利用线粒体Cyt b基因全序列探讨部分鸥类的系统发育关系

利用线粒体细胞色素b(Cyt b)基因全序列,对采自陕西红碱淖湿地繁殖的遗鸥Larus relictus、棕头鸥Larus brunnicephalus、普通燕鸥Sterna hirundo和鸥嘴噪鸥Gelochlidon nilotica的序列特征进行了分析.联合已知该基因全序列的其它32种鸟类,构建了36种鸟类之间的系统发育关系,并确定了4种鸥在系统发育中的地位.结果表明:4种鸥Cytb基因全长均为1 143 bp;MP、ML和Bayes树拓扑结构大致相同,支持遗鸥、渔鸥Larus ichthyaetus和地中海鸥Larus audouinii、Larus melancephalus划归为黑头鸥族;棕头鸥划归为面具族;遗鸥与地中海鸥亲缘关系较近,与渔鸥次之,与棕头鸥亲缘关系较远;普通燕鸥和鸥嘴噪鸥均划归为黑帽族;燕鸥属和凤头燕鸥属亲缘关系较近,噪鸥属较为古老,是较早分化出的一支;鞘嘴鸥科作为单型科,受不同选择压力导致和鸥类亲缘关系甚远;建议将灰头鸥Larus cirrocephalus移人巾头鸥族;鸥科、燕鸥科和剪嘴鸥科的拓扑结构未能准确解析,需要进一步分析研究.     

棕头鸥线粒体基因组全序列测定与分析

基于长距PCR扩增及保守引物步移法测定并注释了棕头鸥(Larus brunnicephalus)的线粒体基因组全序列。结果表明,棕头鸥线粒体基因组全长16 769 bp,GenBank登录号JX155863。基因含量和排列次序与红原鸡一致,包含13个蛋白编码基因、22个tRNA、2个rRNA和一个D-loop区(控制区)。除COI基因以GTG、ND3基因以ATT为起始密码子外,其余11个蛋白质编码基因均以ATG起始。11个蛋白质编码基因以典型的完全终止密码子AGG、TAG、TAA或AGA终止,COIII和ND4基因为不完全终止密码子T。预测了22个tRNA基因的二级结构,发现tRNASer(AGN)缺少DHU臂,tRNAPhe的TψC臂出现第4种排列形式。预测的棕头鸥12S和16S rRNA二级结构分别包括4个结构域47个茎环和6个结构域60个茎环。其他鸟类控制区发现的F-box、E-box、D-box、C-box、B-box、Bird similarity-box和CSB-boxes(1-3)也存在于棕头鸥中,预测了控制区H链复制起始序列OH和双向复制起始序列LSP/HSP。系统发育分析支持将棕头鸥划归为面具鸥族(Masked gulls)。     

陕西红碱淖普通燕鸥和鸥嘴噪鸥的繁殖生态比较

2009年4～7月,采用定点观察法和逐巢清点法,对陕西省红碱淖地区普通燕鸥(Sterna hirundo)和鸥嘴噪鸥(Gelochelidon nilotica)的繁殖生态进行了比较研究。结果表明,两者都是4月末迁至红碱淖,并于5月中旬进入繁殖期。普通燕鸥和鸥嘴噪鸥都选择在湖心岛上营巢,普通燕鸥巢址沿岛边缘四周呈线状分布,而鸥嘴噪鸥位于岛中央向外扩散呈块状分布。对食物调查发现,两者在食物资源利用上存在部分生态位分离。巢址分布格局差异性和食物资源利用生态位部分分离是两者能在同一领域共存的主要原因。对雏鸟的体重等形态参数进行Gompertz曲线方程拟合,结果表明,两种雏鸟生长状况的差异性从另一面也可以反应二者种间竞争压力的缓和。另外,从一定的角度分析了两者与遗鸥(Larus relictus)的伴生关系。     

红嘴巨燕鸥云南鸟类种的新记录

在最近整理标本的过程中,作者发现1981年4月13日采自云南昆明滇池草海的一只红嘴巨燕鸥(Sterna caspia),为云南鸥科(Laridae)鸟类种的新记录。据约翰.马敬能等(2000)记录,红嘴巨燕鸥(Sterna caspiaPallas,1770,Caspian Tern)中文名为红嘴巨鸥。作者考虑该种鸟类隶属于鸥科的燕鸥属(Sterna),故建议将中文名修订为“红嘴巨燕鸥”。鉴别特征:体形较大,体重610g,体长470mm,嘴峰长60mm,翅长340mm,尾长160mm,跗长40mm。前额、头顶至后枕白色,布有黑色纵纹,枕部和眼下的纵纹较为密集而粗著,眼先和额部的纵纹较纤细而稀疏。背部和两翅表面银灰…     

河北沿海发现小凤头燕鸥

正2017年7月25日,在河北省唐山市海港开发区金沙岛一季节性水塘(39°10′26″N,118°58′16″E)观察到1只小凤头燕鸥(Thalasseus bengalensis),该鸟停歇约10 min后飞离该地。至8月7日,在该地点多次记录到单只小凤头燕鸥停歇洗浴。附近亦有普通燕鸥(Sterna hirundo)、白额燕鸥(S.albifrons)、反嘴鹬(Recurvirostra avosetta)、环颈鸻(Charadrius alexandrinus)、青脚滨鹬(Calidris temminckii)等水鸟在此停歇或觅食。所发现的小凤头燕鸥     

湖北省鸟类新记录——红嘴巨燕鸥

正2020年5月21日,在湖北省武汉市天兴洲(114°27'57"E,30°42'51"N,海拔6 m)进行武汉市重点区域鸟类调查时观察到3只红嘴巨燕鸥Hydroprogne caspia (图1:左),发现地位于武汉市黄陂区武湖街道熟地村附近的长江江滩,该区域水位较低,河床露出大片沙洲,沙洲间遍布浅滩与水洼(图1:右),吸引了鸥科Laridae、鹭科Arderidae等众多水鸟觅食。观察时同域还分布有白额燕鸥Sterna albifrons、普通燕鸥S.hirundo等。     

浙江韭山列岛的黑嘴端凤头燕鸥繁殖群调查初报

2004年7月28日～8月2日,在考察浙江象山韭山列岛省级海洋生态自然保护区时,发现了正处于繁殖中期的黑嘴端凤头燕鸥(Sterna bernsteini)的群体混群于大凤头燕鸥(S．bergii)的繁殖群中。据估测,大凤头燕鸥的种群数量为3500～4500只,黑嘴端凤头燕鸥的种群数量为10～20只。这是目前继2000年马祖群岛发现黑嘴端凤头燕鸥繁殖群之后的第2个繁殖群体。     

西藏阿里班公错斑头雁的种间巢寄生行为

2016年6月2日,我们在对西藏阿里地区班公错鸟岛进行鸟类调查时,发现了斑头雁(Anser indicus)将卵产于棕头鸥(Larus brunnicephalus)的巢中,是一种间巢寄生行为。对于发生这种现象的原因,我们初步推测,一种原因可能是繁殖地的巢址和巢材资源短缺,鸟岛上巢材可能无法满足两个鸟种筑巢的需要,个别斑头雁由于巢材短缺,无法顺利筑巢,因此将卵产于棕头鸥的巢中。另一种可能原因是,某些斑头雁由于巢被破坏或卵被捕食,在迁徙之前已没有时间再完成下一轮的繁殖活动,由于斑头雁与棕头鸥食性差异较大,但由于斑头雁为早成鸟,孵出的雏雁不必接受棕头鸥纯肉食的饲喂,也使得这种巢寄生成为可能。     

射阳盐场湿地禽类资源考察初报

在江苏省中部沿海的射阳盐场,1989年2月至1990年2月经考察共发现110种湿地禽类生活或迁徒于该人工湿地。其中有丹顶鹤、白鹳、黑鹳三种国家一级保护珍禽,以及角(辟鸟)(?)、斑嘴鹈鹕、小苇(升鸟)、白琵鹭、黑脸琵鹭、灰鹤、白额雁、小杓鹬、小青脚鹬九种国家二级保护珍禽。共记录到中日保护候鸟湿地禽84种。110种湿地禽类占国内湿地禽类总数46.03%,其中留鸟6种,夏候鸟15种,冬候鸟51种,旅鸟38种。考察中发现黑嘴鸥、环颈鸻为江苏省留鸟分布新记录;黄斑苇鸻、蛎鹬、黑翅长脚鹬、红脚鹬、白额燕鸥、普通燕鸥为江苏鸟类繁殖新纪录;角(辟鸟)(?)、黑颈(辟鸟)(?)、红嘴巨鸥、鸥嘴噪鸥、三趾鹬、灰斑鸻、渔鸥为江苏冬候鸟新纪录。     

西藏墨竹工卡县发现北极鸥

<正>2015年4月5至6日,在西藏自治区拉萨河中上游、米拉山西侧(墨竹工卡县境内)的尼玛加热乡直孔电站水库(30°01′44.39″N,91°50′36.99″E,海拔3 898 m)观察到1只亚成年鸥类,该鸟较棕头鸥(Larus brunnicephalus)个体大,嘴为浅粉色,喙尖端黑色,跗跖和趾为粉色,全身大体白色,羽有褐色纵纹,背羽和尾羽具有更显著褐色纵纹(图1),经鉴定为北极鸥(L.hyperboreus)(约翰·马敬能等2000,Mark 2009,曲利明2014)。查阅相     

RPB2 sequences reveal a close phylogenetic relationship between tetraploid Hordelymus and diploid Hordeum species in Triticeae (Poaceae)

The origin of Hordelymus genome has been debated for years, and no consensus conclusion was reached. In this study, we sequenced and analyzed the RPB2 (RNA polymerase subunit II) gene from Hordelymus europaeus (L.) Harz, and its potential diploid ancestor species those were suggested in previous studies. The focus of this study was to examine the phylogenetic relationship of Hordelymus genomes with its potential donor Hordeum, Psathyrostachys, and Taeniatherum species. Two distinguishable copies of sequences were obtained from H. europaeus. The obvious difference between the two copies of sequences is a 24 bp indel (insertion/deletion). Phylogenetic analysis showed a strong affinity between Hordeum genome and Hordelymus with 85% bootstrap support. These results suggested that one genome in tetraploid H. europaeus closely related to the genome in Hordeum species. Another genome in H. europaeus is sister to the genomes in Triticeae species examined here, which corresponds well with the recently published EF-G data. No obvious relationship was found between Hordelymus and either Ta genome donor, Taeniatherum caput-medusae or Ns genome donor, Psathyrostachys juncea. Our data does not support the presence of Ta and Ns genome in H. europaeus, and further confirms that H. europaeus is allopolyploid.     

A molecular analysis of some Eastern Atlantic grouper from the Epinephelus and Mycteroperca genus

Mitochondrial cytochrome b (397 bp) and 16S rDNA (516 bp) sequences analysis was used to investigate the phylogenetic relationships among some Eastern Atlantic Epinephelinae species. Six species of Epinephelus (E. aeneus, E. caninus, E. costae, E. haifensis, E. marginatus and E. tauvina) and two species of Mycteroperca (M. rubra and M. fusca) were analysed. Neighbour-joining and maximum-parsimony analysis support the paraphyletic grouping of the Epinephelus and Mycteroperca analysed. The maximum pairwise nucleotide divergence value in cyt b among all taxa was 0.196 between E. aeneus and E. marginatus and the minimum value was 0.006 between E. costae and M. rubra. Meanwhile, in 16S sequence analysis, the maximum value is 0.093 between E. aeneus and E. tauvina and the minimum value is 0.011 between E. marginatus and M. rubra. Molecular clock estimates for the species suggest a divergence time of 20-24 mya, which coincides with the Miocene period. A molecular analysis was also conducted, using other Epinephelinae sequences from GenBank in order to improve our understanding of the phyletic status of the Epinephelus and Mycteroperca species analysed.     

Evolutionary history of frogfishes (Teleostei: Lophiiformes: Antennariidae): a molecular approach

Fishes of the family Antennariidae (order Lophiiformes) are primarily shallow-water benthic forms found in nearly all tropical and subtropical oceans and seas of the world, with some taxa extending into temperate waters. Despite an earlier attempt based on morphology, no previous hypothesis of intergeneric relationships of the Antennariidae exists. To resolve phylogenetic relationships within the Antennariidae, and to test the validity of species groups within Antennarius, DNA sequences from the mitochondrial 16S and cytochrome oxidase c subunit 1 (COI) genes, and nuclear recombination activating gene 2 (RAG2), for 25 described and four undescribed antennariid species, representing 10 of 12 known genera and one undescribed genus, were unambiguously aligned and analyzed using Bayesian and maximum likelihood methods. The markers were partitioned and analyzed for substitution saturation and only the third codon position of COI (COI-3) was found to have reached saturation. However, analysis of both datasets, one with the saturated data and one without, differed only slightly. All molecular analyses recovered two major clades, one comprised of Fowlerichthys, Antennarius, Histrio, and Antennatus; and another containing Rhycherus, Antennariidae gen. et sp. nov., Kuiterichthys, Phyllophryne, Echinophryne, Tathicarpus, Lophiocharon, and Histiophryne. Evidence is presented to illustrate a correlation between phylogeny, geographic distribution, and reproductive life history. The results of these analyses provide the first hypothesis of evolutionary relationships within the Antennariidae.     

A molecular phylogeny of thermophilic fungi

Sequences from 86 fungal genomes and from the two outgroup genomes Arabidopsis thaliana and Drosophila melanogaster were analyzed to construct a robust molecular phylogeny of thermophilic fungi, which are potentially rich sources of industrial enzymes. To provide experimental reference points, growth characteristics of 22 reported thermophilic or thermotolerant fungi, together with eight mesophilic species, were examined at four temperatures: 22 °C, 34 °C, 45 °C, and 55 °C. Based on the relative growth performances, species with a faster growth rate at 45 °C than at 34 °C were classified as thermophilic, and species with better or equally good growth at 34 °C compared to 45 °C as thermotolerant. We examined the phylogenetic relationships of a diverse range of fungi, including thermophilic and thermotolerant species, using concatenated amino acid sequences of marker genes mcm7, rpb1, and rpb2 obtained from genome sequencing projects. To further elucidate the phylogenetic relationships in the thermophile-rich orders Sordariales and Eurotiales, we used nucleotide sequences from the nuclear ribosomal small subunit (SSU), the 5.8S gene with internal transcribed spacers 1 and 2 (ITS 1 and 2), and the ribosomal large subunit (LSU) to include additional species for analysis. These phylogenetic analyses clarified the position of several thermophilic taxa. Thus, Myriococcum thermophilum and Scytalidium thermophilum fall into the Sordariales as members of the Chaetomiaceae, Thermomyces lanuginosus belongs to the Eurotiales, Malbranchea cinnamomea is a member of the Onygenales, and Calcarisporiella thermophila is assigned to the basal fungi close to the Mucorales. The mesophilic alkalophile Acremonium alcalophilum clusters with Verticillium albo-atrum and Verticillium dahliae, placing them in the recently established order Glomerellales. Taken together, these data indicate that the known thermophilic fungi are limited to the Sordariales, Eurotiales, and Onygenales in the Ascomycota and the Mucorales with possibly an additional order harbouring C. thermophila in the basal fungi. No supporting evidence was found for thermophilic species belonging to the Basidiomycota.     

Rapid identification of lymnaeid snails and their infection with Fasciola gigantica in Thailand

Freshwater snails of the family Lymnaeidae are the intermediate hosts of the liver fluke Fasciola worldwide. While distinct species have been identified at the molecular level in other parts of the world such data have not been published for Thailand. In this study we collected Lymnaeidae from different localities across Thailand and analyzed their 16S rDNA sequences as a molecular signature for classification. In addition to the ubiquitous Radix rubiginosa, we have confirmed the presence of Austropeplea viridis and Radix swinhoei, for the latter of which the ribosomal rDNA sequences are reported for the first time, in North-Thailand. Based on the obtained 16S rDNA data three primer pairs were designed that allowed rapid identification of these snail species by PCR. To determine their infection status, PCR primers for F.gigantica cathepsin L were used in parallel with the snail 16S rDNA species-specific primers in multiplex PCR analyses. Western blot analysis of total snail protein with a monoclonal anti-F.gigantica cathepsin L antibody confirmed positive cathepsin L PCR results. The developed diagnostic PCR will be of use in risk assessment for transmission of fascioliasis in Thailand.     

Endosymbiotic bacteria nodulating a new endemic lupine Lupinus mariae-josephi from alkaline soils in Eastern Spain represent a new lineage within the Bradyrhizobium genus

Lupinus mariae-josephi is a recently described endemic Lupinus species from a small area in Eastern Spain where it thrives in soils with active lime and high pH. The L. mariae-josephi root symbionts were shown to be very slow-growing bacteria with different phenotypic and symbiotic characteristics from those of Bradyrhizobium strains nodulating other Lupinus. Their phylogenetic status was examined by multilocus sequence analyses of four housekeeping genes (16S rRNA, glnII, recA, and atpD) and showed the existence of a distinct evolutionary lineage for L. mariae-josephi that also included Bradyrhizobium jicamae. Within this lineage, the tested isolates clustered in three different sub-groups that might correspond to novel sister Bradyrhizobium species. These core gene analyses consistently showed that all the endosymbiotic bacteria isolated from other Lupinus species of the Iberian Peninsula were related to strains of the B. canariense or B. japonicum lineages and were separate from the L. mariae-josephi isolates. Phylogenetic analysis based on nodC symbiotic gene sequences showed that L. mariae-josephi bacteria also constituted a new symbiotic lineage distant from those previously defined in the genus Bradyrhizobium. In contrast, the nodC genes of isolates from other Lupinus spp. from the Iberian Peninsula were again clearly related to the B. canariense and B. japonicum bv. genistearum lineages. Speciation of L. mariae-josephi bradyrhizobia may result from the colonization of a singular habitat by their unique legume host.     

Endophytic occupation of peanut root nodules by opportunistic Gammaproteobacteria

Several bacterial isolates were recovered from surface-sterilized root nodules of Arachis hypogaea L. (peanut) plants growing in soils from Córdoba, Argentina. The 16S rDNA sequences of seven fast-growing strains were obtained and the phylogenetic analysis showed that these isolates belonged to the Phylum Proteobacteria, Class Gammaproteobacteria, and included Pseudomonas spp., Enterobacter spp., and Klebsiella spp. After storage, these strains became unable to induce nodule formation in Arachis hypogaea L. plants, but they enhanced plant yield. When the isolates were co-inoculated with an infective Bradyrhizobium strain, they were even found colonizing pre-formed nodules. Analysis of symbiotic genes showed that the nifH gene was only detected for the Klebsiella-like isolates and the nodC gene could not be amplified by PCR or be detected by Southern blotting in any of the isolates. The results obtained support the idea that these isolates are opportunistic bacteria able to colonize nodules induced by rhizobia.     

Pseudoscardovia suis gen. nov., sp. nov., a new member of the family Bifidobacteriaceae isolated from the digestive tract of wild pigs (Sus scrofa)

Seventeen fructose-6-phosphate phosphoketolase-positive bacterial strains were isolated from the digestive tract of wild pigs (Sus scrofa). Most of them were identified as Bifidobacterium boum according to sequences of 16S rRNA gene. Two strains isolated from the small intestine content had unusual morphology of cells in comparison with bifidobacteria. Cells growing in liquid anaerobic media were regular shaped rods arranged mostly in pairs. These isolates showed relatively low 16S rRNA gene sequence similarities (maximum identity of 94%) to members of the family Bifidobacteriaceae. Nevertheless, phylogenetic analyses of 16S rRNA, hsp60 and xfp gene sequences revealed that these strains are more related to recently described Neoscardovia, Aeriscardovia and other scardovial genera, than to Bifidobacterium species. Partial gene sequences of other phylogenetic markers showed low (65.8–89.5%) similarities to genome sequences of bifidobacteria and Gardnerella vaginalis. The major fatty acids detected in cells of the representative strain DPTE4^T were C_16:0, C_18:1, C_14:0. The peptidoglycan type of the DPTE4^T strain was A3β l-Orn(l-Lys)-l-Ser(l-Ala)-l-Ala₂. Polar lipid analysis revealed two phosphoglycolipids and phospholipids, a glycolipid and diphosphatidylglycerol. The results of phylogenetic, genotypic and phenotypic analyses support the proposal of a novel taxa, Pseudoscardovia suis gen. nov., sp. nov. (type strain = DPTE4^T = DSM 24744^T = CCM 7942^T).     

Evolutionary relatedness of mackerels of the genus Scomber based on complete mitochondrial genomes: Strong support to the recognition of Atlantic Scomber colias and Pacific Scomber japonicus as distinct species

Mackerels of the genus Scomber are commercially important species, but their taxonomic status is still controversial. Although previous phylogenetic data support the recognition of Atlantic Scomber colias and Pacific Scomber japonicus as separate species, it is only based on the analysis of partial mitochondrial and nuclear DNA sequences. In an attempt to shed light on this relevant issue, we have determined the complete mitochondrial DNA sequence of S. colias, S. japonicus, and Scomber australasicus. The total length of the mitogenomes was 16,568 bp for S. colias and 16,570 bp for both S. japonicus and S. australasicus. All mitogenomes had a gene content (13 protein-coding, 2 rRNAs, and 22 tRNAs) and organization similar to that observed in Scomber scombrus and most other vertebrates. The major noncoding region (control region) ranged between 865 and 866 bp in length and showed the typical conserved blocks. Phylogenetic analyses revealed a monophyletic origin of Scomber species with regard to other scombrid fish. The major finding of this study is that S. colias and S. japonicus were significantly grouped in distinct lineages within Scomber cluster, which phylogenetically constitutes evidence that they may be considered as separate species. Additionally, molecular data here presented provide a useful tool for evolutionary as well as population genetic studies.