基于线粒体DNA和微卫星标记的大石鸡分子生态学的研究
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摘要
大石鸡(Alectoris magna)隶属于鸟纲(Aves)、鸡形目(Galliforms)、雉科(Phasianidae)、石鸡属(Alectoris),是我国的特有种,分布区狭窄,分化为两个亚种,即指名亚种(A.m.magna)和兰州亚种(A.m. lanzhouensis)。本文以线粒体DNA (mtDNA)的控制区(CR)和细胞色素b (Cytb)以及微卫星(SSR)为分子标记,研究了我国12个地理种群的大石鸡分子生态学以及大石鸡与石鸡之间的渐渗杂交。本文的主要目的是：(1)采用不同分子标记检测大石鸡不同地理种群的遗传多样性,揭示不同的环境因子对大石鸡遗传多样性的影响；(2)通过分子手段构建大石鸡整个分布区内的系统地理结构,检验其是否存在明显的系统地理分化；(3)分析比较不同分子标记构建的系统地理结构之间是否存在差异；(4)分析种群的遗传分化和种群历史动态,阐述更新世冰川作用和气候变化对大石鸡系统发生的影响；(5)通过分析杂交种群的杂交率和杂交种群的遗传多样性,检测渐渗杂交对大石鸡种群遗传多样性的影响；(6)进一步确定大石鸡与石鸡渐渗杂交的范围,推测杂交时间；(7)从遗传学角度探讨大石鸡的保护问题。本研究中,分子生态学的部分共对大石鸡12个地理种群的258个样本进行了分析,其中包括173个样本的mtDNA CR部分序列(1127bp)、230个样本的mtDNA Cytb部分序列(807bp)以及257个样本的8个多态性微卫星位点。渐渗杂交的部分采用了大石鸡分布区内15个地理种群的287个具大石鸡形态的样本的CR部分序列(473bp)和267个具大石鸡形态的样本的Cytb部分序列(807bp),以及宋森毕业论文中25个地理种群的285个具石鸡形态的样本的CR部分序列以及杨志松毕业论文中8个的地理种群的48个具石鸡形态的样本的Cytb部分序列。获得的主要研究结果如下：
1.大石鸡mtDNA CR和mtDNA Cytb的碱基含量都显示A+T的含量超过了一半,符合1ntDNA控制区是“A和T丰富区”。173个样本的mtDNA CR序列中共发现33个变异位点,定义了44种单倍型,核苷酸多样性和单倍型多样性分别为0.00449和0.916。230个样本的mtDNA Cytb序列中共发现13个变异位点,定义了14种单倍型,核苷酸多样性和单倍型多样性分别为0.00216和0.738。8对微卫星位点平均等位基因数为18.875,平均期望杂合度和观察杂合度分别为0.90和0.88,总体遗传多样性低于其它分布于青藏高原和黄土高原的鸟类。
2.MtDNA CR的核苷酸多样性与降水量显著负相关,说明气候因子中降水量是影响大石鸡遗传多样性的一个非常重要的因素,降水量越小,大石鸡遗传多样性越高。微卫星的观测杂合度与相对湿度变异系数呈显著正相关,说明气候越不稳定,大石鸡的遗传多样性越高。
3.mtDNA CR、Cytb和拼接序列的贝叶斯树和网络图显示大石鸡12个地理种群的样本可以分为三个平行的进化分支,这三个分支没有显示出明显的地理分化,微卫星分析也获得了相同的结果,表明大石鸡并没有明显的系统地理结构。
4.不同分子标记的AMOVA的结果显示,虽然大多数的遗传变异存在于种群内,但是地理群组内种群间以及地理群组间也存在显著的遗传,只是分化程度比较低,Fst值也显示大多种群间的遗传分化都显著。1mtDNA控制区的单倍型组成表明柴达木盆地与其它群组之间只有一个共享单倍型,说明柴达木盆地的种群与其它两个地理群组的种群之间具有一定的遗传分化,造成遗传分化的主要原因可能是更新世冰期的冰川作用,但由于冰期持续时间较短,进入间冰期之后,冰川消融,产生隔离作用的屏障消失,柴达木盆地的种群与其它种群之间又会发生广泛的基因交流,减弱了因冰期隔离所造成的遗传分化,使得地理群组之间的遗传分化水平低,而且缺乏明显的系统地理结构。
5.柴达木盆地的种群分布于网络图的两端,位于网络图右端的这一部分柴达木盆地的个体在CR和Cytb的网络图中都与其它群组的样本没有共享单倍型,推测这一部分个体在物种形成之初就已经存在于柴达木盆地,经历了中更新世以来的多次冰川的隔离作用,尤其是规模最大的倒数第三次冰期,被隔离的时间比较早,它们和其它群组的个体之间的遗传分化比较明显。位于控制区和拼接序列网络图左端的这一部分柴达木盆地的个体,在CR的网络图中与其它群组的个体之间有一个共享单倍型,但在Cytb网络图中,这一部分个体全部与其它群组的个体共享一个单倍型,推测这一部分样本是从陇中黄土高原扩散过去的种群所演化而来的,被隔离的时间比较晚,因此与其他群组的遗传分化不明显。
6.错配分布和中性检验的结果支持大石鸡兰州亚种经历过种群扩张,扩张的时间为0.23-0.18Mya,这段时期在青藏高原冰期划分上属于倒数第二次冰期(0.33Mya-0.13Mya),而在第四纪气候划分上属于第四寒冷期(0.24-0.15Mya),气候特征为干冷多风,植被类型属于荒漠型植被,草原的发育和森林的退缩是造成大石鸡种群扩张的主要原因。
7.大石鸡和石鸡之间的杂交是石鸡基因向大石鸡的单向渗透,属于渐渗杂交。仅在六盘山地区的大石鸡种群中发现了杂种,基本都位于六盘山山脉周缘到礼县的位置的长度大约为400km,宽度约为130km的杂交带中。杂种具有石鸡的线粒体基因型和大石鸡的核基因型。渐渗杂交对大多数大石鸡种群的遗传多样性并没有产生明显的影响,但靠近六盘山的种群杂交率很高,甚至达到了100%,基因的不对称渗透可能导致这些地区的大石鸡种群发生遗传灭绝。根据mtDNA CR部分序列计算的杂交时间为0.049-0.062Myr,与宋森计算的大多数石鸡种群的扩张时间(0.027-0.060Mya)相对应。
8.线粒体DNA控制区和细胞色素b的贝叶斯分析均显示大石鸡在系统发生树上没有互为单系发生的种群存在,因此应该将大石鸡作为一个独立的进化显著单元(ESU)来对待。AMOVA结果显示大部分遗传变异分布于种群内,但种群间和群组间也存在显著的遗传变异,除了民和、靖远、会宁、礼县和海原种群外,其它种群间的Fst均显著,所以应该把民和、靖远、会宁、礼县和海原种群作为一个管理单元,其它种群分别作为独立的管理单元(MU)来实现短期内的管理和保护。
The rusty-necklaced partridge (Alectoris magna) is an endemic species of birds in China belonging to Aves, Galliformes, Phasianidae, Alectoris with two described subspecies A.m.magna and A.m.lanzhouensis. In this study, the molecular ecology of A.magna was studied from12populations across the entire distributional ranges based on mitochondrial DNA (CR+Cytb) and microsatellite markers. Introgression between A.magna and Alectoris chukar was also studied using mtDNA (CR+Cytb) and microsatellite markers. The aims of this study are to:(1) examine the effects of environmental factors on population genetic diversity of the12A.magna populations;(2) reconstruct the phylogeographic relationship of A.magan and detect whether there exists obvious phylogeographic differentiation in this species;(3) compare the phylogeographic structures based on different molecular markers;(4) demonstrate the roles of Pleistocene glaciation and climate oscillation played in the population structure, based on the analyses of genetic differentiation and population demography;(5) detect the effects of hybridization on the genetic diversity of A.magna;(6)confirm the geographic ranges of hybridization and speculate the time when the hybridization happened;(7)discuss the genetic conservation of A.magna.
In this study, partial mtDNA CR sequences (1127bp) of173specimens, partial mtDNA Cytb sequences(807bp) of230specimens, and eight microsatellite loci for257specimens from12populations were used to analyze the molecular ecology of A.magna. Partial mtDNA CR sequences(473bp)of287specimens and Partial mtDNA Cytb sequences(807bp)of267specimens from15populations of A.magna, as well as partial sequences (473bp) of285specimens from25populations of Alectoris chukar and partial sequences (807bp) of48specimens from eight populations of A. chukar, were used to analyze the hybridization. The main results include:
1. There were significant differences in base composition among12A.magna populations. The value of A+T preponderated over a half of the total base content, which was consistent with mtDNA control—region including abundance A and T. Forty-four haplotypes were defined by34variable sites with the mean haplotype diversity of0.916and the nucleotide diversity of0.00449based on mtDNA CR. Fourteen haplotypes were defined by14variable sites with the mean haplotype diversity of0.738and the nucleotide diversity of0.00216based on mtDNA Cytb. The average expected and observed heterozygosity was0.90and0.88, respectively. The genetic diversity of A.magna was lower than other birds distributed on Tibetan Plateau and Loess Plateau.
2. A significantly negtive correlation was observed between nucleotide diversity of mtDNA CR and rainfall, indicating the more abundant the precipitation, the lower the genetic diversity. Precipitation played an important role in genetic diversity of A.magna. A significantly positive correlation was observed between expeted heterozygosity (HE) and variation coefficients of annual mean relative humidity (VCH), indicating the more unstable the climate, the higher the genetic diversity.
3. For mtDNA CR, Cytb and combined sequences, all of the haplotypes formed three paraphyletic groups without evident spatial clustering. The similar results was also observed in the analysis based on microsatellites markers, indicating the lack of phylogeographic structure in A.magna.
4. AMOVA analyses suggested that the variation among individuals within populations (ΦST) was maximized and the variation among regional groups(ΦCT) was minimized. However, ΦST,ΦCT and the variation among populations (ΦSC) were all statistically significant. Most of populations pairwise Fst-value was also statistically significant. Only one haplotype was shared by the specimens from Qaidam Basin and the other regional groups, indicating the low genetic differentiation between the populations from Qaidam Basin and the other regional groups. The populations in Qaidam Basin might be isolated from the other populations by the glaciation occurred in Pleistocene glacial period. However, the glacial ablation in the following interglacial period resulted in the disappearance of barriers. Extensive gene flow occurred between all populations of A.magna, decreasing the genetic differentiation among populations.
5. For the CR and combined data set, the specimens from Qaidam Basin were distributed in both ends of the networks. The Qaidam specimens distributed in the right end have no shared haplotype with specimens from the other regional groups in all of the networks based on CR、 Cytb and combined sequences. They might be native to Qaidam Basin. However, the Qaidam specimens distributed in the left ends have shared haplotypes with specimens from the other regional groups in all of the three haplotype network. They might be derived from the specimens from the other regioanl groups and be isolated more recently than the specimens native to Qaidam Basin. Thus, they showed lower genetic differentiation with specimens from other regional groups.
6. The analysis of mismatch distribution and test of selective neutrality indicated that subspecies A.m.lanzhouensis had experienced population expansion at0.23-0.18Mya, co-occurring with the Penultimate Glaciation(0.33-0.13Mya) and the fifth cold period (0.24-0.15Mya), when the climate was dry and cold and the desert-steppe extended.
7. The A.chukar's mitochondrial genotype could be found in A.magna, but A.magna's mitochondrial genotype could not be found in A.chukar. Thus, we can confirm that there existed introgression hybridization between A.magna and A.chukar. The introgression hybridization was only found in the surronding of the Liupan Mountains to Lixian County. Only A.chukar's mitochondrial genotype and A.magna's nuclear genotype could be observed in the hybrids. High level of introgression was observed in populations near to Liupan Mountains. The hybrid rate have reached100%in Longde. The asymmetrical introgression may result in the extinction of the population of A.magna distrubuted near to Liupan Mountains. The time when hybridization happened was about0.049-0.062Myr, which is consistent with the population expansion time of A.chukar (0.027-0.060Mya).
8. Bayes analysis based on CR and Cytb revealed limited phylogenetic distinction between geographically distant populations of the rusty-necklaced partridge, and tentative support for a single evolutionarily significant unit (ESU) range. AMOVA revealed that the most genetic variation was distributed within populations. However, the genetic variations among groups and poulations were also statistically significant. The population pairwise Fst-value was not statistically significant among Minghe(MH), Jingyuan(JY), Huining(HN), Li country(LX) and Haiyuan(HY), but statistically significant among the other populations. According to the criteria of Mus, MH, JY, HN, LX and HY should be treated as a MU and the other populations should be treated as independent MUs.
1.大石鸡mtDNA CR和mtDNA Cytb的碱基含量都显示A+T的含量超过了一半,符合1ntDNA控制区是“A和T丰富区”。173个样本的mtDNA CR序列中共发现33个变异位点,定义了44种单倍型,核苷酸多样性和单倍型多样性分别为0.00449和0.916。230个样本的mtDNA Cytb序列中共发现13个变异位点,定义了14种单倍型,核苷酸多样性和单倍型多样性分别为0.00216和0.738。8对微卫星位点平均等位基因数为18.875,平均期望杂合度和观察杂合度分别为0.90和0.88,总体遗传多样性低于其它分布于青藏高原和黄土高原的鸟类。
2.MtDNA CR的核苷酸多样性与降水量显著负相关,说明气候因子中降水量是影响大石鸡遗传多样性的一个非常重要的因素,降水量越小,大石鸡遗传多样性越高。微卫星的观测杂合度与相对湿度变异系数呈显著正相关,说明气候越不稳定,大石鸡的遗传多样性越高。
3.mtDNA CR、Cytb和拼接序列的贝叶斯树和网络图显示大石鸡12个地理种群的样本可以分为三个平行的进化分支,这三个分支没有显示出明显的地理分化,微卫星分析也获得了相同的结果,表明大石鸡并没有明显的系统地理结构。
4.不同分子标记的AMOVA的结果显示,虽然大多数的遗传变异存在于种群内,但是地理群组内种群间以及地理群组间也存在显著的遗传,只是分化程度比较低,Fst值也显示大多种群间的遗传分化都显著。1mtDNA控制区的单倍型组成表明柴达木盆地与其它群组之间只有一个共享单倍型,说明柴达木盆地的种群与其它两个地理群组的种群之间具有一定的遗传分化,造成遗传分化的主要原因可能是更新世冰期的冰川作用,但由于冰期持续时间较短,进入间冰期之后,冰川消融,产生隔离作用的屏障消失,柴达木盆地的种群与其它种群之间又会发生广泛的基因交流,减弱了因冰期隔离所造成的遗传分化,使得地理群组之间的遗传分化水平低,而且缺乏明显的系统地理结构。
5.柴达木盆地的种群分布于网络图的两端,位于网络图右端的这一部分柴达木盆地的个体在CR和Cytb的网络图中都与其它群组的样本没有共享单倍型,推测这一部分个体在物种形成之初就已经存在于柴达木盆地,经历了中更新世以来的多次冰川的隔离作用,尤其是规模最大的倒数第三次冰期,被隔离的时间比较早,它们和其它群组的个体之间的遗传分化比较明显。位于控制区和拼接序列网络图左端的这一部分柴达木盆地的个体,在CR的网络图中与其它群组的个体之间有一个共享单倍型,但在Cytb网络图中,这一部分个体全部与其它群组的个体共享一个单倍型,推测这一部分样本是从陇中黄土高原扩散过去的种群所演化而来的,被隔离的时间比较晚,因此与其他群组的遗传分化不明显。
6.错配分布和中性检验的结果支持大石鸡兰州亚种经历过种群扩张,扩张的时间为0.23-0.18Mya,这段时期在青藏高原冰期划分上属于倒数第二次冰期(0.33Mya-0.13Mya),而在第四纪气候划分上属于第四寒冷期(0.24-0.15Mya),气候特征为干冷多风,植被类型属于荒漠型植被,草原的发育和森林的退缩是造成大石鸡种群扩张的主要原因。
7.大石鸡和石鸡之间的杂交是石鸡基因向大石鸡的单向渗透,属于渐渗杂交。仅在六盘山地区的大石鸡种群中发现了杂种,基本都位于六盘山山脉周缘到礼县的位置的长度大约为400km,宽度约为130km的杂交带中。杂种具有石鸡的线粒体基因型和大石鸡的核基因型。渐渗杂交对大多数大石鸡种群的遗传多样性并没有产生明显的影响,但靠近六盘山的种群杂交率很高,甚至达到了100%,基因的不对称渗透可能导致这些地区的大石鸡种群发生遗传灭绝。根据mtDNA CR部分序列计算的杂交时间为0.049-0.062Myr,与宋森计算的大多数石鸡种群的扩张时间(0.027-0.060Mya)相对应。
8.线粒体DNA控制区和细胞色素b的贝叶斯分析均显示大石鸡在系统发生树上没有互为单系发生的种群存在,因此应该将大石鸡作为一个独立的进化显著单元(ESU)来对待。AMOVA结果显示大部分遗传变异分布于种群内,但种群间和群组间也存在显著的遗传变异,除了民和、靖远、会宁、礼县和海原种群外,其它种群间的Fst均显著,所以应该把民和、靖远、会宁、礼县和海原种群作为一个管理单元,其它种群分别作为独立的管理单元(MU)来实现短期内的管理和保护。
The rusty-necklaced partridge (Alectoris magna) is an endemic species of birds in China belonging to Aves, Galliformes, Phasianidae, Alectoris with two described subspecies A.m.magna and A.m.lanzhouensis. In this study, the molecular ecology of A.magna was studied from12populations across the entire distributional ranges based on mitochondrial DNA (CR+Cytb) and microsatellite markers. Introgression between A.magna and Alectoris chukar was also studied using mtDNA (CR+Cytb) and microsatellite markers. The aims of this study are to:(1) examine the effects of environmental factors on population genetic diversity of the12A.magna populations;(2) reconstruct the phylogeographic relationship of A.magan and detect whether there exists obvious phylogeographic differentiation in this species;(3) compare the phylogeographic structures based on different molecular markers;(4) demonstrate the roles of Pleistocene glaciation and climate oscillation played in the population structure, based on the analyses of genetic differentiation and population demography;(5) detect the effects of hybridization on the genetic diversity of A.magna;(6)confirm the geographic ranges of hybridization and speculate the time when the hybridization happened;(7)discuss the genetic conservation of A.magna.
In this study, partial mtDNA CR sequences (1127bp) of173specimens, partial mtDNA Cytb sequences(807bp) of230specimens, and eight microsatellite loci for257specimens from12populations were used to analyze the molecular ecology of A.magna. Partial mtDNA CR sequences(473bp)of287specimens and Partial mtDNA Cytb sequences(807bp)of267specimens from15populations of A.magna, as well as partial sequences (473bp) of285specimens from25populations of Alectoris chukar and partial sequences (807bp) of48specimens from eight populations of A. chukar, were used to analyze the hybridization. The main results include:
1. There were significant differences in base composition among12A.magna populations. The value of A+T preponderated over a half of the total base content, which was consistent with mtDNA control—region including abundance A and T. Forty-four haplotypes were defined by34variable sites with the mean haplotype diversity of0.916and the nucleotide diversity of0.00449based on mtDNA CR. Fourteen haplotypes were defined by14variable sites with the mean haplotype diversity of0.738and the nucleotide diversity of0.00216based on mtDNA Cytb. The average expected and observed heterozygosity was0.90and0.88, respectively. The genetic diversity of A.magna was lower than other birds distributed on Tibetan Plateau and Loess Plateau.
2. A significantly negtive correlation was observed between nucleotide diversity of mtDNA CR and rainfall, indicating the more abundant the precipitation, the lower the genetic diversity. Precipitation played an important role in genetic diversity of A.magna. A significantly positive correlation was observed between expeted heterozygosity (HE) and variation coefficients of annual mean relative humidity (VCH), indicating the more unstable the climate, the higher the genetic diversity.
3. For mtDNA CR, Cytb and combined sequences, all of the haplotypes formed three paraphyletic groups without evident spatial clustering. The similar results was also observed in the analysis based on microsatellites markers, indicating the lack of phylogeographic structure in A.magna.
4. AMOVA analyses suggested that the variation among individuals within populations (ΦST) was maximized and the variation among regional groups(ΦCT) was minimized. However, ΦST,ΦCT and the variation among populations (ΦSC) were all statistically significant. Most of populations pairwise Fst-value was also statistically significant. Only one haplotype was shared by the specimens from Qaidam Basin and the other regional groups, indicating the low genetic differentiation between the populations from Qaidam Basin and the other regional groups. The populations in Qaidam Basin might be isolated from the other populations by the glaciation occurred in Pleistocene glacial period. However, the glacial ablation in the following interglacial period resulted in the disappearance of barriers. Extensive gene flow occurred between all populations of A.magna, decreasing the genetic differentiation among populations.
5. For the CR and combined data set, the specimens from Qaidam Basin were distributed in both ends of the networks. The Qaidam specimens distributed in the right end have no shared haplotype with specimens from the other regional groups in all of the networks based on CR、 Cytb and combined sequences. They might be native to Qaidam Basin. However, the Qaidam specimens distributed in the left ends have shared haplotypes with specimens from the other regional groups in all of the three haplotype network. They might be derived from the specimens from the other regioanl groups and be isolated more recently than the specimens native to Qaidam Basin. Thus, they showed lower genetic differentiation with specimens from other regional groups.
6. The analysis of mismatch distribution and test of selective neutrality indicated that subspecies A.m.lanzhouensis had experienced population expansion at0.23-0.18Mya, co-occurring with the Penultimate Glaciation(0.33-0.13Mya) and the fifth cold period (0.24-0.15Mya), when the climate was dry and cold and the desert-steppe extended.
7. The A.chukar's mitochondrial genotype could be found in A.magna, but A.magna's mitochondrial genotype could not be found in A.chukar. Thus, we can confirm that there existed introgression hybridization between A.magna and A.chukar. The introgression hybridization was only found in the surronding of the Liupan Mountains to Lixian County. Only A.chukar's mitochondrial genotype and A.magna's nuclear genotype could be observed in the hybrids. High level of introgression was observed in populations near to Liupan Mountains. The hybrid rate have reached100%in Longde. The asymmetrical introgression may result in the extinction of the population of A.magna distrubuted near to Liupan Mountains. The time when hybridization happened was about0.049-0.062Myr, which is consistent with the population expansion time of A.chukar (0.027-0.060Mya).
8. Bayes analysis based on CR and Cytb revealed limited phylogenetic distinction between geographically distant populations of the rusty-necklaced partridge, and tentative support for a single evolutionarily significant unit (ESU) range. AMOVA revealed that the most genetic variation was distributed within populations. However, the genetic variations among groups and poulations were also statistically significant. The population pairwise Fst-value was not statistically significant among Minghe(MH), Jingyuan(JY), Huining(HN), Li country(LX) and Haiyuan(HY), but statistically significant among the other populations. According to the criteria of Mus, MH, JY, HN, LX and HY should be treated as a MU and the other populations should be treated as independent MUs.
引文
安蓓,2009.西藏雪鸡种群遗传结构与分子系统地理学研究[博士论文].兰州：兰州大学.
曹曼曼,2010.我国斑翅山鹑遗传多样性与分子系统地理学研究[硕士论文].兰州：兰州大学.
曹兴山,1996.甘肃第四纪气候期划分.干旱区研究13,28-40.
陈克造,黄第藩,梁狄刚,1964.青海湖的形成和发展.地理学报30,214-233.
陈强,常城,刘迺发,1999.两种邻域分布石鸡间的线粒体DNA渗透.动物学报45,456-463.
陈小勇,罗兰,刘迺发,何德奎,1998.兰州大石鸡不同生活史阶段栖息地选择的初步研究.应用与环境生物学报4,368-373.
陈妍珂,2006.我国六盘山地区大石鸡和石鸡的渐渗杂交[博士论文].兰州：兰州大学.
葛颂,洪德元,1994.遗传多样性及其检测方法.见：钱迎倩,马克平(主编),生物多样性研究的原理与方法.中国科学技术出版社,北京.
郝岗平,吴忠义,陈茂盛,曹鸣庆,黄丛林,杨清,2004.拟南芥CBF4基因位点的单核苷酸多态性(SNP)变化与抗旱表型的相应性.农业生物技术学报12,122-131.
侯连海,1993.周口店更新世鸟类.中国科学院古脊椎动物与人类研究所集刊.科学技术出版社,北京,165-249.
侯鹏,卫明,张立勋,刘发,2002.大石鸡边缘种群的遗传结构.动物学报48,333-338.
胡志昂,王洪新,1998.分子生态学研究进展.生态学报18,565-574.
胡志昂,张亚平,1997.中国动植物的遗传多样性.浙江科学技术出版社,杭州.
黄麒,孟昭强,刘海玲,1990.柴达木盆地察尔汗湖区古气候波动模式的初步研究.中国科学：B辑,652-663.
黄勇平,朱湘雄,2003.分子生态学—生命科学领域的新学科.中国科学院院刊18,84-88.
黄族豪,2005.我国石鸡属鸟类的分子生态学研究[博士论文].兰州：兰州大学.
黄族豪,刘迺发,2004.陇东黄土高原石鸡的分子系统地理结构.动物学报50,576-582.
雷冬梅,张莘,宋春敬,段昌群,2004.分子生态学的理论与方法研究进展.生态科学进展1,135-159.
李秉成,孙建中,2004.黄土高原晚更新世的植被与气候环境.地理研究23,641-648.
李吉均,方小敏,马海洲,朱俊杰,潘保田,陈怀录,1996.晚新生代黄河上游地貌演化与青藏高原隆起.中国科学(D辑)26,316-322.
李吉均,方小敏,潘保田,赵志军,宋友桂,2001.新生代晚期青藏高原强烈隆起及其对周边环境的影响.第四纪研究21,381-391.
李庆伟,马飞,2007.鸟类分子进化与分子系统学.科学出版社,北京.
李裕元,石辉,2001.新构造运动对黄土高原环境变迁的影响.水土保持研究8,123-129.
林栲,李海鹏,2009.DNA水平上检测正选择方法的研究进展.遗传31,896-902.
刘迺发,1984.大石鸡分类地位的研究.动物分类学报9,212-218.
刘迺发,陈小勇,何德奎,1996.兰州地区大石鸡栖息地选择.动物学报42,83-89.
刘迺发,黄族豪,文陇英,2004.大石鸡亚种分化及一新亚种描述(鸡形目,雉科).动物分类学报刘迺发,王香亭,罗文英,1988.宁夏六盘山鸟类区系研究.兰州大学学报(自然科学版),65-75.
刘迺发,文陇英,黄族豪,侯鹏,2006.六盘山地区石鸡和大石鸡间的渐渗杂交.动物学报52，153-159.
刘亚锋,山宝琴,刘亚惠,2005.分子生态学及其研究进展.延安大学学报：自然科学版24,85-87.
康安,朱筱敏,韩德馨,王延斌,康强,2003.柴达木盆地第四纪孢粉组合及古气候波动.地质通报22,12-15.
沈才明,王苏民,1996.若尔盖地区25万年以来的植被与气候.微体古生物学报13,373-385.
施立明,1990.遗传多样性及其保存.生物科学信息2,159-164.
施雅风,1996.青藏高原进入冰冻圈的时代,高度及其对周围地区的影响.见：青藏高原形成,演化,环境变迁与生态系统.科学出版社,北京.
施雅风,1998.第四纪中期青藏高原冰冻圈的演化及其与全球变化的联系.冰川冻土20,197-208.
施雅风,2004.青藏高原大冰盖假说的提出与扬弃.第四纪研究24,10-18.
施雅风,李吉均,李炳元,1998.青藏高原晚新生代隆升和环境变化.广东科学技术出版社,广州.
施雅风,李吉均,李炳元,姚檀栋,王苏民,李世杰,崔之久,王富保,潘保田,方小敏,张青松,1999.晚新生代青藏高原的隆升与东亚环境变化.地理学报54,10-20.
施雅风,郑本兴,1995.青藏高原中东部最大冰期时代高度与气候环境探讨.冰川冻土17,97-112.
施雅风,郑本兴,李世态,1990.青藏高原的末次冰期与最大冰期.冰川冻土12,1-16.
宋森,2011.石鸡的分子生态及系统地理学研究[博士论文].兰州：兰州大学.
孙儒泳,2001.动物生态学原理(第三版).北京师范大学出版社,北京.
田风贵,马志杰,陈智华,2005.分子生态学与生物多样性研究.西南民族大学学报：自然科学版31,115-120.
王静波,胡长龙,徐宏发,2001.线粒体DNA (mtDNA)多态性在动物保护生物学中的应用.生物多样性9,181-187.
汪松,陈灵芝等,1990.中国科学院生物多样性研讨会会议录.中国科学院生物科学与技术局,北京.
王苏民,施雅风,1992.晚第四纪青海湖演化研究析视与讨论.湖泊科学4,1-9.
王文,1998.分子系统学在生物保护中的意义.生物多样性6,138-142.
王香亭,1991.甘肃脊椎动物志.甘肃科学技术出版社,兰州.
汪永庆,张知彬,徐来祥,2001.中心区和边缘区大仓鼠种群的遗传多样性.科学通报46,1644-1650.
王峥峰,彭少麟,2003.杂交产生的遗传危害一以植物为例.生物多样性11,334-339.
王子玉,1986.云台山鸟类考察报告.动物学杂志21,20-28.
卫明,侯鹏,黄族豪,刘迺发,2002.环境因子对大石鸡种群遗传结构的影响.生态学报22,528-534.
肖金学,王文强,廉振民,2008.浅议分子生态学的概念.延安大学学报：自然科学版27,69-71.
肖清华,张旺生,张伟,朱创鑫,王杰,2008.祁连山地区更新世以来冰期雪线变化研究.干旱区研究25,426-432.
徐钦琦,1990.地球轨道与气候演变的关系.科学通报25,180-182.
杨志松,2007.我国石鸡属鸟类系统地理结构及其种间杂交的研究[博士论文].兰州：兰州大学.
杨志松,刘迺发,2009.基于细胞色素b基因研究两种石鸡的渐渗杂交.重庆师范大学学报(自然科学版)26,1-6.
张惠昌,商日媛,1991.兰州地区黄土年代的划分及古气候特征.兰州大学学报(自然科学版)27，131-138.
张军丽,廖斌,王胜龙译,2009.分子生态学(Beebee TJC & Rowe G. (eds.),2004. An Introduction to Molecular Ecology. Oxford University Press.)中山大学出版社,广州.
张荫荪,梁拴柱,陈容伯,1989.石鸡的一新亚种-鄂尔多斯石鸡(鸡形目：雉科).动物分类学报14,496-499.
张亚平,王文,宿兵,1995.大熊猫微卫星DNA的筛选及其应用.动物学研究16,301-306.
郑光美,2002.世界鸟类与分布名录.科学出版社,北京.
郑作新,1978.中国动物志鸟纲第四卷—鸡形目.科学出版社,北京.
Abbott, R.J., James, J.K., Milne, R.I., Gillies, A.,2003. Plant introductions, hybridization and gene flow. Philosophical Transactions of the Royal Society of London. Series B:Biological Sciences 358,1123-1132.
Adams, C.C.,1905. The postglacial dispersal of the North American biota. The Biological Bulletin 9,53-71.
Alsos, I.G., Eidesen, P.B., Ehrich, D., Skrede, I., Westergaard, K., Jacobsen, G.H., Landvik, J.Y., Taberlet, P., Brochmann, C.,2007. Frequent long-distance plant colonization in the changing Arctic. Science 316,1606-1609.
An, B., Zhang, L., Browne, S., Liu, N., Ruan, L., Song, S.,2009. Phylogeography of Tibetan snowcock (Tetraogallus tibetanus) in Qinghai-Tibetan Plateau. Mol Phylogenet Evol 50, 526-533.
Andersson, A.C., Narain, Y., Tegelstr m, H., Fredga, K.,2004. No apparent reduction of gene flow in a hybrid zone between the West and North European karyotypic groups of the common shrew, Sorex araneus. Molecular Ecology 13,1205-1215.
Aris-Brosou, S., Excoffier, L.,1996. The impact of population expansion and mutation rate heterogeneity on DNA sequence polymorphism. Mol Biol Evol 13,494-504.
Arnold, M.L.,1997. Natural hybridization and evolution. Oxford University Press, USA.
Avise, J.C.,1994. Molecular Markers,Natural History and Evolution. Chapman&Hall, New York.
Avise, J.C.,2000. Phylogeography:The History and Formation of Species. Harvard University Press, Cambridge, Massachusetts.
Avise, J.C., Arnold, J., Ball, R.M., Bermingham, E., Lamb, T., Neigel, J.E., Reeb, C.A., Saunders, N.C.,1987. Intraspecific phylogeography:the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics 18,489-522.
Avise, J.C., Ball, R.,1990. Principles of geneological concordance in species concepts and biological taxonomy. In:Futuyma, D.J., Antonovics, J. (Eds.), Oxford Surveys in Evolutionary Biology. Oxford University Press, Oxford.
Avise, J.C., Hamrick, J.L.,1996. Conservation genetics:case histories from nature. Springer.
Avise, J.C., Neigel, J.E., Arnold, J.,1984. Demographic influences on mitochondrial DNA lineage survivorship in animal populations. Journal of Molecular Evolution 20,99-105.
Avise, J.C., Walker, D.,1998. Pleistocene phylogeographic effects on avian populations and the speciation process. Proc Biol Sci 265,457-463.
Babik, W., Branicki, W., Crnobrnja-Isailovic, J., Cogalniceanu, D., Sas, I., Olgun, K., Poyarkov, N., Garcia-Paris, M., Arntzen, J.W., 2005. Phylogeography of two European newt species-discordance between mtDNA and morphology. Molecular Ecology 14,2475-2491.
Badr, A.,2000. On the origin and domestication history of barley (Hordeum vulgare). Molecular Biology and Evolution 17,499-510.
Barluenga, M., St lting, K.N., Salzburger, W., Muschick, M., Meyer, A.,2006. Sympatric speciation in Nicaraguan crater lake cichlid fish. Nature 439,719-723.
Barratt, E., Gurnell, J., Malarky, G., Deaville, R., Bruford, M.,1999. Genetic structure of fragmented populations of red squirrel (Sciurus vulgaris) in the UK. Molecular Ecology 8, S55-S63.
Barrowclough, G., Groth, J., Mertz, L., Guti(?)rrez, R., 2005. Genetic structure, introgression, and a narrow hybrid zone between northern and California spotted owls (Strix occidentalis). Molecular Ecology 14,1109-1120.
Barton, N.H., Hewitt, G.M.,1989. Adaptation, speciation and hybrid zones. Nature 341,497-503.
Beebee, T.J.C., Rowe, G., 2004. An Introduction to Molecular Ecology. Oxford University Press, New York.
Bensen, J.T., Langefeld, C.D., Hawkins, G.A., Green, L.E., Mychaleckyj, J.C., Brewer, C.S., Kiger, D.S., Binford, S.M., Colicigno, C.J., Allred, D.C.,2003. Nucleotide variation, haplotype structure, and association with end-stage renal disease of the human interleukin-1 gene cluster. Genomics 82,194-217.
Bernacchi, D., Beck-Bunn, T., Emmatty, D., Eshed, Y., Inai, S., Lopez, J., Petiard, V., Sayama, H., Uhlig, J., Zamir, D., 1998. Advanced backcross QTL analysis of tomato. Ⅱ. Evaluation of near-isogenic lines carrying single-donor introgressions for desirable wild QTL-alleles derived from Lycopersicon hirsutum and L. pimpinellifolium. TAG Theoretical and Applied Genetics 97, 170-180.
Bernatchez, L., Wilson, C.C.,1998. Comparative phylogeography of Nearctic and Palearctic fishes. Molecular Ecology 7,431-452.
Birky-Jr, C., Fuerst, P., Maruyama, T.,1989. Organelle gene diversity under migration, mutation, and drift:equilibrium expectations, approach to equilibrium, effects of heteroplasmic cells, and comparison to nuclear genes. Genetics 121,613-627.
Brooks, T.M., Mittermeier, R.A., Mittermeier, C.G., Da Fonseca, G.A.B., Rylands, A.B., Konstant, W.R., Flick, P., Pilgrim, J., Oldfield, S., Magin, G.,2002. Habitat loss and extinction in the hotspots of biodiversity. Conservation Biology 16,909-923.
Burke T,Seidler R,Smith H.Editorial. Molec.Ecol,1992,1:1
Cagelli, L., Lefevre, F.,1995. The conservation of Populus nigra L. and gene flow with cultivated poplars in Europe. Forest Genetics 2,135-144.
Cao, M.M., Liu, N.F., Wang, X.L., Guan, M.M.,2010. Genetic diversity and genetic structure of the Daurian Partridge (Perdix dauuricae) in China, assessed by microsatellite variation. Chinese Birds 1,51-64.
Cartens, B.C., Brunsfeld, S.J., Demboski, J.R., Good, J.M., Sullivan, J.,2005. Investigating the Evolutionary History of the Pacific Northwest Mesic Forest Ecosystem:Hpotehesis Testing Within a Comparative Phylogeographic Framework. Evolution 59,1639-1652.
Chen, Q., Chang, C., Liu, N.F.,1999. Mitochondrial DNA Introgression between Two Parapatric Species of Alectoris. Acta Zoologica Sinica 45,456-463.
Chen, Y., Wang, W., Yang, Y., Su, B., Zhang, Y., Xiong, L., He, Z., Shu, C., Yang, D.,1997. Genetic divergence of Cordyceps sinensis as estimated by random amplified polymorphic DNA analysis]. Acta genetica Sinica 24,410-416.
Chen, Y, Zhao, Z., Liu, N.,2006. Genetic structure of Przewalski's rock partridge (Alectoris magna) populations in the Longzhong Loess Plateau, China. Biochemical genetics 44,209-221.
Chetelat, R., Meglic, V.,2000. Molecular mapping of chromosome segments introgressed from Solanum lycopersicoides into cultivated tomato (Lycopersicon esculentum). TAG Theoretical and Applied Genetics 100,232-241.
Cianchi, R., Ungaro, A., Marini, M., Bullini, L.,2003. Differential patterns of hybridization and introgression between the swallowtails Papilio machaon and P. hospiton from Sardinia and Corsica islands (Lepidoptera, Papilionidae). Molecular Ecology 12,1461-1471.
Clements, J.F.,2007. The Clements checklist of birds of the world (6th Edition). Cornell University Press, New York.
Cornuet, J.M., Luikart, G.,1996. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144,2001-2014.
Cramp, S., Simmons, K.E.L.,1980. Handbook of the birds of Europe, the Middle East and North Africa. The birds of the Western Palearctic. OxfordUniversityPress, Oxford.
Crandall, K.A., Bininda-Emonds, O.R.P., Mace, G.M., Wayne, R.K.,2000. Considering evolutionary processes in conservation biology. Trends in Ecology & Evolution 15,290-295.
Crandall, K.A., Templeton, A.R.,1993. Empirical Tests of Some Predictions From Coalescent Theory With Applications to Intraspecific Phylogeny Reconstruction. Genetics 134,959-969.
Crochet, P.A., Desmarais, E., 2000. Slow rate of evolution in the mitochondrial control region of gulls (Aves:Laridae). Molecular Biology and Evolution 17,1797-1806.
De Queiroz, K.,2007. Species concepts and species delimitation. Syst Biol 56,879-886.
Di Rienzo, A., Peterson, A., Garza, J., Valdes, A., Slatkin, M., Freimer, N.,1994. Mutational processes of simple-sequence repeat loci in human populations. Proceedings of the National Academy of Sciences of the United States of America 91,3166-3170.
Edwards, S.V., Beerli, P., 2000. Perspective:gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54,1839-1854.
Ellstrand, N.C., Prentice, H.C., Hancock, J.F.,1999. Gene flow and introgression from domesticated plants into their wild relatives. Annual Review of Ecology and Systematics, 539-563.
Ellstrand, N.C., Whitkus, R., Rieseberg, L.H.,1996. Distribution of spontaneous plant hybrids. Proceedings of the National Academy of Sciences of the United States of America 93, 5090-5093.
Eshed, Y., Zamir, D.,1994. Introgressions fromLycopersicon pennellii can improve the soluble-solids yield of tomato hybrids. TAG Theoretical and Applied Genetics 88,891-897.
Eshed, Y., Zamir, D.,1995. An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. Genetics 141,1147-1162.
Excoffier, L., Laval, G., Schneider, S.,2005. Arlequin (version 3.0):an integrated software package for population genetics data analysis. Evol Bioinform Online 1,47-50.
Excoffier, L., Smouse, P.E., Quattro, J.M.,1992. Analysis of Molecular Variance Inferred From Metric Distances Among DNA Haplotypes:Application to Human Mitochondrial DNA Restriction Data. Genetics 131,479-491.
Ferrier, S., Guisan, A.,2006. Spatial modelling of biodiversity at the community level. Journal of Applied Ecology 43,393-404.
Frankel, O.H., Soule, M.E.,1981. Conservation and evolution. Cambridge University Press, Cambridge, UK.
Fu, Y.X.,1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147,915-925.
Fu, Y.X., Li, W.H.,1993. Statistical tests of neutrality of mutations. Genetics 133,693-709.
Garcia-Ramos, G., Kirkpatrick, M.,1997. Genetic models of adaptation and gene flow in peripheral populations. Evolution,21-28.
Garner, T.W.J., Pearman, P.B., Angelone, S.,2004. Genetic diversity across a vertebrate species' range:a test of the central-peripheral hypothesis. Molecular Ecology 13,1047-1053.
Gibbs, H.L., Corey, S.J., Blouin-Demers, G., Prior, K.A., Weatherhead, P.J.,2006. Hybridization between mtDNA-defined phylogeographic lineages of black ratsnakes (Pantherophis sp.). Molecular Ecology 15,3755-3767.
Gill, F.,1994. Rapid, asymmetrical introgression of mitochondrial DNA in hybridizing populations of Blue-wringed and Golden-wringed warblers. Journal of Ornithology 135, 359-369.
Gligor, M., Ganzhorn, J., Rakotondravony, D., Ramilijaona, O., Razafimahatratra, E., Zischler, H., Hapke, A.,2009. Hybridization between mouse lemurs in an ecological transition zone in southern Madagascar. Molecular Ecology 18,520-533.
Gompert, Z., Forister, M.L., Fordyce, J.A., Nlice, C.C.,2008. Widespread mito-nuclear discordance with evidence for introgressive hybridization and selective sweeps in Lycaeides. Molecular Ecology 17,5231-5244.
Gonzalez-Rodriguez, A., Bain, J., Golden, J., Oyama, K.,2004. Chloroplast DNA variation in the Quercus affinis CQ. laurina complex in Mexico:geographical structure and associations with nuclear and morphological variation. Molecular Ecology 13,3467-3476.
Good, J.M., Hird, S., Reid, N., DEMBOSKI, J.R., STEPPAN, S.J., MARTIN-NIMS, T.R., Sullivan, J.,2008. Ancient hybridization and mitochondrial capture between two species of chipmunks. Molecular Ecology 17,1313-1327.
Groom, M.J., Meffe, G.K., Carroll, C.R.,2006. Principles of conservation biology. Sinauer Associates Sunderland, Massachusetts, USA.
Hansen, M., Loeschcke, V.,1994. Effects of releasing hatcheryreared brown trout to wild trout populations. In:Loeschcke, V., Tomiuk, J. and Jam, S. K.(eds) Conservation Genetics. Birkhauser Verlag, Basle.
Harrison, R.G.,1993. Hybrids and hybrid zones:historical perspective. Oxford University Press, Oxford,UK.
Hewitt, G.,1999. Post-glacial re-colonization of European biota Biol. J. Linnean Soc 68,87-112.
Hewitt, G.M.,1996. Some genetic consequences of ice ages, and their role, in divergence and speciation. Biological Journal of the Linnean Society 58,247-276.
Hewitt, G.M.,2000. The genetic legacy of the Quaternary ice ages. Nature 405,907-913.
Hewitt, G.M.,2001. Speciation, hybrid zones and phylogeography-or seeing genes in space and time. Molecular Ecology 10,537-549.
Hey, J., Kliman, R.M.,1993. Population genetics and phylogenetics of DNA sequence variation at multiple loci within the Drosophila melanogaster species complex. Molecular Biology and Evolution 10,804-822.
Hey, J., Nielsen, R.,2004. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167,747-760.
Hickerson, M.J., Meyer, C.P.,2008. Testing comparative phylogeographic models of marine vicariance and dispersal using a hierarchical Bayesian approach. Bmc Evol Biol 8,322.
Hickerson, M.J., Meyer, C.P., Moritz, C.,2006. DNA barcoding will often fail to discover new animal species over broad parameter space. Syst Biol 55,729-739.
Hoffmann, A.A., Blows, M.W.,1994. Species borders:ecological and evolutionary perspectives. Trends in Ecology & Evolution 9,223-227.
Houlden, B.A., Costello, B.H., Sharkey, D., Fowler, E.V., Melzer, A., Ellis, W., Carrick, F., Baverstock, P.R., Elphinstone, M.S.,1999. Phylogeographic differentiation in the mitochondrial control region in the koala, Phascolarctos cinereus (Goldfuss 1817). Molecular Ecology 8, 999-1011.
Huang, Z., Liu, N., Zhou, T., Ju, B.,2005. Effects of environmental factors on the population genetic structure in chukar partridge (Alectoris chukar). Journal of arid environments 62, 427-434.
Huang, Z., Liu, N., Luo, S., Long, J.,2007a. Phylogeography of rusty-necklaced partridge (Alectoris magna) in northwestern China. Mol Phylogenet Evol 43,379-385.
Huang, Z., Liu, N., Luo, S., Long, J., Xiao, Y.,2007b. Ecological genetics of rusty-necklaced partridge (Alectoris magna):Environmental factors and population genetic variability correlations. Korean Journal of Genetics 29,115-120.
Huang, Z.H., Yang, Z.S., Zhang, J., Liu, N.F.,2009. Introgressive hybridization and population genetic diversity between rusty-necklaced partridge and chukar partridge in northwestern China. Belgian Journal of Zoology 139,15-21.
Huang, Z., Liu, N., Zhou, T., Ju, B.,2005. Effects of environmental factors on the population genetic structure in chukar partridge (Alectoris chukar). Journal of arid environments 62, 427-434.
Hudson, R.R., Coyne, J.A.,2002. Mathematical consequences of the genealogical species concept. Evolution 56,1557-1565.
Huelsenbeck, J.P., Ronquist, F.,2001. MRBAYES:Bayesian inference of phylogenetic trees. Bioinformatics 17,754-755.
Humphries, C.J., Williams, P.H., Vane-Wright, R.I.,1995. Measuring biodiversity value for conservation. Annual Review of Ecology and Systematics 26,93-101.
Jensen, A.B., Palmer, K.A., Boomsma, J.J., Pedersen, B.V.,2005. Varying degrees of Apis mellifera ligustica introgression in protected populations of the black honeybee, Apis mellifera mellifera, in northwest Europe. Molecular Ecology 14,93-106.
Jin, Y.T., Brown, R.P., Liu, N.F.,2008. Cladogenesis and phylogeography of the lizard Phrynocephalus vlangalii (Agamidae) on the Tibetan plateau. Mol Ecol 17,1971-1982.
Jin, Y.T., Liu, N.F.,2008. Ecological Genetics of Phrynocephalus vlangalii on the North Tibetan (Qinghai) Plateau:Correlation between Environmental Factors and Population Genetic Variability. Biochemical genetics 46,598-604.
Johnsgard, P.A., Jones, H.,1988. The quails, partridges, and francolins of the world. Oxford University Press Oxford, Oxford.
Jordan, D.S.,1905. The origin of species through isolation. Science 22,545-562.
Joseph, L., Wilke, T., Alpers, D.,2002. Reconciling genetic expectations from host specificity with historical population dynamics in an avian brood parasite, Horsfield's Bronze-Cuckoo Chalcites basalis of Australia. Molecular Ecology 11,829-837.
Karron, J.D.,1987. A comparison of levels of genetic polymorphism and self-compatibility in geographically restricted and widespread plant congeners. Evolutionary Ecology 1,47-58.
Kimura, M.,1968. Evolutionary rate at the molecular level. Nature 217,624-626.
Kingman, J.,1982a. On the genealogy of large populations. Journal of Applied Probability,27-43.
Kingman, J.F.C.,1982b. The coalescent. Stochastic processes and their applications 13,235-248.
Knowles, L.L., Carstens, B.C.,2007. Delimiting species without monophyletic gene trees. Syst Biol 56,887-895.
Lamoreux, J.F., Morrison, J.C., Ricketts, T.H., Olson, D.M., Dinerstein, E., McKnight, M.W., Shugart, H.H.,2005. Global tests of biodiversity concordance and the importance of endemism. Nature 440,212-214.
Le corre, V., Roux, F., Reboud, X.,2002. DNA polymorphism at the FRIGIDA gene in Arabidopsis thaliana:extensive nonsynonymous variation is consistent with local selection for flowering time. Molecular Biology and Evolution 19,1261-1271.
Leache, A.D., Cole, C.J.,2007. Hybridization between multiple fence lizard lineages in an ecotone: locally discordant variation in mitochondrial DNA, chromosomes, and morphology. Molecular Ecology 16,1035-1054.
Leavitt, D.H., Bezy, R.L., Crandall, K.A., Sites Jr, J.W.,2007. Multi-locus DNA sequence data reveal a history of deep cryptic vicariance and habitat-driven convergence in the desert night lizard Xantusia vigilis species complex (Squamata:Xantusiidae). Molecular Ecology 16, 4455-4481.
Lesica, P., Allendorf, F.W.,1995. When are peripheral populations valuable for conservation? Conservation Biology 9,753-760.
Levin, D.A., Francisco-Ortega, J., Jansen, R.K.,1996. Hybridization and the extinction of rare plant species. Conservation Biology 10,10-16.
Lexer, C., Randell, R.A., Rieseberg, L.H.,2003. Experimental hybridization as a tool for studying selection in the wild. Ecology 84,1688-1699.
Li, L., Wang, R.Q., Wang, Z.R., Wang, S.P., Li, S.H.,1996. The studies of Naidong Camellia biodiversity in Qingdao (Ⅱ)——Genetic diversity analysis of populations. Biodiversity Science 4,1-6.
Li, Z.K., Fu, B.Y., Gao, Y.M., Xu, J.L., Ali, J., Lafitte, H., Jiang, Y.Z., Rey, J.D., Vijayakumar, C.H.M., Maghirang, R.,2005. Genome-wide introgression lines and their use in genetic and molecular dissection of complex phenotypes in rice (Oryza sativa L.). Plant molecular biology 59,33-52.
Librado, P., Rozas, J.,2009. DnaSP v5:a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25,1451-1452.
Lin, S., Sasaki, T., Yano, M.,1998. Mapping quantitative trait loci controlling seed dormancy and heading date in rice, Oryza sativa L., using backcross inbred lines. TAG Theoretical and Applied Genetics 96,997-1003.
Liu, J., Yu, G., Chen, X.,2002. Palaeoclimate simulation of 21 ka for the Tibetan Plateau and Eastern Asia. Climate Dynamics 19,575-583.
Liu, N.,1992. Ecology of Przewalski's rock partridge (Alectoris magna). Gibier Faune Sauvage 9, 605-615.
Liu, Y., Zhan, X., Wang, N., Chang, J., Zhang, Z.,2010. Effect of geological vicariance on mitochondrial DNA differentiation in Common Pheasant populations of the Loess Plateau and eastern China. Mol Phylogenet Evol 55,409-417.
Lorenzen, E.D., de Neergaard, R., Arctander, P., SIEGISMUND, H.R.,2007. Phylogeography, hybridization and Pleistocene refugia of the kob antelope (Kobus kob). Molecular Ecology 16, 3241-3252.
Luikart, G., Allendorf, F., Cornuet, J., Sherwin, W.,1998. Distortion of allele frequency distributions provides a test for recent population bottlenecks. Journal of Heredity 89,238-247.
Lucchini, V., Randi, E.,1998. Mitochondrial DNA sequence variation and phylogeographical structure of rock partridge (Alectoris graeca) populations. Heredity 81,528-536.
Maan, S.S.,1987. Interspecific and intergeneric hybridization in wheat. In:Heyne, E. G. (Ed.), Wheat and Wheat Improvement. ASA, CSSA and SSSA, Madison.
Madge, S., McGowan, P.J.K., Kirwan, G.M.,2002. Pheasants, partridges and grouse:a guide to the pheasants, partridges, quails, grouse, guineafowl, buttonquails and sandgrouse of the world. Christopher Helm London.
Mallet, J.,2005. Hybridization as an invasion of the genome. Trends in Ecology & Evolution 20, 229-237.
Mayr, E.,1942. Systematics and the origin of species. Columbia university press, New York
McLachlan, J.S., Clark, J.S., Manos, P.S.,2005. Molecular indicators of tree migration capacity under rapid climate change. Ecology 86,2088-2098.
McNeely, J.A., Miller, K.R., Reid, W.V.C., Mittermeier, R.A., Werner, T.B.,1990. Conserving the World's Biological Diversity. Washington D.C. and Gland, Switzerland.
Mebert, K.,2008. Good species despite massive hybridization:genetic research on the contact zone between the watersnakes Nerodia sipedon and N. fasciata in the Carolinas, USA. Molecular Ecology 17,1918-1929.
Melo-Ferreira, J., Boursot, P., Randi, E., Kryukov, A., Suchentrunk, F., Ferrand, N., Alves, P., 2007. The rise and fall of the mountain hare (Lepus timidus) during Pleistocene glaciations: expansion and retreat with hybridization in the Iberian Peninsula. Molecular Ecology 16, 605-618.
Merrell, D.J.,1981. Ecological Genetics, Longman, London.
Meyer, C.P., Paulay, G.,2005. DNA barcoding:error rates based on comprehensive sampling. PLoS Biology 3,2229-2238.
Michalakis, Y., Excoffier, L.,1996. A generic estimation of population subdivision using distances between alleles with special reference for microsatellite loci. Genetics 142,1061-1064.
Morando, M., Avila, L.J., Sites, J.W.,2003. Sampling strategies for delimiting species:genes, individuals, and populations in the Liolaemus elongatus-kriegi complex (Squamata: Liolaemidae) in Andean-Patagonian South America. Syst Biol 52,159-185.
Moritz, C.,1994. Defining evolutionarily significant units for conservation. TRENDS in Ecology and Evolution 9,373-374.
Moritz, C.,1995. Uses of molecular phylogenies for conservation. Philosophical Transactions of the Royal Society of London. Series B:Biological Sciences 349,113-118.
Moritz, C., Dowling, T., Brown, W.,1987. Evolution of animal mitochondrial DNA:relevance for population biology and systematics. Annual Review of Ecology and Systematics,269-292.
Moritz, C., Faith, D.P.,1998. Comparative phylogeography and the identification of genetically divergent areas for conservation. Molecular Ecology 7,419-429.
Moritz, C., Patton, J., Schneider, C., Smith, T.,2000. Diversification of rainforest faunas:an integrated molecular approach. Annual Review of Ecology and Systematics 31,533-563.
Myers, N., Mittermeier, R.A., Mittermeier, C.G., da Fonseca, G.A.B., Kent, J.,2000. Biodiversity hotspots for conservation priorities. Nature 403,853-858.
Nardon, C., Deceliere, G., Loevenbruck, C., Weiss, M., Vieira, C., Biemont, C.,2005. Is genome size influenced by colonization of new environments in dipteran species? Molecular Ecology 14, 869-878.
Neigle, J.E., Avise, J.C.,1986. Phylogenetic relationships of mitochondrial DNA under various demographic models of speciation. In:Nero EandKarlin S(eds). Evolutionary Processes and Theory. Academic Press, New York.
Nevo, E.,1981. Genetic variation and climatic selection in the lizard Agama stellio in Israel and Sinai. TAG Theoretical and Applied Genetics 60,369-380.
Nicolas, V., Mboumba, J.F., Verheyen, E., Denys, C., Lecompte, E., Olayemi, A., Missoup, A.D., Katuala, P., Colyn, M.,2008. Phylogeographic structure and regional history of Lemniscomys striatus (Rodentia:Muridae) in tropical Africa. Journal of biogeography 35,2074-2089.
Nolte, A., Gompert, Z., Buerkle, C,2009. Variable patterns of introgression in two sculpin hybrid zones suggest that genomic isolation differs among populations. Molecular Ecology 18, 2615-2627.
Noy-Meir, I.,1973. Desert ecosystems:environment and producers. Annual Review of Ecology and Systematics 4,25-51.
Nylander, J.A.A.,2004. MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University.
Orme, C.D.L., Davies, R.G., Burgess, M., Eigenbrod, F., Pickup, N., Olson, V.A., Webster, A.J., Ding, T.S., Rasmussen, P.C., Ridgely, R.S.,2005. Global hotspots of species richness are not congruent with endemism or threat. Nature 436,1016-1019.
Pons, J., Barraclough, T.G, Gomez-Zurita, J., Cardoso, A., Duran, D.P., Hazell, S., Kamoun, S., Sumlin, W.D., Vogler, A.P.,2006. Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst Biol 55,595-609.
Posada, D., Crandall, K.A.,2001. Intraspecific gene genealogies:trees grafting into networks. Trends Ecol Evol 16,37-45.
Prentice, H.C., Lonn, M., Lefkovitch, L.P., Runyeon, H.,1995. Associations between allele frequencies in Festuca ovina and habitat variation in the alvar grasslands on the Baltic island of Oland. Journal of Ecology,391-402.
Pritchard, J.K., Stephens, M., Donnelly, P.,2000. Inference of Population Structure Using Multilocus Genotype Data. Genetics 155,945-959.
Qu, J., Liu, N., Bao, X., Wang, X.,2009. Phylogeography of the ring-necked pheasant (Phasianus colchicus) in China. Mol Phylogenet Evol 52,125-132.
Qu, Y., Ericson, P.G.P., Lei, F., Gebauer, A., Kaiser, M., Helbig, A.J.,2006. Molecular phylogenetic relationship of snow finch complex (genera Montifringilla, Pyrgilauda, and Onychostruthus) from the Tibetan plateau. Mol Phylogenet Evol 40,218-226.
Qu, Y., Lei, F.,2009. Comparative phylogeography of two endemic birds of the Tibetan plateau, the white-rumped snow finch (Onychostruthus taczanowskii) and the Hume's ground tit (Pseudopodoces humilis). Mol Phylogenet Evol 51,312-326.
Qu, Y, Lei, F., Zhang, Y, Lu, X.,2010. Comparative phylogeography of five avian species: implications for Pleistocene evolutionary history in the Qinghai-Tibetan plateau. Molecular Ecology 19,338-351.
Randi, E.,1996. A Mitochondrial Cytochrome b Phylogeny of the Alectoris Partridges. Mol Phylogenet Evol 6,214-227.
Randi, E., Alkon, P.U.,1994. Genetic structure of Chukar (Alectoris chukar) populations in Israel. The Auk 111,416-426.
Randi, E., Bernard-Laurent, A.,1999. Population genetics of a hybrid zone between the red-legged partridge and rock partridge. The Auk 116,324-337.
Randi, E., Tabarroni, C., Rimondi, S., Lucchini, V., Sfougaris, A.,2003. Phylogeography of the rock partridge (Alectoris graeca). Molecular Ecology 12,2201-2214.
Raup, D.M.,1986. Biological extinction in earth history. Science 231,1528-1533.
Raymond, M., Rousset, F.,1995. An exact test for population differentiation. Evolution 49, 1280-1283.
Rieseberg, L.H.,1997. Hybrid origins of plant species. Annual Review of Ecology and Systematics 28,359-389.
Rieseberg, L.H.,2000. Crossing relationships among ancient and experimental sunflower hybrid lineages. Evolution 54,859-865.
Rieseberg, L.H., Carney, S.E.,1998. Plant hybridization. New Phytologist 140,599-624.
Rieseberg, L.H., Raymond, O., Rosenthal, D.M., Lai, Z., Livingstone, K., Nakazato, T., Durphy, J.L., Schwarzbach, A.E., Donovan, L.A., Lexer, C.,2003. Major ecological transitions in wild sunflowers facilitated by hybridization. Science 301,1211-1216.
Rieseberg, L.H., Van Fossen, C., Desrochers, A.M.,1995. Hybrid speciation accompanied by genomic reorganization in wild sunflowers. Nature 375,313-316.
Rieseberg, L.H., Wendel, J.F.,1993a. Introgression and its consequences in plants. Hybrid zones and the evolutionary process,70-109.
Rieseberg, L.H., Wendel, J.F.,1993b. Introgression and its consequences in plants. In:Harrison R.G.(eds.), Hybrid Zons and the Evolutionary Process. Oxford University Press, New York.
Rogers, A.R., Harpending, H.,1992. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 9,552-569.
Rooney, A.P., Honeycutt, R.L., Derr, J.N.,2001. Historical Population Size Change of Bowhead Whales Inferred from DNA Sequence Polymorphism Data. Evolution 55,1678-1685.
Rosenberg, N.A.,2003. The shapes of neutral gene genealogies in two species:probabilities of monophyly, paraphyly, and polyphyly in a coalescent model. Evolution 57,1465-1477.
Rosenberg, N.A.,2007. Statistical tests for taxonomic distinctiveness from observations of monophyly. Evolution 61,317-323.
Rousset, F.,1997. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145,1219-1228.
Rowe, G., Beebee, T.J.C.,2003. Population on the verge of a mutational meltdown? Fitness costs of genetic load for an amphibian in the wild. Evolution 57,177-181.
Ryder, O.A.,1986. Species conservation and systematics:the dilemma of subspecies. Trends in Ecology & Evolution 1,9-10.
Rubidge, E.M., Taylor, E.B.,2004. Hybrid zone structure and the potential role of selection in hybridizing populations of native westslope cutthroat trout (Oncorhynchus clarki lewisi) and introduced rainbow trout (O. mykiss). Molecular Ecology 13,3735-3749.
Saetre, G.P., Borge, T., Lindell, J., Mourn, T., Primmer, C.R., Sheldon, B.C., Haavie, J., Johnsen, A., Ellegren, H.,2001. Speciation, introgressive hybridization and nonlinear rate of molecular evolution in flycatchers. Molecular Ecology 10,737-749.
Salzburger, W., Baric, S., Sturmbauer, C.,2002. Speciation via introgressive hybridization in East African cichlids? Molecular Ecology 11,619-625.
Schneider, S., Excoffier, L.,1999. Estimation of Past Demographic Parameters From the Distribution of Pairwise Differences When the Mutation Rates Vary Among Sites:Application to Human Mitochondrial DNA. Genetics 152,1079-1089.
Scheiner, S.M.,1993. Genetics and evolution of phenotypic plasticity. Annual Review of Ecology and Systematics 24,35-68.
Schwarz, D., Matta, B.M., Shakir-Botteri, N.L., McPheron, B.A.,2005. Host shift to an invasive plant triggers rapid animal hybrid speciation. Nature 436,546-549.
Senn, H.V., Pemberton, J.M.,2009. Variable extent of hybridization between invasive sika (Cervus nippon) and native red deer (C. elaphus) in a small geographical area. Molecular Ecology 18, 862-876.
Shi, Y.F.,2002. Characteristics of late Quaternary monsoonal glaciation on the Tibetan Plateau and in East Asia. Quaternary International 97-98,79-91.
Shi, Y.F., Zheng, B.X., Li, S.J.,1990. Last glaciation and maximum glaciation in Qinghai-Xizang (Tibet) plateau. Journal of Glaciology and Geocryology 12,1-15.
Simonsen, K.L., Churchill, G.A., Aquadro, C.F.,1995. Properties of statistical tests of neutrality for DNA polymorphism data. Genetics 141,413-429.
Sites, J.W., Marshall, J.C.,2004. Delimiting species:a Renaissance issue in systematic biology. Trends in Ecology & Evolution 18,462-470.
Slatkin, M.,1987. Gene flow and the geographic structure of natural populations. Science 236, 787-792.
Slatkin, M., Hudson, R.R.,1991. Pairwise Comparisons of Mitochondrial DNA Sequences in Stable and Exponentially Growing Populations. Genetics 129,555-562.
Snow, A.A., Andersen, B., J rgensen, R.B.,1999. Costs of transgenic herbicide resistance introgressed from Brassica napus into weedy B. rapa. Molecular Ecology 8,605-615.
Soule, M.,1973. The epistasis cycle:a theory of marginal populations. Annual Review of Ecology and Systematics 4,165-187.
Spathelf, M., Waite, T., 2007. Will hotspots conserve extra primate and carnivore evolutionary history? Diversity and Distributions 13,746-751.
Stevison, L.S., Kohn, M.H.,2009. Divergence population genetic analysis of hybridization between rhesus and cynomolgus macaques. Molecular Ecology 18,2457-2475.
Swenson, N.G., Howard, D.J.,2005. Clustering of contact zones, hybrid zones, and phylogeographic breaks in North America. American Naturalist 166,581-591.
Swofford, D.L.,2002. PAUP*. Phylogenetic analysis using parsimony (*and other methods).
Taberlet, P., Cheddadi, R.,2002. Quaternary refugia and persistence of biodiversity. Science 297, 2009-2010.
Taberlet, P., Fumagalli, L., Wust-Saucy, A.G., Cosson, J.F.,1998. Comparative phylogeography and postglacial colonization routes in Europe. Molecular Ecology 7,453-464.
Taberlet, P., Luikart, G.,1999. Non-invasive genetic sampling and individual identification. Biological Journal of the Linnean Society 68,41-55.
Tajima, F.,1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123,585-595.
Tanksley, S., Nelson, J.,1996. Advanced backcross QTL analysis:a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. TAG Theoretical and Applied Genetics 92,191-203.
Tang, Q., Liu, H., Mayden, R., Xiong, B.,2006. Comparison of evolutionary rates in the mitochondrial DNA cytochrome b gene and control region and their implications for phylogeny of the Cobitoidea (Teleostei:Cypriniformes). Mol Phylogenet Evol 39,347-357.
Templeton, A.R.,2001. Using phylogeographic analyses of gene trees to test species status and processes. Molecular Ecology 10,779-791.
Thompson, C., Thompson, B., Ades, P., Cousens, R., Garnier-Gere, P., Landman, K., Newbigin, E., Burgman, M.,2003. Model-based analysis of the likelihood of gene introgression from genetically modified crops into wild relatives. Ecological Modelling 162,199-209.
Trigo, T., Freitas, T., Kunzler, G., Cardoso, L., Silva, J., Johnson, W., O'BRIEN, S., Bonatto, S., Eizirik, E.,2008. Inter-species hybridization among Neotropical cats of the genus Leopardus, and evidence for an introgressive hybrid zone between L. geoffroyi and L. tigrinus in southern Brazil. Molecular Ecology 17,4317-4333.
Turelli, M., Barton, N.H., Coyne, J.A.,2001. Theory and speciation. Trends in Ecology & Evolution 16,330-343.
Vallender, R., Robertson, R., Friesen, V., Lovette, I.,2007. Complex hybridization dynamics between golden-winged and blue-winged warblers (Vermivora chrysoptera and Vermivora pinus) revealed by AFLP, microsatellite, intron and mtDNA markers. Molecular Ecology 16, 2017-2029.
Vanhala, T., Van Rijn, C., Buntjer, J., Stam, P., Nevo, E., Poorter, H., Van Eeuwijk, F.,2004. Environmental, phenotypic and genetic variation of wild barley (Hordeum spontaneum) from Israel. Euphytica 137,297-309.
Vaurie, C.,1966. The birds of the palearctic fauna:a systematic reference, non-passeriformes. Witherby, London.
Via, S.,2001. Sympatric speciation in animals:the ugly duckling grows up. Trends in Ecology & Evolution 16,381-390.
Wang, D.G., Fan, J.B., Siao, C.J., Berno, A., Young, P., Sapolsky, R., Ghandour, G., Perkins, N.,
Winchester, E., Spencer, J.,1998. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280,1077-1082.
Wares, J.P., Cunningham, C.W.,2001. Phylogeography and historical ecology of the North Atlantic intertidal. Evolution 55,2455-2469.
Watson, G.E.,1962. Three sibling species of Alectoris partridge. Ibis 104,353-367.
Watterson, G.A.,1984. Allele frequencies after a bottleneck. Theoretical Population Biology 26, 387-407.
Weir, B., Cockerham, C.C.,1984. Estimating F-statistics for the analysis of population structure. Evolution,1358-1370.
Wiens, J.J.,2004. What is speciation and how should we study it? The American Naturalist 163, 914-923.
Williams, J.W., Jackson, S.T., Kutzbach, J.E.,2007. Projected distributions of novel and disappearing climates by 2100 AD. Proceedings of the National Academy of Sciences 104, 5738-5742.
Wilson, E.,1988. The current state of biological diversity. National Academy Press, Washington, DC.
Yaakub, S.M., Bellwood, D.R., Herwerden, L., Walsh, F.M.,2006. Hybridization in coral reef fishes:introgression and bi-directional gene exchange in Thalassoma (family Labridae). Mol Phylogenet Evol 40,84-100.
Yu, N., Zheng, C., Zhang, Y.P., Li, W.H.,2000. Molecular systematics of pikas (genus Ochotona) inferred from mitochondrial DNA sequences. Mol Phylogenet Evol 16,85-95.
Zhang, D., Fengquan, L., Jianmin, B.,2000. Eco-environmental effects of the Qinghai-Tibet Plateau uplift during the Quaternary in China. Environmental Geology 39,1352-1358.
Zhang, F., Jiang, Z.,2006. Mitochondrial phylogeography and genetic diversity of Tibetan gazelle (Procapra picticaudata):implications for conservation. Mol Phylogenet Evol 41,313-321.
Zink, R.M., Pavlova, A., Drovetski, S., Rohwer, S.,2008. Mitochondrial phylogeographies of five widespread Eurasian bird species. Journal of Ornithology 149,399-413.
曹曼曼,2010.我国斑翅山鹑遗传多样性与分子系统地理学研究[硕士论文].兰州：兰州大学.
曹兴山,1996.甘肃第四纪气候期划分.干旱区研究13,28-40.
陈克造,黄第藩,梁狄刚,1964.青海湖的形成和发展.地理学报30,214-233.
陈强,常城,刘迺发,1999.两种邻域分布石鸡间的线粒体DNA渗透.动物学报45,456-463.
陈小勇,罗兰,刘迺发,何德奎,1998.兰州大石鸡不同生活史阶段栖息地选择的初步研究.应用与环境生物学报4,368-373.
陈妍珂,2006.我国六盘山地区大石鸡和石鸡的渐渗杂交[博士论文].兰州：兰州大学.
葛颂,洪德元,1994.遗传多样性及其检测方法.见：钱迎倩,马克平(主编),生物多样性研究的原理与方法.中国科学技术出版社,北京.
郝岗平,吴忠义,陈茂盛,曹鸣庆,黄丛林,杨清,2004.拟南芥CBF4基因位点的单核苷酸多态性(SNP)变化与抗旱表型的相应性.农业生物技术学报12,122-131.
侯连海,1993.周口店更新世鸟类.中国科学院古脊椎动物与人类研究所集刊.科学技术出版社,北京,165-249.
侯鹏,卫明,张立勋,刘发,2002.大石鸡边缘种群的遗传结构.动物学报48,333-338.
胡志昂,王洪新,1998.分子生态学研究进展.生态学报18,565-574.
胡志昂,张亚平,1997.中国动植物的遗传多样性.浙江科学技术出版社,杭州.
黄麒,孟昭强,刘海玲,1990.柴达木盆地察尔汗湖区古气候波动模式的初步研究.中国科学：B辑,652-663.
黄勇平,朱湘雄,2003.分子生态学—生命科学领域的新学科.中国科学院院刊18,84-88.
黄族豪,2005.我国石鸡属鸟类的分子生态学研究[博士论文].兰州：兰州大学.
黄族豪,刘迺发,2004.陇东黄土高原石鸡的分子系统地理结构.动物学报50,576-582.
雷冬梅,张莘,宋春敬,段昌群,2004.分子生态学的理论与方法研究进展.生态科学进展1,135-159.
李秉成,孙建中,2004.黄土高原晚更新世的植被与气候环境.地理研究23,641-648.
李吉均,方小敏,马海洲,朱俊杰,潘保田,陈怀录,1996.晚新生代黄河上游地貌演化与青藏高原隆起.中国科学(D辑)26,316-322.
李吉均,方小敏,潘保田,赵志军,宋友桂,2001.新生代晚期青藏高原强烈隆起及其对周边环境的影响.第四纪研究21,381-391.
李庆伟,马飞,2007.鸟类分子进化与分子系统学.科学出版社,北京.
李裕元,石辉,2001.新构造运动对黄土高原环境变迁的影响.水土保持研究8,123-129.
林栲,李海鹏,2009.DNA水平上检测正选择方法的研究进展.遗传31,896-902.
刘迺发,1984.大石鸡分类地位的研究.动物分类学报9,212-218.
刘迺发,陈小勇,何德奎,1996.兰州地区大石鸡栖息地选择.动物学报42,83-89.
刘迺发,黄族豪,文陇英,2004.大石鸡亚种分化及一新亚种描述(鸡形目,雉科).动物分类学报刘迺发,王香亭,罗文英,1988.宁夏六盘山鸟类区系研究.兰州大学学报(自然科学版),65-75.
刘迺发,文陇英,黄族豪,侯鹏,2006.六盘山地区石鸡和大石鸡间的渐渗杂交.动物学报52，153-159.
刘亚锋,山宝琴,刘亚惠,2005.分子生态学及其研究进展.延安大学学报：自然科学版24,85-87.
康安,朱筱敏,韩德馨,王延斌,康强,2003.柴达木盆地第四纪孢粉组合及古气候波动.地质通报22,12-15.
沈才明,王苏民,1996.若尔盖地区25万年以来的植被与气候.微体古生物学报13,373-385.
施立明,1990.遗传多样性及其保存.生物科学信息2,159-164.
施雅风,1996.青藏高原进入冰冻圈的时代,高度及其对周围地区的影响.见：青藏高原形成,演化,环境变迁与生态系统.科学出版社,北京.
施雅风,1998.第四纪中期青藏高原冰冻圈的演化及其与全球变化的联系.冰川冻土20,197-208.
施雅风,2004.青藏高原大冰盖假说的提出与扬弃.第四纪研究24,10-18.
施雅风,李吉均,李炳元,1998.青藏高原晚新生代隆升和环境变化.广东科学技术出版社,广州.
施雅风,李吉均,李炳元,姚檀栋,王苏民,李世杰,崔之久,王富保,潘保田,方小敏,张青松,1999.晚新生代青藏高原的隆升与东亚环境变化.地理学报54,10-20.
施雅风,郑本兴,1995.青藏高原中东部最大冰期时代高度与气候环境探讨.冰川冻土17,97-112.
施雅风,郑本兴,李世态,1990.青藏高原的末次冰期与最大冰期.冰川冻土12,1-16.
宋森,2011.石鸡的分子生态及系统地理学研究[博士论文].兰州：兰州大学.
孙儒泳,2001.动物生态学原理(第三版).北京师范大学出版社,北京.
田风贵,马志杰,陈智华,2005.分子生态学与生物多样性研究.西南民族大学学报：自然科学版31,115-120.
王静波,胡长龙,徐宏发,2001.线粒体DNA (mtDNA)多态性在动物保护生物学中的应用.生物多样性9,181-187.
汪松,陈灵芝等,1990.中国科学院生物多样性研讨会会议录.中国科学院生物科学与技术局,北京.
王苏民,施雅风,1992.晚第四纪青海湖演化研究析视与讨论.湖泊科学4,1-9.
王文,1998.分子系统学在生物保护中的意义.生物多样性6,138-142.
王香亭,1991.甘肃脊椎动物志.甘肃科学技术出版社,兰州.
汪永庆,张知彬,徐来祥,2001.中心区和边缘区大仓鼠种群的遗传多样性.科学通报46,1644-1650.
王峥峰,彭少麟,2003.杂交产生的遗传危害一以植物为例.生物多样性11,334-339.
王子玉,1986.云台山鸟类考察报告.动物学杂志21,20-28.
卫明,侯鹏,黄族豪,刘迺发,2002.环境因子对大石鸡种群遗传结构的影响.生态学报22,528-534.
肖金学,王文强,廉振民,2008.浅议分子生态学的概念.延安大学学报：自然科学版27,69-71.
肖清华,张旺生,张伟,朱创鑫,王杰,2008.祁连山地区更新世以来冰期雪线变化研究.干旱区研究25,426-432.
徐钦琦,1990.地球轨道与气候演变的关系.科学通报25,180-182.
杨志松,2007.我国石鸡属鸟类系统地理结构及其种间杂交的研究[博士论文].兰州：兰州大学.
杨志松,刘迺发,2009.基于细胞色素b基因研究两种石鸡的渐渗杂交.重庆师范大学学报(自然科学版)26,1-6.
张惠昌,商日媛,1991.兰州地区黄土年代的划分及古气候特征.兰州大学学报(自然科学版)27，131-138.
张军丽,廖斌,王胜龙译,2009.分子生态学(Beebee TJC & Rowe G. (eds.),2004. An Introduction to Molecular Ecology. Oxford University Press.)中山大学出版社,广州.
张荫荪,梁拴柱,陈容伯,1989.石鸡的一新亚种-鄂尔多斯石鸡(鸡形目：雉科).动物分类学报14,496-499.
张亚平,王文,宿兵,1995.大熊猫微卫星DNA的筛选及其应用.动物学研究16,301-306.
郑光美,2002.世界鸟类与分布名录.科学出版社,北京.
郑作新,1978.中国动物志鸟纲第四卷—鸡形目.科学出版社,北京.
Abbott, R.J., James, J.K., Milne, R.I., Gillies, A.,2003. Plant introductions, hybridization and gene flow. Philosophical Transactions of the Royal Society of London. Series B:Biological Sciences 358,1123-1132.
Adams, C.C.,1905. The postglacial dispersal of the North American biota. The Biological Bulletin 9,53-71.
Alsos, I.G., Eidesen, P.B., Ehrich, D., Skrede, I., Westergaard, K., Jacobsen, G.H., Landvik, J.Y., Taberlet, P., Brochmann, C.,2007. Frequent long-distance plant colonization in the changing Arctic. Science 316,1606-1609.
An, B., Zhang, L., Browne, S., Liu, N., Ruan, L., Song, S.,2009. Phylogeography of Tibetan snowcock (Tetraogallus tibetanus) in Qinghai-Tibetan Plateau. Mol Phylogenet Evol 50, 526-533.
Andersson, A.C., Narain, Y., Tegelstr m, H., Fredga, K.,2004. No apparent reduction of gene flow in a hybrid zone between the West and North European karyotypic groups of the common shrew, Sorex araneus. Molecular Ecology 13,1205-1215.
Aris-Brosou, S., Excoffier, L.,1996. The impact of population expansion and mutation rate heterogeneity on DNA sequence polymorphism. Mol Biol Evol 13,494-504.
Arnold, M.L.,1997. Natural hybridization and evolution. Oxford University Press, USA.
Avise, J.C.,1994. Molecular Markers,Natural History and Evolution. Chapman&Hall, New York.
Avise, J.C.,2000. Phylogeography:The History and Formation of Species. Harvard University Press, Cambridge, Massachusetts.
Avise, J.C., Arnold, J., Ball, R.M., Bermingham, E., Lamb, T., Neigel, J.E., Reeb, C.A., Saunders, N.C.,1987. Intraspecific phylogeography:the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics 18,489-522.
Avise, J.C., Ball, R.,1990. Principles of geneological concordance in species concepts and biological taxonomy. In:Futuyma, D.J., Antonovics, J. (Eds.), Oxford Surveys in Evolutionary Biology. Oxford University Press, Oxford.
Avise, J.C., Hamrick, J.L.,1996. Conservation genetics:case histories from nature. Springer.
Avise, J.C., Neigel, J.E., Arnold, J.,1984. Demographic influences on mitochondrial DNA lineage survivorship in animal populations. Journal of Molecular Evolution 20,99-105.
Avise, J.C., Walker, D.,1998. Pleistocene phylogeographic effects on avian populations and the speciation process. Proc Biol Sci 265,457-463.
Babik, W., Branicki, W., Crnobrnja-Isailovic, J., Cogalniceanu, D., Sas, I., Olgun, K., Poyarkov, N., Garcia-Paris, M., Arntzen, J.W., 2005. Phylogeography of two European newt species-discordance between mtDNA and morphology. Molecular Ecology 14,2475-2491.
Badr, A.,2000. On the origin and domestication history of barley (Hordeum vulgare). Molecular Biology and Evolution 17,499-510.
Barluenga, M., St lting, K.N., Salzburger, W., Muschick, M., Meyer, A.,2006. Sympatric speciation in Nicaraguan crater lake cichlid fish. Nature 439,719-723.
Barratt, E., Gurnell, J., Malarky, G., Deaville, R., Bruford, M.,1999. Genetic structure of fragmented populations of red squirrel (Sciurus vulgaris) in the UK. Molecular Ecology 8, S55-S63.
Barrowclough, G., Groth, J., Mertz, L., Guti(?)rrez, R., 2005. Genetic structure, introgression, and a narrow hybrid zone between northern and California spotted owls (Strix occidentalis). Molecular Ecology 14,1109-1120.
Barton, N.H., Hewitt, G.M.,1989. Adaptation, speciation and hybrid zones. Nature 341,497-503.
Beebee, T.J.C., Rowe, G., 2004. An Introduction to Molecular Ecology. Oxford University Press, New York.
Bensen, J.T., Langefeld, C.D., Hawkins, G.A., Green, L.E., Mychaleckyj, J.C., Brewer, C.S., Kiger, D.S., Binford, S.M., Colicigno, C.J., Allred, D.C.,2003. Nucleotide variation, haplotype structure, and association with end-stage renal disease of the human interleukin-1 gene cluster. Genomics 82,194-217.
Bernacchi, D., Beck-Bunn, T., Emmatty, D., Eshed, Y., Inai, S., Lopez, J., Petiard, V., Sayama, H., Uhlig, J., Zamir, D., 1998. Advanced backcross QTL analysis of tomato. Ⅱ. Evaluation of near-isogenic lines carrying single-donor introgressions for desirable wild QTL-alleles derived from Lycopersicon hirsutum and L. pimpinellifolium. TAG Theoretical and Applied Genetics 97, 170-180.
Bernatchez, L., Wilson, C.C.,1998. Comparative phylogeography of Nearctic and Palearctic fishes. Molecular Ecology 7,431-452.
Birky-Jr, C., Fuerst, P., Maruyama, T.,1989. Organelle gene diversity under migration, mutation, and drift:equilibrium expectations, approach to equilibrium, effects of heteroplasmic cells, and comparison to nuclear genes. Genetics 121,613-627.
Brooks, T.M., Mittermeier, R.A., Mittermeier, C.G., Da Fonseca, G.A.B., Rylands, A.B., Konstant, W.R., Flick, P., Pilgrim, J., Oldfield, S., Magin, G.,2002. Habitat loss and extinction in the hotspots of biodiversity. Conservation Biology 16,909-923.
Burke T,Seidler R,Smith H.Editorial. Molec.Ecol,1992,1:1
Cagelli, L., Lefevre, F.,1995. The conservation of Populus nigra L. and gene flow with cultivated poplars in Europe. Forest Genetics 2,135-144.
Cao, M.M., Liu, N.F., Wang, X.L., Guan, M.M.,2010. Genetic diversity and genetic structure of the Daurian Partridge (Perdix dauuricae) in China, assessed by microsatellite variation. Chinese Birds 1,51-64.
Cartens, B.C., Brunsfeld, S.J., Demboski, J.R., Good, J.M., Sullivan, J.,2005. Investigating the Evolutionary History of the Pacific Northwest Mesic Forest Ecosystem:Hpotehesis Testing Within a Comparative Phylogeographic Framework. Evolution 59,1639-1652.
Chen, Q., Chang, C., Liu, N.F.,1999. Mitochondrial DNA Introgression between Two Parapatric Species of Alectoris. Acta Zoologica Sinica 45,456-463.
Chen, Y., Wang, W., Yang, Y., Su, B., Zhang, Y., Xiong, L., He, Z., Shu, C., Yang, D.,1997. Genetic divergence of Cordyceps sinensis as estimated by random amplified polymorphic DNA analysis]. Acta genetica Sinica 24,410-416.
Chen, Y, Zhao, Z., Liu, N.,2006. Genetic structure of Przewalski's rock partridge (Alectoris magna) populations in the Longzhong Loess Plateau, China. Biochemical genetics 44,209-221.
Chetelat, R., Meglic, V.,2000. Molecular mapping of chromosome segments introgressed from Solanum lycopersicoides into cultivated tomato (Lycopersicon esculentum). TAG Theoretical and Applied Genetics 100,232-241.
Cianchi, R., Ungaro, A., Marini, M., Bullini, L.,2003. Differential patterns of hybridization and introgression between the swallowtails Papilio machaon and P. hospiton from Sardinia and Corsica islands (Lepidoptera, Papilionidae). Molecular Ecology 12,1461-1471.
Clements, J.F.,2007. The Clements checklist of birds of the world (6th Edition). Cornell University Press, New York.
Cornuet, J.M., Luikart, G.,1996. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144,2001-2014.
Cramp, S., Simmons, K.E.L.,1980. Handbook of the birds of Europe, the Middle East and North Africa. The birds of the Western Palearctic. OxfordUniversityPress, Oxford.
Crandall, K.A., Bininda-Emonds, O.R.P., Mace, G.M., Wayne, R.K.,2000. Considering evolutionary processes in conservation biology. Trends in Ecology & Evolution 15,290-295.
Crandall, K.A., Templeton, A.R.,1993. Empirical Tests of Some Predictions From Coalescent Theory With Applications to Intraspecific Phylogeny Reconstruction. Genetics 134,959-969.
Crochet, P.A., Desmarais, E., 2000. Slow rate of evolution in the mitochondrial control region of gulls (Aves:Laridae). Molecular Biology and Evolution 17,1797-1806.
De Queiroz, K.,2007. Species concepts and species delimitation. Syst Biol 56,879-886.
Di Rienzo, A., Peterson, A., Garza, J., Valdes, A., Slatkin, M., Freimer, N.,1994. Mutational processes of simple-sequence repeat loci in human populations. Proceedings of the National Academy of Sciences of the United States of America 91,3166-3170.
Edwards, S.V., Beerli, P., 2000. Perspective:gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54,1839-1854.
Ellstrand, N.C., Prentice, H.C., Hancock, J.F.,1999. Gene flow and introgression from domesticated plants into their wild relatives. Annual Review of Ecology and Systematics, 539-563.
Ellstrand, N.C., Whitkus, R., Rieseberg, L.H.,1996. Distribution of spontaneous plant hybrids. Proceedings of the National Academy of Sciences of the United States of America 93, 5090-5093.
Eshed, Y., Zamir, D.,1994. Introgressions fromLycopersicon pennellii can improve the soluble-solids yield of tomato hybrids. TAG Theoretical and Applied Genetics 88,891-897.
Eshed, Y., Zamir, D.,1995. An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. Genetics 141,1147-1162.
Excoffier, L., Laval, G., Schneider, S.,2005. Arlequin (version 3.0):an integrated software package for population genetics data analysis. Evol Bioinform Online 1,47-50.
Excoffier, L., Smouse, P.E., Quattro, J.M.,1992. Analysis of Molecular Variance Inferred From Metric Distances Among DNA Haplotypes:Application to Human Mitochondrial DNA Restriction Data. Genetics 131,479-491.
Ferrier, S., Guisan, A.,2006. Spatial modelling of biodiversity at the community level. Journal of Applied Ecology 43,393-404.
Frankel, O.H., Soule, M.E.,1981. Conservation and evolution. Cambridge University Press, Cambridge, UK.
Fu, Y.X.,1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147,915-925.
Fu, Y.X., Li, W.H.,1993. Statistical tests of neutrality of mutations. Genetics 133,693-709.
Garcia-Ramos, G., Kirkpatrick, M.,1997. Genetic models of adaptation and gene flow in peripheral populations. Evolution,21-28.
Garner, T.W.J., Pearman, P.B., Angelone, S.,2004. Genetic diversity across a vertebrate species' range:a test of the central-peripheral hypothesis. Molecular Ecology 13,1047-1053.
Gibbs, H.L., Corey, S.J., Blouin-Demers, G., Prior, K.A., Weatherhead, P.J.,2006. Hybridization between mtDNA-defined phylogeographic lineages of black ratsnakes (Pantherophis sp.). Molecular Ecology 15,3755-3767.
Gill, F.,1994. Rapid, asymmetrical introgression of mitochondrial DNA in hybridizing populations of Blue-wringed and Golden-wringed warblers. Journal of Ornithology 135, 359-369.
Gligor, M., Ganzhorn, J., Rakotondravony, D., Ramilijaona, O., Razafimahatratra, E., Zischler, H., Hapke, A.,2009. Hybridization between mouse lemurs in an ecological transition zone in southern Madagascar. Molecular Ecology 18,520-533.
Gompert, Z., Forister, M.L., Fordyce, J.A., Nlice, C.C.,2008. Widespread mito-nuclear discordance with evidence for introgressive hybridization and selective sweeps in Lycaeides. Molecular Ecology 17,5231-5244.
Gonzalez-Rodriguez, A., Bain, J., Golden, J., Oyama, K.,2004. Chloroplast DNA variation in the Quercus affinis CQ. laurina complex in Mexico:geographical structure and associations with nuclear and morphological variation. Molecular Ecology 13,3467-3476.
Good, J.M., Hird, S., Reid, N., DEMBOSKI, J.R., STEPPAN, S.J., MARTIN-NIMS, T.R., Sullivan, J.,2008. Ancient hybridization and mitochondrial capture between two species of chipmunks. Molecular Ecology 17,1313-1327.
Groom, M.J., Meffe, G.K., Carroll, C.R.,2006. Principles of conservation biology. Sinauer Associates Sunderland, Massachusetts, USA.
Hansen, M., Loeschcke, V.,1994. Effects of releasing hatcheryreared brown trout to wild trout populations. In:Loeschcke, V., Tomiuk, J. and Jam, S. K.(eds) Conservation Genetics. Birkhauser Verlag, Basle.
Harrison, R.G.,1993. Hybrids and hybrid zones:historical perspective. Oxford University Press, Oxford,UK.
Hewitt, G.,1999. Post-glacial re-colonization of European biota Biol. J. Linnean Soc 68,87-112.
Hewitt, G.M.,1996. Some genetic consequences of ice ages, and their role, in divergence and speciation. Biological Journal of the Linnean Society 58,247-276.
Hewitt, G.M.,2000. The genetic legacy of the Quaternary ice ages. Nature 405,907-913.
Hewitt, G.M.,2001. Speciation, hybrid zones and phylogeography-or seeing genes in space and time. Molecular Ecology 10,537-549.
Hey, J., Kliman, R.M.,1993. Population genetics and phylogenetics of DNA sequence variation at multiple loci within the Drosophila melanogaster species complex. Molecular Biology and Evolution 10,804-822.
Hey, J., Nielsen, R.,2004. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167,747-760.
Hickerson, M.J., Meyer, C.P.,2008. Testing comparative phylogeographic models of marine vicariance and dispersal using a hierarchical Bayesian approach. Bmc Evol Biol 8,322.
Hickerson, M.J., Meyer, C.P., Moritz, C.,2006. DNA barcoding will often fail to discover new animal species over broad parameter space. Syst Biol 55,729-739.
Hoffmann, A.A., Blows, M.W.,1994. Species borders:ecological and evolutionary perspectives. Trends in Ecology & Evolution 9,223-227.
Houlden, B.A., Costello, B.H., Sharkey, D., Fowler, E.V., Melzer, A., Ellis, W., Carrick, F., Baverstock, P.R., Elphinstone, M.S.,1999. Phylogeographic differentiation in the mitochondrial control region in the koala, Phascolarctos cinereus (Goldfuss 1817). Molecular Ecology 8, 999-1011.
Huang, Z., Liu, N., Zhou, T., Ju, B.,2005. Effects of environmental factors on the population genetic structure in chukar partridge (Alectoris chukar). Journal of arid environments 62, 427-434.
Huang, Z., Liu, N., Luo, S., Long, J.,2007a. Phylogeography of rusty-necklaced partridge (Alectoris magna) in northwestern China. Mol Phylogenet Evol 43,379-385.
Huang, Z., Liu, N., Luo, S., Long, J., Xiao, Y.,2007b. Ecological genetics of rusty-necklaced partridge (Alectoris magna):Environmental factors and population genetic variability correlations. Korean Journal of Genetics 29,115-120.
Huang, Z.H., Yang, Z.S., Zhang, J., Liu, N.F.,2009. Introgressive hybridization and population genetic diversity between rusty-necklaced partridge and chukar partridge in northwestern China. Belgian Journal of Zoology 139,15-21.
Huang, Z., Liu, N., Zhou, T., Ju, B.,2005. Effects of environmental factors on the population genetic structure in chukar partridge (Alectoris chukar). Journal of arid environments 62, 427-434.
Hudson, R.R., Coyne, J.A.,2002. Mathematical consequences of the genealogical species concept. Evolution 56,1557-1565.
Huelsenbeck, J.P., Ronquist, F.,2001. MRBAYES:Bayesian inference of phylogenetic trees. Bioinformatics 17,754-755.
Humphries, C.J., Williams, P.H., Vane-Wright, R.I.,1995. Measuring biodiversity value for conservation. Annual Review of Ecology and Systematics 26,93-101.
Jensen, A.B., Palmer, K.A., Boomsma, J.J., Pedersen, B.V.,2005. Varying degrees of Apis mellifera ligustica introgression in protected populations of the black honeybee, Apis mellifera mellifera, in northwest Europe. Molecular Ecology 14,93-106.
Jin, Y.T., Brown, R.P., Liu, N.F.,2008. Cladogenesis and phylogeography of the lizard Phrynocephalus vlangalii (Agamidae) on the Tibetan plateau. Mol Ecol 17,1971-1982.
Jin, Y.T., Liu, N.F.,2008. Ecological Genetics of Phrynocephalus vlangalii on the North Tibetan (Qinghai) Plateau:Correlation between Environmental Factors and Population Genetic Variability. Biochemical genetics 46,598-604.
Johnsgard, P.A., Jones, H.,1988. The quails, partridges, and francolins of the world. Oxford University Press Oxford, Oxford.
Jordan, D.S.,1905. The origin of species through isolation. Science 22,545-562.
Joseph, L., Wilke, T., Alpers, D.,2002. Reconciling genetic expectations from host specificity with historical population dynamics in an avian brood parasite, Horsfield's Bronze-Cuckoo Chalcites basalis of Australia. Molecular Ecology 11,829-837.
Karron, J.D.,1987. A comparison of levels of genetic polymorphism and self-compatibility in geographically restricted and widespread plant congeners. Evolutionary Ecology 1,47-58.
Kimura, M.,1968. Evolutionary rate at the molecular level. Nature 217,624-626.
Kingman, J.,1982a. On the genealogy of large populations. Journal of Applied Probability,27-43.
Kingman, J.F.C.,1982b. The coalescent. Stochastic processes and their applications 13,235-248.
Knowles, L.L., Carstens, B.C.,2007. Delimiting species without monophyletic gene trees. Syst Biol 56,887-895.
Lamoreux, J.F., Morrison, J.C., Ricketts, T.H., Olson, D.M., Dinerstein, E., McKnight, M.W., Shugart, H.H.,2005. Global tests of biodiversity concordance and the importance of endemism. Nature 440,212-214.
Le corre, V., Roux, F., Reboud, X.,2002. DNA polymorphism at the FRIGIDA gene in Arabidopsis thaliana:extensive nonsynonymous variation is consistent with local selection for flowering time. Molecular Biology and Evolution 19,1261-1271.
Leache, A.D., Cole, C.J.,2007. Hybridization between multiple fence lizard lineages in an ecotone: locally discordant variation in mitochondrial DNA, chromosomes, and morphology. Molecular Ecology 16,1035-1054.
Leavitt, D.H., Bezy, R.L., Crandall, K.A., Sites Jr, J.W.,2007. Multi-locus DNA sequence data reveal a history of deep cryptic vicariance and habitat-driven convergence in the desert night lizard Xantusia vigilis species complex (Squamata:Xantusiidae). Molecular Ecology 16, 4455-4481.
Lesica, P., Allendorf, F.W.,1995. When are peripheral populations valuable for conservation? Conservation Biology 9,753-760.
Levin, D.A., Francisco-Ortega, J., Jansen, R.K.,1996. Hybridization and the extinction of rare plant species. Conservation Biology 10,10-16.
Lexer, C., Randell, R.A., Rieseberg, L.H.,2003. Experimental hybridization as a tool for studying selection in the wild. Ecology 84,1688-1699.
Li, L., Wang, R.Q., Wang, Z.R., Wang, S.P., Li, S.H.,1996. The studies of Naidong Camellia biodiversity in Qingdao (Ⅱ)——Genetic diversity analysis of populations. Biodiversity Science 4,1-6.
Li, Z.K., Fu, B.Y., Gao, Y.M., Xu, J.L., Ali, J., Lafitte, H., Jiang, Y.Z., Rey, J.D., Vijayakumar, C.H.M., Maghirang, R.,2005. Genome-wide introgression lines and their use in genetic and molecular dissection of complex phenotypes in rice (Oryza sativa L.). Plant molecular biology 59,33-52.
Librado, P., Rozas, J.,2009. DnaSP v5:a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25,1451-1452.
Lin, S., Sasaki, T., Yano, M.,1998. Mapping quantitative trait loci controlling seed dormancy and heading date in rice, Oryza sativa L., using backcross inbred lines. TAG Theoretical and Applied Genetics 96,997-1003.
Liu, J., Yu, G., Chen, X.,2002. Palaeoclimate simulation of 21 ka for the Tibetan Plateau and Eastern Asia. Climate Dynamics 19,575-583.
Liu, N.,1992. Ecology of Przewalski's rock partridge (Alectoris magna). Gibier Faune Sauvage 9, 605-615.
Liu, Y., Zhan, X., Wang, N., Chang, J., Zhang, Z.,2010. Effect of geological vicariance on mitochondrial DNA differentiation in Common Pheasant populations of the Loess Plateau and eastern China. Mol Phylogenet Evol 55,409-417.
Lorenzen, E.D., de Neergaard, R., Arctander, P., SIEGISMUND, H.R.,2007. Phylogeography, hybridization and Pleistocene refugia of the kob antelope (Kobus kob). Molecular Ecology 16, 3241-3252.
Luikart, G., Allendorf, F., Cornuet, J., Sherwin, W.,1998. Distortion of allele frequency distributions provides a test for recent population bottlenecks. Journal of Heredity 89,238-247.
Lucchini, V., Randi, E.,1998. Mitochondrial DNA sequence variation and phylogeographical structure of rock partridge (Alectoris graeca) populations. Heredity 81,528-536.
Maan, S.S.,1987. Interspecific and intergeneric hybridization in wheat. In:Heyne, E. G. (Ed.), Wheat and Wheat Improvement. ASA, CSSA and SSSA, Madison.
Madge, S., McGowan, P.J.K., Kirwan, G.M.,2002. Pheasants, partridges and grouse:a guide to the pheasants, partridges, quails, grouse, guineafowl, buttonquails and sandgrouse of the world. Christopher Helm London.
Mallet, J.,2005. Hybridization as an invasion of the genome. Trends in Ecology & Evolution 20, 229-237.
Mayr, E.,1942. Systematics and the origin of species. Columbia university press, New York
McLachlan, J.S., Clark, J.S., Manos, P.S.,2005. Molecular indicators of tree migration capacity under rapid climate change. Ecology 86,2088-2098.
McNeely, J.A., Miller, K.R., Reid, W.V.C., Mittermeier, R.A., Werner, T.B.,1990. Conserving the World's Biological Diversity. Washington D.C. and Gland, Switzerland.
Mebert, K.,2008. Good species despite massive hybridization:genetic research on the contact zone between the watersnakes Nerodia sipedon and N. fasciata in the Carolinas, USA. Molecular Ecology 17,1918-1929.
Melo-Ferreira, J., Boursot, P., Randi, E., Kryukov, A., Suchentrunk, F., Ferrand, N., Alves, P., 2007. The rise and fall of the mountain hare (Lepus timidus) during Pleistocene glaciations: expansion and retreat with hybridization in the Iberian Peninsula. Molecular Ecology 16, 605-618.
Merrell, D.J.,1981. Ecological Genetics, Longman, London.
Meyer, C.P., Paulay, G.,2005. DNA barcoding:error rates based on comprehensive sampling. PLoS Biology 3,2229-2238.
Michalakis, Y., Excoffier, L.,1996. A generic estimation of population subdivision using distances between alleles with special reference for microsatellite loci. Genetics 142,1061-1064.
Morando, M., Avila, L.J., Sites, J.W.,2003. Sampling strategies for delimiting species:genes, individuals, and populations in the Liolaemus elongatus-kriegi complex (Squamata: Liolaemidae) in Andean-Patagonian South America. Syst Biol 52,159-185.
Moritz, C.,1994. Defining evolutionarily significant units for conservation. TRENDS in Ecology and Evolution 9,373-374.
Moritz, C.,1995. Uses of molecular phylogenies for conservation. Philosophical Transactions of the Royal Society of London. Series B:Biological Sciences 349,113-118.
Moritz, C., Dowling, T., Brown, W.,1987. Evolution of animal mitochondrial DNA:relevance for population biology and systematics. Annual Review of Ecology and Systematics,269-292.
Moritz, C., Faith, D.P.,1998. Comparative phylogeography and the identification of genetically divergent areas for conservation. Molecular Ecology 7,419-429.
Moritz, C., Patton, J., Schneider, C., Smith, T.,2000. Diversification of rainforest faunas:an integrated molecular approach. Annual Review of Ecology and Systematics 31,533-563.
Myers, N., Mittermeier, R.A., Mittermeier, C.G., da Fonseca, G.A.B., Kent, J.,2000. Biodiversity hotspots for conservation priorities. Nature 403,853-858.
Nardon, C., Deceliere, G., Loevenbruck, C., Weiss, M., Vieira, C., Biemont, C.,2005. Is genome size influenced by colonization of new environments in dipteran species? Molecular Ecology 14, 869-878.
Neigle, J.E., Avise, J.C.,1986. Phylogenetic relationships of mitochondrial DNA under various demographic models of speciation. In:Nero EandKarlin S(eds). Evolutionary Processes and Theory. Academic Press, New York.
Nevo, E.,1981. Genetic variation and climatic selection in the lizard Agama stellio in Israel and Sinai. TAG Theoretical and Applied Genetics 60,369-380.
Nicolas, V., Mboumba, J.F., Verheyen, E., Denys, C., Lecompte, E., Olayemi, A., Missoup, A.D., Katuala, P., Colyn, M.,2008. Phylogeographic structure and regional history of Lemniscomys striatus (Rodentia:Muridae) in tropical Africa. Journal of biogeography 35,2074-2089.
Nolte, A., Gompert, Z., Buerkle, C,2009. Variable patterns of introgression in two sculpin hybrid zones suggest that genomic isolation differs among populations. Molecular Ecology 18, 2615-2627.
Noy-Meir, I.,1973. Desert ecosystems:environment and producers. Annual Review of Ecology and Systematics 4,25-51.
Nylander, J.A.A.,2004. MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University.
Orme, C.D.L., Davies, R.G., Burgess, M., Eigenbrod, F., Pickup, N., Olson, V.A., Webster, A.J., Ding, T.S., Rasmussen, P.C., Ridgely, R.S.,2005. Global hotspots of species richness are not congruent with endemism or threat. Nature 436,1016-1019.
Pons, J., Barraclough, T.G, Gomez-Zurita, J., Cardoso, A., Duran, D.P., Hazell, S., Kamoun, S., Sumlin, W.D., Vogler, A.P.,2006. Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst Biol 55,595-609.
Posada, D., Crandall, K.A.,2001. Intraspecific gene genealogies:trees grafting into networks. Trends Ecol Evol 16,37-45.
Prentice, H.C., Lonn, M., Lefkovitch, L.P., Runyeon, H.,1995. Associations between allele frequencies in Festuca ovina and habitat variation in the alvar grasslands on the Baltic island of Oland. Journal of Ecology,391-402.
Pritchard, J.K., Stephens, M., Donnelly, P.,2000. Inference of Population Structure Using Multilocus Genotype Data. Genetics 155,945-959.
Qu, J., Liu, N., Bao, X., Wang, X.,2009. Phylogeography of the ring-necked pheasant (Phasianus colchicus) in China. Mol Phylogenet Evol 52,125-132.
Qu, Y., Ericson, P.G.P., Lei, F., Gebauer, A., Kaiser, M., Helbig, A.J.,2006. Molecular phylogenetic relationship of snow finch complex (genera Montifringilla, Pyrgilauda, and Onychostruthus) from the Tibetan plateau. Mol Phylogenet Evol 40,218-226.
Qu, Y., Lei, F.,2009. Comparative phylogeography of two endemic birds of the Tibetan plateau, the white-rumped snow finch (Onychostruthus taczanowskii) and the Hume's ground tit (Pseudopodoces humilis). Mol Phylogenet Evol 51,312-326.
Qu, Y, Lei, F., Zhang, Y, Lu, X.,2010. Comparative phylogeography of five avian species: implications for Pleistocene evolutionary history in the Qinghai-Tibetan plateau. Molecular Ecology 19,338-351.
Randi, E.,1996. A Mitochondrial Cytochrome b Phylogeny of the Alectoris Partridges. Mol Phylogenet Evol 6,214-227.
Randi, E., Alkon, P.U.,1994. Genetic structure of Chukar (Alectoris chukar) populations in Israel. The Auk 111,416-426.
Randi, E., Bernard-Laurent, A.,1999. Population genetics of a hybrid zone between the red-legged partridge and rock partridge. The Auk 116,324-337.
Randi, E., Tabarroni, C., Rimondi, S., Lucchini, V., Sfougaris, A.,2003. Phylogeography of the rock partridge (Alectoris graeca). Molecular Ecology 12,2201-2214.
Raup, D.M.,1986. Biological extinction in earth history. Science 231,1528-1533.
Raymond, M., Rousset, F.,1995. An exact test for population differentiation. Evolution 49, 1280-1283.
Rieseberg, L.H.,1997. Hybrid origins of plant species. Annual Review of Ecology and Systematics 28,359-389.
Rieseberg, L.H.,2000. Crossing relationships among ancient and experimental sunflower hybrid lineages. Evolution 54,859-865.
Rieseberg, L.H., Carney, S.E.,1998. Plant hybridization. New Phytologist 140,599-624.
Rieseberg, L.H., Raymond, O., Rosenthal, D.M., Lai, Z., Livingstone, K., Nakazato, T., Durphy, J.L., Schwarzbach, A.E., Donovan, L.A., Lexer, C.,2003. Major ecological transitions in wild sunflowers facilitated by hybridization. Science 301,1211-1216.
Rieseberg, L.H., Van Fossen, C., Desrochers, A.M.,1995. Hybrid speciation accompanied by genomic reorganization in wild sunflowers. Nature 375,313-316.
Rieseberg, L.H., Wendel, J.F.,1993a. Introgression and its consequences in plants. Hybrid zones and the evolutionary process,70-109.
Rieseberg, L.H., Wendel, J.F.,1993b. Introgression and its consequences in plants. In:Harrison R.G.(eds.), Hybrid Zons and the Evolutionary Process. Oxford University Press, New York.
Rogers, A.R., Harpending, H.,1992. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 9,552-569.
Rooney, A.P., Honeycutt, R.L., Derr, J.N.,2001. Historical Population Size Change of Bowhead Whales Inferred from DNA Sequence Polymorphism Data. Evolution 55,1678-1685.
Rosenberg, N.A.,2003. The shapes of neutral gene genealogies in two species:probabilities of monophyly, paraphyly, and polyphyly in a coalescent model. Evolution 57,1465-1477.
Rosenberg, N.A.,2007. Statistical tests for taxonomic distinctiveness from observations of monophyly. Evolution 61,317-323.
Rousset, F.,1997. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145,1219-1228.
Rowe, G., Beebee, T.J.C.,2003. Population on the verge of a mutational meltdown? Fitness costs of genetic load for an amphibian in the wild. Evolution 57,177-181.
Ryder, O.A.,1986. Species conservation and systematics:the dilemma of subspecies. Trends in Ecology & Evolution 1,9-10.
Rubidge, E.M., Taylor, E.B.,2004. Hybrid zone structure and the potential role of selection in hybridizing populations of native westslope cutthroat trout (Oncorhynchus clarki lewisi) and introduced rainbow trout (O. mykiss). Molecular Ecology 13,3735-3749.
Saetre, G.P., Borge, T., Lindell, J., Mourn, T., Primmer, C.R., Sheldon, B.C., Haavie, J., Johnsen, A., Ellegren, H.,2001. Speciation, introgressive hybridization and nonlinear rate of molecular evolution in flycatchers. Molecular Ecology 10,737-749.
Salzburger, W., Baric, S., Sturmbauer, C.,2002. Speciation via introgressive hybridization in East African cichlids? Molecular Ecology 11,619-625.
Schneider, S., Excoffier, L.,1999. Estimation of Past Demographic Parameters From the Distribution of Pairwise Differences When the Mutation Rates Vary Among Sites:Application to Human Mitochondrial DNA. Genetics 152,1079-1089.
Scheiner, S.M.,1993. Genetics and evolution of phenotypic plasticity. Annual Review of Ecology and Systematics 24,35-68.
Schwarz, D., Matta, B.M., Shakir-Botteri, N.L., McPheron, B.A.,2005. Host shift to an invasive plant triggers rapid animal hybrid speciation. Nature 436,546-549.
Senn, H.V., Pemberton, J.M.,2009. Variable extent of hybridization between invasive sika (Cervus nippon) and native red deer (C. elaphus) in a small geographical area. Molecular Ecology 18, 862-876.
Shi, Y.F.,2002. Characteristics of late Quaternary monsoonal glaciation on the Tibetan Plateau and in East Asia. Quaternary International 97-98,79-91.
Shi, Y.F., Zheng, B.X., Li, S.J.,1990. Last glaciation and maximum glaciation in Qinghai-Xizang (Tibet) plateau. Journal of Glaciology and Geocryology 12,1-15.
Simonsen, K.L., Churchill, G.A., Aquadro, C.F.,1995. Properties of statistical tests of neutrality for DNA polymorphism data. Genetics 141,413-429.
Sites, J.W., Marshall, J.C.,2004. Delimiting species:a Renaissance issue in systematic biology. Trends in Ecology & Evolution 18,462-470.
Slatkin, M.,1987. Gene flow and the geographic structure of natural populations. Science 236, 787-792.
Slatkin, M., Hudson, R.R.,1991. Pairwise Comparisons of Mitochondrial DNA Sequences in Stable and Exponentially Growing Populations. Genetics 129,555-562.
Snow, A.A., Andersen, B., J rgensen, R.B.,1999. Costs of transgenic herbicide resistance introgressed from Brassica napus into weedy B. rapa. Molecular Ecology 8,605-615.
Soule, M.,1973. The epistasis cycle:a theory of marginal populations. Annual Review of Ecology and Systematics 4,165-187.
Spathelf, M., Waite, T., 2007. Will hotspots conserve extra primate and carnivore evolutionary history? Diversity and Distributions 13,746-751.
Stevison, L.S., Kohn, M.H.,2009. Divergence population genetic analysis of hybridization between rhesus and cynomolgus macaques. Molecular Ecology 18,2457-2475.
Swenson, N.G., Howard, D.J.,2005. Clustering of contact zones, hybrid zones, and phylogeographic breaks in North America. American Naturalist 166,581-591.
Swofford, D.L.,2002. PAUP*. Phylogenetic analysis using parsimony (*and other methods).
Taberlet, P., Cheddadi, R.,2002. Quaternary refugia and persistence of biodiversity. Science 297, 2009-2010.
Taberlet, P., Fumagalli, L., Wust-Saucy, A.G., Cosson, J.F.,1998. Comparative phylogeography and postglacial colonization routes in Europe. Molecular Ecology 7,453-464.
Taberlet, P., Luikart, G.,1999. Non-invasive genetic sampling and individual identification. Biological Journal of the Linnean Society 68,41-55.
Tajima, F.,1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123,585-595.
Tanksley, S., Nelson, J.,1996. Advanced backcross QTL analysis:a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. TAG Theoretical and Applied Genetics 92,191-203.
Tang, Q., Liu, H., Mayden, R., Xiong, B.,2006. Comparison of evolutionary rates in the mitochondrial DNA cytochrome b gene and control region and their implications for phylogeny of the Cobitoidea (Teleostei:Cypriniformes). Mol Phylogenet Evol 39,347-357.
Templeton, A.R.,2001. Using phylogeographic analyses of gene trees to test species status and processes. Molecular Ecology 10,779-791.
Thompson, C., Thompson, B., Ades, P., Cousens, R., Garnier-Gere, P., Landman, K., Newbigin, E., Burgman, M.,2003. Model-based analysis of the likelihood of gene introgression from genetically modified crops into wild relatives. Ecological Modelling 162,199-209.
Trigo, T., Freitas, T., Kunzler, G., Cardoso, L., Silva, J., Johnson, W., O'BRIEN, S., Bonatto, S., Eizirik, E.,2008. Inter-species hybridization among Neotropical cats of the genus Leopardus, and evidence for an introgressive hybrid zone between L. geoffroyi and L. tigrinus in southern Brazil. Molecular Ecology 17,4317-4333.
Turelli, M., Barton, N.H., Coyne, J.A.,2001. Theory and speciation. Trends in Ecology & Evolution 16,330-343.
Vallender, R., Robertson, R., Friesen, V., Lovette, I.,2007. Complex hybridization dynamics between golden-winged and blue-winged warblers (Vermivora chrysoptera and Vermivora pinus) revealed by AFLP, microsatellite, intron and mtDNA markers. Molecular Ecology 16, 2017-2029.
Vanhala, T., Van Rijn, C., Buntjer, J., Stam, P., Nevo, E., Poorter, H., Van Eeuwijk, F.,2004. Environmental, phenotypic and genetic variation of wild barley (Hordeum spontaneum) from Israel. Euphytica 137,297-309.
Vaurie, C.,1966. The birds of the palearctic fauna:a systematic reference, non-passeriformes. Witherby, London.
Via, S.,2001. Sympatric speciation in animals:the ugly duckling grows up. Trends in Ecology & Evolution 16,381-390.
Wang, D.G., Fan, J.B., Siao, C.J., Berno, A., Young, P., Sapolsky, R., Ghandour, G., Perkins, N.,
Winchester, E., Spencer, J.,1998. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280,1077-1082.
Wares, J.P., Cunningham, C.W.,2001. Phylogeography and historical ecology of the North Atlantic intertidal. Evolution 55,2455-2469.
Watson, G.E.,1962. Three sibling species of Alectoris partridge. Ibis 104,353-367.
Watterson, G.A.,1984. Allele frequencies after a bottleneck. Theoretical Population Biology 26, 387-407.
Weir, B., Cockerham, C.C.,1984. Estimating F-statistics for the analysis of population structure. Evolution,1358-1370.
Wiens, J.J.,2004. What is speciation and how should we study it? The American Naturalist 163, 914-923.
Williams, J.W., Jackson, S.T., Kutzbach, J.E.,2007. Projected distributions of novel and disappearing climates by 2100 AD. Proceedings of the National Academy of Sciences 104, 5738-5742.
Wilson, E.,1988. The current state of biological diversity. National Academy Press, Washington, DC.
Yaakub, S.M., Bellwood, D.R., Herwerden, L., Walsh, F.M.,2006. Hybridization in coral reef fishes:introgression and bi-directional gene exchange in Thalassoma (family Labridae). Mol Phylogenet Evol 40,84-100.
Yu, N., Zheng, C., Zhang, Y.P., Li, W.H.,2000. Molecular systematics of pikas (genus Ochotona) inferred from mitochondrial DNA sequences. Mol Phylogenet Evol 16,85-95.
Zhang, D., Fengquan, L., Jianmin, B.,2000. Eco-environmental effects of the Qinghai-Tibet Plateau uplift during the Quaternary in China. Environmental Geology 39,1352-1358.
Zhang, F., Jiang, Z.,2006. Mitochondrial phylogeography and genetic diversity of Tibetan gazelle (Procapra picticaudata):implications for conservation. Mol Phylogenet Evol 41,313-321.
Zink, R.M., Pavlova, A., Drovetski, S., Rohwer, S.,2008. Mitochondrial phylogeographies of five widespread Eurasian bird species. Journal of Ornithology 149,399-413.