我国高山鹑类分子系统发生研究
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摘要
我国高山鹑类传统分类包括5属、11种、29个亚种,它们主要分布于我国青藏高原及周围的山地、我国中北部地区。本研究共采集我国高山鹑类4属(雪鸡属Tetraogallus、石鸡属Alectoris、山鹑属Perdix和雉鹑属Tetraophasis)、9种23亚种(喜马拉雅雪鸡的4个亚种、藏雪鸡3个亚种,石鸡5个亚种、大石鸡2亚种,灰山鹑1个亚种、斑翅山鹑3个亚种、高原山鹑3个亚种,雉鹑、四川雉鹑)的样本以及其它雉科鸟类样本,包括从genebank上下载相关序列,研究共涉及鸡形目雉科鸟类30属67种82亚种,包括我国雉科鸟类21属55种中的20属41种,利用核基因c-mos、线粒体DNA细胞色素b基因(Cyt b)、NADH脱氢酶第二亚基(ND2)基因、控制区(control region)多种分子标记,来分析探讨我国高山鹑类的分子系统发生及物种形成过程。
对c-mos、CYT B、ND2、control region四个核苷酸序列片段单独及合并来进行系统发生分析,不同序列片段合并后的一致性检验采取incongruence-length-difference (ILD)检验,采用最大简约法MP (maximum parsimony)和贝叶斯法(Bayesian analyses)来分析建树；采用斑翅山鹑化石作内部锚定,雉科起源时间作为外部锚定,通过BEAST 1.4.8软件分析三个编码基因的合并片段(c-mos+CYT B+ND2)以及控制区序列,来估算相关类群的分歧时间。
研究的主要结果如下：
1、高山鹑类cytb基因与ND2基因密码子各位点碱基含量属间一致性很高,各属的碱基替代多数是沉默的,密码子第二位点最保守,第三位点进化最快。4属中核苷酸多样性雉鹑属较低；cytb基因核苷酸替代中异义替代(nonsynonymous)比例最高的是雉鹑属(22.58%),但其ND2基因核苷酸异义替代却在4属中最低(17.14%)；4属中Cytb、ND2基因转换颠换比(Ti/Tv)最高的都是雉鹑属。
2、我国雉科鸟类应该划分为四个支系群：①雪鸡属、石鸡属和鹌鹑属支系,代表着典型的鹑族类；②雉属、锦鸡属、鹇属、长尾雉属、马鸡属、虹雉属和雉鹑属、角雉属、勺鸡属、血雉属以及山鹑属这一大的支系,作为雉族类群；③原鸡属、竹鸡属和鹧鸪属；④孔雀属和孔雀雉属支系。
3、分类地位一直不太确定的血雉属和角雉属,其分子系统发生位置应该在雉族类群内的基部,是比较原始的雉类。系统发生不明的山鹧鸪属,其分子系统发生位于其它雉科鸟类支系之外,表明了这一类群物种的古老性。
4、分子系统发生研究表明雉鹑属和虹雉属有很近的亲缘关系,并且这一姊妹群明确地归入雉族类群；从形态、习性及分布特征方面比较,二者一致性也较高。在青藏高原强烈隆升前,虹雉属祖先和雉鹑属祖先就已经在横断山地区分化形成；雉鹑属祖先在早更新世高原希夏邦马冰期被隔离于高原东部边缘的一些较低的山地盆地,分化形成雉鹑和四川雉鹑,目前两个种的分布区相接格局是冰期结束后的再扩散造成的。
5、系统发生位置一直有争议的山鹑属应当置于雉族类群中。山鹑属内3种以及斑翅山鹑、高原山鹑种内亚种间的分子系统发生关系都表明,山鹑属的起源是在青藏高原。高原山鹑分歧形成时间为3.63-3.77百万年,在上新世中、末期广泛分布生活于青藏高原地区的山鹑属祖先物种在高原隆升过程中,存留于高原低洼盆地区域的祖先种群逐步适应高原环境的变迁,从冰期中存活下来而形成高原山鹑；被迫向北部扩散移动的种群,在中国中部因第二次大的冰期(大约2.05-1.28百万年)而迫使它们分裂成两大部分,向低的平原地区移动,西部支系演化成灰山鹑,东部支系进化为斑翅山鹑,地质环境的变化以及化石的记录都支持这一观点。
6、藏雪鸡三个涉及到的亚种间无明显的系统地理结构,在高原经历中更新世末的大间冰期时,藏雪鸡的不同种群被隔离分化形成亚种,之后的各个冰期,各亚种间都有一定的再扩散和交流。喜马拉雅雪鸡的四个亚种间表现出较为明晰的系统发生关系,经历了沿塔里木盆地的西南缘山地向东扩散和亚种形成路线。从种内亚种间分子系统发生关系、喜马拉雅雪鸡与藏雪鸡分歧时间的估算以及高原及其周边地质环境演变方面可以认定,喜马拉雅雪鸡和藏雪鸡是在高原隆升前(也就是说在3.6百万年前)就已经分化形成了,在青藏高原隆升初期的多瑙河冰期(3.5-2.6百万年),淡腹组的一支由天山东部地区向东南扩散至青藏东部地区的一些高山,伴随着青藏高原的隆升而形成藏雪鸡；暗腹组雪鸡的一支形成喜马拉雅雪鸡后在高原隆升中期(大约0.88百万年前)开始向高原上扩散并形成各亚种。
7、石鸡和大石鸡两种的分歧时间为2.76或2.82百万年,分子系统发生树表明,所涉及的5个石鸡亚种间无系统地理结构,石鸡的祖先种群在冰期被隔离在不同“避难所”,在间冰期从避难所向外扩散,后又被冰期隔离出一些小种群,经历遗传瓶颈,分化形成不同的亚种。在冰期结束后,不同的亚种间又有相互的扩散渗透,从而造成目前的混乱状态。
The alpine partridges in China consist of 5 genera,11 species and 29 subspecies of Galliformes taxonomic groups distributing mainly on and around Qingzang plateau. The samples we collected are composed of 4 genera,9 species and 23 subspecies of it, i.e.4 subspecies of Tetraogallus himalayensis,3 subspecies of T. tibetanus,5 subspecies of Alectoris chukar,2 subspecies of A. magna,1 subspecies of Perdix perdix,3 subspecies of P. dauuricae,3 subspecies of P. hodgsoniae,1 of Tetraophasis obscures and T. szechenyii. Together with other Phasianidae samples and the categories from Genebank, Taxa studied herein include 41 Phasianidae species and 20 of 21 phasianidae genera in China and 67 species and 30 genera in the world. The nuclear gene and several mitochondrial genes sequences, representing these Galliformes groups, were analyzed to (1) ascertain the evolutionary relationship between the alpine partridges and other related phasianid genera, (2) produce a molecular phylogeny of the extant species of the alpine partridges, and (3) correlate the inferred molecular phylogeny and extent of interspecific genetic divergence with Pliocene/Pleistocene biogeographical scenarios in the Qinghai-Tibet Plateau region to suggest speciational patterns in these alpine partridges.
The different gene segments were separated and concatenated for analysis simultaneously. Congruence among the different DNA data sets was evaluated using the incongruence-length-difference (ILD) test. Each data set was subjected to maximum parsimony (MP) using PAUP*4.0b10 and Bayesian analyses using MrBayes 3.0. Bayesian analysis of combined data (c-mos+CYT B+ND2) and D-loop data were also used separately to estimate the divergence times for clades of these alpine partridges by software BEAST 1.4.8.
We obtained the nucleotide sequences including partial c-mos gene (613bp), ND2 gene(1023bp), control region (1056bp) and complete CYT B gene (1143bp). The ILD test of different combined dataset were acceptable(>0.05). Among the alpine partridge genera, CYT B and ND2 showed similar composition of nucleotide pair and similar rates and types of nucleotide substitutions. The percentage of nonsynonymous substitution is comparatively higher in genus Tetraophasis on CYT B nucleotide sequences, but not on ND2. The transition to transversion ratio (Ti/Tv) is also higher in genus Tetraophasis.
The genera of Phasianidae in China should be classified into 4 clades:(1) Tetraogallus/Alectoris/Coturnix, (2) Phasianus/Chrysolophus/Lophura/Syrmaticus/ Crossoptilon/Tetraophasis and Lophophorus, also including Ithaginis/Tragopan/ Pucrasia/Perdix, (3) Gallus/Bambusicola/Francolinus, (4)Pavo and Polyplectron.
Blood Pheasant (genus Ithaginis) and Tragopan had uncertain positions in traditional classification but should been placed in tribe Phasianini in molecular phylogenetic analysis. Genus Arborophila was basal in whole Phasianidae clade, indicated it's age-old phylogenetic position.
Tetraophasis was sister to genus Lophophorus doubtlessly and the clade should also been placed in pheasants. The divergence time between them indicated that the clade Tetraophasis and the clade Lophophorus had been formed in the region of Hengduan Mountains before the uplift of the Tibetan Plateau, and the ancestor populations of Tetraophasis had been segregated into two partitions by the early Pleistocene glaciation and then formed the two species of Tetraophasis.
All three species of genus Perdix were grouped into a monophyletic cluster and should be placed into the pheasant group in our analyses. Tibetan partridges(Perdix hodgsoniae) were consistently placed basal to other Perdix species, and P. dauuricae przewalskii and P. hodgsoniae hodgsoniae, the subspecies distributed in main land of Tibet plateau, were basal to the other two subspecies in their own clade, respectively. These phylogenetic relationships suggested that the Perdix were originated from Tibet region. Divergence time estimates indicated that the Tibetan partridge split from the ancestor of Daurian partridge and gray partridge about 3.63 myr ago, we consider that the grassland-adapted ancestor of the typical partridges spread to the plateau during the middle Pliocene (4.52-2.75 myr ago). Throughout the course of the Qingzang Movement and the Pleistocene glaciations, some populations of the ancestor stayed in some basins, survived the glaciations and gave rise to Tibetan partridge. Other groups were forced to move north by rapid ascension of the Plateau, whereafter the big second glacier (approximately 2.05-1.28 myr ago) in central China compelled them to split into west and east branches, which now form the prey partridge in the west and the Daurian partridge in the east.
The three subspecies of Tetraogallus tibetanus studied herein showed no significant phylogeographic structure, we suggested that it's resulted from the adaptation to the climatic conditions and glacial cycles on the Qinghai-Tibetan Plateau. The phylogeny of 4 subspecies within Tetraogallus himalayensis indicated their eastward dispersal course along the south margin of Tarim Basin during the medium-term uplift (approximately 0.88 myr ago) of Qingzang plateau. Our studies also suggested that divergence between T. tibetanus and T. himalayensis took place before the sudden uplift of the Plateau.
Divergence time estimates between Alectoris chukar and A. magna indicated that the two species split away about 2.76 myr ago, and the molecular phylogenetic analysis showed no phylogeographic partitions among the 5 subspecies of A. chukar.
对c-mos、CYT B、ND2、control region四个核苷酸序列片段单独及合并来进行系统发生分析,不同序列片段合并后的一致性检验采取incongruence-length-difference (ILD)检验,采用最大简约法MP (maximum parsimony)和贝叶斯法(Bayesian analyses)来分析建树；采用斑翅山鹑化石作内部锚定,雉科起源时间作为外部锚定,通过BEAST 1.4.8软件分析三个编码基因的合并片段(c-mos+CYT B+ND2)以及控制区序列,来估算相关类群的分歧时间。
研究的主要结果如下：
1、高山鹑类cytb基因与ND2基因密码子各位点碱基含量属间一致性很高,各属的碱基替代多数是沉默的,密码子第二位点最保守,第三位点进化最快。4属中核苷酸多样性雉鹑属较低；cytb基因核苷酸替代中异义替代(nonsynonymous)比例最高的是雉鹑属(22.58%),但其ND2基因核苷酸异义替代却在4属中最低(17.14%)；4属中Cytb、ND2基因转换颠换比(Ti/Tv)最高的都是雉鹑属。
2、我国雉科鸟类应该划分为四个支系群：①雪鸡属、石鸡属和鹌鹑属支系,代表着典型的鹑族类；②雉属、锦鸡属、鹇属、长尾雉属、马鸡属、虹雉属和雉鹑属、角雉属、勺鸡属、血雉属以及山鹑属这一大的支系,作为雉族类群；③原鸡属、竹鸡属和鹧鸪属；④孔雀属和孔雀雉属支系。
3、分类地位一直不太确定的血雉属和角雉属,其分子系统发生位置应该在雉族类群内的基部,是比较原始的雉类。系统发生不明的山鹧鸪属,其分子系统发生位于其它雉科鸟类支系之外,表明了这一类群物种的古老性。
4、分子系统发生研究表明雉鹑属和虹雉属有很近的亲缘关系,并且这一姊妹群明确地归入雉族类群；从形态、习性及分布特征方面比较,二者一致性也较高。在青藏高原强烈隆升前,虹雉属祖先和雉鹑属祖先就已经在横断山地区分化形成；雉鹑属祖先在早更新世高原希夏邦马冰期被隔离于高原东部边缘的一些较低的山地盆地,分化形成雉鹑和四川雉鹑,目前两个种的分布区相接格局是冰期结束后的再扩散造成的。
5、系统发生位置一直有争议的山鹑属应当置于雉族类群中。山鹑属内3种以及斑翅山鹑、高原山鹑种内亚种间的分子系统发生关系都表明,山鹑属的起源是在青藏高原。高原山鹑分歧形成时间为3.63-3.77百万年,在上新世中、末期广泛分布生活于青藏高原地区的山鹑属祖先物种在高原隆升过程中,存留于高原低洼盆地区域的祖先种群逐步适应高原环境的变迁,从冰期中存活下来而形成高原山鹑；被迫向北部扩散移动的种群,在中国中部因第二次大的冰期(大约2.05-1.28百万年)而迫使它们分裂成两大部分,向低的平原地区移动,西部支系演化成灰山鹑,东部支系进化为斑翅山鹑,地质环境的变化以及化石的记录都支持这一观点。
6、藏雪鸡三个涉及到的亚种间无明显的系统地理结构,在高原经历中更新世末的大间冰期时,藏雪鸡的不同种群被隔离分化形成亚种,之后的各个冰期,各亚种间都有一定的再扩散和交流。喜马拉雅雪鸡的四个亚种间表现出较为明晰的系统发生关系,经历了沿塔里木盆地的西南缘山地向东扩散和亚种形成路线。从种内亚种间分子系统发生关系、喜马拉雅雪鸡与藏雪鸡分歧时间的估算以及高原及其周边地质环境演变方面可以认定,喜马拉雅雪鸡和藏雪鸡是在高原隆升前(也就是说在3.6百万年前)就已经分化形成了,在青藏高原隆升初期的多瑙河冰期(3.5-2.6百万年),淡腹组的一支由天山东部地区向东南扩散至青藏东部地区的一些高山,伴随着青藏高原的隆升而形成藏雪鸡；暗腹组雪鸡的一支形成喜马拉雅雪鸡后在高原隆升中期(大约0.88百万年前)开始向高原上扩散并形成各亚种。
7、石鸡和大石鸡两种的分歧时间为2.76或2.82百万年,分子系统发生树表明,所涉及的5个石鸡亚种间无系统地理结构,石鸡的祖先种群在冰期被隔离在不同“避难所”,在间冰期从避难所向外扩散,后又被冰期隔离出一些小种群,经历遗传瓶颈,分化形成不同的亚种。在冰期结束后,不同的亚种间又有相互的扩散渗透,从而造成目前的混乱状态。
The alpine partridges in China consist of 5 genera,11 species and 29 subspecies of Galliformes taxonomic groups distributing mainly on and around Qingzang plateau. The samples we collected are composed of 4 genera,9 species and 23 subspecies of it, i.e.4 subspecies of Tetraogallus himalayensis,3 subspecies of T. tibetanus,5 subspecies of Alectoris chukar,2 subspecies of A. magna,1 subspecies of Perdix perdix,3 subspecies of P. dauuricae,3 subspecies of P. hodgsoniae,1 of Tetraophasis obscures and T. szechenyii. Together with other Phasianidae samples and the categories from Genebank, Taxa studied herein include 41 Phasianidae species and 20 of 21 phasianidae genera in China and 67 species and 30 genera in the world. The nuclear gene and several mitochondrial genes sequences, representing these Galliformes groups, were analyzed to (1) ascertain the evolutionary relationship between the alpine partridges and other related phasianid genera, (2) produce a molecular phylogeny of the extant species of the alpine partridges, and (3) correlate the inferred molecular phylogeny and extent of interspecific genetic divergence with Pliocene/Pleistocene biogeographical scenarios in the Qinghai-Tibet Plateau region to suggest speciational patterns in these alpine partridges.
The different gene segments were separated and concatenated for analysis simultaneously. Congruence among the different DNA data sets was evaluated using the incongruence-length-difference (ILD) test. Each data set was subjected to maximum parsimony (MP) using PAUP*4.0b10 and Bayesian analyses using MrBayes 3.0. Bayesian analysis of combined data (c-mos+CYT B+ND2) and D-loop data were also used separately to estimate the divergence times for clades of these alpine partridges by software BEAST 1.4.8.
We obtained the nucleotide sequences including partial c-mos gene (613bp), ND2 gene(1023bp), control region (1056bp) and complete CYT B gene (1143bp). The ILD test of different combined dataset were acceptable(>0.05). Among the alpine partridge genera, CYT B and ND2 showed similar composition of nucleotide pair and similar rates and types of nucleotide substitutions. The percentage of nonsynonymous substitution is comparatively higher in genus Tetraophasis on CYT B nucleotide sequences, but not on ND2. The transition to transversion ratio (Ti/Tv) is also higher in genus Tetraophasis.
The genera of Phasianidae in China should be classified into 4 clades:(1) Tetraogallus/Alectoris/Coturnix, (2) Phasianus/Chrysolophus/Lophura/Syrmaticus/ Crossoptilon/Tetraophasis and Lophophorus, also including Ithaginis/Tragopan/ Pucrasia/Perdix, (3) Gallus/Bambusicola/Francolinus, (4)Pavo and Polyplectron.
Blood Pheasant (genus Ithaginis) and Tragopan had uncertain positions in traditional classification but should been placed in tribe Phasianini in molecular phylogenetic analysis. Genus Arborophila was basal in whole Phasianidae clade, indicated it's age-old phylogenetic position.
Tetraophasis was sister to genus Lophophorus doubtlessly and the clade should also been placed in pheasants. The divergence time between them indicated that the clade Tetraophasis and the clade Lophophorus had been formed in the region of Hengduan Mountains before the uplift of the Tibetan Plateau, and the ancestor populations of Tetraophasis had been segregated into two partitions by the early Pleistocene glaciation and then formed the two species of Tetraophasis.
All three species of genus Perdix were grouped into a monophyletic cluster and should be placed into the pheasant group in our analyses. Tibetan partridges(Perdix hodgsoniae) were consistently placed basal to other Perdix species, and P. dauuricae przewalskii and P. hodgsoniae hodgsoniae, the subspecies distributed in main land of Tibet plateau, were basal to the other two subspecies in their own clade, respectively. These phylogenetic relationships suggested that the Perdix were originated from Tibet region. Divergence time estimates indicated that the Tibetan partridge split from the ancestor of Daurian partridge and gray partridge about 3.63 myr ago, we consider that the grassland-adapted ancestor of the typical partridges spread to the plateau during the middle Pliocene (4.52-2.75 myr ago). Throughout the course of the Qingzang Movement and the Pleistocene glaciations, some populations of the ancestor stayed in some basins, survived the glaciations and gave rise to Tibetan partridge. Other groups were forced to move north by rapid ascension of the Plateau, whereafter the big second glacier (approximately 2.05-1.28 myr ago) in central China compelled them to split into west and east branches, which now form the prey partridge in the west and the Daurian partridge in the east.
The three subspecies of Tetraogallus tibetanus studied herein showed no significant phylogeographic structure, we suggested that it's resulted from the adaptation to the climatic conditions and glacial cycles on the Qinghai-Tibetan Plateau. The phylogeny of 4 subspecies within Tetraogallus himalayensis indicated their eastward dispersal course along the south margin of Tarim Basin during the medium-term uplift (approximately 0.88 myr ago) of Qingzang plateau. Our studies also suggested that divergence between T. tibetanus and T. himalayensis took place before the sudden uplift of the Plateau.
Divergence time estimates between Alectoris chukar and A. magna indicated that the two species split away about 2.76 myr ago, and the molecular phylogenetic analysis showed no phylogeographic partitions among the 5 subspecies of A. chukar.
引文
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