Genetic Diversity of Chinese Water Deer (Hydropotes inermis inermis): Implications for Conservation

The Chinese water deer (Hydropotes inermis inermis) is endemic to China. Historically, the species was widely distributed, but now, habitat loss and poaching have reduced its range and number drastically. In order to provide useful information for its conservation, we have investigated the genetic diversity and population structure of the Chinese water deer by analyzing the 403 bp fragment of the mitochondrial DNA (mtDNA) control region (D-loop). Eighteen different haplotypes were detected in 40 samples. Overall, Chinese water deer have a relatively high-genetic diversity compared to other rare cervid species, with a haplotype diversity of 0.923±0.025 and nucleotide diversity of 1.318 ± 0.146%. No obvious phylogenetic structure among haplotypes was found for samples of different origin. An analysis of molecular variance (AMOVA) showed significant differentiation between the Zhoushan and the mainland population (F_ST= 0.088, P < 0.001; Φ _ST = 0.075, P = 0.043), which suggests that exchanges of individuals between Zhoushan and the mainland should be avoided. We also recommend that a breeding center be set up for the mainland population.     

獐在上海地区重引入的社会价值初探

上海地区在长期的工农业发展过程中丧失了大量的自然生态环境,尤其是大型哺乳动物严重缺乏.近年来上海市加紧生态保护与恢复性建设工作,期望建立起一个完整的生态系统,因此需要重引入大型哺乳动物.獐(Hydropotes inermis)因其较强的适应性、极广的食性和对湿地环境的偏好而成为重引入的适合物种.而任何物种的重引入不仅要经过科学论证,还需要得到当地居民的支持才具有可持续性,但已有的重引入项目中鲜有此类研究的报导.为此我们以社会价值为标准,以此衡量獐在上海重引入的社会意义和上海市居民的支持程度.研究结果初步表明獐的重引入具有4909万元的社会价值,并受到92.4%的上海居民的支持.     

舟山群岛獐的食性研究

利用野外观察、粪便显微组织学分析和投喂实验等方法对舟山群岛獐的食性进行了研究。结果表明,研究地的獐所食植物共有137种,隶属于6l科l15属,其中豆科植物在取食种类和取食频次上均多于其它科植物。尽管獐对植物科和种的选择在四季间没有显著差别,但取食科和种的数量依然从春天到冬天呈递减趋势,并且冬天与其它3个季节差别较大。獐的食物中,每个季节都含有非禾草类草本植物、禾草类草本植物、木本植物和蕨类植物,且其食物组成在季节间亦无显著差异;除木本植物外,獐对其它3类植物的选择在季节间有显著差异。獐在冬天较多选择木本植物,而其它季节较多选择草本植物,但木本植物和非禾草类草本植物在四季食物组成中均占较高比例,而禾草类植物所占的比例很小。因此,笔者认为舟山群岛的獐应该偏向于嫩食者。     

獐(Hydropotes inermis)的警戒行为模式及逃跑起始距离的适应性变化

为了掌握獐的警戒行为特征并为重引入项目提供管理依据,以人为干扰源观察獐的警戒反应,发现其警戒模式包括听 (listen) 或扫视 (scan) ,盯视 (stare) ,走开 (walk away) ,跑开 (run away),吼叫 (bark) 和压脖 (stretch) 。利用逃跑起始距离对上海松江圈养 (自由采食) 獐、上海华夏圈养(人工饲喂) 獐和江苏盐城野生獐进行警戒性比较,得出：人工饲喂獐警戒性最小,野生獐警戒性最大。可通过野化训练提高人工饲喂獐的警戒性;人类活动、种群密度、围栏和区域面积可能影响獐的警戒性。     

Detection of Tick-Borne Pathogens in the Korean Water Deer (Hydropotes inermis argyropus) from Jeonbuk Province,Korea

The objective of this study was to investigate the prevalence of tick-borne pathogens in the Korean water deer (Hydropotes inermis argyropus). Pathogens were identified using PCR which included Anaplasma, Ehrlichia, Rickettsia, and Theileria. Rickettsia was not detected, whereas Anaplasma, Ehrlichia, and Theileria infections were detected in 4, 2, and 8 animals, respectively. The most prevalent pathogen was Theileria. Of the 8 Theileria-positive animals, 2 were mixed-infected with 3 pathogens (Anaplasma, Ehrlichia, and Theileria) and another 2 animals showed mixed-infection with 2 pathogens (Anaplasma and Theileria). Sequencing analysis was used to verify the PCR results. The pathogens found in this study were identified as Anaplasma phagocytophilum, Ehrlichia canis, and Theileria sp. To the best of our knowledge, this is the first report identifying these 3 pathogens in the Korean water deer. Our results suggest that the Korean water deer may serve as a major reservoir for these tick-borne pathogens, leading to spread of tick-borne diseases to domestic animals, livestock, and humans. Further studies are needed to investigate their roles in this respect.     

Prevalence of Anaplasma and Bartonella spp. in Ticks Collected from Korean Water Deer (Hydropotes inermis argyropus)

Deer serve as reservoirs of tick-borne pathogens that impact on medical and veterinary health worldwide. In the Republic of Korea, the population of Korean water deer (KWD, Hydropotes inermis argyropus) has greatly increased from 1982 to 2011, in part, as a result of reforestation programs established following the Korean War when much of the land was barren of trees. Eighty seven Haemaphysalis flava, 228 Haemaphysalis longicornis, 8 Ixodes nipponensis, and 40 Ixodes persulcatus (21 larvae, 114 nymphs, and 228 adults) were collected from 27 out of 70 KWD. A total of 89/363 ticks (266 pools, 24.5% minimum infection rate) and 5 (1.4%) fed ticks were positive for Anaplasma phagocytophilum using nested PCR targeting the 16S rRNA and groEL genes, respectively. The 16S rRNA gene fragment sequences of 88/89 (98.9%) of positive samples for A. phagocytophilum corresponded to previously described gene sequences from KWD spleen tissues. The 16S rRNA gene fragment sequences of 20/363 (5.5%) of the ticks were positive for A. bovis and were identical to previously reported sequences. Using the ITS specific nested PCR, 11/363 (3.0%) of the ticks were positive for Bartonella spp. This is the first report of Anaplasma and Bartonella spp. detected in ticks collected from KWD, suggesting that ticks are vectors of Anaplasma and Bartonella spp. between reservoir hosts in natural surroundings.     

Genetic diversity of Chinese water deer (Hydropotes inermis inermis): implications for conservation

The Chinese water deer (Hydropotes inermis inermis) is endemic to China. Historically, the species was widely distributed, but now, habitat loss and poaching have reduced its range and number drastically. In order to provide useful information for its conservation, we have investigated the genetic diversity and population structure of the Chinese water deer by analyzing the 403 bp fragment of the mitochondrial DNA (mtDNA) control region (D-loop). Eighteen different haplotypes were detected in 40 samples. Overall, Chinese water deer have a relatively high-genetic diversity compared to other rare cervid species, with a haplotype diversity of 0.923+/-0.025 and nucleotide diversity of 1.318 +/- 0.146%. No obvious phylogenetic structure among haplotypes was found for samples of different origin. An analysis of molecular variance (AMOVA) showed significant differentiation between the Zhoushan and the mainland population (F(ST)= 0.088, P < 0.001; Phi( ST ) = 0.075, P = 0.043), which suggests that exchanges of individuals between Zhoushan and the mainland should be avoided. We also recommend that a breeding center be set up for the mainland population.     

从细胞色素b基因序列探讨我国林蛙属动物的系统发生关系

对中国林蛙属动物进行了DNA水平的分子系统发生研究,测定了中国林蛙属7种15个样品,侧褶蛙属2种2个样品Cyt b基因长约360bp片段的序列。对这些序列的系统发生分析表明：（1）中国林蛙甘肃种群与东北种群序列差异较大,但尚难根据序列差异来判断它们是不同的亚种还是不同的物种;（2）7种林蛙中,中国林蛙与黑龙江林蛙的亲缘关系最近,与桓仁林蛙最远;（3）支持将昭觉林蛙,镇海林蛙,峨眉林蛙和长肢林蛙归入日本林蛙种组Rana japonica group。     

獐在吉林省的重新发现

獐(Hydropotes inermis)在历史上曾广泛分布于中国的辽东半岛、华北平原及长江两岸,在1949年以后的多篇文献中没有发现对吉林省獐分布的记载。2017年12月至2018年3月,利用红外相机于吉林省白山市(原浑江市)白山原麝国家级自然保护区拍摄到獐有效照片21张,有效视频时长总计600 s。在后续的野外调查中,研究者现场拍摄到獐幼崽活体及大量獐的活动痕迹,确认獐在吉林省重新发现。     

从D环和细胞色素b基因序列探讨懒猴属的分子系统发育关系(英文)

本研究测定了懒猴属(Nycticebus)D环的部分序列和细胞色素b基因的全序列(1140bp),分析了该属物种之间的系统发育进化关系。在DNA水平上,序列分析结果一致地提供了新的分类学证据：支持Rataiszczak和Groves的观点,即N．intermedus只是N．pygmaeus的成体(Ratajszczak,1998;Groves,1971)。对两种序列的数据做了联合及个别分析,获得相似的系统树,支持懒猴属由两个单系群组成：第一群由N．pygmaeus聚成,第二群由N．coucang聚成。该结果也提供了新的分子遗传证据,支持懒猴属由N．coucang和N．pygmaeus两物种组成。     

基于线粒体Cyt b基因(开鸟)亚科部分鸟类的系统进化与黑(开鸟)的分类地位初探

鉴于黑的分类归属一直未能有定论 ,本文中通过分析线粒体细胞色素b基因的序列 ,并重建亚科的系统发生 ,在此基础上探讨黑的分类归属。在重建的系统树中 ,亚科物种之间表现为平行枝的关系 ;亚科物种间的序列分歧在属内与两个属间之间变化不明显 ,提示亚科的物种可能是来自于一个快速辐射演化事件的群体。对细胞色素b基因的序列分析结果以及重建的分子系统进化树提示 ,将黑独立为Dupetor属是不适合的 ,因而我们支持Bock的观点 ,将黑置于苇属之内。     

太湖新银鱼线粒体D-loop和Cytb片段序列结构与进化速率比较

共获得49个太湖新银鱼(Neosalanx taihuensis)个体的线粒体细胞色素b(Cyt b)全序列和控制区(D-loop)部分序列。所测线粒体D-loop部分序列长度变化范围为648～680bp,识别到位于前端的一个串联重复序列、一个终止相关序列(ETAS),3个中央保守区保守序列(CSB-F、CSB-E、CSB-D)及一个保守序列区保守序列(CSB-1),结构与其他鱼类的研究结果类似。太湖新银鱼线粒体Cyt b和D-loop片段的相对进化速率的比较研究结果表明,太湖新银鱼D-loop总的序列多态性位点的比例为0.83%,低于线粒体Cyt b部分总的序列多态性位点的比例(1.31%)。假设太湖新银鱼Cyt b基因平均进化速率相对值为1,贝叶斯(Bayes)MCMC模拟给出Cyt b基因的相对速率区间估计为1.000±0.131,而D-loop基因的相对速率为0.859±0.261,表明太湖新银鱼D-loop基因的进化速率低于Cyt b基因,同时,后验概率分布的变异方差也比较大。说明Cyt b基因比D-loop基因具有相对较高的进化速率,也相对更接近分子钟假设。因此,可以认为Cyt b基因比D-loop基因更适于太湖新银鱼种内及近缘种间相关分子生态及系统地理格局的研究。     

Detection and Quantification of Pfiesteria piscicida by Using the Mitochondrial Cytochrome b Gene

Mitochondrial cytochrome b was isolated from the dinoflagellate Pfiesteria piscicida, and the utility of the gene for species identification was examined. One of the primer sets designed was shown to be highly specific for P. piscicida. A time step PCR protocol was used to demonstrate the potential of this primer set for quantification of this species.     

剑尾鱼线粒体细胞色素b基因的序列分析

目的　克隆和测定剑尾鱼 (Xiphophorushelleri)线粒体细胞色素b基因 (cytb)的全序列。方法　提取剑尾鱼肝脏的总DNA。设计合成特异引物进行PCR扩增。扩增产物经琼脂糖电泳检测、纯化后克隆到pGEM Teasyvectorsystem中的T载体上 ,筛选转化子 ,提取质粒 ,酶切鉴定。挑取重组质粒pGEM T xhcytb 11进行序列测定。结果　获得了剑尾鱼线粒体cytb基因的全序列 ,共 114 0bp。结论　用BLAST与GenBank中的线粒体DNA序列进行比较 ,显示剑尾鱼与其他鱼类的cytb基因具有较高的同源性 ;根据剑尾鱼与其他 13种鱼的cytb基因序列同源性所建立的进化树 ,与传统的分类地位基本吻合     

基于线粒体DNA细胞色素b基因和控制区序列分析西藏雅鲁藏布江黄斑褶鮡种群遗传多样性

采用线粒体DNA（mtDNA）Cyt b基因和D-loop控制区为分子标记,对分布于西藏雅鲁藏布江大峡谷以上里龙段和以下墨脱段2个群体的黄斑褶 （Pseudecheneis sulcata）共60个样本进行遗传多样性研究。获得联合基因有效序列长度为1 893 bp,包括Cyt b基因1 060 bp和D-loop控制区833 bp。结果显示,里龙和墨脱2个群体的单倍型多样性值（Hd）均较高（0.701和0.761）,核苷酸多样性值（π）均较低（0.001 00和0.001 09）;高频率的单倍型Hap1和Hap2为2个群体所共享,推测为祖先单倍型;同时,里龙和墨脱群体分别存在5个和6个特有单倍型,且在2个群体中不共享;分子方差分析（AMOVA）显示遗传变异主要来源于种群内部,群体间呈中度遗传分化水平（Fst = 0.090 44,P < 0.05）;中性检验（Tajima''s D、Fu''s Fs）和核苷酸不配对（SSD、Hir）分析结果揭示,黄斑褶 种群曾经历过种群扩张现象。本研究推测,黄斑褶 2个群体间的基因流动存在障碍,雅鲁藏布大峡谷的海拔落差及水文情势等生态屏障可能是阻碍黄斑褶 迁徙和交流的主要原因。     

12S rRNA和Cyt b基因序列测定在獐乳制品鉴定中的应用

采用改良的蛋白酶K消化和酚/氯仿抽提的方法从脂肪含量很高的动物乳制品及胃组织中提取出基因组总DNA,利用特异引物扩增了线粒体12S rRNA基因和Cyt b基因的部分片段,测定了12S rRNA和Cyt b基因的PCR扩增产物序列,使用BLAST搜索软件将其序列与GenBank中的同源序列进行比对,并利用DNAMAN分析软件分析序列同源性。结果表明3件检材均来源于獐Hydropotes inermis。本研究所用方法在野生动物乳制品鉴定中具有较高的应用价值。     

Variability of Nucleotide Sequences of Mitochondrial DNA Cytochrome b Gene in Chars of the Genus Salvelinus

Nucleotide sequences of two (405- and 1050-bp) regions of mitochondrial DNA (mtDNA) cytochrome c gene were established in chars of the genus Salvelinus from Russian Far East and Siberia. Based on the divergence and phylogenetic analysis of nucleotide sequences of the mtDNA cytochrome b gene, S. laecomaenis was shown to carry the most ancient mitochondrial lineage, which is close to the ancestral one. The archaic mtDNA of S. levanidovi occupied an isolated position on the phylogenetic trees. The mtDNA lineage of the southern S. malma was close to the S. alpinus–S. malma malmacomplex group. Within the S. alpinus–S. m. malma complex, three groups of mtDNA types having particular geographic distributions were distinguished. The Kolyma–Chukotka group includes lake S. taranetzi, S. boganidae, andS. elgyticus from Chukotka, lake chars from Kolyma. The Okhotsk group is represented by northernS. malma, lake chars from northern Sea of Okhotsk, and anadromous S. taranetzi. The Siberian group is close to the Okhotsk one and consists of Taimyr and Baikal region chars as well as Arctic char from Finland. The divergence of char mitochondrial lineages was dated to the Pliocene–Pleistocene.     

塔里木马鹿(Cervus elaphus yarkandensis)遗传结构及遗传多样性分析

目的:塔里木马鹿(Cervus elaphus yarkandensis)为马鹿的新疆特有亚种,自20世纪50年代以来,由于自然和人为因素影响,种群数量急剧下降,现已隔离成3个孤立的小种群,即沙雅种群、尉犁种群和且末种群.为了更好地保护这一濒危野生动物.方法:基于塔里木马鹿线粒体控制区部分序列对3个种群的控制区结构和遗传多样性进行了研究.结果:在34个序列比对中得到342bp的片段,含变异位点12个,占分析序列长度的3.51%,由此定义了6个单倍型.显示出3个种群总的核苷酸多样性较低(0.01351±0.00063),单倍型多样性较高(0.693±0.051);就单个种群而言,且末种群的遗传多样性最低,而沙雅种群最高.从Tajima's D和Fu and Li's D值的估算结果来看,塔里木马鹿尉犁和沙雅种群相对于中性进化的歧异度并没有明显的偏离(P>0.1),且末种群则出现了明显的偏离(分别为P<0.05和P<0.02),这预示着3个塔里木马鹿种群间可能存在一定的平衡选择.分子变异分析表明,沙雅和尉犁种群间基因流Nm大于4,说明这2个塔里木马鹿种群间存在着非常丰富的基因流,且末种群分别与沙雅、尉犁种群间基因流Nm均小于1,而且末种群分别与沙雅和尉犁种群产生了明显的遗传分化(Fst分别为0.409;0.718,P值均小于0.001),以及3个塔里木马鹿种群单倍型间的序列差异为0.012.结论:以上数据都显示了3个塔里木马鹿种群的单倍型间已经出现了明显分化.结合系统发生关系分析,应将沙雅种群和尉犁种群联合建立管理单元进行重点保护.     

Phylogeographic Patterns and Evolution of the Mitochondrial DNA Control Region in Two Neotropical Cats (Mammalia, Felidae)

The ocelot (Leopardus pardalis) and margay (L. wiedii) are sister-species of Neotropical cats which evolved from a lineage that migrated into South America during the formation of the Panamanian land bridge 3–5 million years ago. Patterns of population genetic divergence of each species were studied by phylogenetic analyses of mitochondrial DNA (mtDNA) control region sequences in individuals sampled across the distribution of these taxa. Abundant genetic diversity and remarkably concordant phylogeographic partitions for both species were observed, identifying parallel geographic regions which likely reflect historical faunal barriers. Inferred aspects of phylogeography, population genetic structure, and demographic history were used to formulate conservation recommendations for these species. In addition, observed patterns of sequence variation provided insight into the molecular evolution of the mtDNA control region in closely related felids. Received: 26 January 1998 / Accepted: 14 May 1998