草兔线粒体基因组全序列及其系统发育关系分析

草兔(Lepus capensis)在我国数量多,分布广,但人们对草兔的系统地理学、草兔与其他兔类的系统发育关系了解不多,其亚种水平的分类也长期存在争议。本研究通过LA-PCR 技术对草兔线粒体基因组全序列进行PCR 扩增、序列测定和分析,并基于线粒体基因组12 个蛋白质编码基因10 776 bp的核苷酸序列,采用贝叶斯法(BI)和最大似然法(ML)构建哺乳纲(Mammalia) 灵长总目(Euarchontoglires)5 个目12 种动物的系统发育关系,结果支持兔形目(Lagomorpha)的单系起源,其中草兔与欧洲野兔(L. europaeus)亲缘关系最近,两者互为姐妹群,进而与家兔(Oryctolagus cuniculus)构成姐妹群关系。此外,基于线粒体细胞色素b 基因全序列,构建31 个兔类个体的系统发育关系,结果显示,草兔与雪兔(L. timidus),云南兔(L. comus) 与高原兔(L.oiostolus),东北兔(L. mandschuricus)与塔里木兔(L. yarkandensis) 有较近的亲缘关系,而在草兔内部,中国的草兔与南非草兔亲缘关系较远,采自江苏盐城的草兔与来自山东、陕西、四川的草兔聚为一支,具有明显较近的亲缘关系。该研究为更好地探讨草兔系统发育关系提供了进一步的分子生物学资料.     

中国狼（Canis lupus chanco）线粒体全基因组序列分析

参照近缘物种线粒体全基因组序列,设计14 对特异引物,采用PCR产物直接测序法测得中国狼线粒体基因组全序列,并分析其基因组特点和各基因的定位.用pDRAW32软件,预测12种限制性酶的酶切图谱.结果表明,中国狼线粒体基因组全长16 774 bp, 包括13 个蛋白质编码基因、2 个rRNA 基因、22 个tRNA 基因和1个非编码控制区.除ND2、 ND3和ND5 基因以ATA作为起始密码子外,其它基因的起始密码子均为ATG.除COXⅢ、 ND4、 ND3基因的终止密码子分别为不完全的T,T,TA;ND2,COXⅡ,Cytb基因的终止密码子分别是TAG、TAG、AGA外;其余基因均以TAA作为终止密码子,而欧亚狼和狗COXⅡ基因则以TAA终止.基于近缘哺乳动物15种近缘物种的线粒体基因组的12S rRNA 和 16S rRNA 基因全序列,用邻近法、最大简约法和最大似然法构建系统进化树,系统进化关系与传统的系统分类基本一致.并在已有文献的基础上,探讨了中国狼的进化地位.     

中国树花线粒体基因组特征及系统发育分析

中国树花是广布于北半球的一种地衣,具有抗病毒、抗菌、抗氧化、抗肿瘤、抗炎和治疗糖尿病等生物活性。本研究首次对中国树花Ramalina sinensis的线粒体基因组进行测序、组装和注释,结果表明其线粒体基因组是一个长度为38 265 bp的环状分子,共编码42个基因(15个蛋白质编码基因(PCGs)、2个rRNA基因和25个tRNA基因),碱基组成具有明显AT偏好性,其中24个tRNA被成功预测为典型三叶草结构。密码子偏好性分析显示该线粒体基因组对A/U结尾的密码子具有明显偏好性。树花科地衣共线性分析没有发现大面积的基因重排现象。与间枝树花R. intermedia的线粒体基因组比较分析显示这2个物种有着较为亲密的适应性进化关系。15个PCGs的Ka/Ks值各不相同,说明这些基因正在接受不同的选择压力。系统发育分析表明中国树花与间枝树花的亲缘关系很紧密。本研究为树花属的资源保护、系统进化以及遗传多样性研究提供基础数据。     

赤狐线粒体全基因组及系统发育分析

测定了赤狐的线粒体基因组全序列,总长度为16 723 bp,碱基组成为：31.3% A、26.1% C、14.8% G、27.8% T。和大多数哺乳动物一样,赤狐的线粒体全基因组包含13个蛋白质编码基因、2个核糖体RNA基因、22个转运RNA基因和1个控制区。除ND3基因起始密码子为不常见的ATT外,赤狐与北极狐、狼、家犬、郊狼的线粒体蛋白质编码遵循相同模式。在控制区的保守序列区段1和2之间发现一段较长的富含AC的随机重复序列。为了验证赤狐与其他犬科动物的系统发育关系,利用12个重链蛋白质编码基因,分别通过邻接法和最大简约法构建了系统发育树。结果表明：赤狐与北极狐是姐妹群,它们在犬科中都属于赤狐型分支,而灰狼、家犬和郊狼则属于狼型分支,与现有的系统进化研究结果一致。     

基于线粒体基因组的藏马高原适应及系统发育分析

研究测定了西藏那曲（4,500m）、云南中甸（3,300m）、云南德钦（3,300m）地区3匹藏马线粒体全基因组序列。3个地区的藏马线粒体基因组全长以及结构均与韩国济州岛的马类似,但比瑞典马线粒体基因组短。藏马基因组在DNA序列上的两两相似性达993％。通过对线粒体蛋白编码区的分析发现,NADH6基因的蛋白序列在三匹藏马中均表现快速进化的现象。这表明NADH6基因在藏马高原适应进化过程中扮演着重要角色。此外,利用7匹藏马的D—loop区域序列以及与其亲缘关系较近的马的序列首次构建的藏马的系统发育树显示,那曲藏马与中甸、德钦藏马属于不同的分支,且存在较大的遗传多样性,表明藏马可能为多地区起源。     

黑茶中“金花菌”线粒体基因组序列测定及系统发育分析

本研究对黑茶中优势微生物“金花菌”线粒体基因序列进行测定与生物信息分析,并探究其与近缘种微生物的系统发育关系。结果表明,“金花菌”线粒体基因组是一条全长77 649bp的环状DNA分子,其ATCG 4种碱基所占比例分别为34.14%、37.64%、15.61%、12.61%,具有显著的A-T偏向性。基因组共编码42个基因（15个蛋白质编码基因,2个rRNA基因和25个tRNA）,与近缘种相比缺失了trnT-TGT且多了1个trnM-CAT拷贝,排列顺序上则较为保守。蛋白质编码基因编码频率较高的氨基酸分别为Leu、Ile、Ser、Phe和Val;RSCU频率最高的4个密码子依次是UUA、AUA、UUU和AAU。25个tRNA基因均可形成典型三叶草结构,并存在有35处G-U错配。系统发育分析表明：与“金花菌”分类地位上最密切是Aspergillus pseudoglaucus。依据菌株形态学与系统发育分析的结果,本研究支持将“金花菌”归类于Aspergillus属并使用A. cristatus这一名称的分类观点。     

象甲科线粒体基因组特征及系统发育分析

昆虫线粒体基因组广泛应用于系统发育关系的重新建立、分子进化、谱系地理学及物种诊断等领域。为揭示象甲科昆虫线粒体全基因组序列的主要结构特征,探究其系统发育相关信息,为进化遗传学研究和分子标记选取等提供参考依据,本研究利用比较基因组学和生物信息学方法,对NCBI上已公布的35种象甲科物种线粒体全基因组序列进行了分析。结果显示:(1)象甲科tRNA基因存在排序及数目异常情况,不同物种中蛋白质编码基因和2种rRNAs排列相同,线粒体全基因组具有明显AT偏向;(2)COX1、ATP6、ND5、ND4、ND4L和ND1基因除标准三联密码子外,还存在特殊的起始密码子AAT、TTG和GTG;(3)13种蛋白质编码基因的进化速率顺序为COX3ATP8ND2ND5ND1ND4ND6ND4LND3ATP6CytbCOX1COX2;(4)13个蛋白编码基因和rRNAs基因中,ND5、rrnL、ND4和ND2基因变异位点数较高,可作为备选的分子标记;(5)各亚科的系统发育关系可能为(((小蠹亚科Scolytinae+长小蠹亚科Platypodinae)+(隐喙象亚科Cryptorhynchinae+魔喙象亚科Molytinae+象虫亚科Curculioninae)+((孢喙象亚科Cyclominae+粗喙象亚科Entiminae)+(隐颏象亚科Dryophthorinae+长小蠹亚科))),为象甲科的系统发育分析有提供参考。     

短尾蝮蛇线粒体基因组全序列分析

参照近缘物种的线粒体基因序列设计并筛选得到8对引物,结合TA克隆和步移测序获得了全长17227bp的短尾蝮蛇线粒体基因组全序列.与多数蛇类线粒体基因组类似,其共编码包括13个蛋白、2个rRNA和22个tRNA在内的37个基因,另外还包含2个非编码的富含AT的控制区.基因间排列紧凑,多数基因间间隔极短甚至发生重叠.除nad1、cox1和nad3外,多数蛋白编码基因均以ATG作为起始密码子,终止密码子的使用则存在TAA、AGA、AGG和不完全的T4种情况.基于合并的19个tRNA基因序列组合数据采用NJ、MP和ME3种算法对21种蛇进行了初步的系统发育分析,结果表明,各主要分类单元之间的亲缘关系与前人基于形态学、线粒体12SrRNA和cytb基因序列研究的结论完全一致,这证实了基于合并的线粒体tRNA基因序列进行蛇类物种DNA分子系统学研究的可行性.     

虾虎鱼类线粒体全基因组序列结构特征分析及系统发育关系探讨

虾虎鱼类体态变异大、体型小、种类多, 形态鉴定及谱系分类较为困难。为深入开展虾虎鱼类的鉴定、分类及遗传进化等研究, 文章对已获得的26种虾虎鱼线粒体全基因组进行分析。结果发现, 虾虎鱼类线粒体基因组的基因组成及排列模式与大多数脊椎动物线粒体基因组特征基本一致; 由于不同物种的控制区存在不同数量的重复序列而导致基因组序列长度存在明显的差异; 26种虾虎鱼线粒体全基因组序列及不同基因中A+T的含量均超过50%, 并存在碱基G偏倚现象。基于37个编码基因序列, 利用Kimura双参数法计算遗传距离, 发现矛尾刺虾虎鱼与斑尾刺虾虎鱼、斑纹舌虾虎鱼与钝吻舌虾虎鱼分别为同种异名。通过对26种虾虎鱼线粒体基因组控制区序列的比较, 识别了终止结合序列区、中央保守区及保守序列区。利用26种虾虎鱼线粒体基因组的36个编码基因序列构建系统发育树, 发现部分聚类结果不同于传统的形态学分类方式, 虾虎鱼科中的5个亚科出现了明显的分化, 近盲虾虎鱼亚科、背眼虾虎鱼亚科、瓢虾虎鱼亚科亲缘关系较近而聚成一大支, 然后与拟虾虎鱼亚科种类形成姐妹类群, 虾虎鱼亚科与其它的4个亚科亲缘关系较远, 单独成为一个类群。根据分子钟估算结果推测虾虎鱼科物种可能起源于始新世晚期至渐新世时段, 在中新世进一步分化为具有现代表征的虾虎鱼种类。     

The complete mitochondrial genome of the Keeled box turtle Pyxidea mouhotii and phylogenetic analysis of major turtle groups

The complete mitochondrial genome （16,837 bp） from the Keeled box turtle （Pyxidea mouhotii） was determined. The genome content, gene order, and base composition conformed to the consensus vertebrate type mtDNA. However, a remarkable feature was found in this molecule： a large number of （ATTATATC） n direct tandem repeats followed by （TA） n microsatellite at the 3＇ end of the control region （D-loop）, which might be useful as molecular markers for studying population genetics and helpful for species identification and conservation. Besides, to review phylogenetic relationships among major turtle lineages, maximum-likelihood （ML） and Bayesian （BI） analyses were conducted based on concatenated sequences of 13 protein-coding genes from 16 taxa. The resultant ML and BI analyses showed homological topologies, which only differed on the exact placement of Platysternon. Nevertheless, the results strongly supported that 1） Pyxidea mouhotii and Cuora aurocapitata formed a monophyletic clade, whereas Cyclemys atripons was not closer to the Pyxidea-Cuora than to Chinemys reevesii, suggesting that Cyclemys and the Cuora group （containing Pyxidea） may have originated from two ancestors; 2） the Geoemydidae with Testudinidae was a sister group rather than with the Emydidae.     

土蜂科线粒体基因组序列测定和分析

【目的】本研究旨在通过针尾部(Aculeata)昆虫线粒体基因组系统发育分析认知土蜂科(Scoliidae)的单系性及系统发育位置。【方法】利用Illumina Hiseq2500二代测序技术测序土蜂科3属5种的线粒体基因组,并进行注释和分析;基于针尾部昆虫36个线粒体基因组13个蛋白质编码基因(protein-coding genes, PCGs)和2个rRNA基因序列采用最大似然法(maximum likelihood, ML)和贝叶斯法(Bayesian inference, BI)法构建系统发育树。【结果】新测序的土蜂科5个线粒体基因组为五带波壁土蜂Colpa quinquecincta线粒体基因组(GenBank登录号：OM103696),齿石波壁土蜂Colpa tartara线粒体基因组(GenBank登录号：OM103697),厚大长腹土蜂Megacampsomeris grossa线粒体基因组(GenBank登录号：OM103796),台湾大长腹土蜂Megacampsomeris formosensis线粒体基因组(GenBank登录号：OM142776)和斯式土蜂Sc...     

Characterization of 59 canine single nucleotide polymorphisms in the Italian wolf (Canis lupus) population

We characterized 59 canine single nucleotide polymorphisms (SNPs) in the endangered Italian wolf (Canis lupus) population, which were discovered by resequencing sequence‐tagged‐site (STS) DNA sequences that are known to contain SNPs in domestic dogs. Dog SNPs were usually found also in wolves. Additional SNPs unique in dogs or wolves were discovered, which is important for detecting hybrids between dogs and wolves. We developed new primer sets and analysed 15 SNPs by Pyrosequencing. The characterized SNPs will provide an important addition to the genetic markers that are currently available for studying wild populations of canids.     

Unexplained patterns of grey wolf Canis lupus natal dispersal

Natal dispersal (movement from the site of birth to the site of reproduction) is a pervasive but highly varied characteristic of life forms. Thus, understanding it in any species informs many aspects of biology, but studying it in most species is difficult. In the grey wolf Canis lupus, natal dispersal has been well studied. Maturing members of both sexes generally leave their natal packs, pair with opposite-sex dispersers from other packs, near or far, select a territory, and produce their own offspring. However, three movement patterns of some natal-dispersing wolves remain unexplained: 1) long-distance dispersal when potential mates seem nearby, 2) round-trip travels from their natal packs for varying periods and distances, also called extraterritorial movements, and often not resulting in pairing, and 3) coincidental dispersal by individual wolves from a given area in the same basic directions and over the same long distances. This perspective article documents and discusses these unexplained dispersal patterns, suggests possible explanations, and calls for additional research to understand them more clearly.     

The complete mitochondrial genome of Paracymoriza prodigalis (Leech, 1889) (Lepidoptera), with a preliminary phylogenetic analysis of Pyraloidea

The complete mitochondrial genome sequence is determined for Paracymoriza prodigalis (Leech, 1889). The 15,326 bp circular molecule possesses a gene organization and order identical to other sequenced Pyraloidea mitochondrial genomes. All tRNAs have the typical clover-leaf structure except for tRNA^Ser(AGN), which lacks the dihydrouridine (DHU) arm. The A+T-rich region of 343 bp includes the features common to the Lepidoptera, including the ‘ATAGA’ followed by an 19-bp poly-T stretch, but the tandem repeat sequences often appearing in available insects are not found. Phylogenetic relationships of eight subfamilies of 14 Pyraloidea species were constructed based on 13 PCGs of mitochondrial genomes using Bayesian inference (BI) and maximum likelihood (ML) methods. These phylogenies of the subfamilies within Pyraloidea accord well with morphological phylogenetic analysis except for the position of Schoenobiinae.     

Complete sequence of the Tibetan Mastiff mitochondrial genome and its phylogenetic relationship with other Canids ( Canis, Canidae)

In this study, the complete sequence of the Tibetan Mastiff mitochondrial genome (mtDNA) was determined, and the phylogenetic relationships between the Tibetan Mastiff and other species of Canidae were analyzed using the coyote (Canis latrans) as an outgroup. The complete nucleotide sequence of the Tibetan Mastiff mtDNA was 16 710 bp, and included 22 tRNA genes, 2S rRNA gene, 13 protein-coding genes and one non-coding region (D-loop region), which is similar to other mammalian mitochondrial genomes. The characteristics of the protein-coding genes, non-coding region, tRNA and rRNA genes among Canidae were analyzed in detail. Neighbor-joining and maximum-parsimony trees of Canids constructed using 12 mitochondrial protein-coding genes showed that as the coyotes and Tibetan wolves clustered together, so too did the gray wolves and domestic dogs, suggesting that the Tibetan Mastiff originated from the gray wolf as did other domestic dogs. Domestic dogs clustered into four clades, implying at least four maternal origins (A to D). The Tibetan Mastiff, which belongs to clade A, appears to be closely related to the Saint Bernard and the Old English Sheepdog.     

内蒙古达赉湖自然保护区狼冬季的生境选择

内蒙古达赉湖自然保护区狼的生境受到了自然环境变化压力和人为干扰的严重影响。为了解内蒙古达赉湖自然保护区狼的冬季生境特征,于2008年10-12月,在内蒙古达赉湖国家级自然保护区对狼的冬季生境选择进行了研究。野外共测量了59个20m×20m样方中的11个生态因子,运用聚类分析和主成分分析法,对狼的冬季生境选择因子进行了分析。结果表明,狼的生境主要特征为:隐蔽程度中等以上,水源距离100m,生境类型为高草阔地、干旱苇塘和河套,植被类型是以芦苇和柳灌丛为优势种的沼泽植被,植被高度1.0m,食物丰富度良好,居民点距离1000m,距草原道路距离1000m,牧场距离500m。影响狼冬季生境选择的主要因子为植被高度、植被类型和隐蔽级。次要因子为距围栏距离、雪深、距水源距离、生境类型、距牧场距离、食物丰富度和距居民点距离。     

Characterization of the complete mitochondrial genome of Cryptotermes domesticus (Blattodea: Kalotermitidae): Genome description and phylogenetic implications

The complete mitochondrial genome of Cryptotermes domesticus (Haviland) was sequenced and annotated to study its characteristics and the phylogenetic relationship of C. domesticus to other termite species. The mitogenome of C. domesticus is a circular, close, and double-stranded molecule with a length of 15,655 bp. The sequenced mitogenome contains 37 typical genes, which are highly conserved in gene size, organization, and codon usage. Transfer RNA genes (tRNAs) also have typical secondary structures. All of the 13 protein-coding genes (PCGs) start with an ATN codon, except for nad4, which starts with GTG and terminates with the terminal codon TAA and TAG or the incomplete form T-- (cox2 and nad5). Most tRNAs have a typical cloverleaf structure, except for trnS1, in which this form is replaced by a simple loop and lacks the dihydrouridine (DHU) arm. The nucleotide diversity (Pi) and nonsynonymous (Ka)/synonymous (Ks) mutation rate ratios indicate that nad1, cox1, and cox3 are the most conserved genes, and that cox1 has the lowest rate of evolution. In addition, an 89 bp repeated sequence was found in the A + T-rich region. Phylogenetic analysis was performed using Bayesian inference (BI) and maximum likelihood (ML) methods based on 13 PCGs, and the monophyly of Kalotermitidae was supported.     

Environmental and social factors influencing wolf (Canis lupus) howling behavior

Animals communicate in a variety of ways and calls are used for a number of important behaviors. Temperature, wind, time of day, and human activities can affect animals’ use of calls, particularly over long distances. Effects of group size on the use of calls can be particularly influential in territorial social carnivores. Where gray wolves (Canis lupus) are hunted by humans, for example, howling may make it easier for hunters to locate individuals and ultimately increase mortality. We hypothesized that a suite of factors would affect wolves’ responses to simulated howling. Specifically, we predicted that howling behavior would increase with (a) group size, (b) pup age, and (c) during crepuscular time periods and howling behavior would decrease (a) where wolves were harvested and (b) when it was hot or windy. Contrary to our prediction, larger groups did not respond as quickly to simulated wolf howls as smaller groups did and minimum and maximum daily temperatures were not good predictors of wolf howling response rates. Individuals in small litters of pups may have responded more quickly to howls than those in large litters because they are eager to seek safety from and have socialization with adults returning from foraging bouts. Although harvest did not appear to affect vocal communication by wolves, group size, pup age, time of day, wind, and number of howls emitted greatly affected wolves’ behavior and responses during howling surveys. Howling responses did not change because of harvest; response rates from wolves were nearly identical with (2.2%) and without (2.3%) harvest. The year-round benefits of long-distance vocal communication may outweigh the costs of increased mortality arising from howling during harvest season.