从细胞色素b基因全序列分析岩羊和山羊、绵羊的系统发生关系

本测定了来自四川和青海岩羊的细胞色素b基因全序列(1140bp),结合从GenBank中检索获得的山羊、北山羊、绵羊和盘羊4个近缘种细胞色素b核苷酸同源区序列进行比较,分析了碱基组成和变异情况以及核苷酸序列差异。分别采用简约法和距离矩阵法构建分子系统树,得到了基本相同的拓扑结构,从分子水平初步探讨了岩羊的系统起源问题。岩羊与山羊属的山羊、北山羊有着比绵羊属的绵羊、盘羊更近的亲缘关系。岩羊与山羊、北山羊的分歧时间大约在3—6百万年,而与盘羊、绵羊的分歧时间大约在6-8百万年。     

基于细胞色素b基因的中国岩羊不同地理种群遗传差异分析

为了揭示中国岩羊不同地理种群的遗传差异,探讨岩羊亚种分化的分子机制,采用中国岩羊不同地理种群的细胞色素b(Cyt b)基因的全序列,分析了碱基变异情况、遗传距离以及核苷酸序列差异。用最大似然法和贝叶斯法构建分子系统树并对获得的拓扑结构进行分析。结果发现,西藏亚种与四川亚种Cyt b基因平均序列差异为4.2%(±0.007),处于偶蹄目亚种的序列差异范围内,支持了目前对岩羊西藏亚种的分类地位。四川亚种内部各地理种群之间的遗传距离(0.033±0.0 111)与它们分别到西藏种群的遗传距离(0.042±0.007)差异不显著(t=1.824,P=0.084),说明四川亚种内部各地理种群间已经发生较显著的遗传分化。其中,四川、甘肃和青海种群亲缘关系较近,并与四川亚种内部的其它种群已产生了显著的遗传分化。因此认为四川亚种内部各地理种群的种下分化需要深入研究。     

基于线粒体Cyt b和核基因ZFY探讨羊族物种之间的系统发生关系

为了阐明羊族物种之间的系统发生关系并解决岩羊属中矮岩羊物种的有效性问题,本文测定了来自金沙江河谷地区栖息于林线以上岩羊和林线以下矮岩羊共226份粪便DNA样品的线粒体Cyt b基因全序列(1 140 bp)和核基因ZFY部分序列(612 bp),结合从Gen Bank中检索到的羊族物种同源DNA序列进行比较,利用最大简约法和最大似然法构建分子系统发育树,根据获得的拓扑结构初步探讨它们的系统进化关系。结果表明,绵羊属的绵羊与山羊属、塔尔羊属、岩羊属各物种亲缘关系最远,喜马拉雅塔尔羊和岩羊属、山羊属的亲缘关系最近。在进化树的岩羊属这一分支中,金沙江河谷地带岩羊和矮岩羊与内蒙古、青海、四川其它地理种群的岩羊聚为一支,同时分布在这一区域的部分岩羊和矮岩羊在Cyt b基因和ZFY基因单倍型上存在共享现象。历史上的气候事件可能造成金沙江河谷地带岩羊和矮岩羊种群之间相互迁移,偏雄性扩散促进了各地理种群之间的基因交流。因此不支持矮岩羊为独立的物种,建议将金沙江河谷地带的岩羊和矮岩羊都划分到岩羊四川亚种(Pseudois nayaur szechuanensis)。由于它们的形态和生态上存在一定的分化,建议将林线以下矮岩羊作为一个独立的管理单元进行保护与管理。     

基于DNA条形码和微卫星标记分析矮岩羊的进化地位

岩羊Pseudois nayaur是目前岩羊属Pseudois中承认的唯一物种,主要分布在青藏高原及其周边山脉地区,是该地区代表性的大型有蹄类动物。岩羊种内存在矮岩羊这一个形态特异的种群,其分类地位一直处在争议当中。本次研究从岩羊分布区域内搜集到26个岩羊样品,其中包括5个矮岩羊样品,选取了COⅠ基因DNA条形码标准区域和8个微卫星标记位点探讨了矮岩羊与岩羊不同地理种群的系统进化关系,同时分析了矮岩羊的进化地位。结果表明矮岩羊和岩羊间目前处于基因交流半隔离状态,不应该被分为2个不同的物种或者亚种,而矮岩羊应该被作为岩羊四川亚种P.n.szechuanensis中一个形态变异的特殊分类群。另外,结合生境选择和生态观察的结果推测矮岩羊目前可能已经处于单独进化的早期阶段。     

岩羊不同种群细胞色素b基因序列差异的初步分析

测定了来自四川和宁夏两个种群的岩羊Pseudois nayaur共10个个体的线粒体DNA细胞色素b基因全序列(1140 bp),分析了碱基组成和变异情况以及核苷酸序列差异,计算了岩羊种群的核苷酸多样性,采用简约法和距离矩阵法构建了不同的分子系统树,得到了相似的拓扑结构,从分子水平初步探讨了岩羊不同种群的遗传结构.结果显示:岩羊整个群体的遗传多态性较高,四川种群的遗传变异水平较宁夏种群的高;同时,四川种群岩羊个体之间的平均序列差异为2.15,宁夏种群岩羊个体之间的平均序列差异为0.71,四川种群和宁夏种群之间的序列差异为2.61,这反映了四川种群和宁夏种群种群内的差异以及四川种群和宁夏种群种群间的差异都属于个体间的变化;然而四川种群的个体11(Si11)与该种群内的其它个体的平均序列差异和平均Kimura两参数距离远高于它与宁夏种群个体间的相应数值,存在着较为明显的分歧.形成这一现象的原因可能要涉及到岩羊在中国的地理演化和扩散问题.     

从线粒体细胞色素b基因探讨矮岩羊物种地位的有效性

用采自四川省的岩羊和矮岩羊共18个头骨或皮张标本，分析了线粒体Cyt6基因1140bp的全序列(其中一个样品只测到802bp的基因片段)。用NJ、MP、ML等系统发育分析法分别重建的系统发育树的拓扑结构完全一致，均不支持矮岩羊是单系群。结果提示：所研究的全部样品都属于同一个物种，即岩羊P．nayaur，不支持矮岩羊的物种地位。根据基于17个样品Cyt6基因全序列的系统发育树和遗传变异以及地理分布，这些岩羊样品聚为5支，根据地理区划和本文分析结果，四川的岩羊可分为摩天岭、川西、川西北、川西南和川北5个种群。基于17个样品Cyt6基因1137bp的编码区，共定义了岩羊的16种单元型，在5个种群间未发现共享的单元型。     

矮岩羊(Pseudois schaeferi)行为谱及PAE编码系统

2007年3～12月,对四川竹巴笼自然保护区的矮岩羊（Pseudois schaeferi）进行了行为谱工作的研究,建立了矮岩羊行为谱及其PAE（posture,act and environment）编码系统。研究分辨和记录了矮岩羊的11种姿势,83种动作和118种行为,还区别了各种行为在雄性、雌性和幼体之间的相对发生频次以及发生季节。     

岩羊和矮岩羊头骨形态特征比较

本文报道了岩羊和矮岩羊的头骨形态学资料,涉及头骨特征描述和一些形态学指标测定,被测定的指标主要有上颊齿列基长、眼窝长、乳突间距、眶间距、颧宽、枕颅高、枕髁宽、脑颅最大宽、眶下孔距、上颌臼齿外宽、角基最窄、最小角尖距、角尖距、最大角间距、角基周长、角基长径、角基短径、角外侧长,应用判别分析和单变量分析对岩羊和矮岩羊头骨的测量值进行统计与分析,以探讨这两个种头骨之间的形态差异。结果表明：（1）岩羊和矮岩羊头骨在形态上十分相似,但矮岩羊的头骨细长,脑颅狭窄,角直且朝上翘,角内侧具一明显角棱,亦较直,角基部狭窄,老年个体角基部愈合;岩羊的脑颅宽大,角粗大而长,向两侧分开,弯曲度较大,内侧角棱弯曲呈长S型,角尖朝向后方,角基部较宽,不愈合在一起。（2）岩羊和矮岩羊头骨的18项形态测量指标中乳突间距、眶间距、颧宽、脑颅最大宽、上颌臼齿外宽、角基周长、角基长径差异极显著（P〈0.01）,枕颅高、枕髁宽、眶下孔距、角尖距、最大角间距、角基短径、角外侧长差异显著（P〈0.05）;典型判别的正确率：岩羊为100%,矮岩羊为83.3%,交互验证法检验的结果,判别正确率：岩羊100%,矮岩羊为83.3%。这两个判别函数可以从角上区别岩羊和矮岩羊。     

我国的特产动物——矮岩羊

矮岩羊(Pseudois schaeferi Haltenorth1903)1977年由澳大利亚学者Groves从大岩羊(P.nayaur)中分出,订为一新种,结束了岩羊属为单型属的历史。模式标本于1930年采于四川省巴塘县竹巴笼,后带出国外。为了弄清矮岩羊目前是否存在、数量分布和生活习性等等,我们于1988年5月、9—10月两次到模式产地进行了考察,采得国内第一批珍贵的地模标本,并获得一些生态资料。1形态特征矮岩羊个体较小,大约仅大岩羊的一半。头顶有洞角一对,雌雄差异很大,是野外分辨性别最明显的特征。雄性角粗大(长250mm左右),角自头顶略向两侧伸出,两角内侧各具一明显的纵…     

繁盛的羊类大家族

羊类是一个繁杂且繁盛的动物类群,体型及习性多种多样。狭义上而言,所谓羊类系属于哺乳纲、偶蹄目、牛科、羊亚科、羊族的物种,常见的有野山羊、盘羊(家绵羊的野生种)、北山羊和岩羊等;广义上而言,牛科动物除了美洲野牛、欧洲野牛、非洲野牛、野黄牛和野水牛等少数种类之外,均可称之为羊类物种。习惯上,有人将羊族动物称为山羊类,将其他羊类动物称为羚羊类,因此,牛科物种可简约分为牛类、山羊类、羚羊类。无论是山羊还是羚羊,都可认为是"羊类"这个大家族的成员,其进化地位和种属分类极为复杂,尚存在诸多争议。     

Molecular phylogeography and genetic differentiation of blue sheep Pseudois nayaurszechuanensis and Pseudois schaeferi in China

Within the genus Pseudois (Bovidae, Artiodactyla), two challenges are faced by taxonomists. First, the designation of the two subspecies of blue sheep, Pseudois nayaur nayaur and Pseudois nayaurszechuanensis, tends to be questionable with the accumulation of morphological and molecular data. Second, the taxonomic status of the dwarf blue sheep (Pseudois schaeferi) has been controversial since its discovery, and molecular analyses with relatively small sample sizes have not painted a clear picture. We collected samples and DNA sequence data from a broad geographic range in China to investigate the population structure of Pseudois nayaurszechuanensis and its phylogenetic relationship with Pseudois schaeferi. Employing mitochondrial cytochrome b and control region sequences, as well as the nuclear gene zona pellucida glycoprotein 3, further investigation was performed to extend upon previous studies. We found that the population of Helan Mountain of Ningxia Hui Autonomous Region has significantly differentiated from the populations in Qinghai, Gansu and Sichuan provinces, and may be classified as a new subspecies according to the 75% rule. The dwarf blue sheep was found to be some individuals of Pseudois nayaurszechuanensis with morphological variations and is not a species or subspecies, since they did not fall into a monophyletic group in the phylogenetic analyses with blue sheep. Gene flow between dwarf blue sheep and common blue sheep might have occurred in different areas of western Sichuan, which would result in the paraphyly of dwarf blue sheep.     

Molecular evidence for the subspecific differentiation of blue sheep (Pseudois nayaur) and polyphyletic origin of dwarf blue sheep (Pseudois schaeferi)

Blue sheep (Pseudois nayaur), a Central Asian ungulate with restricted geographic distribution, exhibits unclear variation in morphology and phylogeographic structure. The composition of species and subspecies in the genus Pseudois is controversial, particularly with respect to the taxonomic designation of geographically restricted populations. Here, 26 specimens including 5 dwarf blue sheep (Pseudois schaeferi), which were collected from a broad geographic region in China, were analyzed for 2 mitochondrial DNA fragments (cytochrome b and control region sequences). In a pattern consistent with geographically defined subspecies, we found three deeply divergent mitochondrial lineages restricted to different geographic regions. The currently designated two subspecies of blue sheep, Pseudois nayaur nayaur and Pseudois nayaur szechuanensis, were recognized in the phylogenetic trees. In addition, the Helan Mountain population showed distinct genetic characteristics from other geographic populations, and thus should be classified as a new subspecies. In contrast, dwarf blue sheep clustered closely with some blue sheep from Sichuan Province in the phylogenetic trees. Therefore, dwarf blue sheep appear to be a subset of Pseudois nayaur szechuanensis. After considering both population genetic information and molecular clock analysis, we obtained some relevant molecular phylogeographic information concerning the historical biogeography of blue sheep. These results also indicate that western Sichuan was a potential refugium for blue sheep during the Quaternary period.     

Genetic distinctiveness of endangered dwarf blue sheep (Pseudois nayaur schaeferi): evidence from mitochondrial control region and Y-linked ZFY intron sequences

To elucidate the controversial systematic relationship of blue sheep (Pseudois nayaur) and endangered dwarf blue sheep, we sequenced part of the mtDNA control region and Y-linked ZFY intron, and carried out phylogenetic analyses. Mitochondrial results revealed that the dwarf blue sheep is a strongly supported monophyletic group, with an average of 12.21% sequence divergence from the blue sheep. This is the first genetic evidence for the distinctness of the dwarf blue sheep. ZFY intron results showed an average of 0.51% sequence divergence, and one shared haplotype between the dwarf blue sheep and blue sheep. By analyzing an expanded data set that incorporated ZFY intron sequences of two additional Ovis (sheep) species-O. nivicola and O. ammon--we demonstrated that ZFY intron provides good resolution at the species and genus levels. The ZFY intron sequence divergence between dwarf blue sheep and blue sheep was comparable to that within the two Ovis species. Moreover, we found intraspecific sequence variation in ZFY intron for all three species examined. We propose that dwarf blue sheep be designated as a subspecies of blue sheep, P. n. schaeferi.     

New aspects of an old discussion - phylogenetic relationships of Ammotragus and Pseudois within the subfamily Caprinae based on comparison of the 12S rDNA sequences

A mitochondrial 12S rDNA fragment was amplified by PCR and directly sequenced from eight members of the Caprinae ( Ammotragus lervia, Capra aegagrus, Ovis ammon, O. musimon, O. nivicola, O. orientalis, O. vignei and Pseudois nayaur ). Multiple alignment of the sequences and genetic distance calculation with the'distance of Taijama and Nei and the algorithms of Saitou and Nei (neighbour-joining - NJ) showed that Pseudois is grouped together with Capra and Ammotragus . All members of the genus Oxis formed a second cluster. Phylogenetic analyses supported these results. NJ-analyses and maximum parsimony (MP) trees did not support the present phylogenetic classification. Bootstrap values of 95% (NJ) and 96% (MP) confirms the grouping of P. nayaur and C. aegagrus . Another clade, O. ammon and O. orientalis supported weakly by bootstrap values of 65% (MP) and 70% (NJ) and the clade O. musimonand O. vignei had bootstrap values of 50% (MP) and 60% (NJ). So the phylogenetic relationship within the genus Oxis is still unsafe. But the parsimony analyses lead to the conclusion that Ammotragus represents an old lineage that diverged from ancestral caprines together with true sheep a long time ago and that both true goats and blue sheep forms represent one evolutionary lineage.     

Molecular phylogeny and phylogeography of genus Pseudois (Bovidae,Cetartiodactyla): New insights into the contrasting phylogeographic structure

Blue sheep, Pseudois nayaur, is endemic to the Tibetan Plateau and the surrounding mountains, which are the highest‐elevation areas in the world. Classical morphological taxonomy suggests that there are two subspecies in genus Pseudois (Bovidae, Artiodactyla), namely Pseudois nayaur nayaur and Pseudois nayaur szechuanensis. However, the validity and geographic characteristics of these subspecies have never been carefully discussed and analyzed. This may be partially because previous studies have mainly focused on the vague taxonomic status of Pseudois schaeferi (dwarf blue sheep). Thus, there is an urgent need to investigate the evolutionary relationship and taxonomy system of this genus. This study enriches a previous dataset by providing a large number of new samples, based on a total of 225 samples covering almost the entire distribution of blue sheep. Molecular data from cytochrome b and the mitochondrial control region sequences were used to reconstruct the phylogeny of this species. The phylogenetic inferences show that vicariance plays an important role in diversification within this genus. In terms of molecular dating results and biogeographic analyses, the striking biogeographic pattern coincides significantly with major geophysical events. Although the results raise doubt about the present recognized distribution range of blue sheep, they have corroborated the validity of the identified subspecies in genus Pseudois. Meanwhile, these results demonstrate that the two geographically distinct populations, the Helan Mountains and Pamir Plateau populations, have been significantly differentiated from the identified subspecies, a finding that challenges the conventional taxonomy of blue sheep.     

Mitogenomic analysis of the genus Pseudois: Evidence of adaptive evolution of morphological variation in the ATP synthase genes

The genus Pseudois includes two variable taxa, blue sheep (Pseudois nayaur) and dwarf blue sheep (Pseudois schaeferi), that exhibit notable geographic variation in morphology and ecological niche, suggesting the potential for significant adaptive differentiation between these two goats. Blue sheep are broadly distributed in the Tibetan Plateau and peripheral mountains through Central Asia, while dwarf blue sheep are only found in the gorges of the upper Yangtze River (Jinsha River) near Batang county, Sichuan province and adjacent mountains. Although they are all adapted to high altitude environments, endangered dwarf blue sheep show unique morphological variation and niche shifts compared to blue sheep. Mitochondria play important roles in oxygen usage and energy metabolism. The energetically demanding lifestyles of these high altitude species may have altered the selective regimes on mitochondrial genes encoding proteins related to cellular respiration. Here, we compared the sequences of 13 protein-coding genes in the mitochondrial genome of dwarf blue sheep with those of blue sheep to understand the genetic basis of morphological variation. Using neighbor-joining, maximum-likelihood and Bayesian approaches, we estimated rates of synonymous (d(S)) and nonsynonymous (d(N)) substitutions. Independent analyses showed that no ω ratio was larger than 1, suggesting that all mitochondrial 13 genes were under the purifying selection. Surprisingly, we found that the ω ratio (d(N)/d(S)) of the ATP synthase complex (ATP6 and ATP8) in blue sheep is sixteen times that of dwarf blue sheep (0.340 compared to 0.021). This result was confirmed by a separate analysis of ATP synthase genes from two additional P. schaeferi individuals and two P. nayaur individuals. We hypothesize that the large body size and diverse feeding styles are factors influencing the nonsynonymous substitutions in the ATP synthase complex of blue sheep.     

贺兰山同域分布岩羊和马鹿发情季节的生境选择差异

2007年和2008年9—12月,在宁夏贺兰山国家级自然保护区和内蒙古贺兰山国家级自然保护区利用痕迹检验法和直接观察法对同域分布的岩羊和马鹿发情季节生境选择进行研究。通过在选定的15条沟段里进行调查,分别测定了岩羊和马鹿的177个和154个样方的18种生态因子。结果表明,发情季节岩羊和马鹿在植被类型、地形特征、优势乔木、坡向、坡位、灌木密度、灌木高度、植被盖度、坡度、海拔高度、距水源距离、人为干扰距离、距裸岩距离和隐蔽级等生态因子选择上存在极显著差异(P0.01),乔木高度存在显著差异(P0.05),而其余生态因子无显著差异(P0.05),相对于马鹿选择的生境而言,岩羊发情季节更偏爱选择地势陡峭的山地疏林草原带,优势乔木以较高的灰榆为主,灌木密度低但高度较高,植被盖度较低,坡度较大的阳坡中上部,海拔较低,接近水源和裸岩,隐蔽程度低的生境。典则系数显示发情季节岩羊和马鹿的生境选择几乎完全分离,Wilk’sλ值也显示发情季节岩羊和马鹿的生境选择具有很高的差异性(Wilk’sλ=0.123,χ2=679.172,df=10,P0.001)。发情季节岩羊和马鹿的Fisher线性判别函数分别为:F岩羊=3.638×乔木高度+0.242×乔木距离+7.766×灌木高度+0.663×灌木距离+0.232×植被盖度+0.191×坡度+0.001×距水源距离+0.008×距裸岩距离+0.307×隐蔽级-31.078;F马鹿=4.850×乔木高度+0.321×乔木距离+12.024×灌木高度+0.929×灌木距离+0.192×植被盖度+0.482×坡度+0.002×距水源距离-0.001×人为干扰距离-0.003×距裸岩距离+0.511×隐蔽级-50.787。逐步判别分析表明在区分发情季节岩羊和马鹿生境方面有一系列生态因子发挥作用,依照贡献值的大小依次为坡度、人为干扰距离、隐蔽级、距裸岩距离、乔木高度、乔木距离、距水源距离、灌木高度、灌木距离和植被盖度,由这10个变量构成的方程对发情季节岩羊和马鹿生境的正确区分率达到99.7%。     

贺兰山岩羊冬季对卧息地的选择

20 0 3年 11～ 12月 ,在贺兰山采用样带法对岩羊冬季卧息地的选择性进行了研究。共观察到 94个岩羊的卧息地 ,结果表明岩羊对优势乔木的利用有选择性 (x2 =17 0 1,df=5 ,P <0 0 5 ) ,偏好利用灰榆占优势的卧息地 ,避免选择油松和青海云杉占优势的卧息地 ;对坡向选择性利用 (x2 =30 6 9,df=2 ,P <0 0 5 ) ,偏好位于阳坡的卧息地 ,避免利用阴坡 ;对植被类型、坡位和风向的利用无选择性。对卧息地样方与在样带中随机设置的样方进行比较 ,发现卧息地具有乔木密度低、食物丰富度低、隐蔽程度高、接近水源、接近裸岩、风速低和雪覆盖浅等特征。贺兰山的岩羊经常选择岩洞作为卧息地 ,占总卧息地的 6 2 77%。对 5 9个岩洞和 35个非岩洞卧息地进行比较 ,表明岩洞卧息地的坡度大、隐蔽程度高、风速低、保温性好、食物丰富度低和无雪覆盖。岩羊通常选择较宽的、深度和高度适中的岩洞作为卧息地。对各种生境因子的主成分分析表明前 7个特征值的累积贡献率已经达到了 80 0 9% ,可以较好地反映岩羊卧息地的生境特征 ,第 1主成分中隐蔽级、风向、风速、距裸岩距离和雪深具有重要作用 ,其余 6个主成分中优势乔木、坡向、坡位和坡度也很重要     

贺兰山岩羊冬春季取食生境的比较

2003年11～12月和2004年4～6月,在贺兰山设定了25条固定样线,采用直接观察法对岩羊冬春季的取食生境选择进行了研究。结果表明,岩羊冬季对12种取食生境生态因子有选择性,偏爱选择位于山地疏林草原带,优势乔木为灰榆,乔木密度〈4株、高度4～6m,灌木密度〉5株、高度〉1．3m,食物质量〉50g,人为干扰距离〈500m,距裸岩距离〈2m的地方取食。而春季对11种取食生境生态因子有选择性,偏爱选择山地疏林草原带,优势乔木为灰榆,乔木密度〈4株、高度〈6m,灌木密度5～10株、高度1．3～1．7m,食物质量〉100g,海拔高度〈2000m,距水源距离〈500m,隐蔽级50％～75％的地点。冬春季岩羊对植被类型、地形特征、优势乔木、乔木密度、乔木高度、灌木密度、灌木距离、食物丰富度、坡向、坡度、距水源距离、人为干扰距离和隐蔽级的选择存在显著差异。主成分分析表明,冬季第1主成分的贡献率达24．493％,其中绝对值较大的权系数出现在植被类型、优势乔木、乔木高度、乔木距离、灌木密度、灌木高度、海拔高度、距水源距离和人为干扰距离等生态因子：春季第1主成分的贡献率达28．777％,其中绝对值较大的权系数出现在植被类型、乔木距离、灌木高度、灌木距离、食物丰富度、海拔高度和人为干扰距离等生态因子。随着北方地区冬春季食物数量和质量的剧烈变化,贺兰山岩羊对取食生境的利用对策也将发生一定程度的改变,与其他分布区的岩羊相比,贺兰山独特的地理位置和特殊生境使其在取食生境选择上存在很大差异。