鹟科五种鸟线粒体DNA序列变化与亲缘关系的研究

首次对鹟科（Muscicapidae）画眉亚科三种鸟----画眉（Garrulax canorus）、红嘴相思鸟（Leiothrix lutea）、棕头雅雀(Paradoxornis webbiana);鸫亚科的乌鸫（Turdinae merula）线粒体DNA的12S rRNA基因片段的DNA序列进行了测定,并与北美画眉亚科弯嘴鹛属（Pomatostomus）的灰冠弯嘴鹛（P.temporalis）同源序列进行分析比较并构建分子进化树。实验结果与传统形态学论述存在一定的差异,与同工酶研究结果相同：画眉与红嘴相思鸟的亲缘关系最近,棕头鸦雀较乌鸫与画眉亚科的关系更近,为将其置于画眉亚科提供了分子证据。 Abstract：The classfication on Muscicapinae disturbed us for a long time.The important thing is to find an appropriate character to resolve it.It is the first time that we testified the mitochondrial 12S rRNA gene fragment sequence of four birds (G.canorus,L.lutea,P.webbianus and T.merula-owing to Muscicapinae) and aligned with the same sequence of P.temporalis.Using the mitochondrial 12S rRNA sequences date,we built phylogenetic trees.The results indicated that that the relationship between Garrulax canorus and Leiothrix lutea in the four birds was closer which is congruent with morphology.According to the results of isoenzyme and DNA sequencing data,we can draw a conclusion that Paradoxornis webbianus has closer relationship to Timaliinae than that of Turdus merula,and that putting Paradoxonithinae to Timaliinae was reasonable.     

画眉科鸟类系统发育及分类地位商榷

原记录在中国有分布的鹛类计142种,占世界鹛类纪录种总数284种的50%.由于该类群的种类繁多,形态和生态习性多样,其分类问题历来受分类学者的关注,且争议较大.本文尝试以分子生物学手段来解决传统分类中遗留的问题.在系统发育分析中共有20属59种鹛类作为内群、14个相关物种作为外群,分子标记分别采用线粒体细胞色素b(Cty 6,846 bp)和核内重组引导基因(RAG-1,870 bp),以最大似然法和贝叶斯法重建系统发育树.结果表明,画眉科鸟类明显被分为2大支系,一支由噪鹛Garrulax、希鹛Minla、薮鹛Liocichla、相思鸟Leiothrix、奇鹛Heterophasia、穗鹛Stachyris、钩嘴鹛Pomatorhinus、凤鹛Yuhina、及部分雀鹛Alcippe等属的种类构成,另一支由鸦雀属Paradoxornis和山鹛Rhopophilus pekinensis、及部分雀鹛属的种类构成,2支都有相当高的支持率;各个属之间的相互关系大致得到解决,传统分类体系中噪鹛属、雀鹛属、鸦雀属、凤鹛属、穗鹛属的单系性不能成立;证实绣眼鸟属Zosteropidae、山鹛和林莺属Sylvia鸟类的亲缘关系较近,而白腹凤鹛Yuhina.zantholeuca、鹏鹛属Pteruthius和文须雀Panurus biarmicus与鹛类的亲缘关系较远;并提出小鳞胸鹪鹛Pnoepyga pusilla有可能不是画眉科种类,其分类地位需要重新认识.     

繁殖期贵阳本地鸟类贸易现状

动物贸易是生物多样性丧失的重要原因,在物种的繁殖期进行捕捉和贸易对种群更是不利。为分析和评价贵阳本地鸟类在繁殖期间的生存现状和保护需求,于2014年3—6月调查了贵阳市油榨街花鸟市场上被交易的鸟类。共记录到114种当地鸟类,种数超过贵阳当地鸟类总数的50%,其中7种为保护物种。用于"斗鸟"的灰喉鸦雀Paradoxornis alphonsianus被交易的数量最高,画眉Garrulax canornus、红嘴相思鸟Leiothrix lutea、暗绿绣眼鸟Zosterops japonicas、红尾水鸲Rhyacornis fuliginosus和黄喉鹀Emberiza elegans等数量次之。接近80%的陆栖或半陆栖的鸟类及其雏鸟在繁殖期间都面临着很高的被捕捉风险。除了开展人工繁育,还建议开展野生鸟类的性别识别和性比研究,以减少野生雌鸟的损失和评价鸟类物种保护的优先性,同时加大宣传,将笼养鸟类者发展为支持鸟类研究和保护的重要力量。     

The single nucleotide polymorphisms of the chicken myostatin gene are associated with skeletal muscle and adipose growth

Myostatin, a new member of the TGF-p superfamily, is predominantly expressed in skeletal muscle cells and functions as a negative regulator of skeletal muscle growth in animals. Recently, we have reported three single nucleotide polymorphisms (SNPs) in the chicken my-ostatin gene. Herein, we investigate the association of those SNPs with the production traits in a F2 chicken line derived from Broilers crossing to Silky with the least square analysis. The results show that the BB and AA genotypes are strongly associated with abdominal fat weight (AFW), abdominal fat percentage (AFP), and birth weight (BW) (P < 0.05). Breast muscle percentage (BMP) of the AA type is higher than that of the AB type. The breast muscle weight and breast muscle percentages of F2 individuals have significant difference between CC and DD genotypes (P< 0.05). Breast muscle weight (BMW) of EF birds is higher than that of EE birds (P< 0.05). In this report, we present the first genetic evidence to show that chicken myostatin not o     

Bioinspired 4D Trajectory Generation for a UAS Rapid Point-to-Point Movement

A bioinspired trajectory generation approach for Unmanned Aerial System （UAS） rapid Point-to-Point （PTP） movement was presented. The approach was based on general tau theory developed by biologists from observing and studying the behavior of birds and some other animals. We applied the bioinspired approach to the rapid PTP movement problem of a rotary UAS and derived two different trajectory planning strategies, namely, the tau coupling strategy and the intrinsic tau gravity guidance strategy. Based on general tau theory, according to the dynamic model of UAS, we presented a new strategy named intrinsic tau jerk guidance which can fit the movement that the initial acceleration of the UAS is zero. With new strategies, flight trajectory generation examples with a UAS were presented. The kinematics and dynamics analyses of the UAS for rapid PTP movement were presented with simulation results which show that the generated trajectories were feasible.     

幼龄红嘴相思鸟小脑皮层组织学结构

为了探讨不同日龄幼龄红嘴相思鸟（Leiothrix lutea）小脑皮质的组织学结构变化,本文分别以1、5、9日龄幼龄红嘴相思鸟为研究对象,通过H.E.和甲苯胺蓝法进行染色,光镜下观察红嘴相思鸟小脑冠状切面的显微结构。结果显示,1日龄时小脑皮层由外颗粒层（EGL）、浦肯野细胞层（PCL）和内颗粒层（IGL）3层构成,外颗粒层较厚且清晰,而浦肯野细胞层和内颗粒层界限不清楚;5日龄和9日龄时小脑皮质均可见外颗粒层、分子层（ML）、浦肯野细胞层和内颗粒层4层结构。对不同日龄红嘴相思鸟小脑皮质各层厚度进行单因素方差分析显示,随日龄增长,小脑皮质、分子层和内颗粒层厚度极显著增厚（P < 0.01）,浦肯野细胞体积也极显著增加（P < 0.01）;外颗粒层厚度变化不明显（P < 0.01）,呈现先增厚后变薄的趋势,与皮质厚度的比例逐渐减小。研究表明,幼龄红嘴相思鸟在出生后,随日龄增长,小脑皮质层逐渐发育成熟。内颗粒层与外颗粒层的相对变化规律表明内颗粒层细胞是由外颗粒层细胞迁移而来。     

Nelumbonaceae:Systematic position and species diversification revealed by the complete chloroplast genome

<正>Nelumbonaceae is a morphologically unique family of angiosperms and was traditionally placed in Nymphaeales;more recently,it was placed in Proteales based on molecular data,or in an order of its own,Nelumbonales. To determine the systematic position of the family and to date the divergence time of the family and the divergence time of its two intercontinentally disjunct species,we sequenced the entire chloroplast genome of Nelumbo lutea and most of the chloroplast genes of,N.nucifera.We carried out phylogenetic and molecular dating analyses of the two species and representatives of 47 other plant families,representing the major lineages of angiosperms, using 83 plastid genes.The N.lutea genome was 163 510 bp long,with a total of 130 coding genes and an overall GC content of 38%.No significant structural differences among the genomes of N.lutea,Nymphaea alba, and Platanus occidentalis were observed.The phylogenetic relationships based on the 83 plastid genes revealed a close relationship between Nelumbonaceae and Platanaceae.The divergence times were estimated to be 109 Ma between the two families and 1.5 Ma between the two Nelumbo species.The estimated time was only slightly longer than the age of known Nelumbo fossils,suggesting morphological stasis within Nelumbonaceae.We conclude that Nelumbonaceae holds a position in or close to Proteales.We further conclude that the two species of Nelumbo diverged recently from a common ancestor and do not represent ancient relicts on different continents.     

Metabolic enzymes in seasonally acclimatized and cold acclimated rufous-collared sparrow inhabiting a Chilean Mediterranean environment

Due to the higher energy requirements of birds during winter, it is predicted that the activities of metabolic enzymes （e.g., citrate synthase, CS and cytochrome C oxidase, COX） should increase in tandem with increases in rates of energy expendi ture （e.g., basal metabolic rate, BMR）. However, there is mixed support for the hypothesis of enzymatic acclimatization. Fur thermore, there is little information about the effect of ambient temperature on energetics and tissue enzyme activity levels in passerines inhabiting seasonal Mediterranean environments. In this study we evaluated the interplay between BMR and enzyme activities of freshly caught individuals of the passerine Zonotrichia capensis in winter and summer in a Mediterranean environment from central Chile, and also in warm （30℃） and cold （15℃） labacclimated birds. The results revealed a lack of seasonal variation in BMR, thermal conductance and in the activity of CS and COX. However, we found higher BMR and lower thermal conductance in coldacclimated than in warmacclimated birds. Also, total CS activity was higher in the flight muscles of coldacclimated than in warmacclimated birds. We found also a significant correlation between BMR and total CS activity in pectoral muscle. Although some authors have suggested that BMR mainly depends on the metabolic intensity and mass of internal organs, our results revealed that skeletal muscles such as the flight muscles may also affect BMR. Finally, differences in the accli mation and acclimatization responses in Rufouscollared sparrows suggest that largescale oscillations in the physical environment might maintain the capacity for flexibility in thermogenic traits through generations .     

Avian genetic ecotoxicology： DNA of the canary in a coalmine

Genotoxic chemicals, through damage and alteration of the genetic material of wild organisms, pose significant threats to the persistence of wild animal populations. Their damaging effects can ultimately impair the health of the ecosystem and its provision of services to human society. Bird species are good candidates for the role of sentinels of the effects of genotoxins, thanks to （i） the diversity of their ecological niches, （ii） their ubiquity across environments, （iii） their conspicuousness, abundance and approachability, together with （iv） their well-known life histories and the availability of historical data series. Avian diversity increases the likelihood that adequate model species be available for monitoring genotoxicants and assessing their impact. This paper reviews the methods utilized by genetic ecotoxicological studies of wild birds, highlighting their benefits and shortcomings. It also summarizes the genetic ecotoxicological studies so far conducted. In spite of a paucity of studies, several classes of genotoxicants have already been investigated across a variety of species and environments, thus supporting the versatility of birds as monitors of genotoxic contamination. Future technical advancements and applications are suggested, with par- ticular reference to the analysis of mutational events, gene expression and methylation patterns. Finally, I argue that the development of avian genetic ecotoxicology will contribute to the understanding of natural variation in the underlying machinery for coping with DNA damage and oxidative stress, both of which are increasingly recognized as proximate factors in the evolution of life history adaptations [Current Zoology 60 （2）： 285-298, 2014].     

The OsDHODH1 Gene is Involved in Salt and Drought Tolerance in Rice

In the present paper, we identified and cloned OsDHODH1 encoding a putative cytosolic dihydroorotate dehydrogenase （DHODH） in rice. Expression analysis indicated that OsDHODH1 is upregulated by salt, drought and exogenous abscisic acid （ABA）, but not by cold. By prokaryotic expression, we determined the enzymatic activity of OsDHODH1 and found that overproduction of OsDHODH1 significantly improved the tolerance of Escherichia coil cells to salt and osmotic stresses. Overexpression of the OsDHODH1 gene in rice increased the DHODH activity and enhanced plant tolerance to salt and drought stresses as compared with wild type and OsDHODHl-antisense transgenic plants. Our findings reveal, for the first time, that cytosolic dihydroorotate dehydrogenase is involved in plant stress response and that OsDHODH1 could be used in engineering crop plants with enhanced tolerance to salt and drought.     

Isolation of cDNA clones coding for mitochondrial 16S ribosomal RNA from the crustacean Artemia

cDNA clones coding for Artemia mitochondrial 16S ribosomal RNA (rRNA) have been isolated. The clones cover from nucleotide 650 of the RNA molecule to its 3' end. The comparison of Artemia sequence with both vertebrate and invertebrate mitochondrial 16S rRNA sequences has shown the existence of regions of high similarity between them. A model for the secondary structure of the 3' half of Artemia mitochondrial 16S rRNA is proposed. The size of the rRNA molecule has been estimated at 1.35 kb. Despite the similarity of the Artemia gene to insect rRNA in size, sequence and secondary structure, the G + C content of the Artemia gene (42%) is closer to that of mammals than to the insect genes. The number of mitochondria in Artemia has been estimated at 1500 per diploid genome in the cyst and 4000 in the nauplius. In contrast, the amount of mt 16S rRNA is constant at all stages of Artemia development.     

The complete mitochondrial DNA sequence of the Mekong giant catfish (Pangasianodon gigas), and the phylogenetic relationships among Siluriformes

The Mekong giant catfish (Pangasianodon gigas) is the largest scale-less freshwater fish of the world, and a critically endangered species. We determined the complete nucleotide sequence (16,533 bp) of the mitochondrial genome of the Mekong giant catfish, and conducted phylogenetic analyses based on mitochondrial protein (the combined amino acid sequences of all 13 mitochondrial protein coding genes) and rRNA (the combined nucleotide sequences of mitochondrial 12S and 16S rRNA genes) data sets in order to further clarify the relative phylogenetic position of P. gigas, and to recover phylogenetic relationships among 15 out of the 33 families of Siluriformes. Phylogenetic analyses (maximum parsimony, minimum evolution, maximum likelihood, Bayesian inference) of the protein data set were congruent with a basal split of the order into Loricarioidei and Siluroidei, and supported a closer relationship of the Mekong giant catfish (family Pangasiidae) to Siluridae than to Bagridae. The rRNA-based Bayesian phylogeny recovered Callichthyidae as the sister group of all other analyzed non-diplomystid catfish families, rendering Loricarioidei paraphyletic. In addition, Loricariidae were recovered as paraphyletic due to the inclusion of Astroblepidae. However, none of the two relationships received bootstrap support in the maximum parsimony, minimum evolution, and maximum likelihood analyses, and should be interpreted with caution. The derived position of Cetopsidae within Siluroidei, the sister group relationship of Pseudopimelodidae and Pimelodidae, and a close relationship of Doradidae and Auchenipteridae to the exclusion of Mochokidae were strongly supported. Pangasiidae was placed as a single lineage without clear affinities.     

Molecular phylogeny of lugworms (Annelida, Arenicolidae) inferred from three genes

Arenicolids comprise a group of four genera in which about 30 nominal species are described. Whereas the biology of many arenicolids is well known, the phylogenetic relationships of these worms are inadequately studied. A close relationship of Arenicolidae and Maldanidae is generally accepted. The phylogenetic relationships of arenicolid taxa were reconstructed based on sequence data of the mitochondrial 16S rRNA gene, the nuclear 18S rRNA gene, and a small fraction of the nuclear 28S rRNA gene. Members of all described arenicolid genera are included in the data set. Phylogenetic analyses were conducted using Maximum Likelihood, Bayesian inference, and Maximum Parsimony. The monophyly of the Maldanidae, as well as of the Arenicolidae is supported by all conducted analyses. Two well supported major clades are highest ranked sister taxa in the Arenicolidae: one containing all Abarenicola species and one containing Arenicola, Arenicolides, and Branchiomaldane. Evidence is given for a closer relationship between the two investigated Branchiomaldane species and Arenicolides ecaudata in the combined analysis. In the light of the molecular data the best explanation for structural and morphological observations is that Branchiomaldane evolved by progenesis.     

Contributions to molecular systematics of water scavenger beetles (Hydrophilidae,Coleoptera)

Phylogenetic relationships within Hydrophilidae were examined by analyses of separate and combined nuclear and mitochondrial markers (28S rRNA, 18S rRNA, 16S rRNA, 12S rRNA, COI and COII genes). The preferred (Bayesian) tree topology suggests a sister group relationship between Spercheidae and Hydrophilidae, supporting the ‘hydrophilid lineage’; Epimetopidae are placed on the base of the ‘helophorid branch’, the monophyly of Sphaeridiinae is highly supported, nested deeply within Hydrophilidae closest to Enochrus, making Hydrophilinae and Acidocerini paraphyletic; Hydrobius appears as sister taxon to (Hydrochara + Hydrophilus) without a closer relationship to Acidocerini; the hydrophiloid–histeroid sister group relationship is confirmed. The topology of several taxa remains contradictory, and requires further investigations with a larger taxon sampling and additional molecular markers.     

从12S rRNA基因第三结构域序列分析探讨蜘蛛若干重要类群的亲缘关系

本文将12S rRNA基因序列分析应用于研究若干重要蜘蛛类群的系统关系,以对传统的分类研究结论进行验证和补充,并且探讨12S rRNA基因序列分析在蜘蛛系统发生研究中的适用性。根据12S rRNA基因第3结构域构建的分子系统树得出结论:1.圆网类(即妖面蛛总科与园蛛总科)并非单系;2.隙蛛与暗蛛较漏斗蛛具有更近的亲缘关系;3.壁钱和拟壁钱并不近缘;4.有筛器类蜘蛛为复系类群;5.12S rRNA基因第3结构域片段对推断近缘科属间的系统发生关系是有效的遗传标记。     

蒙古狼线粒体基因组序列分析及其系统发育地位

应用Long-PCR和克隆测序法得到蒙古狼(Canis lupus chanco)线粒体基因组全序列,结合GenBank中现有犬科动物线粒体基因组数据,应用最大简约法(MP)、最大似然法(ML)和Bayesian分析法对蒙古狼的系统发育地位进行了探讨。结果如下:蒙古狼线粒体基因组全长16709bp,包含13个蛋白质编码基因、22个tRNA基因、2个rRNA基因和1个非编码区。序列碱基的组成存在明显的A-T偏好性。tRNA基因中除tRNA-Ser(AGY)缺少双氢尿嘧啶(DHU)臂以外,其余均能折叠成典型的三叶草二级结构。大多数蛋白质编码基因的起始和终止密码子与犬科动物有报道相同,COXⅡ基因的起始密码子为ATA,与其他犬科动物不同。基于12S rRNA+16S rRNA+H链上的12个蛋白质编码基因的联合数据的系统发育分析发现,在已报道的狼亚种数据中,西藏狼(Canis lupus laniger)的分化时间最早,其次为阿拉伯狼(Canis lupus arabs),蒙古狼与欧亚狼(Canis lupuslupus)的系统发育地位最为接近。     

Nuclear counterparts of the cytoplasmic mitochondrial 12S rRNA gene: A problem of ancient DNA and molecular phylogenies

Monkey mummy bones and teeth originating from the North Saqqara Baboon Galleries (Egypt), soft tissue from a mummified baboon in a museum collection, and nineteenth/twentieth-century skin fragments from mangabeys were used for DNA extraction and PCR amplification of part of the mitochondrial 12S rRNA gene. Sequences aligning with the 12S rRNA gene were recovered but were only distantly related to contemporary monkey mitochondrial 12S rRNA sequences. However, many of these sequences were identical or closely related to human nuclear DNA sequences resembling mitochondrial 12S rRNA (isolated from a cell line depleted in mitochondria) and therefore have to be considered contamination. Subsequently in a separate study we were able to recover genuine mitochondrial 12S rRNA sequences from many extant species of nonhuman Old World primates and sequences closely resembling the human nuclear integrations. Analysis of all sequences by the neighbor-joining (NJ) method indicated that mitochondrial DNA sequences and their nuclear counterparts can be divided into two distinct clusters. One cluster contained all temporary cytoplasmic mitochondrial DNA sequences and approximately half of the monkey nuclear mitochondriallike sequences. A second cluster contained most human nuclear sequences and the other half of monkey nuclear sequences with a separate branch leading to human and gorilla mitochondrial and nuclear sequences. Sequences recovered from ancient materials were equally divided between the two clusters. These results constitute a warning for when working with ancient DNA or performing phylogenetic analysis using mitochondrial DNA as a target sequence: Nuclear counterparts of mitochondrial genes may lead to faulty interpretation of results.Correspondence to: A.C. van der Kuyl