Sound production by the Shi drum Umbrina cirrosa and comparison with the brown meagre Sciaena umbra: a passive acoustic monitoring perspective

Sounds produced by the Shi drum Umbrina cirrosa were short trains of pulses with an average pulse period of 180 ms, pulse duration of c. 40 ms and an average peak frequency of 400 Hz; average values of acoustical properties differed from those recorded from the brown meagre Sciaena umbra in previous studies. The present study provides a preliminary tool for discriminating between these two species while conducting passive acoustic monitoring. The potential effects of ontogeny on sound production in both species are discussed and recommendations are made for further research.     

Polymorphism of mtDNA regions in brown hare (Lepus europaeus) populations from Vojvodina (Serbia and Montenegro)

It is well known that there is heterogeneity of mitochondrial DNA (mtDNA) within and among natural populations of same species. The polymorphism level of particular regions of mtDNA gives valuable results in detection of population genetic structure. The aim of this paper was to detect polymorphism of three mtDNA regions: cytochrome oxidase I (COI), Control region, and 12S/16S rRNA, by the mtDNA RFLP-PCR method, in three Lepus europaeus populations from Vojvodina province (Serbia and Montenegro). Polymorphism was detected within the two regions, COI and Control region, while 12S/16S rRNA region was monomorphic in all 77 individuals. Eight haplotypes were detected in the brown hare population in Vojvodina, and three were unique for the Srem brown hare population.     

花生根瘤菌群体遗传多样性和系统发育研究

利用16S rRNA RFLP,16S rRNA序列分析和16S－23S IGS PCR RFLP技术对43株花生根瘤菌和来自其他种属的15个参比菌株进行了群体遗传多样性和系统分析。16S rRNA PCR RFLP分析结果表明,所有供试花生根瘤菌均属于慢生根瘤菌属,在系统发育上与B.japonicum的亲缘关系最近,具有相同的16S rRNA RFLP基因型,而与B.elkanii相对较远。16S rRNA 序列分析结果表明,供试花生根瘤菌在系统发育上更接近于B.liaoningense,序列间差异小于1％,而B.liaoningense在系统发育上与B.japonicum相距很近,其序列间差异小于1％,16S－23S rRNA IGS RFLP分析结果表明,尽管花生根瘤菌与B.japonicum和B.elkanii的亲缘关系很近,但在71％的相似性水平上供试花生根瘤菌仍各自聚为一群,并可进一步分为A、B、C和D4个亚群,该分群还明显反映了地理因素对群体遗传多样性和系统发育的影响。     

茜草内生菌的分离鉴定及其抗菌活性物质研究

对中药植物茜草(Rubia cordifoliaL)的内生菌进行了分离和抗菌活性筛选,获得一株具有广谱抗菌活性的内生细菌。该细菌对常见的3种人类病原菌和4种植物病原菌具有拮抗作用。传统分类学和基于16S rRNA基因的分子分类学证据表明,该内生细菌为一株新的枯草芽孢杆菌,命名为Bacillus subtilisRC4。B.subtilisRC4在综合马铃薯培养基(pH值5.0)中于28℃振荡培养60h,产生的代谢物对白色念珠菌的抗菌活性最强。抗菌活性物质在100℃受热20min,活性维持80%以上,且在pH值2.0~11.0范围内稳定。经硅胶柱层析和高效液相色谱分离,得到主要抗菌活性化合物,质谱分析表明其分子量约为288Da。     

产中性纤维素酶耐碱芽孢杆菌的筛选及酶学性质研究

采用CMC碱性平板筛选方法,从造纸厂碱性淤泥中获得产中性纤维素酶的耐碱枯草芽孢杆菌C3004。根据其形态特征、生理生化特性和16S rRNA序列分析鉴定该菌株为枯草芽孢杆菌,并命名为Bacillus subtilis C3004。液体摇瓶培养24 h产生CMC酶活力达46.6 U/mL。酶学性质初步研究显示,CMC酶反应的pH值以7.0左右为适;在弱酸和碱性条件下也具有较高的酶活和一定的稳定性;反应温度以50℃左右为宜;且具有较好的热稳定性。Mn~(2+)与Fe~(3+)对酶反应有促进作用,Cu~(2+)、Mg~(2+)和Zn~(2+)对酶反应有抑制作用。该菌可在碱性(pH 8.5～10)条件下培养,具有不易被杂菌污染的特点。     

基于线粒体16S rRNA基因对中国狼蛛科(Lycosidae)系统发育研究

将自测的中国狼蛛科Lycosidae4亚科6属26种和从GenBank中检索到的北美2种豹蛛的mtD-NA-16S rRNA序列进行比较;以漏斗蛛科1种蜘蛛作为外群,对碱基序列的组成和遗传距离进行了分析,采用Bayesian方法和最大简约法(MP)构建分子系统树。研究结果表明:16SrRNA基因的部分序列为340bp到360bp,A T含量平均为75%,存在较强的A T含量偏向性;序列共有157个碱基存在变异,其中79个简约信息位点。狼蛛科各属间的遗传距离介于0.026￣0.200之间。2种建树方法均表明:科内的属及属内的种优先聚在一起;水狼蛛属相对马蛛属是狼蛛科中较为原始的类群,分化较早;獾蛛属作为1个单系群与熊蛛属合为1个并系,属于狼蛛亚科。狼蛛科6属间的分子系统关系为(Pirata(Hippasa(Trochsa Arctosa(Pardosa Wadicosa))))。     

Genomic analyses of the Formosan harvest mouse (Micromys minutus) and comparisons to the brown Norway rat (Rattus norvegicus) and the house mouse (Mus musculus)

The harvest mouse, Micromys minutus (MMIN), has a very wide range of distribution (from the British Isles across the Euroasian continent to Japan and Taiwan). We studied an isolated population of MMIN in Taiwan, which is at the southeastern margin of the species’ geographic distribution, and compared its genetic complement with those of the same species previously reported from other geographic locations and with two model rodent species, the house mouse (Mus musculus) and the brown Norway rat (Rattus norvegicus). The diploid number (2N) of MMIN was 68, consistent with that reported for other populations. However, variations were noted in the fundamental number (FN) and the shape and banding patterns of the individual chromosomes among populations. The FN of MMIN was estimated to be 72, including 2 bi-armed autosomes, 31 one-armed autosomes, and one pair of one-armed sex chromosomes. Here, we propose the first ideogram for MMIN. C-banding, Ag-NOR, and the locations of 18S rRNA gene sequences (MMIN chromosomes no. 10, 14, 19, 29, 31, 33, and X) mapped by fluorescence in situ hybridization (FISH) are also reported. Additionally, we compared the 18S rDNA sequences and performed cross-species X chromosome painting (FISH) for M. minutus, M. musculus, and R. norvegicus. The results indicate that both genetic elements are rather conserved across species. Thus, implications for the phylogenetic position of Micromys were limited.     

Brief communication: immunoglobulin (Gm and Km) allotypes in two populations of Catalonia (Spain)

Serum samples from two populations of Catalonia, Spain, 208 from Olot (Gerona) and 209 from Tortosa (Tarragona), were typed for G1m (1, 2, 3, 17), G3m (5, 10, 11, 13, 14, 15, 16, 26), and Km (1). The Gm patterns of the Catalonian populations are characterized by the presence of four haplotypes, Gm 1,17;21,26 Gm 1,2,17;21,26 Gm 1,3;5,10,11,13,14,26 and Gm 3;5,10,11,13,14,26. The homogeneity for haplotype Gm 1,17;21,26 among our data and other European populations suggests the existence of an isofrequency line which starts from the Mediterranean zone of Iberian Peninsula and continues through the northwestern part of Europe. From this line a decreasing cline towards the south can be observed. For the haplotype Gm 1,2;17,21,26, affinities are observed between Catalonian populations and other populations from central Europe. This confirms the existence of a gradient towards low values from NW to SE. The presence of the typical Mongoloid haplotype Gm 1,3;5,10,11,13,14,26 is discussed in this paper. No significant differences in the frequencies of the Km1 allele were observed among the European populations.     

斑节对虾两个野生亲虾种群遗传多样性

采用RAPD和mtDNA 16S rRNA基因序列分析方法对海南和马来西亚斑节对虾(Penaeus monodon)种群进行了遗传多样性和遗传分化研究.结果表明:15个RAPD随机引物共检测到82个位点,海南和马来西亚种群的多态位点比例分别为75.90％和76.83％,杂合度分别为0.199和0.218,遗传多样性指数分别为0.276和0.288,种群间的遗传距离为0.015;16S rRNA基因检测的种内遗传变异较低,马来西亚和海南种群的核苷酸多样性分别为0.011和0,种群之间的遗传距离为0.008;马来西亚种群比海南种群的遗传变异水平要高得多,且海南种群可能起源于马来西亚种群;进行遗传选育时可考虑引进马来西亚亲虾作为奠基群体.     

日本囊对虾4个地理群体线粒体16S rRNA序列及遗传结构分析

对我国东南沿海日本囊对虾(Marsupenaeus japonicus)的4个地理群体广东群体(GD)、台湾群体(TW)、福建群体(FJ)和浙江群体(ZJ)的线粒体16S rRNA基因片段进行PCR扩增,对产物进行测序后分析。经比对获得470bp的核苷酸分析序列,发现了16个变异位点,得到了10种单倍型。广东、台湾、福建和浙江群体的核苷酸多样性依次分别为0.0008、0.0010、0.0051、0.0015,各群体均存在独有的单倍型和共有单倍型。群体遗传距离分析表明各群体间保持着一定的遗传差异,其中福建群体与其他群体之间存在着较远的遗传距离并保持了较高的遗传多样性。另外,利用其423bp的16S rRNA同源序列探讨了对虾科6个属共12种对虾的系统进化关系,囊对虾属与沟对虾属亲缘关系较近聚为一支,其他4个属的10种对虾聚为一支。     

Genetic diversity and population connectivity of the Asian green mussel Perna viridis in South China Sea,inferred from mitochondria DNA markers

The Asian green mussel Perna viridis is ecologically and economically important in the coastal regions of China. In order to characterize the genetic diversity and population connectivity of P. viridis in South China Sea, a 664 bp region of mitochondrial COI gene and a 293 bp region of 16S rRNA gene were sequenced and analyzed for 78 and 92 individuals from four populations in South China Sea, respectively. A total of 15 haplotypes were defined by 14 variable nucleotide sites in COI gene, and 7 haplotypes by 6 variable nucleotide sites in 16S rRNA gene. High haplotype diversity and low nucleotide diversity were observed in COI gene, while moderate haplotype diversity and low nucleotide diversity were observed in 16S rRNA gene. Pairwise F_ST values of COI gene were all negative and those of 16S rRNA gene ranged from −0.01409 to 0.10289. The results showed that no significant genetic divergence (or shallow genetic structure) and high levels of population connectivity among the four populations of P. viridis in South China Sea.     

Genetic identity between populations when mutation rates vary within and across loci

A formula is derived for the probability that two genes taken at random from the same locus in two populations isolated at time t ago are of the same allelic type. The model assumed is a neutral one where there are possibly different mutation rates between different alleles. Inequalities are derived for this probability. A particular result is that for a fixed overall mutation rate, the probability is least for the infinite alleles model. Inequalities and approximations are found for Nei's genetic identity at one locus when mutation rates vary, and also for the identity across loci when the overall mutation rates per locus vary. Genetic identity at the molecular level is considered and a probability generating function found for the number of segregating sites between two randomly chosen gametes from two divergent populations, under various models.     

mtDNA analysis reveals the ongoing speciation on Greek populations of Microtus (Terricola) thomasi (Arvicolidae,Rodentia)

The present article extends our previous work on the phylogenetic history of Microtus (Terricola) thomasi, analysing cytochrome b, 12S rRNA, 16S rRNA and the control region in 65 Greek populations. The analysis revealed three clades: one grouping the populations from Peloponnisos (Southern Greece); the second, the populations from Agios (Ag.) Stefanos and Evvoia island (Central East Greece); and the third, all the remaining populations with no geographical substructure. Genetic distances were low for most populations, with only the populations of Evvoia and Ag. Stefanos being substantially distant. Thus, although this species has a recent colonization history and probably descends from a highly polymorphic ancestor, a monophyletic and highly differentiated lineage is formed in Greece and is distributed in Ag. Stefanos and Evvoia. Molecular differentiation, distinct geographical distribution and restriction of gene flow between this lineage and the rest of the Greek populations provide evidence for its probable subspecific status, Microtus (Tericola) thomasi atticus. A possible mechanism leading the differentiation process of the proposed subspecies is suggested, based on the displacement of this species in central Greece by its congeneric, probably better‐fitted Microtus (Microtus) guentheri and the subsequent separation of Ag. Stefanos and Evvoia from the remaining Greek populations. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 117–130.     

基于形态特征和部分基因序列的中国蚱科四个种的分类订正

为了澄清形态相似种锯齿股蚱Tetrix dentifemura和粗体蚱T. grossus及红背悠背蚱Euparatettix erythronotus和九万山悠背蚱E. jiuwanshanensis的分类问题,我们分别从形态学分类和DNA数据对这4种蚱进行了分析。形态学特征分析结果显示：锯齿股蚱和粗体蚱形态相同之处非常多,而形态的不同之处主要表现在两者后翅的长度差异相对较大;红背悠背蚱和九万山悠背蚱在形态上共同之处很多,仅在头顶与颜面隆起的形状、触角与侧单眼着生位置以及后足股节长度等方面有微小差异。对蚱科2属4种昆虫的Cyt b,16S rRNA和18S rRNA基因部分序列进行了测定,3个片段共2 902 bp。发现蚱属的锯齿股蚱和粗体蚱的这三个基因同源序列完全一致,悠背蚱属的红背悠背蚱和九万山悠背蚱的同源序列也完全一致。结合形态学比较和基因序列分析结果,提出粗体蚱和九万山悠背蚱分别是齿股蚱和红背悠背蚱的同物异名。     

Genetic structure of expanding wolf (Canis lupus) populations in Italy and Croatia,and the early steps of the recolonization of the Eastern Alps

After centuries of range contraction and demographic declines wolves are now expanding in Europe, colonizing regions from where they have been absent for centuries. Wolf colonizing the western Alps originate by the expansion of the Italian population. Vagrant wolves of Italian and Dinaric-Balkan origins have been recently observed in the Eastern Alps. In this study we compared the genetic structure of wolf populations in Italy and Croatia, aiming to identify the sources of the ongoing recolonization of the Eastern Alps. DNA samples, extracted from 282 Italian and 152 Croatian wolves, were genotyped at 12 autosomal microsatellites (STR), four Y-linked STR and at the hypervariable part of the mitochondrial DNA control-region (mtDNA CR1). Wolves in Croatia and Italy underwent recent demographic bottlenecks, but they differ in genetic diversity and population structure. Wolves in Croatia were more variable at STR loci (N_A = 7.4, H_O = 0.66, H_E = 0.72; n = 152) than wolves in Italy (N_A = 5.3, H_O = 0.57, H_E = 0.58; n = 282). We found four mitochondrial DNA (mtDNA CR1) and 11 Y-STR haplotypes in Croatian wolves, but only one mtDNA CR1 and three Y-STR haplotypes in Italy. Wolves in Croatia were subdivided into three genetically distinct subpopulations (in Dalmatia, Gorski kotar and Lika regions), while Italian wolves were not sub-structured. Assignment testing shows that the eastern and central Alps are recolonized by wolves dispersing from both the Italian and Dinaric populations. The recolonization of the Alps will predictably continue in the future and the new population will be genetically admixed and very variable with greater opportunities for local adaptations and survival.     

三角帆蚌五个野生群体线粒体DNA 16S rRNA遗传特性

对中国主要淡水湖泊(鄱阳湖、洞庭湖、太湖、洪泽湖及巢湖)三角帆蚌5个野生群体的线粒体DNA 16S rRNA基因片段进行了扩增和测序,得到473bp的碱基序列,没有发现插入/缺失突变的核苷酸位点。检测到了32个多态性核苷酸位点,共7种单倍型。鄱阳湖群体的222(C→G)和325(A→G)位点,太湖群体的233(A→G)位点,巢湖群体的40(A→G)、138(A→T)和294(C→T)位点,洪泽湖群体的241(A→C)位点的变异可以作为区分群体分子遗传标记位点。洞庭湖群体未发现特异位点。在5个群体间鄱阳湖群体多态性位点、核苷酸多态性、单倍型多态性和单倍型数量4个指标都最高,表明鄱阳湖群体具有最为丰富的遗传结构,遗传变异最大,可作为三角帆蚌选育的基础群体。     

从线粒体基因探讨中国大头蛙群的分类及其属内地位

Partial sequences of the mitochondrial 12S rRNA and 16S rRNA gene were determined for 8 populations of three species of Chinese Limnonectes, and aligned with the published sequences of Limnonectes from other parts of the world. When Nanorana parker, Paa boulengeri, Fejervarya limnocharis and Hoplobatrachus rugulosus was used as outgroup taxa (Accession Nos. AY158705, AY313685, AF206111, AF206491, AY322311). The sequences of the 12S rRNA and 16S rRNA genes totaled 950 nueleotide positions with gaps including 510 variable sites. We reconstructed phylogenetie trees using Clustal X 1.8, Mega 2.1 and PHYLIP 3.5e software, and using the maximum parsimony and maximum likelihood methods, respectively. Our analyses suggest that these fanged frogs from China are another monophyletie group in addition to the four monophyletie groups identified by previous studies. The Chinese Limnonectes were grouped into three elades (BCL 55% ). The first elade contains one species (BCL 100% ), from a population of Limnoneetes fragilis from Hainan Province. The second contains four individuals (BCL 100% ), i. e. two populations of Limnonectes kuhlii from Yunnan Province. The third contains one species (BCL 100% ), i. e. five populations of Limnonectes fujianensis from Fujian Province and 1 from Taiwan Province. The resulted phylogenetie trees indicate L. fragilis is basal to L. kuhlii L. fujianensis 。     

Genomic variation in the mitochondrially encoded cytochrome b (MT-CYB) and 16S rRNA (MT-RNR2) genes: characterization of eight endangered Pecoran species

In an effort to develop species-specific identification markers, we examined genetic variants and molecular signatures within genes encoding mitochondrial cytochrome b and 16S rRNA in eight endangered Pecoran species endemic to the Indian peninsula. Our results revealed that the cytochrome b gene exhibited higher sequence diversity than the 16S rRNA gene, both between and within species. However, the 16S rRNA gene harboured a larger number of species-specific mutation sites compared with the cytochrome b gene, suggesting that it could be useful for species identification. Indeed, we successfully used 'forensically informative nucleotide sequencing' (FINS) analysis of the 16S rRNA gene to identify two previously unknown biological specimens.     

不同身体质量指数人群肠道菌群结构及共存网络解析

[背景] 人体能量稳态失衡表现为体重过轻、超重和肥胖,肠道菌群与人体能量稳态的维持有关,但不同身体质量指数（Body Mass Index,BMI）人群的肠道菌群特征仍需进一步探究。[目的] 基于美国肠道计划公开数据库,解析4类BMI人群肠道菌群的特征,并探究4类BMI人群肠道菌群共存网络特征及差异,为基于肠道菌群来干预肥胖及体重过轻等不健康状态提供新的理论依据。[方法] 从美国肠道计划数据集中筛选具有BMI信息的肠道菌群样本,并根据世界卫生组织规定的BMI划分标准将筛选后的样本分为4类：体重过轻（BMI<18.5 kg/m²）,正常体重（18.5 kg/m²2）,超重（25 kg/m²2）,肥胖（BMI>30 kg/m²）;通过计算和比较肠道菌群的α多样性和β多样性探究4类BMI人群肠道菌群的整体结构特征及差异;通过多元线性回归模型对不同BMI分类与肠道菌群进行相关性分析,并且将地域、年龄、性别因素作为混杂因素加入到模型中进行校正;采用SparCC分别计算4类BMI人群肠道菌群中菌属相关性,并分别构建肠道菌群共存网络。[结果] 经过Wilcoxon秩和检验,发现体重过轻、超重、肥胖人群的肠道菌群α多样性都显著低于正常体重人群;β多样性分析结果表明4类BMI人群肠道菌群的整体结构存在显著差异;4类BMI人群肠道中厚壁菌门（Firmicutes）和拟杆菌门（Bacteroidetes）的相对含量无显著差异;通过MaAsLin分析,并且将地域、年龄、性别因素作为混杂因素加入到模型中进行校正,共得到49个与BMI类型显著相关的物种;4类BMI人群肠道菌群共存网络的拓扑结构具有一定差异,体重过轻和正常体重人群肠道菌群共存网络的复杂度较高,超重和肥胖人群肠道菌群共存网络的复杂度较低。[结论] 4类BMI人群肠道菌群的多样性、整体结构和共存网络间均存在差异。