismatch analysis and Fu`Fs test. The results support that the individuals in Yunnan, which were treated as A. draco, should be identified as A. ilex. The genetic distance (K2P-ds+v) between A. ilex and A. draco is 0.091. It is significantly beyond species-level genetic distance within Apodemus (0.080), which supports A. ilex may be regarded as a separate species rather than a synonym of A. draco. Various geographic population of Apodemus ilex were divided into two clades and separated by Lancangjiang River. Each Clade can further divided into two sub-clades. AMOVA analysis revealed that genetic variation was primarily contributed by the difference between the two main clades. Mismatch analysis and Fu`Fs test revealed that each population and the two main clades of A. ilex had experienced multiple expanding accidents, which maybe caused by the reiteration between glacial and interglacial age. Phylogeny tree and Network analysis revealed geographic isolation have obvious influence on the population differentiation, and isolation effect of Lancangjiang River is the most significant. Relax molecular clock analysis based on Lognormal model revealed the divergence time of A. draco with A. ilex is 2.98 Ma (95％HPD: 4.32-1.88). A. ilex divided into two clades at 1.13 Ma (95％HPD: 1.95-0.65), and it may happened in Poyang glaciation (1.2-0.9 Ma).The divergence time between sub-clades in two main clades are closed to each other. Divergence time in clade 1 is 0.67 Ma（95％HPD: 1.17-0.34）and in clade 2 is 0.64 Ma (95％HPD: 1.17-0.36). Isolate population have nearly closed divergence time in differentiation，that implies the differentiation may affected by paleoclimate such as glacial and interglacial age.
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