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.     

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.     

Analysis of the matrilineal genetic structure of population in the early Iron Age from Tarim Basin, Xinjiang, China

Ancient mtDNA data of human remains were analyzed from four early Iron Age Tarim Basin sites （Yuansha, Zaghunluq, Sampula and Niya） in the southern Silk Road region. Haplogroup distributions show that ancient Tarim Basin population was comprised of well-differentiated Western and Eastern matrilineal lineages. Some West lineage of Tarim Basin population originated from Near East and Iran region. Of the East lineages, North and Northeast Asia originated lineages were the main components, and a few Southeast Asian lineages also existed, which indicated a more extensive origin and a more complex admixture. The genetic structure of ancient Tarim Basin population is relatively close to the modern populations of Xinjiang, which implied that the early Iron Age is an important period during the formation of the modern Xinjiang population.     

Relationships of Aegilops tauschii revealed by DNA fingerprints: the evidence for agriculture exchange between China and the West

Genetic diversity and relationships of wild goat grass (Aegilops tauschii Cosson) from Iran and Xinjiang, west China, as well as its weedy type from the Yellow River region of Shaanxi and Henan provinces in China were analyzed by simple sequence repeat (SSR) fingerprinting. A high level of genetic diversity in Aegilops tauschii accessions from Iran was observed, and the richness of genetic diversity was followed by accessions from Shaanxi, Henan, and Xinjiang. The weedy type of Aegilops tauschii showed a close genetic relationship with the wild type from different regions in Iran. The results indicated that the weedy Aegilops tauschii found in the Yellow River region was most likely introduced from Iran—the diversity center of Aegilops tauschii. The weedy Aegilops tauschii populations found in the Yellow River region may be brought into the central part of China as a weed species together with common wheat (Triticum aestivum L.) from the west during various periods of time in history. This finding has provided strong evidence for the introduction of common wheat from the West into China via the Silk Road, and also demonstrated the important role of the Silk Road in the exchange of agriculture and other relevant technologies between China and the West.     

High genetic diversity in population of <Emphasis Type="Italic">Lepturichthys fimbriata</Emphasis> from the Yangtze River revealed by microsatellite DNA analysis

Lepturichthys fimbriata (Günther) is one of the benthic and rock-attached fish species that is typically found in torrential flows of the upper reaches of the Yangtze River in China. Several dams in the Yangtze River (the Ertan Dam, the Three Gorges Dam, the Gezhouba Dam, the Xiluodu Dam and the Xiangjiaba Dam (the latter two dams are under construction)) may have significant effects on the habitat and spawning behaviors of L. fimbriata, and could ultimately threaten the survival of this fish. We studied the population genetic diversity of L. fimbriata samples collected at three sites within the Yangtze River and one of its tributaries, the Yalong River. Genetic diversity patterns were determined by analyzing genetic data from 14 polymorphic microsatellite loci isolated in Jinshaia sinensis (Sauvage et Dabry). A high genetic diversity among these L. fimbriata local populations was indicat- ed by the number of microsatellite alleles (A) and the expected heterozygosity. No reductions of genetic diversity in any L. fimbriata population were observed. However, significant population differentiations were observed among three local populations by pairwise comparisons (P<0.001). We deduced that L. fimbriata local populations were not small ones. In addition, the habitat behaviors of rock-attachment and possible residence of L. fimbriata could account for the genetic differences found in local populations.     

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.     

The yellow sea green tides were dominated by one species, Ulva (Enteromorpha) prolifera, from 2007 to 2011

Green tides have occurred in the Yellow Sea successively from 2007 to 2011. Genetic analysis of the 5-year green-tide-forming algae needs to be performed to determine the source of the biomass and understand the mechanism of the green tide blooms. In this study, free-floating green algae were collected at different sites in the Yellow Sea in 2010 and 2011. Data on 182 free-floating samples and 155 attached Ulva samples from previous studies on the Yellow Sea green tides from 2007 to 2009 were also taken into consideration. Morphology observation and molecular phylogenetic analyses indicated that the Yellow Sea green tides were dominated by a single species, Ulva prolifera, from 2007 to 2011. Considering that at least five Ulva species inhabit the north coast of China, the unialgal composition of the green tides implied that (1) there may be some special physiology and propagation pathways of U. prolifera for its rapid expansion, (2) the mechanisms of the Yellow Sea green tide formation were similar for the last five years, and (3) the intra-species genetic variation and population structure of U. prolifera need to be studied to determine the exact origin of the bloom-forming biomass.     

RAPD Analysis for Genetic Variation within the Endangered Quillwort Isoetes hypsophila （Isoetaceae）

The genetie variation in the critically endangered species Isoetes hypsophila was investigated using Random Amplified Polymorphism DNA (RAPD) markers. Thirteen primers were screened from sixty primers, and a total of 104 DNA fragments were scored, of which, 52 were polymorphic loci. Low-level genetic diversity within populations with PPB values ranging from 7.69% to 25.96% was found. An Analysis of Molecular Variance (AMOVA) indicated that the most of variance (78.30%) occurred between Yunnan and Sichuan. The variances among populations within regions and within populations were only 3.89% and 17.82%, respectively.     

Genetic diversity in the male-specific <Emphasis Type="Italic">SRY</Emphasis> gene of <Emphasis Type="Italic">Lepus yarkandensis</Emphasis>

Lepus yarkandensis, an endemic hare species in the Tarim Basin of China, has been suffering from habitat fragmentation due to desert expansion. To evaluate the effect of habitat fragmentation on its genetic diversity, the genetic diversity based on male-specific SRY gene marker is examined. A relatively low level of SRY genetic diversity is found compared to previous studies with mtDNA data, possibly due to the low SRY mutation rate and positive selection. Furthermore, one haplotype exists in eight populations along the Tarim River but not in many other relatively isolated populations, suggesting that habitat fragmentation may affect population divergence. Despite this, our pairwise Fst analysis shows no significant differentiation among populations, and this may be mainly caused by positive selection on the SRY gene in that 88 percent of individuals share the same haplotype. Finally, the phylogenetic analysis shows deep differentiation between L. yarkandensis and other two hare species (L. capensis and L. europaeus).     

Microsatellite polymorphisms of Sichuan golden monkeys

Previous study using protein electrophoresis shows no polymorphism in 44 nuclear loci of Sichuan golden monkey （Rhinopithecus roxellana）, which limits our understandings of its population genetic patterns in the nuclear genome. In order to obtain sufficient information, we scanned 14 microsatellite loci in a sample of 32 individuals from its three major habitats （Minshan, Qinling and Shennongjia）. A considerable amount of polymorphisms were detected. The average heterozygosities in the local populations were all above 0.5. The differentiations among local populations were significant. There was evidence of geneflow among subpopulations, but geneflow between Qinling and Shennongjia local populations was the weakest. Minshan and Qinling populations might have gone through recent bottlenecks. The estimation of the ratio of the effective population sizes among local populations was close to that from census sizes. Comparisons to available mitochondria data suggested that R. roxellana＇s social structures played an important role in shaping its population genetic patterns. Our study showed that the polymorphism level of R. roxellana was no higher than other endangered species; therefore, measures should be taken to preserve genetic diversity of this species.     

Molecular phylogenetics of <Emphasis Type="Italic">Gymnocypris</Emphasis> (Teleostei: Cyprinidae) in Lake Qinghai and adjacent drainages

149 complete mitochondrial DNA (mtDNA) cytochrome b (Cyt b) genes (1140 bp) of Gymnocypris przewalskii, Gymnocypris eckloni and Gymnocypris scolistomus from the Lake Qinghai, Yellow River and Qaidam Basin were sequenced and analyzed. Consistent dendrogram indicated that the samples collected from the same species do not constitute a separate monophyletic group and all the samples were grouped into three highly divergent lineages (A, B and C). Among them, Lineage A contained all samples of G. przewalskii from the Lake Qinghai and partial samples of the G. eckloni from the Yellow River. Lineage B contained the remaining samples of G. eckloni from the Yellow River. Lineage C was composed of a monophyletic group by G. eckloni from the Qaidam Basin. Analysis of molecular variance (AMOVA) indicated that most of genetic variations were detected within these three mtDNA lineages (93.12%), suggesting that there are three different lineages of Gymnocypris in this region. Our Cyt b sequence data showed that G. przewalskii was not a polytypic species, and G. scolistomus was neither an independent species nor a subspecies of G. eckloni. The divergent mtDNA lineages of G. eckloni from the Yellow River suggested that gene flow between the different populations was restricted to a certain extent by several gorges on the upper reach of the Yellow River. Lineage B of G. eckloni might be the genetic effect from the ancestor which was incorporated with the endemic schizothoracine fishes when the headward erosion of the Yellow River reached to its current headwaters of late. The G. eckloni from Basin Qaidam was a monophyletic group (lineage C) and F_st values within G. eckloni from the Yellow River were higher than 0.98, suggesting that the gene flow has been interrupted for a long time and the G. eckloni from Basin Qaidam might have been evolved into different species by ecology segregation. The correlation between the rakers number of Gymnocypris and population genetic variation was not significant. All Gymnocypris populations exhibited a low nucleotide diversity (π = 0.00096–0.00485). Therefore the Gymnocypris populations from Basin Qaidam could have experienced severe bottleneck effect in history. Our result suggested Gymnocypris populations of Basin Qaidam should give a high priority in conservation programs.     

Process-based modeling analyses of Sabina przewalskii growth response to climate factors around the northeastern Qaidam Basin

Sabina przewalskii is the longest living endemic tree species in the northeastern Tibetan Plateau,and has been widely employed in tree ring based climate research in China.However,most dendroclimatic reconstructions have been primarily based on empirical relationships between tree growth and climate factors identified by statistical assessment.To date,the physiological relationships between tree growth and their limiting climate factors have not been properly assessed.Here,we simulated the physiological response of Sabina przewalskii tree growth to major limiting climate factors based on the Vaganov-Shashkin (VS) model.The VS modeled results validated the relationships between tree ring and climate factors constructed by statistical models,both approaches suggesting that precipitation during the early growing season,especially in May and June,has significant effect on tree growth,while temperature mainly affects tree growth by warming-induced drought and by extending the growing season.Under current and projected climate scenarios,our modeling results predict an increase in radial growth of Sabina przewalskii around the Qaidam Basin,with the potential outcome that regional forests will increase their capacity to sequester carbon.     

2种三疣梭子蟹居群线粒体Cyt b和S-rRNA基因片段序列变异研究

目的：通过对2种三疣梭子蟹居群样线粒体C弘b和S-rRNA基因片段的序列分析,探讨其遗传变异,为种质资源的管理、保存和利用提供依据．方法：采集山东潍坊和福建厦门两个不同居群的三疣梭子蟹样,提取其线粒体DNA．由Genebank获得三疣梭子蟹完整线粒体DNA序列（登陆号：NC_005037）,设计扩增Cyt b和S-rRNA基因片段引物,经PCR扩增获得预期产物,纯化后测序．结果：以提取的线粒体DNA为模板扩增出特异性强的Cyt b和S-rRNA基因片段,与预期条带长度429bp和465bp吻合;2个基因片段的AT含量均高于GC含量;Cyt b基因片段有3个位点发生了突变,S-rRNA只有1个位点发生了突变;在两种居群的4个突变位点中,2个位置突变为相同的碱基,且所有突变位点均呈转换方式．结论：Cyt b基因序列比S-rRNA基因序列具有相对高的突变率;研究的2个基因片段的突变位点的碱基置换主要呈转换方式;来自2个三疣梭子蟹居群样本的线粒体S-rRNA基因的突变发生在同一位点且突变为相同碱基,表明2个居群具有较近的亲缘关系．     

黄河口近岸海域大型底栖动物群落特征

为了解黄河口近岸海域大型底栖生物资源的现状和变化,本研究于2016年8月、11月和2017年5月、8月、11月进行拖网调查。对拖网获得的生物样品进行鉴定,并称重和计数,以获取物种组成、优势物种、生物量和丰度等指标数据。使用优势度计算方法和PRIMER 6.0统计软件对群落特征进行分析。结果共获得大型底栖动物109种,其中甲壳动物37种,鱼类35种,软体动物34种,棘皮动物2种,其他动物(海葵Actiniaria sp.)1种。在该区域发现优势种19种,其中甲壳动物11种,软体动物4种,鱼类4种。黄河口近海大型底栖动物总平均丰度和总平均生物量分别为0.48ind./m~2、1.44g/m~2,均是软体动物贡献率最高。丰富度指数(D)、均匀度指数(J′)和Shannon-Wiener多样性指数(H′)平均值分别为2.44±0.33、0.88±0.03、3.64±0.08。CLUSTER聚类分析和MDS标序分析表明,在40%相似性水平上,每次调查结果可以分为3—5组,各组之间差异显著。黄河口近海大型底栖动物以小个体的甲壳动物、软体动物及低经济价值的鱼类为主,底栖物种有小型化趋势。黄河口近海底栖群落结构差异较大,总体受污染扰动情况明显。     

Genetic consequences of postglacial colonization by the endemic Yarkand hare （Lepus yarkandensis） of the arid Tarim Basin

Orogenesis of the Qinghai-Tibetan Plateau,which occurred in a stepwise manner,contributed to the extreme aridity of the Tarim Basin,resulting in vulnerable and unstable ecosystems.Quaternary climatic oscillations may have affected the ecosystems and,consequently,the distributions and genetic structuring of the Tarim Basin’s biota.We used nucleotide sequence data from 2 mitochondrial (mt) DNA genes (Cyt b and the D-loop) to test hypotheses associated with the matrilineal and demographical histories of the Tarim Basin’s endemic Yarkand hare (Lepus yarkandensis).Range-wide sampling involving 20 populations and 224 individuals detected 126 haplotypes that clustered into 5 major lineages in both the phylogenetic tree and median-joining network.Populations from the northern and eastern Tarim Basin shared a similar history,as did those from the western and southern regions.Demographical analysis and genetic diversity estimations suggested that the western and southern regions might have served as glacial refugia for the Yarkand hare during Quaternary climatic oscillations.The distribution of the Yarkand hare,especially in the northern and eastern parts,probably represented 3 postglacial colonization events,dated to 0.21,0.090 and 0.054 MYA,which corresponded to known interglacial periods.Given the relatively complete geographic isolation between the eastern and southern populations,the Yarkand hare likely dispersed during postglacial periods from the southwest to the north,and then onward to the east.The absence of water likely forced the species into refugia,and this differed from other Pleistocene biogeographical drivers.The demographical and historical patterns have important implications for conservation.     

青海湖裸鲤寄生湟鱼棘头虫的种群季节动态研究

以在青海湖收集的寄生于青海湖裸鲤的湟鱼棘头虫（Ｅｃｈｉｎｏｒｈｙｎｃｈｕｓ ｇｙｍｎｏｃｙｐｒｉｉ）４个季节的样本研究湟鱼棘头虫种群的季节动态,结果表明：种群的平均丰度,感染强度和感染率都没有明显季节变化。这与湟鱼棘头虫温度依赖死亡、中间宿主的季节数量动态,宿主食性的季改变有关。湟鱼棘头虫种群在宿主种群的分布在各季度中都是聚集性的,这与宿主食性的分化及第一中间宿主（钩虾）的分布不均匀性有关。雄虫体     

涉案偶蹄目动物DNA条形码构建

【目的】利用线粒体DNA条形码标记鉴定涉案偶蹄目动物,为解决偶蹄目动物残体、制品的鉴定难题提供技术参考。【方法】对16个偶蹄目动物物种共67份样本,采用试剂盒提取DNA,扩增、测定物种的线粒体DNA的COI基因、Cyt b基因片段;在GenBank上Blast搜索进行同源性分析;利用MEGA 7.0软件分别比较这两个基因片段种内和种间遗传距离,构建系统发育树。【结果】在同源性分析中,西伯利亚狍(Capreolus pygargus)的Cyt b基因片段与GenBank中西伯利亚狍、欧洲狍(Capreolus capreolus)基因序列的同源性均为99.64%~99.82%,该片段不能区分西伯利亚狍与欧洲狍这两个近缘种。其余测序结果与数据库中参考序列一致且相似度较高。对于COI片段,种内遗传距离为0~1.4%,种间遗传距离为1.8%~18.8%。对于Cyt b基因片段种内遗传距离为0~0.5%,种间遗传距离为4.0%~15.8%。两个片段的种内遗传差异均小于种间遗传差异,存在较为明显的条形码间隔。COI和Cyt b基因片段的系统发育树中,同物种的不同个体均能形成具有较高支持度的单分支;不同物种之间界限清晰,每个物种的所有个体均能够形成具有较高支持度的单分支。【结论】基于COI和Cyt b基因片段构建的DNA条形码均可用于对涉案偶蹄目动物的物种鉴定。在物种鉴定中,可采用两个片段联合使用的方式,尤其是对于近缘种的鉴定,以降低错误风险。     

Subspecies in Przewalski’s gazelle Procapra przewalskii and its conservation implication

Przewalski’s gazelle Procapra przewalskii is an endangered species endemic to China. A question remains about subspecific variation in this species. Skulls of Przewalski’s gazelle collected from its current remnant ranges around the Qinghai Lake in combination with those collected prior to the 20th century were measured and analyzed using Hierarchical Cluster Analysis in order to clarify the question. Unexpectedly, P. p. diversicornis, extirpated from its historic range, has spread to the Qinghai Lake region where it has replaced nominotypical P. p. przewalskii and is now restricted to a few small isolated populations around the lake. We discuss the causes of this unexpected replacement. In this study, we discuss the possibility of a new form, possibly a new subspecies, in the Guide Basin, adjacent to Qinghai Lake; it is unclear whether the new form has long existed and was only discovered in recent years, or whether it evolved in recent times due to the geographical isolation and anthropogenic landscape features. The study sheds light on the processes of microevolution and subspeciation in Procapra przewalskii, and based on the findings, we propose measures for conservation strategies for Przewalski’s gazelle.