基于线粒体控制区分析雉鸡甘肃亚种的种群遗传结构与保护遗传研究
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摘要
雉鸡(Phasianus colchicus)是全世界最重要的猎禽之一,适应性强,分布广泛。我国共有19个亚种的分布,其中甘肃亚种分布于中国西北部地区。本研究以进化速率相对较快的线粒体控制区全序列基因片段为遗传标记,对雉鸡甘肃亚种10个种群的132个样本进行了种群遗传结构分析和保护遗传研究。本文研究的主要目的为:(1)探究雉鸡种下单元的遗传变异,了解雉鸡甘肃亚种不同种群间的分化程度及在特殊生境下不同种群间的基因交流情况;(2)揭示雉鸡甘肃亚种的种群遗传结构;(3)重建雉鸡甘肃亚种的系统地理结构,阐明气候和环境变化对其系统进化的作用;(4)为雉鸡起源中心假说提供依据,给出可能的进化扩散路线;(5)结合形态差异的描述,分析雉鸡甘肃亚种的遗传变异与形态地理变异的关系;(6)从遗传学角度探讨雉鸡甘肃亚种的保护问题。主要结果如下:
用直接测序法对线粒体控制区全序列进行分析,测出碱基含量G+C=40.5%。共发现50个变异位点,定义了54种单倍型。由8个种群共享的单倍型H1比例最高,为祖先单倍型。平均核苷酸多样较低(0.0031),而平均单倍型多样性较高(0.9421)。通过计算固定指数、基因流和Fu's Fs检验发现,种群间遗传分化不显著,且经历过快速扩张,可能由于缺少隔离,基因交流频繁所致。根据种群间遗传距离计算分歧时间约为8-28万年。
支持雉鸡起源于西南横断山脉的假说,从西南向东北和西北可能是其扩散的路线。各单倍型在系统树中相互混杂,没有形成明显的地理分支,属于“系统发生连续,无空间隔离”的地理格局。推测由于线粒体的母性遗传,其变异与父性遗传的白色眉纹项圈等变异并不完全一致。为缓冲栖息地片段化和人类活动对其的影响,对遗传多样性较高的成县、大通种群,以及严重隔离的漳县种群应优先保护。
Common pheasant(Phasianus colchicus)is a world-widely distributed species as one of the most important game birds with numerous subspecies,while in China, there are 19.Our study is to demonstrate genetic structure and conservation genetics of common pheasant Gansu subspecies(P.c.strauchi),which is an endemic resident of Gansu,Ningxia and Qinghai provinces in northwestern China.
Mitochondrial DNA(mtDNA)genome has proven to be useful in many avian phylogenetic and population studies,and the control region(CR)plays an important role in replication and transcription in the mitochondrial(mt)genome.Its supposedly high rate of DNA substitution makes it a suitable marker for our study.In our study,a total of 132 samples from 10 populations of P.c.strauchi were collected from ten localities in Gansu,Ningxia and Qinghai provinces.We obtained those samples during three consecutive autumns 2005,2006 and 2007.The entire mtDNA control region genes were PCR amplified and sequenced directly.We used different softwares to calculate the genetic structure within and among P.c.strauchi populations.The aims of our study are:(1)to calculate the genetic diversity of common pheasant at a level of subspecies;to demonstrate the divergence variation and gene flows among P.c.strauchi populations in different habitats;(2)to reveal the population genetic structure of P.c.strauchi;(3)to reconstruct the phylogeographic structure of P.c. strauchi and to infer the impacts of environmental and climate change on its systematic evolutionary process;(4)to give support to the nascence-center hypothesis of pheasants;to infer the possible dispersal route in P.c.strauchi evolutionary history; (5)to compare the morphological variation and genetic diversity referred to descriptions of P.c.strauchi morphological characters;(6)to discuss the conservation status of P.c.strauchi as viewed from genetics.
The results of our study are as below:
The average nucleotide composition G+C=40.5%,which was typical for avian mitochondrial DNA control regions.A total of 50 variable sites defined 54 haplotypes. The most common haplotype was H1 with 26 individuals from 8 populations.The theory predicts that the most frequent and widespread haplotypes are ancestral.Based on this coalescent theory,it suggested that the haplotype H1 was ancestral.
The average nucleotide diversity was at a low level(0.0031),while the average haplotype diversity was at a high level(0.9421).The value of Fst and value of Nm implied there was no,however,significant genetic divergence among populations mainly because populations lacking of spatial separation and communicating frequently.Fu's Fs test indicated that P.c.strauchi has suffered a rapid spatial expanding during its evolutionary history.Diverge time was suggested 0.08 Ma to 0.28 Ma by calculating genetic distance among populations.
The results gave support to hypothesis that the nascence-center of pheasants was in Hengduan Mountain range in southwestern China,which indicated the possible dispersal route of P.c.strauchi was from southwest to northeast and northwest during its evolutionary history.A total of 54 haplotypes interweaved in the phylogenetic tree and did not cluster into separate branches according to separate sampling localities as imaged.The phylogeographic structure of P.c.strauchi belonged to "phylogenetic continuity,lack of spatial separation".Due to the maternal inheritance of mitochondrial DNA while paternal inheritance of morphologic characters such as white eyebrow and white collar,it didn't show strict congruence between genetic differentiation and morphologic variation.For the sake of decreasing impacts coming from both habitat fragmentation and human behavior to P.c.strauchi,we should give first protection priority to Chengxian(CX)and Datong(DT) populations which had high genetic diversity and to Zhangxian(ZX)population which had been isolated sharply.
用直接测序法对线粒体控制区全序列进行分析,测出碱基含量G+C=40.5%。共发现50个变异位点,定义了54种单倍型。由8个种群共享的单倍型H1比例最高,为祖先单倍型。平均核苷酸多样较低(0.0031),而平均单倍型多样性较高(0.9421)。通过计算固定指数、基因流和Fu's Fs检验发现,种群间遗传分化不显著,且经历过快速扩张,可能由于缺少隔离,基因交流频繁所致。根据种群间遗传距离计算分歧时间约为8-28万年。
支持雉鸡起源于西南横断山脉的假说,从西南向东北和西北可能是其扩散的路线。各单倍型在系统树中相互混杂,没有形成明显的地理分支,属于“系统发生连续,无空间隔离”的地理格局。推测由于线粒体的母性遗传,其变异与父性遗传的白色眉纹项圈等变异并不完全一致。为缓冲栖息地片段化和人类活动对其的影响,对遗传多样性较高的成县、大通种群,以及严重隔离的漳县种群应优先保护。
Common pheasant(Phasianus colchicus)is a world-widely distributed species as one of the most important game birds with numerous subspecies,while in China, there are 19.Our study is to demonstrate genetic structure and conservation genetics of common pheasant Gansu subspecies(P.c.strauchi),which is an endemic resident of Gansu,Ningxia and Qinghai provinces in northwestern China.
Mitochondrial DNA(mtDNA)genome has proven to be useful in many avian phylogenetic and population studies,and the control region(CR)plays an important role in replication and transcription in the mitochondrial(mt)genome.Its supposedly high rate of DNA substitution makes it a suitable marker for our study.In our study,a total of 132 samples from 10 populations of P.c.strauchi were collected from ten localities in Gansu,Ningxia and Qinghai provinces.We obtained those samples during three consecutive autumns 2005,2006 and 2007.The entire mtDNA control region genes were PCR amplified and sequenced directly.We used different softwares to calculate the genetic structure within and among P.c.strauchi populations.The aims of our study are:(1)to calculate the genetic diversity of common pheasant at a level of subspecies;to demonstrate the divergence variation and gene flows among P.c.strauchi populations in different habitats;(2)to reveal the population genetic structure of P.c.strauchi;(3)to reconstruct the phylogeographic structure of P.c. strauchi and to infer the impacts of environmental and climate change on its systematic evolutionary process;(4)to give support to the nascence-center hypothesis of pheasants;to infer the possible dispersal route in P.c.strauchi evolutionary history; (5)to compare the morphological variation and genetic diversity referred to descriptions of P.c.strauchi morphological characters;(6)to discuss the conservation status of P.c.strauchi as viewed from genetics.
The results of our study are as below:
The average nucleotide composition G+C=40.5%,which was typical for avian mitochondrial DNA control regions.A total of 50 variable sites defined 54 haplotypes. The most common haplotype was H1 with 26 individuals from 8 populations.The theory predicts that the most frequent and widespread haplotypes are ancestral.Based on this coalescent theory,it suggested that the haplotype H1 was ancestral.
The average nucleotide diversity was at a low level(0.0031),while the average haplotype diversity was at a high level(0.9421).The value of Fst and value of Nm implied there was no,however,significant genetic divergence among populations mainly because populations lacking of spatial separation and communicating frequently.Fu's Fs test indicated that P.c.strauchi has suffered a rapid spatial expanding during its evolutionary history.Diverge time was suggested 0.08 Ma to 0.28 Ma by calculating genetic distance among populations.
The results gave support to hypothesis that the nascence-center of pheasants was in Hengduan Mountain range in southwestern China,which indicated the possible dispersal route of P.c.strauchi was from southwest to northeast and northwest during its evolutionary history.A total of 54 haplotypes interweaved in the phylogenetic tree and did not cluster into separate branches according to separate sampling localities as imaged.The phylogeographic structure of P.c.strauchi belonged to "phylogenetic continuity,lack of spatial separation".Due to the maternal inheritance of mitochondrial DNA while paternal inheritance of morphologic characters such as white eyebrow and white collar,it didn't show strict congruence between genetic differentiation and morphologic variation.For the sake of decreasing impacts coming from both habitat fragmentation and human behavior to P.c.strauchi,we should give first protection priority to Chengxian(CX)and Datong(DT) populations which had high genetic diversity and to Zhangxian(ZX)population which had been isolated sharply.
引文
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