Human-specific changes of genome structure detected by genomic triangulation

Knowledge of the rhesus macaque genome sequence enables reconstruction of the ancestral state of the human genome before the divergence of chimpanzees. However, the draft quality of nonhuman primate genome assemblies challenges the ability of current methods to detect insertions, deletions, and copy-number variations between humans, chimpanzees, and rhesus macaques and hinders the identification of evolutionary changes between these species. Because of the abundance of segmental duplications, genome comparisons require the integration of genomic assemblies and data from large-insert clones, linkage maps, and radiation hybrid maps. With genomic triangulation, an integrative method that reconstructs ancestral states and the structural evolution of genomes, we identified 130 human-specific breakpoints in genome structure due to rearrangements at an intermediate scale (10 kilobases to 4 megabases), including 64 insertions affecting 58 genes. Comparison with a human structural polymorphism database indicates that many of the rearrangements are polymorphic.     

基于Cytb基因的东印度洋鸢乌贼系统发育关系和种群遗传结构

通过测定东印度洋北部、赤道、南部3个鸢乌贼（Sthenoteuthis oualaniensis）群体的线粒体DNA细胞色素b（Cytb）基因序列,分析了东印度洋鸢乌贼的系统发育关系。研究表明,东印度洋鸢乌贼整体具有高单倍型多样性（h=0.939）和高核苷酸多样性（π=0.015）。3个鸢乌贼群体间的F_st值为0.661,群体间遗传分化水平很高,具有明显的遗传分化现象,可分为以东印度洋北部群体为主的谱系1（东印度洋北部谱系）和主要由东印度洋赤道与南部群体组成的谱系2（东印度洋南部谱系）,且谱系2经历过群体扩张。东印度洋巨大的南北水文差异可能是鸢乌贼产生南北谱系分化的原因,在东印度洋鸢乌贼资源的利用和管理方面应考虑南北谱系的差异和特点。     

动物园环境丰容对恒河猴行为的影响

为了探索环境丰容对恒河猴行为的影响,对比观察研究了山西阳泉南山公园动物园猴山环境丰容条件和单独笼养的恒河猴行为的变化,发现环境丰容对恒河猴有明显影响,表现在丰容环境条件下恒河猴积极行为增加,消极和异常行为减少,结果表明实施环境丰容有利于恒河猴天性的恢复与展示。     

Microchronology and demographic evidence relating to the size of pre-columbian north american Indian populations

Recent estimates for the size of the aggregate North American Indian population in A.D. 1492 vary from about 18 million to less than 2 million. The unusually favorable archaeological characteristics of Mohawk Iroquois sites in eastern New York have allowed a detailed demographic reconstruction of one case for the period A.D. 1400 to 1776. The case indicates that exogenous epidemics did not reach the region until the 17th century and supports arguments favoring the lower populations estimates for North America as a whole.     

Exploring the genetic features and signatures of selection in South China indigenous pigs

To explore the genetic features and signatures of selection in indigenous pigs from South China and Duroc pigs, 259 pigs from six populations were genotyped using single-nucleotide polymorphism(SNP) BeadChips. Principal component analysis(PCA), effective population size(Ne), linkage disequilibrium(LD), and signatures of selection were explored and investigated among the six pig populations. The results showed the Ne of five South China indigenous pig populations has been decreasing rapidly since 100 generations ago. The LD between pairwise SNP distance at 100 kb ranged from 0.16 to 0.20 for the five indigenous pig populations, while it was 0.32 for the Duroc population. However, the LD of all six pig populations showed the opposite order at long distances(5 Mb). Furthermore, 15 potential signatures of selection associated with meat quality and age at puberty were exclusively detected in South China indigenous pigs, while eight potential signatures of selection associated with growth traits were detected in Duroc pigs. Our work provides valuable insights for the utilization and conservation of South China indigenous pigs.     

中国野生大豆群体特征和地理分化的遗传分析

【目的】从分子标记等位变异水平上探讨中国野生大豆群体的遗传特征、连锁不平衡特点和地理生态分化的遗传机制,并以重要生态性状全生育期为代表解析性状地理分化的遗传基础。【方法】从全国24个省区不同地理生态型的野生大豆材料中抽选174份组成代表性样本,选用204个SSR标记,利用TASSEL及STRUCTURE 2.2软件进行群体连锁不平衡（linkage disequilibrium,LD）和群体遗传结构分析。在此基础上对群体的地理分化、亚群体特异性及全生育期位点等位变异的地理分化进行遗传分析。【结果】中国野生大豆群体蕴含丰富的遗传变异,20条连锁群中,I和C2连锁群有相对较多的位点平均等位变异和遗传分化。不论是共线性组合,还是非共线性组合,都有一定程度的LD存在,说明历史上发生过连锁群间的大量重组;野生群体D ′平均值为0.34,高值多,比栽培大豆高,说明野生群体发生过更多的重组,保留下较高的LD。采用H-W平衡模型将野生群体聚成4类,模型聚类亚群划分与地理生态分类相关、有交叉,推测各地理亚群体发生过材料的迁移。各地理亚群经长期自然选择,各位点等位基因的频率发生变化,还有新生的与绝灭的,因此,各地理亚群间产生明显的等位基因分化。与地理生态性状全生育期关联的有15个位点160个等位变异,其中,亚群特有等位变异共58个,来自14个位点,同一位点可以在多个亚群体产生不同的特有等位变异,其效应从南至北逐渐下降,这说明生态区间不仅有强烈的遗传分化,而且是有规律的遗传分化。【结论】中国野生大豆群体遗传多样性高,共线、非共线位点间连锁不平衡程度高,4个生态亚群体间位点高度遗传分化,产生大量地区特有等位变异,全生育期还表现由南向北降效的规律性遗传分化。     

云杉天然群体基因分化与种质资源异地保存抽样策略

采用聚丙烯酰胺垂直板凝胶电泳和水平淀粉凝胶电泳对云杉全分布区10个天然群体的300个个体进行酶电泳分析,研究天然群体的等位基因数量和频率分化,共测定8种酶系统,得到17个清晰酶位点和27个等位基因.10个群体检测到的等位基因数均值为24.7个(变幅为23～27个).据基因频率进行分类,检测到全域基因和广域基因数量分别为19个和7个,分别占总基因的70.37%和25.93%;特有基因只有1个,即铁布群体的Idh-2-C,占总基因的3.7%.10个群体基因频率的均值没有太大差异,相同位点的广域基因频率在群体间均存在差异.通过计算机模拟建立云杉天然群体种质资源保存的群体和群体内个体两个层次的基因捕获曲线.群体的等位基因频率与地理生态因子的相关分析表明:Fdh-2-B基因频率与生态梯度值呈显著负相关(r=-0.661 1*).构建了云杉天然群体核心种质保存的抽样策略,经综合分析,抽取全分布区内铁布、卓尼、阿坝、小金、热务沟、凤县和曲谷7个群体,每个群体保存25个拟式无亲缘关系的个体,可以保护云杉种内95%～99%的基因资源.     

Molecular Diversity and Association Analysis of Drought and Salt Tolerance in Gossypium hirsutum L. Germplasm

Association mapping is a useful tool for the detection of genes selected during plant domestication based on their linkage disequilibrium (LD). This study was carried out to estimate genetic diversity, population structure and the extent of LD to develop an association framework in order to identify genetic variations associated with drought and salt tolerance traits. 106 microsatellite marker primer pairs were used in 323 Gossypium hirsutum germplasms which were grown in the drought shed and salt pond for evaluation. Polymorphism (PIC=0.53) was found, and three groups were detected (K=3) with the second likelihood ΔK using STRUCTURE software. LD decay rates were estimated to be 13-15 cM at r2 0.20. Significant associations between polymorphic markers and drought and salt tolerance traits were observed using the general linear model (GLM) and mixed linear model (MLM) (P 0.01). The results also demonstrated that association mapping within the population structure as well as stratification existing in cotton germplasm resources could complement and enhance quantitative trait loci (QTLs) information for marker-assisted selection.     

西南部分地区圈养非人灵长类贾第虫感染情况调查及多位点基因序列分析

为了解西南部分地区非人灵长类贾第虫的感染情况及其集聚体和基因亚型分布,收集了西南地区部分动物园、养殖场以及试验动物养殖基地的207份猕猴、长臂猿、金丝猴和食蟹猴新鲜粪便,采用饱和蔗糖漂浮法处理样品,提取DNA,经巢式PCR扩增β-giardin(bg)、tpi和gdh基因,扩增产物经测序后进行分子生物学分析。结果表明:西南部分地区圈养非人灵长类贾第虫感染率为7.73%(16/207),16份阳性样品均为集聚体B(assemblage B)。感染的品种包括猕猴、长臂猿及食蟹猴。长臂猿感染率最高(38.89%),不同品种非人灵长类贾第虫感染率差异极显著(P<0.01)。所有阳性样品均成功扩增出bg、tpi和gdh三个基因的特异性产物。多位点基因序列分析和种系进化树分析结果显示,bg及tpi基因位点多态性变异明显,gdh位点多态性变异较小。本次调查结果表明,西南部分地区非人灵长类所携带的贾第虫具有人兽共患风险。     

Mobile DNA in Old World monkeys: a glimpse through the rhesus macaque genome

The completion of the draft sequence of the rhesus macaque genome allowed us to study the genomic composition and evolution of transposable elements in this representative of the Old World monkey lineage, a group of diverse primates closely related to humans. The L1 family of long interspersed elements appears to have evolved as a single lineage, and Alu elements have evolved into four currently active lineages. We also found evidence of elevated horizontal transmissions of retroviruses and the absence of DNA transposon activity in the Old World monkey lineage. In addition, approximately 100 precursors of composite SVA (short interspersed element, variable number of tandem repeat, and Alu) elements were identified, with the majority being shared by the common ancestor of humans and rhesus macaques. Mobile elements compose roughly 50% of primate genomes, and our findings illustrate their diversity and strong influence on genome evolution between closely related species.     

Properties of gamma-ray burst progenitor stars

We determined some basic properties of stars that produce spectacular gamma-ray bursts at the end of their lives. We assumed that accretion of the outer portion of the stellar core by a central black hole fuels the prompt emission and that fall-back and accretion of the stellar envelope later produce the plateau in the x-ray light curve seen in some bursts. Using x-ray data for three bursts, we estimated the radius of the stellar core to be approximately (1 - 3) x 10(10) cm and that of the stellar envelope to be approximately (1 - 2) x 10(11) cm. The density profile in the envelope is fairly shallow, with rho approximately r(-2) (where rho is density and r is distance from the center of the explosion). The rotation speeds of the core and envelope are approximately 0.05 and approximately 0.2 of the local Keplerian speed, respectively.     

Different mutations in Ashkenazi Jewish and non-Jewish French Canadians with Tay-Sachs disease

Tay-Sachs disease patients of Ashkenazi Jewish and non-Jewish French Canadian origin are affected with a clinically identical form of this inherited disease. Both have a similar gene frequency for the disorder, which is tenfold higher than that found in the general population. Unlike other patients with the disease, who often display variation at the clinical or biochemical level, the absence of such differences between these two groups has prompted the idea that they may harbor the same mutation. In this report, a complementary DNA clone coding for the alpha chain of human beta-hexosaminidase has been used to analyze the genetic lesions in the alpha-chain locus of two patients with Tay-Sachs disease from each of these groups. On the basis of DNA hybridization analyses, the alpha-chain gene of the Ashkenazi patients appears intact while the alpha-chain gene of French Canadian patients has a 5' deletion of approximately 5 to 8 kilobases.     

陕南卷丹10个野生种群数量性状变异分析

为揭示陕南地区卷丹Lilium lancifolium野生种群的表型变异程度和规律, 以该区10个有代表性的卷丹野生种群, 每个种群30个个体为试材, 对其茎、叶、花的茎粗、叶片数、着花量等16个数量性状指标进行方差分析、相关性分析及聚类分析, 探讨种群间及种群内表型多样性的变异特点。结果表明:①卷丹数量性状在种群间和种群内均存在一定程度的变异, 不同性状的平均变异系数为2.07%(花丝长)~35.38%(着花量), 种群间的平均变异系数为7.52%(汉台区天台山乡种群)~17.18%(城固县石槽河乡种群)。②相关性分析表明, 着花量(r=0.684, P < 0.05, n=10), 外瓣宽长比(r=0.651, P < 0.05, n=10), 柱头宽(r=0.729, P < 0.05, n=10)与海拔高度有显著正相关性, 中部叶宽长比(r=-0.743, P < 0.05, n=10), 花丝长(r=-0.795, P < 0.01, n=10)与海拔高度有显著负相关性; 且茎秆高度(r=0.733, P < 0.01, n=10), 叶片数(r=0.718, P < 0.01, n=10), 着花量(r=0.752, P < 0.01, n=10)与生境有显著正相关性, 上部叶宽长比(r=-0.707, P < 0.05, n=10), 内瓣宽长比(r=-0.681, P < 0.05, n=10)与生境有显著负相关性; ③Q聚类分析显示, 陕南地区10个卷丹野生种群可以初步分为2组, 汉台区天台山乡种群单独为一组。     

乌拉山自然保护区白桦种群的年龄结构和点格局分析

白桦群落是乌拉山森林植被的主要类型之一,在高海拔阴坡、半阴坡以纯林形式分布.根据乌拉山自然保护区白桦林不同林龄结构设置3个典型样地,采用种群径级结构代替年龄结构、点格局分析(Ripley''s K-Function)方法探讨了乌拉山白桦种群年龄结构、空间分布规律和种群动态.结果表明:(1)乌拉山自然保护区白桦种群径级结构呈典型的“金字塔”型,种群自然更新良好,属增长型种群;(2)由于种内不同个体间为争夺空间和资源,种群在第Ⅲ、Ⅳ径级死亡率较高,自疏作用明显;(3)白桦种群的存活曲线接近于Deevey Ⅰ型曲线;(4)在研究尺度内白桦种群以幼树、中龄树为主时呈聚集分布,而成龄树或老龄树占多数时呈随机分布,即随着种群年龄的增加,其分布格局逐渐由集群分布向随机分布转变.乌拉山白桦种群在小于1.5m的尺度呈聚集分布,即具有2株以上个体“丛生”现象.在环境条件相似的情况下,白桦种群自身的生物、生态学特性是影响其分布格局的最主要因素.     

Estimates of mass and angular momentum in the oort cloud

Estimates can be made of unseen mass (in the form of cometary nuclei) at the heliocentric distances between 3 x 10(3) and 2 x 10(4) astronomical units(AU) under the assumptions (i) that the Oort cloud is a rarefied halo surrounding the core (dense, inner cometary cloud) and (ii) that the mass and albedo of comet Halley is typical for comets both in the core and the Oort cloud populations. The mass appears to be approximately 0.03 solar masses, with angular momentum of the order of 10(52) to 10(53) g-cm(2)/s. This mass is of the order of the total mass of the planetary system before the loss of volatiles. This leads to an estimate of a mass M(o) approximately 100 M( plus sign in circle) (where M( plus sign in circle) is the mass of Earth) concentrated in the Oort cloud (r > 2 x 10(4) AU) with an angular momentum that may exceed the present angular momentum of the whole planetary system by one order of magnitude. The present angular momentum of the Oort cloud appears to be of the same order as the total angular momentum of the planetary system before the loss of volatiles.     

Prevention of vaginal SHIV transmission in rhesus macaques through inhibition of CCR5

Topical agents, such as microbicides, that can protect against human immunodeficiency virus (HIV) transmission are urgently needed. Using a chimeric simian/human immunodeficiency virus (SHIV SF162), which is tropic for the chemokine receptor CCR5, we report that topical application of high doses of PSC-RANTES, an amino terminus-modified analog of the chemokine RANTES, provided potent protection against vaginal challenge in rhesus macaques. These experimental findings have potentially important implications for understanding vaginal transmission of HIV and the design of strategies for its prevention.     

马拉硫磷对东亚飞蝗不同种群遗传结构的分化研究

以接近于LD50的马拉硫磷处理东亚飞蝗Locustamigratoriamanilensis(Meyen)天津北大港和山东无棣种群个体,用SSRP-PCR标记技术分析检验东亚飞蝗在不同选择压力下,存活个体与死亡个体的基因型与马拉硫磷致死作用的可能相关关系。结果表明,无棣种群死亡组的多态性明显高于存活组,而北大港种群存活组的多态性高于死亡组,北大港群体的多态性高于无棣群体。各多态位点与马拉硫磷致死性相关性检测表明:第一,相同引物的不同位点对马拉硫磷的敏感性不同,不同种群对马拉硫磷致死性存在相关性的位点不同;第二,不同处理的东亚飞蝗在同一引物扩增出的同一位点对马拉硫磷毒性的反应不同。这些结果表明,马拉硫磷对东亚飞蝗在不同引物扩增的不同位点有选择致死作用。Nei’s遗传距离值在两个种群中都是在死亡组和存活组最高,表明马拉硫磷对东亚飞蝗种群的遗传结构产生了一定的分化作用。     

利用ISSR标记对天麻的贵州种群遗传多样性分析

摘要:该文利用ISSR分子标记技术,对分布于贵州的药用植物天麻的9个种群的遗传多样性水平和遗传结构进行分析,为传统的中药材天麻的遗传、育种及种质资源的保护和合理利用提供依据.该研究用12条ISSR引物共扩增出120条大小在200～1 600 bp清晰的谱带,其中97条具有多态性,总的多态位点百分率为80.83%,表明在物种水平上有较高的遗传变异;种群水平的多态性相对较低,多态百分率在17.5%～40.83%,平均25.56%.用POPGENE软件计算各种群间和种群内的遗传参数,结果表明:物种水平上的Nｅｉ’ｓ遗传多样性（He）为0.042～0.153,平均0.073; Shannon信息指数为0.332 6±0.224 1;Nｅｉ’ｓ基因分化系数（Gst）为0.637 7,表明种群间的遗传变异占总变异的63.77%,而种群内的遗 传变异占总变异的36.23%,这与有限的基因流有关;而种群间有限的基因流（Ｎｍ=0.284 1）可能是由于种子的传播距离、种子极低的生活率以及种群间的地理隔离和营养繁殖等因素所致.      

Demographic characteristics and population dynamical patterns of solitary birds

In birds and many other animals, there are large interspecific differences in the magnitude of annual variation in population size. Using time-series data on populations of solitary bird species, we found that fluctuations in population size of solitary birds were affected by the deterministic characteristics of the population dynamics as well as the stochastic factors. In species with highly variable populations, annual variation in recruitment was positively related to the return rate of adults between successive breeding seasons. In stable populations, more recruits were found in years with low return rates of breeding adults. This identifies a gradient, associated with the position of the species along a "slow-fast" continuum of life history variation, from highly variable populations with a recruitment-driven demography to stable, strongly density-regulated populations with a survival-restricted demography. These results suggest that patterns in avian population fluctuations can be predicted from a knowledge of life-history characteristics and/or temporal variation in certain demographic traits.     

湖北省棉花黄萎病菌致病力分化和遗传多样性分析

测定了源于湖北省棉区的15个棉黄萎病菌单孢菌株（简称湖北菌株）和2个落叶型棉黄萎病菌菌株T9和V991对4个棉花品种上的致病力。采用随机引物聚合酶链反应（RAPD）技术分析了这些菌株的遗传多样性。结果表明：供试的17个棉黄萎病菌之间的致病力存在显著差异（P〈0．05）。在各个棉花品种上,15个湖北菌株中都有致病力与T9或V991的致病力差异不显著的菌株。综合分析表明：菌株T9的致病力最强,6个湖北菌株的致病力相当或强于菌株V991,7个湖北菌株的致病力中等,2个湖北菌株的致病力较弱。4个供试棉花品种中中棉12较耐黄萎病。RAPD分析表明供试的27个随机引物（10碱基）中10个可以从17个菌株的基因组DNA中稳定地扩增出多态性DNA片段。对扩增片段统计结果表明,供试菌株间遗传相似系数变化幅度为0．37～1．00。聚类分析表明,在阈值0．68处,17个黄萎病菌菌株可划分为2个RAPD群（RAPD group,简称RG）,湖北省的9个菌株和V991属于RG1,另外6个菌株和T9属于RG2。综合以上结果可以看出湖北省的棉黄萎病菌种群存在着明显的致病力分化和丰富的遗传多样性。