我国斑翅山鹑遗传多样性与分子系统地理学研究
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摘要
斑翅山鹑(Perdix dauuricae)是一种广布性草原鸟类,隶属鸡形目(Galliformes)雉科(Phasianidae)山鹑属(Genus Perdix),是具有很高经济价值的猎用禽。本研究选用微卫星DNA作为分子标记,分别从家鸡(Gallus gallus)和鹌鹑(Coturnix coturnix)的微卫星引物中共筛选出8个微卫星DNA标记位点,对分布于我国的斑翅山鹑种群进行遗传多样性和分子系统地理学研究。比较了来自青藏高原的5个地理种群、黄土高原9个地理种群、六盘山2个地理种群、内蒙古高原3个地理种群、华北平原的2个地理种群、东北平原1个地理种群和天山山脉的1个地理种群共23个地理种群285个样本个体之间的遗传多样性情况以及系统地理格局。
8个微卫星位点在斑翅山鹁23个地理种群中均获得成功扩增,通过对微卫星数据的的分析,我们获得到了如下主要结果及结论：
(1)遗传多样性研究：8个微卫星位点共检测到94个等位基因,每个位点平均等位基因数为11.75。所有位点都呈现多态性。平均期望杂合度(HE)和观测杂合度(Ho)分别为0.58和0.72。8个位点的多态信息含量从0.56(MCW280)到0.87(UBC0006)。平均多态信息含量(PIC)为0.73。这些结果表明斑翅山鹑为遗传多样性较丰富的群体。斑翅山鹑在我国北方地区分布广泛,生态环境多样性高；更新世冰期隔离作用以及间冰期森林的隔离作用造成斑翅山鹑栖息地片段化,这些因素导致斑翅山鹑表现出较高遗传多样性。通过对23个地理种群遗传多样性比较我们发现位于青藏高原柴达木盆地地区的种群以及华北地区种群遗传多样性较高,这可能与这些地区进化历史时间长,且具有适于斑翅山鹑生活的稳定生态环境有关。
(2)遗传分化研究：根据对斑翅山鹑23个地理种群的遗传分化分析表明斑翅山鹑各地理种群之间遗传差异不大,但极为极显著(FST=0.10,RST=0.11,P<0.001)。AMOVA分析表明遗传差异主要发生在地理种群内81.03%(FST=0.20166,P<0.001)。而地理种群间只有9.19%(FSC=0.12278,P<0.001),不同组之间的遗传变异为9.78%(FCT=0.10979,P<0.05)。斑翅山鹑各地理种群间遗传分化明显,从一个方面反映出斑翅山鹑对环境的适应性较好且具有较高的进化潜力。用Mantel检验对斑翅山鹑23个地理种群的遗传分化FsT／(1-FST)与地理距离之间的相关性分析表明二者成不显著正相关,表明遗传距离差异并不单纯由地理距离决定。
(3)种群聚类分析：根据Nei氏遗传距离用UPGMA方法进行聚类分析以及用贝叶斯聚类法和多因子分析法(FCA)进行的聚类分析结果都表明斑翅山鹑23个地理种群可聚为两大支,A和B。其中分支A主要包含了分布于黄土高原及青藏高原的种群。分支B是由分布于六盘山地区、华北平原、东北平原、天山山脉以及内蒙古高原的种群所组成的。基于对分歧时间的估算,分支A与B的分歧时间大约发生0.33百万年前,这一时期为中更新世晚期,处于民德冰期的间冰期。在这一时期青藏高原的隆升对印度洋暖湿气流的阻挡作用使得我国北方的干旱化与荒漠化加剧,出现了一系列大的沙漠。沙漠的存在对适应于草原环境的斑翅山鹑种群之间的基因流构成了天然屏障,故而造成了斑翅山鹑两大分支A与B之间的分歧。分支A又进一步分化为两个支,A1和A2。A1由来自于黄土高原的种群组成,分支A2由分布于青藏高原的种群组成。这两个分之间的分歧时间大约发生在0.20百万年前,这一时期处于里斯冰期间冰期。间冰期森林的大量扩展阻隔了斑翅山鹑种群间的基因交流,使其产生分歧分化。B支同样分化为两个支系,B1和B2。B1的种群来自于六盘山,B2是由分布于我国北方的内蒙古高原、东北平原以、华北平原及天山山脉的种群组成。B1与B2的分歧时间大约是0.19百万年之前,我们推测,形成这一格局的原因可能是由于六盘山地区降水极为丰富自成局部小气候,加上北部毛乌素沙漠的隔离作用,使得六盘山地区的两个种群与其他种群隔离起来。
另外,生态遗传学分析遗传多样性与环境因子的关系显示：斑翅山鹑遗传多样性参数随着经度和纬度的升高而有降低的趋势,而斑翅山鹑遗传多样性最高的种群主要分布在青藏高原的柴达木盆地附近,我们推测斑翅山鹑有可能起源于柴达木盆地地区。
通过Bottleneck分析表明斑翅山鹑23个地理种群中部分种群曾经历了瓶颈效应。结合遗传多样性的数据和瓶颈效应分析结果,我们建议应对宁夏六盘山地区种群、柴达木盆地地区种群、华北的WC和XH种群以及甘肃的JN种群个ZJC种群加强重视和监管,力求保证这些地理种群数量足以保持其遗传多样性。
The Daurian Partridge (Perdix dauuricae) is a kind of widespread birds in grassland, belong to Genus Perdix of Phasianidae in Galliformes. They are a kind of hunting birds which have high economic value. We sampled 23 populations which were five populations in Qinghai-tibetan Plateau, nine populations from Loess Plateau, two popualtions in Liupan Mountain, three populations in Inner Mongolia Plateau, two populations in North China Plain, one populations in Northeast Plain and one poulation in Tianshan Mountains.We obtained 285 samples which were successfully and completely amplified by microsatellite marker to investigate the genetic diversity differentation, geographic structure and the molecular phylogeography of the Daurian Partridge.
We selected eight microsatellite loci, developed in the domestic chicken and quail, for utility in Daurian Partridge. The main results and conclusion are as below:
(1) The genetic diversity for Daurian Partridge. A total of 94 alleles at the 8 loci tested with an average of 11.75 alleles per locus were found in Daurian Partridge populations. The average of observed heterozygosity value (HO) was 0.58 and the average of expected hetergozygosity value (HE) was 0.72. The polymorphism information content (PIC)values ranged from 0.56 (MCW280) to 0.87 (UBC0006). The average value of PIC was 0.73. All loci of the samples were polymorphic. The above data indicated that the genetic diversity of the current Daurian Partridge was relatively high. The Daurian Partridge was a kind of birds which distributes widely in Northern China with wide ecological differentiations. High levels of genetic diversity in natural populations can be associated with a wide range ecological types and niche variation. Habitat fragmentation because of Quaternary glaciations isolation and the forest isolation during interglacial. These factors may lead to a high level of genetic diversity of Daurian Partridge.
(2) Population genetic differentiation for Daurian Partridge. Tests for differences in the distribution of allele frequencies indicated highly significant differentiation between all pairs of populations, microsatellite genetic diversity was significantly partitioned among the 23 populations (average multilocus FST= 0.10, RST= 0.11, P＜0.001). The AMOVA analysis revealed that 81.03%(FST=0.20166, P＜0.001) of the total genetic variance resided within populations with a substantial proportion 9.19% (FSC= 0.12278, P＜0.001) and 9.78%(FCT= 0.10979, P＜0.05) of the variance being at the within-group and among-group hierarchical levels, respectively. The obvious genetic differentiation between Daurian Partridge populations, from one side, reflects the Daurian partridge has better adaptability to the environment and has a high evolutionary potential. Mantle test showed that there were no significant positive correlation between FST/(1-FST) and geographical distance. The result told us that the differences between genetic distance were not simply dicided by the geographical distance.
(3) Phylogeographical reconstruction. Analysis of the microsatellite DNA markers indicated that Daurian Partridge were geographically structured. Both the UPGMA and Bayesian clustering analysis of multilocus genotypes provided clear indications of genetic divergence of all Daurian Partridge populations into two distinct clusters A and B.The Factorial correspondence analysis (FCA) also got the same result. The populations in Cluster A come from Loess Plateau and Qinghai-tibetan Plateau, populations in Cluster B come from Liupan Mountain, North China Plain, Northeast Plain, Tianshan Mountains and Inner Mongolia Plateau. Based on the estimated divergence time between the two groups was 0.33 million years ago. During this period, the Qinghai-Tibet Plateau uplift had achieved its current elevation causing the desertification of the northern regions of the Qinghai-Tibetan Plateau expanded rapidly, affecting the extent and quality of arid grassland and scrub habitats, and creating barriers for population distributions and restricting gene flow between populations located in Cluster A and B. Cluster A was further subdivided into two subgroups:A1 and A2. The A1 group was comprised of populations from Loess Plateau, and A2 group consisted of populations from Qinghai-Tibet Plateau.The divergence time was 0.20 million years which corresponds with the Riss interglacial. A wide range of forest expansion during interglacial restricted the gene flow between populations from Loess Plateau, lead to the divergence of the two group populations. Cluster B was also subdivided into two subgroups:B1 and B2, corresponding to populations of the Liupan Mountains and populations in Inner Mongolia Plateau, Northeast Plain, North China Plain and poulation in Tianshan Mountains. We speculate that the Liupan Mountain populations were split from the other populations because of climatic changes and subsequent geographic barriers created by deserts.
The ecological genetics analysis of the relationship between the Daurian Partridge genetic diversity and environmental factors showed that, genetic diversity parameters decreased with the increase of latitude and longitude. The highest genetic diversity of Daurian Partridge populations mainly in the Qaidam Basin of Qinghai-Tibetan Plateau. We speculate that Daurian Partridge may be originated in the Qaidam Basin.
The Bottleneck analysis showed that the Daurian Partridge in some 23 populations have undergone a bottleneck effect. Combined the analysis data of genetic diversity and bottleneck, proposed that we should enhance attention and strengthen supervision to populations in Liupan Mountain, the Qaidam Basin populations, WC and XH population in North China, JN population and ZJC population in Loess Plateau, seek to ensure that the size of these populations were sufficient to maintain the genetic diversity.
8个微卫星位点在斑翅山鹁23个地理种群中均获得成功扩增,通过对微卫星数据的的分析,我们获得到了如下主要结果及结论：
(1)遗传多样性研究：8个微卫星位点共检测到94个等位基因,每个位点平均等位基因数为11.75。所有位点都呈现多态性。平均期望杂合度(HE)和观测杂合度(Ho)分别为0.58和0.72。8个位点的多态信息含量从0.56(MCW280)到0.87(UBC0006)。平均多态信息含量(PIC)为0.73。这些结果表明斑翅山鹑为遗传多样性较丰富的群体。斑翅山鹑在我国北方地区分布广泛,生态环境多样性高；更新世冰期隔离作用以及间冰期森林的隔离作用造成斑翅山鹑栖息地片段化,这些因素导致斑翅山鹑表现出较高遗传多样性。通过对23个地理种群遗传多样性比较我们发现位于青藏高原柴达木盆地地区的种群以及华北地区种群遗传多样性较高,这可能与这些地区进化历史时间长,且具有适于斑翅山鹑生活的稳定生态环境有关。
(2)遗传分化研究：根据对斑翅山鹑23个地理种群的遗传分化分析表明斑翅山鹑各地理种群之间遗传差异不大,但极为极显著(FST=0.10,RST=0.11,P<0.001)。AMOVA分析表明遗传差异主要发生在地理种群内81.03%(FST=0.20166,P<0.001)。而地理种群间只有9.19%(FSC=0.12278,P<0.001),不同组之间的遗传变异为9.78%(FCT=0.10979,P<0.05)。斑翅山鹑各地理种群间遗传分化明显,从一个方面反映出斑翅山鹑对环境的适应性较好且具有较高的进化潜力。用Mantel检验对斑翅山鹑23个地理种群的遗传分化FsT／(1-FST)与地理距离之间的相关性分析表明二者成不显著正相关,表明遗传距离差异并不单纯由地理距离决定。
(3)种群聚类分析：根据Nei氏遗传距离用UPGMA方法进行聚类分析以及用贝叶斯聚类法和多因子分析法(FCA)进行的聚类分析结果都表明斑翅山鹑23个地理种群可聚为两大支,A和B。其中分支A主要包含了分布于黄土高原及青藏高原的种群。分支B是由分布于六盘山地区、华北平原、东北平原、天山山脉以及内蒙古高原的种群所组成的。基于对分歧时间的估算,分支A与B的分歧时间大约发生0.33百万年前,这一时期为中更新世晚期,处于民德冰期的间冰期。在这一时期青藏高原的隆升对印度洋暖湿气流的阻挡作用使得我国北方的干旱化与荒漠化加剧,出现了一系列大的沙漠。沙漠的存在对适应于草原环境的斑翅山鹑种群之间的基因流构成了天然屏障,故而造成了斑翅山鹑两大分支A与B之间的分歧。分支A又进一步分化为两个支,A1和A2。A1由来自于黄土高原的种群组成,分支A2由分布于青藏高原的种群组成。这两个分之间的分歧时间大约发生在0.20百万年前,这一时期处于里斯冰期间冰期。间冰期森林的大量扩展阻隔了斑翅山鹑种群间的基因交流,使其产生分歧分化。B支同样分化为两个支系,B1和B2。B1的种群来自于六盘山,B2是由分布于我国北方的内蒙古高原、东北平原以、华北平原及天山山脉的种群组成。B1与B2的分歧时间大约是0.19百万年之前,我们推测,形成这一格局的原因可能是由于六盘山地区降水极为丰富自成局部小气候,加上北部毛乌素沙漠的隔离作用,使得六盘山地区的两个种群与其他种群隔离起来。
另外,生态遗传学分析遗传多样性与环境因子的关系显示：斑翅山鹑遗传多样性参数随着经度和纬度的升高而有降低的趋势,而斑翅山鹑遗传多样性最高的种群主要分布在青藏高原的柴达木盆地附近,我们推测斑翅山鹑有可能起源于柴达木盆地地区。
通过Bottleneck分析表明斑翅山鹑23个地理种群中部分种群曾经历了瓶颈效应。结合遗传多样性的数据和瓶颈效应分析结果,我们建议应对宁夏六盘山地区种群、柴达木盆地地区种群、华北的WC和XH种群以及甘肃的JN种群个ZJC种群加强重视和监管,力求保证这些地理种群数量足以保持其遗传多样性。
The Daurian Partridge (Perdix dauuricae) is a kind of widespread birds in grassland, belong to Genus Perdix of Phasianidae in Galliformes. They are a kind of hunting birds which have high economic value. We sampled 23 populations which were five populations in Qinghai-tibetan Plateau, nine populations from Loess Plateau, two popualtions in Liupan Mountain, three populations in Inner Mongolia Plateau, two populations in North China Plain, one populations in Northeast Plain and one poulation in Tianshan Mountains.We obtained 285 samples which were successfully and completely amplified by microsatellite marker to investigate the genetic diversity differentation, geographic structure and the molecular phylogeography of the Daurian Partridge.
We selected eight microsatellite loci, developed in the domestic chicken and quail, for utility in Daurian Partridge. The main results and conclusion are as below:
(1) The genetic diversity for Daurian Partridge. A total of 94 alleles at the 8 loci tested with an average of 11.75 alleles per locus were found in Daurian Partridge populations. The average of observed heterozygosity value (HO) was 0.58 and the average of expected hetergozygosity value (HE) was 0.72. The polymorphism information content (PIC)values ranged from 0.56 (MCW280) to 0.87 (UBC0006). The average value of PIC was 0.73. All loci of the samples were polymorphic. The above data indicated that the genetic diversity of the current Daurian Partridge was relatively high. The Daurian Partridge was a kind of birds which distributes widely in Northern China with wide ecological differentiations. High levels of genetic diversity in natural populations can be associated with a wide range ecological types and niche variation. Habitat fragmentation because of Quaternary glaciations isolation and the forest isolation during interglacial. These factors may lead to a high level of genetic diversity of Daurian Partridge.
(2) Population genetic differentiation for Daurian Partridge. Tests for differences in the distribution of allele frequencies indicated highly significant differentiation between all pairs of populations, microsatellite genetic diversity was significantly partitioned among the 23 populations (average multilocus FST= 0.10, RST= 0.11, P＜0.001). The AMOVA analysis revealed that 81.03%(FST=0.20166, P＜0.001) of the total genetic variance resided within populations with a substantial proportion 9.19% (FSC= 0.12278, P＜0.001) and 9.78%(FCT= 0.10979, P＜0.05) of the variance being at the within-group and among-group hierarchical levels, respectively. The obvious genetic differentiation between Daurian Partridge populations, from one side, reflects the Daurian partridge has better adaptability to the environment and has a high evolutionary potential. Mantle test showed that there were no significant positive correlation between FST/(1-FST) and geographical distance. The result told us that the differences between genetic distance were not simply dicided by the geographical distance.
(3) Phylogeographical reconstruction. Analysis of the microsatellite DNA markers indicated that Daurian Partridge were geographically structured. Both the UPGMA and Bayesian clustering analysis of multilocus genotypes provided clear indications of genetic divergence of all Daurian Partridge populations into two distinct clusters A and B.The Factorial correspondence analysis (FCA) also got the same result. The populations in Cluster A come from Loess Plateau and Qinghai-tibetan Plateau, populations in Cluster B come from Liupan Mountain, North China Plain, Northeast Plain, Tianshan Mountains and Inner Mongolia Plateau. Based on the estimated divergence time between the two groups was 0.33 million years ago. During this period, the Qinghai-Tibet Plateau uplift had achieved its current elevation causing the desertification of the northern regions of the Qinghai-Tibetan Plateau expanded rapidly, affecting the extent and quality of arid grassland and scrub habitats, and creating barriers for population distributions and restricting gene flow between populations located in Cluster A and B. Cluster A was further subdivided into two subgroups:A1 and A2. The A1 group was comprised of populations from Loess Plateau, and A2 group consisted of populations from Qinghai-Tibet Plateau.The divergence time was 0.20 million years which corresponds with the Riss interglacial. A wide range of forest expansion during interglacial restricted the gene flow between populations from Loess Plateau, lead to the divergence of the two group populations. Cluster B was also subdivided into two subgroups:B1 and B2, corresponding to populations of the Liupan Mountains and populations in Inner Mongolia Plateau, Northeast Plain, North China Plain and poulation in Tianshan Mountains. We speculate that the Liupan Mountain populations were split from the other populations because of climatic changes and subsequent geographic barriers created by deserts.
The ecological genetics analysis of the relationship between the Daurian Partridge genetic diversity and environmental factors showed that, genetic diversity parameters decreased with the increase of latitude and longitude. The highest genetic diversity of Daurian Partridge populations mainly in the Qaidam Basin of Qinghai-Tibetan Plateau. We speculate that Daurian Partridge may be originated in the Qaidam Basin.
The Bottleneck analysis showed that the Daurian Partridge in some 23 populations have undergone a bottleneck effect. Combined the analysis data of genetic diversity and bottleneck, proposed that we should enhance attention and strengthen supervision to populations in Liupan Mountain, the Qaidam Basin populations, WC and XH population in North China, JN population and ZJC population in Loess Plateau, seek to ensure that the size of these populations were sufficient to maintain the genetic diversity.
引文
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