Complete mitochondrial genome of the Bewick's swan Cygnus columbianus bewickii (Aves, Anseriformes, Anatidae)

The mitochondrial genome of Bewick's swan Cygnus columbianus bewickii was completely sequenced and then the resultant data were compared with those of the whistling swan Cygnus columbianus columbianus. The complete mitochondrial genome sequence of C. c. bewickii was 16,727?bp in length and its gene arrangement pattern, gene content, and genome organization were identical to those of Cygnus species. The similarities of nucleotide and amino acid sequences between the two swans were 99.1% and 99.6%, respectively. Out of the 13 protein-coding genes and 2 rRNA genes, COIII showed the lowest nucleotide sequence similarity with 98.0%. On the other hand, in amino acid sequence similarities, both COII and ATP6 showed the lowest with 98.7% in common. The control region has the 97.8% nucleotide sequence similarity.     

Comparative mechanics of filter feeding in Anas platyrhynchos,Anas clypeata and Aythya fuligula (Aves,Anseriformes)

Summary The straining of seeds ranging in size from 0.01 to 4.6 mm was investigated in the filtering mechanisms of three anseriform species, Anas platyrhynchos, Anas clypeata, and Aythya fuligala. The morphology of the filtering mechanisms was studied by dissection and from microsections. The kinematic work envelope of the beaks was measured by stereotactic manipulation. The actual beak kinematics were analyzed by calculating the changes of the mouth volume from computer simulations and comparing the results with the amounts of water expelled. The performances of the filter and the water pump were measured with special collection boxes. The influence of the lamellae was estimated by removing them in whole or in part and measuring the performances again. The results show that if the size of the strained seeds increases, the gapes and amplitudes also increase (cf. bill rotations). Beak rotation is elevated for small kernels, even more elevated for slightly larger ones, but depressed for large kernels. However, neither frequencies nor phase shifts change between different moving elements. Simulation of these data by stereotactic manipulation of fresh material and by measuring gape sizes and mesh widths shows that the beak kinematics during straining keep mesh widths and gapes carefully adjusted to the seed size. The pumping and the filtering mechanisms influence each other mutually in setting boundary conditions on mouth kinematics. Beyond a certain kernel size, the necessity for mesh-width control sets a boundary on the increase of the water flow. Conversely, phase shifts, frequency changes and change of lingual amplitudes were restricted by the pumping mechanism. Drastic shortening of either dorsal mandibular or maxillary lamellae in Anas platyrhynchos and Aythya fuligula does not effect either the filter performances, the pump performances, or the beak kinematics, but these modifications do change the performances in Anas clypeata. The usually accepted assumption concerning food sieving was thus verified for Anas clypeata and falsified for the other two anseriform species. Therefore, a vortex model in addition to the sieving model, was developed, based on the assumption that local vortices cause inertia of particles so that small kernels are filtered by centrifugation and translation out of the main water flow. Combined effects of sieving and centrifugation occur when larger kernels are filtered. The kinematics of the filtering mechanism are highly flexible; therefore, a wide tolerance for seed sizes exists. However, the morphology of the filtering mechanism differs in the three species. Testing whether the anseriform filter mechanism is so plastic that the mechanism in each species has developed in such a way that the staple food is gathered most economically has shown that filtering of the staple food does indeed occur at the most efficient levels of maxillary rotation.     

The Anatidae and Scolopacidae (Aves: Anseriformes,Charadriiformes) from the late Neogene of Gargano,Italy

The late Neogene (MN13-14) fissure fillings found in the limestone quarries near Apricena (Foggia, Southern Italy) contain a well-diversified fossil bird assemblage. Most of the bird taxa show endemic characteristics following the high degree of insularity of the whole vertebrate assemblage. In addition to the endemic taxa, some non-endemic forms are present, mostly only recently found after the still ongoing revision of the whole bird remains. Here the remains of Anatidae and Scolopacidae are presented. This analysis reveals the occurrence of at least two taxa of Anatidae, Anas velox and Anatidae indet., and two taxa of Scolopacidae, Calidris sp. and an Scolopacidae indet. In addition, some remains are determined as Charadriiformes indet., but they probably represent more than one taxon, even if their bad status of preservation does not allow any further consideration. The detailed study of these remains and their comparison with the other European Neogene taxa already described is carried out.     

Complete mitochondrial genome of the peregrine falcon Falco peregrinus (Aves, Falconiformes, Falconidae): genetic differences between the two individuals

The peregrine falcon Falco peregrinus (Aves, Falconiformes, Falconidae) is one of the most common and widespread raptor species in the world. Here, the complete mitochondrial genome of F. peregrinus from Korea, which is one of the breeding ranges, was sequenced and characterized in detail.     

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)。     

Complete mitochondrial genome of Oxuderces dentatus (Perciformes, Gobioidei)

The complete mitochondrial genome (mitogenome) of Oxuderces dentatus was determined first. The genome was 17,116?bp in length and consisted of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 2 main non-coding regions [the control region (CR) and the origin of the light strand replication], the gene composition and order of which was similar to most other vertebrates. The overall base composition of the heavy strand was T 27.9%, C 26.8%, A 30.2%, and G 15.1%, with a slight A+T bias of 58.1%. In addition to the discrete and conserved sequence blocks, unusual long tandem repeat unit (three 150-bp tandem repeat units and an incomplete copy of 146?bp) was also detected within CR. This mitogenome sequence data would play an important role in population genetics and phylogenetic analysis of the Gobioidei.     

Complete mitochondrial genome of Liobagrus obesus (Siluriformes, Amblycipitidae)

Liobagrus obesus (Siluriformes, Amblycipitidae) is an endemic, endangered species in South Korea. Throughout this study, complete mitochondrial genome of L. obesus was sequenced, which is 16,506 bp in length. Its detail characteristics were described in this study.     

Complete mitochondrial genome of Trypauchen vagina (Perciformes, Gobioidei)

The complete mitochondrial genome of Trypauchen vagina was determined first. The genome is 16,686 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 2 main non-coding regions [the control region (CR) and the origin of the light strand replication], the gene composition and order of which was similar to most other vertebrates. The overall base composition of T. vagina is T 27.6%, C 27.6%, A 29.5%, and G 15.3%, with a slight A+T bias of 57.1%. In addition to the discrete and conserved sequence blocks, an incomplete tandem repeat unit is detected within the CR. This mitogenome sequence data would play an important role in population genetics and phylogenetic analysis of the Gobioidei.     

Complete mitochondrial genome of Oxya chinensis （Orthoptera, Acridoidea）

The complete sequence of Oxya chinensis （0. chinensis） mitochondrial genome is reported here. It is 15,443 bp in length and contains 75.9% A＋T. The protein-coding genes have a similar A＋T content （75.2%）. The initiation codon of the cytochrome oxidase subunit I gene in the mitochondrial genome of O. chinensis appears to be ATC, instead of the tetranucleotides that have been reported in Locusta migratoria （L migratoria） mitochondrial genome. The sizes of the large and small ribosomal RNA genes are 1319 and 850 bp, respectively. The transfer RNA genes have been modeled and showed strong resemblance to the dipteran transfer RNAs, and all anticodons are identical to those of dipteran. The A＋T-rich region is 562 bp, shorter than that of other known Orthoptera insects. The six conserved domains were identified within the A＋T-rich region by comparing its sequence with those of other grasshoppers. The result of phylogenetic analysis based on the dataset containing 12 concatenated protein sequences confirms the close relation-ship of O. chinensis with L migratoria.     

Changes in thyroid function and gonadotrophin activity during sexual development in ducks Anas sp. (Aves: Anatidae)

Age-related changes in plasma iodohormone concentrations in male and female Aylesbury and Khaki Campbell ducklings were determined between the second week after hatching and sexual maturity.
In both sexes and strains the concentration of total thyroxine (T₄) and the free thyroxine index (FT₄1) were low during the first 6–8 weeks after hatching. A marked increase in the T₄ and FT₄1 occurred when the ducklings were nine weeks old; T₄ progressively increased over the following four weeks and remained high thereafter. The T₄ concentration in both sexes was directly related to age.
Concentrations of total tri-iodothyronine (T₃) were more variable than T₄ but were highest before sexual maturation and inversely age-related. An age-related decline in free tri-iodothyronine index (FT₃1) was observed during the first nine weeks.
The possibility that these maturational changes in thyroid function may reflect changes in gonadal activity was assessed by measuring the concentration of luteinizing hormone (LH) in the same plasma samples. Although plasma LH increased with age, in all cases the increase occurred after changes in the thyroid hormones were observed. Moreover, the maturational pattern of LH was related to sex and strain whereas thyroid function was unaffected by sex or strain.
These results demonstrate reciprocal changes in plasma T₃ and T₄ levels in ducks during sexual development, although the stimuli responsible and physiological significance are uncertain.     

Systematic relationships of the palaeogene family Presbyornithidae (Aves: Anseriformes)

The early Tertiary (Paleocene and Eocene) family Presbyornithidae is one of the most completely known group of fossil birds. Essentially all parts of the skeleton are represented in the fossil record, allowing a thorough analysis of the phylogenetic position of the family. Forty-two families of nonpasserine birds representing the orders Ciconiiformes, Anseriformes, Galliformes, Gruiformes and Charadriiformes, were included in a cladistic analysis of 71 skeletal characters. The previously suggested anseriform affinity of the Presbyornithidae was confirmed. Furthermore, the family proved to be closer to the Anatidae than to the Anhimidae or Anseranatidae. The many postcranial similarities with certain charadriiform birds as the Burhinidae, obviously are plesiomorphies. By this observation, a better undestanding of character evolution in nonpasserine skeletal morphology is gained. The often suggested close relationship of anseriform and galliform birds is not confirmed by osteology. Instead, the Anseriformes and the Phoenicopteridae form a monophyletic clade that is the sister to the remaining ciconiiform birds. This result renders the Ciconiiformes sensu Wetmore (1960) polyphyletic.     

Sequencing and phylogenetic analysis of the Pyrgilauda ruficollis(Aves,Passeridae) complete mitochondrial genome

In this study,both long PCR and conserved primers walking sequencing methods were used to determine the complete sequence of the of Pyrgilauda ruficollis mitochondrial genome(KC836121).The results showed that the complete mitochondrial genome of P.ruficollis is 16909 bp in length with 55.0%A+T content,harboring the typical 37 genes.The mitogenome had the same gene order with that of Podoces hendersoni.All protein coding genes started with ATG codon,except ND3 with GTG.For the stop codon usage,most genes terminate with codons TAA or TAG,but ND5 terminated with AGA,while ND1 and COI genes with AGG,and both the genes COIII and ND4 have an incomplete termination codon(T).The secondary structures of 22 tRNA genes were also predicted,showing that all tRNAs can form typical clover-leaf secondary structures,except for the tRNASer(AGN)which loses the DHU arm,while tRNAPhe harbor an extra nucleotide inserted in the TψC arm.The predicted secondary structures of 12S rRNA and16S rRNA exhibit 47 helices in 4 domains and 60 helices in 6 domains respectively.The control region of P.ruficollis with the length of 1 305 bp was located between tRNAGlu and tRNAPhe,and typical domains of which could be found as other bird groups.Using the data from 13 mitochondrial protein-coding genes,results of a final phylogenetic analysis strongly supports the traditional view that P.ruficollis is closely related with Passeridae and Fringillidae.     

Histomorphological changes in the oviduct of the mallard (Aves: Anatidae)

Studies on histomorphometrical changes in different segments (infundibulum, magnum, isthmus, shell gland and vagina) of oviduct of mallard, Anas platyrhynchos during active and quiescent phases of the reproductive cycle have been made. The absolute and per cent length and width of each segment showed a marked change. The magnum showed an increase of 280 per cent. Of all the histological parameters studied the number and height of mucosal folds and mucosal epithelium showed more marked increase in all segments of oviduct. The size of tubular glands and frequency of ciliated and secretory cells were studied in relation to oviductal activity.     

Complete mitochondrial genome of the Walking goby Scartelaos histophorus (Perceformes, Gobiidae)

The Walking goby Scartelaos histophorus (Perciformes, Gobiidae) is an amphibious gobioid fish. In this paper, the complete mitochondrial genome of S. histophorus was first determined. The genome is 16,496 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 1 control region. The overall base composition of S. histophorus is 27.5% for T, 28.0% for C, 28.3% for A, and 16.1% for G, with a slight A+T bias of 55.8%. It has the typical vertebrate mitochondrial gene arrangement.     

云南禄丰晚中新世鸭类标本的再研究与系统发育分析（英文）

1985年侯连海初步报告了发现于云南禄丰中新世古猿地点的部分鸟类化石,建立了一新种石灰坝潜鸭(Aythya shihuibas),并将另一件标本定为河鸭属未定种(Anas sp.)。针对这两件鸭类标本保存的特征进行系统发育分析,并结合二者目前已知的分布情况,可以确定禄丰鸟类至少存在两个不同种(不同的系统发育支系),这和之前的结论相似。石灰坝潜鸭的肱骨腹侧气窝中具有骨质支柱,异于现生潜鸭类,代表了气窝演化的较原始形态,依此认为其很可能为一潜鸭类冠群以外的绝灭支系。另一件原命名为Anas p.的鸭类标本保存非常破碎,无法对其进行较精确的系统发育分析。它很可能为鸭科成员,或许可以称为河鸭类,尽管此属(Anas)为非单系类群。这件禄丰河鸭类标本可能与发现于蒙古中新世-上新世的另一河鸭属未定种关系较近,二者具有相似的特殊特征组合。     

Complete mitochondrial genome of the Amur stickleback Pungitius kaibarae (Gasterosteiformes, Gasterosteidae)

The complete mitochondrial genome was sequenced from the Amur stickleback Pungitius kaibarae. The genome sequence was 16,505 bp in size, and the gene order and contents were identical with the same genera Pungitius sinensis and other previously reported fish mitochondrial genomes. Of 13 protein-coding genes (PCGs), 3 genes (CO2, ND4, and Cytb) had incomplete stop codons. The base composition of P. kaibarae showed anti-G bias (8.86%) on the third position of PCGs.     

Complete mitochondrial genome of the Amur stickleback Pungitius sinensis (Gasterosteiformes, Gasterosteidae)

The complete mitochondrial genome was sequenced from the Amur stickleback Pungitius sinensis. The genome sequence was 16,581 bp in size, and the gene order and contents were identical with those of previously reported fish mitochondrial genomes. Of 13 protein-coding genes (PCGs), four genes (ND2, CO2, ND4, Cytb) had incomplete stop codons. The base composition of P. sinensis showed anti-G bias (9.53%) on the third position of PCGs.     

Complete mitochondrial genome of the Antarctic amphipod Gondogeneia antarctica (Crustacea, amphipod)

The complete sequence of the mitochondrial genome of the Antarctic amphipod Gondogeneia antarctica was determined to be 18,424 bp in length, and to contain 13 protein-coding genes (PCGs), 22 tRNA genes, and large (rrnL) and small (rrnS) rRNA genes. Its total A+T content is 70.1%. The G. antarctica mitogenome is the largest known among those of crustaceans, due to the existence of two relatively large intergenic non-coding sequences. The PCG arrangement of G. antarctica is identical to that of the ancestral pancrustacean ground pattern, although the tRNA arrangement differs somewhat. The complete mitogenome sequences of 68 species of pancrustacea have been added to the NCBI database, only 4 of which represent complete mitogenome sequences from amphipods. This is the first report of a mitogenome sequence of an Antarctic amphipod, and provides insights into the evolution of crustacean mitochondrial genomes, particularly in amphipods.     

Complete mitochondrial genome of the longtooth grouper Epinephelus bruneus (Perciformes, Serranidae)

We determined the complete nucleotide sequence of the mitochondrial (mt) genome for the longtooth grouper, Epinephelus bruneus (Perciformes, Serranidae). This mt genome, consisting of 16,686 base pairs (bp), encoded genes for 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a noncoding control region as those found in other vertebrates, with the gene order identical to that of typical vertebrates. A major noncoding region between the trnP and trnF genes (991 bp) was considered to be the control region (D-loop). Within this sequence, 22 copies of a 17-bp tandem repeat element, 5'-TGATATTACATATATGC-3', were identified in the control region unlike previous reported Epinephelus species.     

Complete mitochondrial genome of the marine medaka Oryzias melastigma (Beloniformes, Adrianichthyidae)

The complete mitochondrial genome was obtained from the assembled genome data sequenced by next-generation sequencer from the marine medaka Oryzias melastigma. The mitochondrial genome sequence was 16,864 bp in size, and the gene order and contents were identical with those of previously reported fish mitochondrial genomes. Of 13 protein-coding genes (PCGs), 4 genes (CO3, ND3, ND4, and Cytb) had incomplete stop codons. The base composition of O. melastigma mitogenome showed high A+T (59.65%) and anti-G bias (8.73%) on the 3rd position of PCGs.