Genetic diversity among Chinese sika deer （Cerrus nippon） populations and relationships between Chinese and Japanese sika deer

Sika deer （Cervus nippon） is a cervid endemic to mainland and insular Asia and endangered. We analyzed variation in the mitochondrial DNA （mtDNA） control region for four subspecies to understand the genetic diversity, population structure and evolutionary history in China. 335 bp were sequenced and eight haplotypes were identified based on 25 variable sites among the populations. Sika deer in China showed lower genetic diversity, sug- gesting a small effective population size due to habitat fragmentation, a low number of founder individuals, or the narrow breeding program. AMOVA analysis indicated that there was significant genetic subdivision among the four populations, but no correlation between the genetic and geographic distance. PhyIogenetic analyses also revealed that Chinese sika deer may be divided into three genetic clades, but the genetic structure among Chinese populations was inconsistent with subspecies designations and present geographic distribution. Including the sequence data of Japanese sika deer, the results indicated that Chinese populations were more closely related to Southern Japanese populations than to the Northern Japanese one, and the Taiwan population was closer to populations of Northeastern China and Sichuan than to those of Southern China.     

Characterization of MHC class II A genes in Hainan Eld’s deer (Cervus eldi hainanus)

The major histocompatibility complex(MHC) genes play pivotal roles in the immune system of vertebrates against antigens.They are also significant indicators of genetic structure,and are vital to species-level population viability analyses and disease risk assessments.In this study,two DRA and two DQA sequences were isolated from Hainan Eld’s deer(Cervus eldi hainanus) using rapid amplification of cDNA ends(RACE) and single-strand conformation polymorphism-heteroduplex(SSCP-HD) analysis.Nucleotide sequence analysis revealed large differences between the two DQA sequences,especially in their exon 2 regions,but only minimal differences between the variants of the DRA gene.Comparison of the predicted amino acid sequences of the Ceel-MHC class Ⅱ A variants with those from six other species revealed that these molecules share high homology among ruminants.A phylogenetic tree of four class Ⅱ A sequences from Hainan Eld’s deer and the other species placed the newly identified DQA and DRA genes on two distinct branches(100%-supportively),and further divided the two DQA sequences into 98%-supportive DQA1 and 99%-supportive DQA2 clusters,respectively.Therefore,this study identified monomorphic Ceel-DQA1 and Ceel-DQA2 genes,and one dimorphic Ceel-DRA gene from Hainan Eld’s deer.     

Microsatellite and mitochondrial DNA assessment of the genetic diversity of captive Saiga antelopes (Saiga tatarica) in China

To estimate the genetic diversity of the only captive Saiga antelope(Saiga tatarica) population in China,40 umbilical cord samples were collected and mitochondrial(control region) and nuclear(microsatellite) variabilities were assessed.Both of the markers revealed low genetic variability(or high genetic homogeneity) within the population.The microsatellites yielded monitoring ranges of 2-6 alleles.The observed heterozygosities ranged from 0.28 to 0.83,and the expected heterozygosities were between 0.27 and 0.71.The Shannon information index(Shannon I) and Polymorphic Information Content(PIC) presented overall means of 0.87 and 0.43,respectively.The gene diversity was 0.49.We found only two haplotypes in the population,and the haplotype and nucleotide diversities were 39.1% and 1.13%,respectively.Founder events,bottlenecks and inbreeding have contributed to the low genetic variation observed in this population.Our findings revealed the extent of genetic diversity maintained in the present population and the urgency of implementing a protection plan,introducing animals from other populations to enhance saiga’s genetic variation.     

Mitochondrial cytochrome b sequence variations and phylogeny of the East Asian bagrid catfishes

The mitochondrial DNA cytochrome b gene was sequenced from 8 bagrid catfishes in China. Aligned with cytochrome b sequences from 9 bagrid catfishes in Japan, Korea and Russia retrieved from GenBank, and selected Silurus meridionalis, Liobagrus anguillicauda, Liobagrus reini and Phenacogrammus interruptus as outgroups, we constructed a matrix of 21 DNA sequences. The Kimura's two-parameter distances were calculated and molecular phylogenetic trees were constructed by using the maximum parsimony (MP) and neighbor-joining (NJ) methods. The results show that (i) there exist 3-bp deletions of mitochondrial cytochrome b gene compared with cypriniforms and characiforms; (ii) the molecular phylogenetic tree suggests that bagrid catfishes form a monophyletic group, and the genus Mystus is the earliest divergent in the East Asian bagrid catfishes, as well as the genus Pseudobagrus is a monophyletic group but the genus Pelteobagrus and Leiocassis are complicated; and (iii) the evolution rate of the East Asian bagrids mitochondrial cytochrome b gene is about 0.18%～0.30% sequence divergence per million years.     

Evolutionary analysis of allotetraploid hybrids of red crucian carp × common carp, based on ISSR, AFLP molecular markers and cloning of cyclins genes

The allotetraploid hybrids of red crucian carp x common carp are the first reported artificially cultured polyploid fish with bisexual fertility and stable inheritance in vertebrate. Using ISSR and AFLP markers and the cyclins genes, the genomes and cyclin gene sequence changes were analyzed between the allotetraploid hybrids and their parents. The results indicated that the allotetraploids inherited many genetic characteristics from their parents and the genetic characteristics were stable after 15 generations. However, the allotetraploids had a closer genetic relationship with their original female parents and represented a bias toward the maternal progenitor. DNA fingerprinting analysis showed that the allotetraploids had undergone sequences deletion from their original parents and that the deleted sequences were mostly from the male parent＇s genome. Some non-parental bands were found in the allotetraploid hybrids. Sequences analysis of the cyclin A1 and B1 genes showed nonsynonymous substitutions of single nucleotides in codons that were different from their original parents, leading to non-parental amino acid loci. We speculate that the non-additivity in the allotetraploids, compared with their progenitors, could be an adjustment to the genomic shock from heterozygosity and polyploidy, allowing maintenance of genetic stability.     

Origin of Gymnocypris przewalskii and phylogenetic history of Gymnocypris eckloni (Teleostei: Cyprinidae)

The origins and phylogenetic patterns were assessed for G. przewalskii and G. eckloni by analyzing the complete mtDNA cytochrome b gene sequence (1140bp). Phylogenetic analyses further supported that there were three mtDNA lineages (A-C) identified in G. przewalskii and G. eckloni, demonstrating that outer rakers of the first gill have little significance in the phylogeny of the Gymnocypris fishes. The network established showed that G . eckloni of the Yellow River specific haplotype Al was a founder and it radiated all haplotypes of G. przewalskii which suggested G . przewalskii might only originate from one of two maternals of G . eckloni from the Yellow River. Fs test and mismatch analysis showed at least two expansion events in the population of G. przewalskii about 0.2734 Ma and 0.0658 Ma, while G. eckloni from Qaidam Basin could have experienced severe bottleneck effect about 0.0693 Ma. The population expansion was detected in subclades Al and A21 with the most recent common ancestor (TMRCA) about 0. 2308±0.01 Ma and 0.1319±0. 015 Ma, respectively, which were within the geological age range of "Gonghe Movement" event that caused the separation of Lake Qinghai from the upper Yellow River. These results suggested the effect of the fish diversification by rapid uplift of the Qing-hai-Tibetan Plateau in the Late Pleistocene.     

New ancient DNA sequences suggest high genetic diversity for the woolly mammoth (Mammuthus primigenius)

Partial DNA sequences of cytochrome b gene (mtDNA) were successfully retrieved from Late Pleistocene fossil bone of Mammuthus primigenius collected from the Xiguitu County ( Yakeshi), Inner Mongolia Autonomous Region and from Zhaodong, Harbin of Heilongjiang Province in northern China. Two ancient DNA fragments (109 bp and 124 bp) were authenticated by reproducible experiments in two different laboratories and by phylogenetic analysis with other Elephantidae taxa. Phylogenetic analysis using these sequences and published data in either separate or combined datasets indicate unstable relationship among the woolly mammoth and the two living elephants, Elephas and Loxodonta . In addition to the short sequences used to attempt the long independent evolution of Elephantidae terminal taxa, we suggest that a high intra-specific diversity existed in Mammuthus primigenius crossing both spatial and temporal ranges, resulting in a complex and divergent genetic background for DNA sequences so far recovered. The high genetic diversity in the extinct woolly mammoth can explain the apparent instability of Elephantidae taxa on the molecular phylogenetic trees and can reconcile the apparent paradox regarding the unresolved Elephantidae trichotomy.     

Molecular biological analysis of remains from Jiangjungou Cemetery in Inner Mongolia

The 364-bp nucleotide sequence in hypervariable region I (HVRI) of mitochondrial DNA is successfully amplified from 9 out of 11 individuals of an ancient population buried in the Jiangjungou Cemetery in Inner Mongolia dated back to the Warring States Period in China. Nine fragments with different variations are obtained. A phylogenetic tree and a multidimensional scaling (MDS) plot are constructed using mtDNA sequences from the ancient population and several modern Asian populations. The results show that ancient population shares a closer genetic relationship with East Asian populations than with North and Central Asian populations. The genetic and historical evidence raise the possibility that the population might be the immigrants from Zhongyuan area, sent by the King Wuling of Zhao State to guard the nation against the attack from Huns.     

Origin of Gymnocypris przewalskii and phylogenetic history of Gymnocypris eckloni (Teleostei: Cyprinidae)

The origins and phylogenetic patterns were assessed for G. przewalskii and G. eckloni by analyzing the complete mtDNA cytochrome b gene sequence （1140bp）. Phylogenetic analyses further supported that there were three mtDNA lineages (A-C) identified in G. przewalskii and G. eckloni, demonstrating that outer rakers of the first gill have little significance in the phylogeny of the Gymnocypris fishes. The network established showed that G. eckloni of the Yellow River specific haplotype A1 was a founder and it radiated all haplotypes of G. przewalskii which suggested G. przewalskii might only originate from one of two maternals of G. eckloni from the Yellow River. Fs test and mismatch analysis showed at least two expansion events in the population of G. przewalskii about 0.2734 Ma and 0.0658 Ma, while G. eckloni from Qaidam Basin could have experienced severe bottleneck effect about 0.0693 Ma. The population expansion was detected in subclades A1 and A21 with the most recent common ancestor (TMRCA) about 0.2308±0.01 Ma and 0.1319±0.015 Ma, respectively, which were within the geological age range of “Gonghe Movement” event that caused the separation of Lake Qinghai from the upper Yellow River. These results suggested the effect of the fish diversification by rapid uplift of the Qinghai-Tibetan Plateau in the Late Pleistocene.     

Phylogenetic positions of some genera and species of the family Buccinidae (Gastropoda: Mollusca) from China based on ribosomal RNA and COI sequences

A phylogenetic analysis of members of the family Buccinidae was conducted using 18S rRNA gene, 28S rRNA gene and the mitochondrial cytochrome oxidase Ⅰ gene. We studied 18 species of Buccinidae that belong to eight different genera and inhabit the China coastal seas. We analyzed the patterns of divergence between an outgroup and basal ingroup taxa, the monophyly of the genus Neptunea, and the position of one unnamed species within the Buccinidae. A phylogenetic tree (neighbor-joining (NJ) method) was reconstructed based on the sequences of 18S rRNA, 28S rRNA and COI, with Rapana venosa as outgroup. The NJ tree indicated that the 18 species could be divided into five groups. The genus Buccinum was monophyletic, whereas Neptunea was shown to be paraphyletic since it included Siphonalia subdilatata and Neptunea sp., a new species. This novel species otherwise clustered consistently with Neptunea cumingi in three other phylogenetic trees, showing a low genetic distance and divergence percentage of sequences belonging to the genus Neptunea. A smaller genetic distance and a smaller difference of 18S rRNA, 28S rRNA and COI sequences between Neptunea cumingii and Neptunea arthritica cumingii confirmed them to be the same species.     

基于线粒体Cytb基因序列的褐石斑鱼种群遗传多样性分析

为评估种质资源状况被世界自然保护联盟(International Union for Conservation of Nature, IUCN)评定为易危物种的褐石斑鱼(Epinephelus bruneus)野生种群的遗传多样性和遗传分化水平，采用PCR方法测定褐石斑鱼西太平洋海区的中国海南岛(HN)、福建厦门(XM)和韩国济州岛(HG)3个地理群体的线粒体细胞色素b(Cytb)基因的部分序列，并对其基因序列遗传变异、谱系结构和群体扩张历史特征进行分析。结果显示，褐石斑鱼3个地理种群(88个个体)共检测出18个多态位点，共有7种单倍型；各地理群体遗传多样性水平较低，而且单倍型在群体间分布不均，韩国群体遗传多样性最高，中国海南和厦门群体遗传多样性较低。地理距离最远的韩国群体和中国海南群体遗传分化最高(F_ST=0.177 5),地理距离最近的中国海南群体和厦门群体的遗传分化最低(F_ST=0.013 4)。Mantel检验结果显示，3个褐石斑鱼群体间遗传距离和地理距离间存在显著相关，距离隔离(Isolation by Distance, IBD)...     

GENETIC DIVERSITY AMONG CHINESE SIKA DEER (CERVUS NIPPON) POPULATIONS AND RELATIONSHIPS BETWEEN CHINESE AND JAPANESE SIKA DEER

SIKA DEER,CERVUS NIPPON,WAS HISTORICALLY WIDE-SPREAD THROUGHOUT NORTHEASTERN ASIA,FROM THE USSURI REGION TO VIETNAM,INCLUDING THE KOREAN PENINSULA,MAINLAND CHINA AND TAIWAN,AND THE JAPANESE ARCHI-PELAGO,AND UP TO13SUBSPECIES HAVE BEEN DESCRIBED[1].THE FOS…     

银额果蝇(Drosophila albomicans)细胞色素b基因的初步研究

通过PCR直接测序和克隆后测序的方法获得了不同银额果蝇单雌系细胞色素b基因的部分序列,并对这些序列进行分析．结果表明银额果蝇单雌系细胞色素b基因存在着一定的地理分化,银额果蝇细胞色素b基因序列不仅在不同地理群体间存在着差异,而且同一地理群体内也存在着差异,有时群体内的差异比群体间的差异还要显著．通过研究再一次说明了银额果蝇的分化已达到亚种和半种水平．     

基于CR及Cytb基因序列的大泷六线鱼野生群体遗传多样性分析

为进一步了解山东省内大泷六线鱼(Hexagrammos otakii)群体遗传背景和分化情况,合理保护与开发利用渔业资源,选取线粒体控制区(CR)和细胞色素b基因(Cytb)对分布于山东省近海沿岸的3个大泷六线鱼野生群体以及北黄海1个离岸大泷六线鱼野生群体的线粒体基因序列进行对比,分析它们的序列特征、遗传多样性和种群历史动态情况。经PCR扩增得到大泷六线鱼野生群体的CR和Cytb基因序列,全长分别为485bp和651bp。基于CR基因序列共检测到40个多态位点,单倍型多样性平均值为0.908,核苷酸多样性平均值为0.006,定义了53种单倍型。基于Cytb基因序列检测到56个多态位点,转换颠换比值为19.04,种内单倍型多样性平均值为0.934,核苷酸多样性平均值为0.005,定义了38种单倍型。对比分析表明,4个大泷六线鱼野生群体均具有高单倍型多样性和低核苷酸多样性。NJ系统进化树、群体间/内平均遗传距离、Fst值、基因流及AMOVA分析结果显示:山东省内近海沿岸大泷六线鱼野生群体和北黄海离岸野生群体遗传差异不显著,群体间存在频繁的基因交流,未形成显著的遗传分化。种群动态结果表明大泷六线鱼于更新世晚期经历了快速扩张,并形成了现有遗传格局。山东省内近海沿岸大泷六线鱼野生群体和北黄海离岸野生群体遗传结构之间不存在显著的地理隔离,这可能与人为增殖放流和秋冬季节黄海沿岸流及暖流有关,从而使得群体之间基因交流广泛。     

The taxonomic status ofMoschus moschiferus anhuiensis

Since the musk deer distributed in the Dabie Mountains, Anhui was defined asMoschus moschiferus anhuiensis, its status has been disputed based on researches of morphology and ecology. This study further probed into its taxonomic status with principal components analysis (PCA) on skull measurements and mtDNA cytochrome b sequences (367 bp) analysis so as to clear its status. It is concluded that the figure and skull in Anhui musk deer are different from other species, and DNA divergence between it and other species is 6.24%–7.90%, which belongs to inter-specific difference. Thus, the study defines this musk deer as one distinct species,Moschus anhuiensis (Wang, Huet al.)     

几种常用饲料在长白山狍瘤胃中降解率的测定

利用3只装有永久性瘤胃瘘管的成年公狍,用尼龙袋法,测定了8种常用饲料在狍瘤胃的干物质有效降解率(DMD)、蛋白质有效降解率(CPD)、有机物有效降解率(OMD),为科学制定狍的饲养标准奠定了基础.玉米面、豆粕、紫花苜蓿、玉米青贮、菊芋叶、高梁、青柞叶、草木樨的DMD分别为百分之62.15,58.21,57.22,26.29,54.23,61.98,40.75,55.89;CPD分别为百分之67.28,68.24,66.15,34.23,65.23,40.09,37.13,54.47;OMD分别为百分之70.01,70.14,66.49,34.47,67.57,58.53,40.41,57.55.     

赤眼鳟线粒体D-loop和Cyt b基因序列的对比分析

 研究了长江和珠江野生赤眼鳟Squaliobarbus curriculus共4个群体24个个体的线粒体控制区（D-loop）和细胞色素b（Cyt b）基因序列,通过PCR扩增与测序,分别获得了长度为598 bp和752 bp的D-loop和Cyt b基因片段。分析表明,D-loop序列共定义了18个单倍型,存在34个简约信息位点,67个多态性位点,发生转换40次,颠换15次,插入/缺失14次。A、T、C、G平均含量分别为33.7%、35.1%、17.5%、13.7%。Cyt b序列共定义了18个单倍型,存在68个简约信息位点,72个多态性位点,发生转换60次,颠换15次,无插入/缺失位点。A、T、C、G平均含量分别为29.3%、26.4%、29.8%、14.5%。Cyt b除简约信息位点百分比大于D-loop外,多态位点百分比和单突变位点百分比均小于D-loop,说明D-loop具有较快的进化速率。D-loop序列的单倍型多样性(H)、平均核苷酸差异数(K)、核苷酸多样性(π)分别0.963 8、16.543 5和0.028 4,Cyt b的H、K和π分别为0.971 0、31.855 1和0.042 6,显示赤眼鳟具有较高的遗传多样性水平,且遗传变异主要存在于群体间。分析群体间的遗传距离和F_ST值,D-loop和Cyt b都一致表明：长江和珠江水系间存在明显的遗传分化,系统树和分子变异等级分析(AMOVA)也支持这一观点。同一水系群体间的遗传差异较小,Cyt b则更小;不同水系群体间的遗传差异较大,Cyt b则更大。故,Cyt b呈现出“小则越小,大则越大”的态势。分析其原因,可能与D-loop和Cyt b进化速率密切相关。