Shape, size and density of daytime surface swarms of the euphausiid Meganyctiphanes norvegica in the Bay of Fundy

Daytime surface swarms of ^{Meganyctiphanes norvegica} in the Bayof Fundy were examined using a variety of techniques to providemeasurements of their shapes, sizes and densities. Shapes andsizes were determined from two aerial photographs: swarms werespherical, ribbon-like or amorphous. were up to 28 6 m longand ranged in area from 0.4–111 7 m². Densities were measuredby a bag-sampling device which gave figures of up to 41 000animals m^–3 by photographic methods which gave figuresof up to 770 000 animals m^–3 and by a plankton net whichgave maximum values of six animals m^–3 Using the photographicmethod the maximum euphausud biomass was estimated to be 154kg m^–3 within swarms and the largest swarm measured wasestimated to contain up to 2 1 tonnes of M. norvegica. Meanpatch biomass estimates for the two aerial photographs rangedfrom 77.8–778 g m^–3 and 15 6–155.6 g m^–3which are similar to figures obtained by other authors usingintegrating sampling techniques at depth.     

Food ingestion and digestive transit time in the euphausiid Meganyctiphanes norvegica as a function of animal size

Laboratory experiments with Meganyctiphanes norvegica of differentsizes (7 to 70 mg dry) fed on Artemia salina show that the dailyspecific ingestion rate varies with animal weight accordingto a power law with a negative exponent of -0.58. This relationis used to calculate the production rate of faeces which ishigher in the smaller individuals when expressed as a percentageof animal weight; a comparison of the M. norvegica data withpublished data for Calanus helgolandicus indicates that thisrate is higher for the smaller species. Under the experimentalconditions used the digestive transit time of food in M. norvegicais appreciably shorter in smaller animals (15 minutes versus30 minutes). The data, combined with other data previously obtainedfor the same ipecies, show that the metabolism of active, well-fedindividuals is about three times higher than the standard metabolism.     

Phylogenetic relationships of elapid snakes based on cytochrome b mtDNA sequences

Published molecular phylogenetic studies of elapid snakes agree that the marine and Australo-Melanesian forms are collectively monophyletic. Recent studies, however, disagree on the relationships of the African, American, and Asian forms. To resolve the relationships of the African, American, and Asian species to each other and to the marine/Australo-Melanesian clade, we sequenced the entire cytochrome b gene for 28 elapids; 2 additional elapid sequences from GenBank were also included. This sample includes all African, American, and Asian genera (except for the rare African Pseudohaje), as well as a representative sample of marine/Australo-Melanesian genera. The data were analyzed by the methods of maximum-parsimony and maximum-likelihood. Both types of analyses yielded similar trees, from which the following conclusions can be drawn: (1) Homoroselaps falls outside a clade formed by the remaining elapids; (2) the remaining elapids are divisible into two broad sister clades, the marine/Australo-Melanesian species vs the African, American, and Asian species; (3) American coral snakes cluster with Asian coral snakes; and (4) the "true" cobra genus Naja is probably not monophyletic as the result of excluding such genera as Boulengerina and Paranaja.     

Identification of mosquito bloodmeals using mitochondrial cytochrome oxidase subunit I and cytochrome b gene sequences

Abstract.  Primer pairs were designed and protocols developed to selectively amplify segments of vertebrate mitochondrial cytochrome oxidase subunit 1 (COI) and cytochrome b (Cyt b ) mtDNA from the bloodmeals of mosquitoes (Diptera: Culicidae). The protocols use two pairs of nested COI primers and one pair of Cyt b primers to amplify short segments of DNA. Resultant sequences are then compared with sequences in GenBank, using the BLAST function, for putative host identification. Vertebrate DNA was amplified from 88% of our sample of 162 wild-caught, blood-fed mosquitoes from Oregon, U.S.A. and GenBank BLAST searches putatively identified 98% of the amplified sequences, including one amphibian, seven mammalian and 14 avian species. Criteria and caveats for putative identification of bloodmeals are discussed.     

基于线粒体Cyt b基因部分序列的中国东方蜜蜂不同地理种群的系统发育

从线粒体DNA水平上对中国境内东方蜜蜂不同地理种群的系统发育进行研究,为保护和合理利用这一宝贵的蜂种资源提供理论基础。对我国10个省市的21群东方蜜蜂mtDNA Cyt b基因片段进行了扩增、测序,并以意大利蜂、卡尼鄂拉蜂、印尼蜂作为外群进行序列分析。采用Minimum-Spanning Network方法构建系统进化树。结果显示：扩增片段长度429bp;在得到的21条同源序列中,共检测出13个变异位点,其中转换数为9,颠换数为4,并且变异位点大都发生在密码子的第三位,无碱基插入或缺失;聚类分析结果显示西方蜜蜂、印尼蜂和东方蜜蜂各为独立的蜂种;在中国东方蜜蜂群体中,吉林、海南和云南的东方蜜蜂各为一个独立的类群,其它地区的东方蜜蜂为一个类群[动物学报54（6）：1005-1013,2008]。     

Molecular phylogeny of icefish Salangidae based on complete mtDNA cytochrome b sequences, with comments on estuarine fish evolution

Phylogenetic relationships among 15 species in the family Salangidae were constructed based on the complete cytochrome b sequence (1141 bp). We confirmed the monophyly of the family Salangidae and defined four primitive lineages within this family: (I) Protosalanx , Neosalanx anderssoni , Neosalanx tangkahkeii , and Neosalanx argentea ; (II) Neosalanx reganius , Neosalanx jordani , Neosalanx oligodontis , and Neosalanx  sp.; (III) Hemisalanx , Salanx , Leucosoma , and Salangichthys ishikawae ; and (IV) Salangichthys microdon . A major finding of our study is the key basal placement of Sg. microdon . According to the tentative estimation, the divergence of the four lineages appears to have been initiated in the early Miocene (21 Mya), with most speciation events occurring 1.05–9.90 Mya. Taxonomic revisions on subfamilial, generic, and specific levels were carried out based on phylogenetic relationships and genetic distance, taking into account some key morphological characters. The speciation mechanism in Salangidae is also discussed, and the evidence shows that geographical isolation, water mass, as well as some ecological factors, may not always play important roles in the speciation of temperate estuarine fish. In the most cases, sympatric salangids are not monophyletic, indicating that their coexistence reflects secondary contact rather than sympatric speciation.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 327–342.     

Phylogenetic relationships among bumble bees (Bombus, latreille) inferred from mitochondrial cytochrome b and cytochrome oxidase I sequences

We conducted a molecular study intending to derive an estimate of the relationships within the genus Bombus (bumble bees) by comparing the mitochondrial cytochrome b and cytochrome oxidase I (COI) genes from 19 species, spanning 10 of approximately 16 European subgenera and 3 subgenera from North and South America. Our trees differ from the most recent classifications of bumble bees. Although bootstrap values for deep branches are low, our sequences show significant data structure and low homoplasy, and all trees share some groups and patterns. In all cases, the subgenus Bombus s. str. clusters among the most derived bumble bees, contrary to other molecular studies. In all trees, B. funebris is the sister taxon of B. robustus, and in five of the six trees, B. wurflenii is the sister taxon to this clade. B. nevadensis is basal to the other species in the analysis of the cytochrome b gene, but appears to be among the most derived according to the analysis of the COI region. The species representing the subgenera Thoracobombus and Fervidobombus are consistently among the earliest diverged. Species that appear in very different positions in different trees are B. nevadensis, B. mesomelas, B. balteatus, and B. hyperboreus. All subgenera with two representatives in our analysis are apparently monophyletic except Fervidobombus, Melanobombus, and Pyrobombus. The groups formed by pocket makers and non-pocket makers within Bombus also appear to be paraphyletic, and therefore some subgenera may not accurately reflect phylogeny.     

Phylogeny of the genus Chironomus (Diptera) inferred from DNA sequences of mitochondrial cytochrome b and cytochrome oxidase I

Two mitochondrial genes, Cytochrome b (Cytb) and Cytochrome c oxidase subunit I (COI), have been used as phylogenetic markers in Chironomids. The nucleotide sequences of 685 bp from Cytb and 596 bp from COI have been determined for 36 Chironomus species from the Palearctic, or Holarctic, and Australasia. The concatenated sequence of 1281 bp from both genes was used to investigate the phylogenetic relationships among these species. The nucleotide sequence alignments were used for construction of phylogenetic trees based on maximum-parsimony and neighbor-joining methods. Both techniques produced similar phylogenies. Monophyly of the genus Chironomus is supported by a bootstrap value of 100% at the basal branch. Six clusters of species have been revealed with high bootstrap values supporting both monophyly of each cluster and the validity of the branching order within each cluster. Four species, C. circumdatus, C. nepeanensis, C. dorsalis, and C. crassiforceps, cannot be placed into any cluster. Cytological phylogenies were constructed using the same set of species, except for C. biwaprimus. These trees showed many similarities to that obtained from the mitochondrial (mt) sequence analysis, but also a number of significant differences. When compared with the tree constructed from the sequence of 23 species available for one of the globin genes, globin 2b (gb2b), there was better support for the mt tree than for the cytological trees. An intron, which varies in its occurrence and position in gb2b, was also investigated and the distribution of the introns supports the phylogenetic history of the genus Chironomus obtained with mt data. The differences observed in the cytological trees seem to be attributable more to the retention of the same chromosome banding sequence across several species, rather than convergent evolutionary events. An important question is the determination of the position of the subgenus Camptochironomus in relation to the representatives of the nominal subgenus Chironomus, since it has been suggested that this is a separate genus. The Camptochironomus species are internal to the trees and have arisen more recently than some of the species of the subgenus Chironomus, indicating that they are not sufficiently differentiated to be considered more than a subgenus.     

Divergence of two forms of Triphoturus in the eastern Pacific based on mtDNA cytochrome b gene sequences and larval morphology

Divergence between two eastern Pacific forms of Triphoturus , currently considered to belong to the same species was tested by DNA sequences of the cytochrome b gene (DNA obtained from larvae collected in northern Chile and from adults in the Southern California Bight) and examination of larval characters. The number of apparently fixed substitutions (12 among 31 variable sites, out of 1001 bases) was high and the pattern of mid‐lateral trunk pigmentation in larvae also differed consistently between the two forms. The results support the separate species status for T. mexicanus (North America) and T. oculeus (Central‐South America).     

基于线粒体基因Cytb和COI的蝗科中五亚科分子系统发育关系分析（直翅目: 蝗总科）（英文）

本研究基于Cytb 基因和COI基因的部分序列来推断17种蝗虫之间的系统发育关系。这17种蝗虫均采自国内,代表了蝗科(Acrididae)5个亚科：黑蝗亚科(Melanoplinae)、斑腿蝗亚科(Catantopinae)、刺胸蝗亚科(Cyrtacanthacridinae)、斑翅蝗亚科(Oedipodinae)和大足蝗亚科(Gomphocerinae)。采用联合序列方法进行分析,结果显示：Cytb 和COI联合序列长度为1 998 bp,其中A和T总含量为72.13%,G和C总含量为27.87%。联合序列共包含了889个保守位点,1 109个变异位点,在这些变异位点中有838个简约信息位点。系统发生树采用邻接法（NJ）、最大简约法（MP）和最大似然法（ML）进行构建。使用蜢总科的变色乌蜢Erianthus versicolor 和 Erianthus sp. 两个种作为外群。结果表明：大足蝗亚科和斑腿蝗亚科的单系性没有得到支持。斑翅蝗亚科内部各种聚成一个大支,在本研究中该亚科的单系性得到支持,与前人的研究结论相同。大足蝗亚科、斑腿蝗亚科、刺胸蝗亚科和黑蝗亚科这4科关系非常近,可以考虑将其合并为一个亚科。同时,我们发现基于Cytb和COI基因联合序列推断蝗科内各亚科间的系统发生关系并不十分可靠。     

基于Cytb和COⅠ基因部分序列的15种麻蝇之间的系统发育关系(双翅目：麻蝇科)

本研究通过测序Cytb基因和COⅠ基因的部分序列来推定15种麻蝇之间的系统发育关系。在世界麻蝇名录中,本研究的15种麻蝇能够代表麻蝇属Sarcophaga的6个亚属。连接序列（972 bp）被用于系统发育分析;分析方法包括了了最大简约法、最大似然法以及贝叶斯法。我们的结果提示了亚麻蝇亚属Parasarcophaga、别麻蝇亚属Boettcherisca以及红麻蝇亚属Liopygia的单系性,同时也表明蛇麻蝇亚属Liosarcophaga和德麻蝇亚属Pandelleisca并不是单源的。不过,目前的研究并不能分辨野德麻蝇S. (Pandelleisca) similis和峨眉叉麻蝇S. (Robineauella) coei的系统发育位置。此外,最大简约分析和似然功能分析在scopariiformis-iwuensis进化枝和polystylata-hui进化枝的关系上产生了不一致的系统发育推断。因此,后续研究不仅需要其他的分子标记,也需要更多的分类取样。     

Molecular phylogeny of the chipmunks inferred from Mitochondrial cytochrome b and cytochrome oxidase II gene sequences

There are currently 25 recognized species of the chipmunk genus Tamias. In this study we sequenced the complete mitochondrial cytochrome b (cyt b) gene of 23 Tamias species. We analyzed the cyt b sequence and then analyzed a combined data set of cyt b along with a previous data set of cytochrome oxidase subunit II (COII) sequence. Maximum-likelihood was used to further test the fit of models of evolution to the cyt b data. Other sciurid cyt b sequence was added to examine the evolution of Tamias in the context of other sciurids. Relationships among Tamias species are discussed, particularly the possibility of a current sorting event among taxa of the southwestern United States and the extreme divergences among the three subgenera (Neotamias, Eutamias, and Tamias).     

Relationship among coelacanths,lungfishes, and tetrapods: A phylogenetic analysis based on mitochondrial cytochrome oxidase I gene sequences

To clarify the relationship among coelacanths, lungfishes, and tetrapods, the amino acid sequences deduced from the nucleotide sequences of mitochondrial cytochrome oxidase subunit I (COI) genes were compared. The phylogenetic tree of these animals, including the coelacanth Latimeria chalumnae and the lungfish Lepidosiren paradoxa, was inferred by several methods. These analyses consistently indicate a coelacanth/lungfish clade, to which little attention has been paid by previous authors with the exception of some morphologists. Overall evidence of other mitochondrial genes reported previously and the results of this study equally support the coelacanth/lungfish and lungfish/tetrapod clades, ruling out the coelacanth/tetrapod clade.Correspondence to: K. Watanabe 0592     

A DNA microarray for identification of selected Korean birds based on mitochondrial cytochrome c oxidase I gene sequences

DNA barcoding with the gene encoding cytochrome c oxidase I (COI) in the mitochondrial genome has been proposed as a standard marker to identify and discover animal species. Some migratory wild birds are suspected of transmitting avian influenza and pose a threat to aircraft safety because of bird strikes. We have previously reported the COI gene sequences of 92 Korean bird species. In the present study, we developed a DNA microarray to identify 17 selected bird species on the basis of nucleotide diversity. We designed and synthesized 19 specific oligonucleotide probes; these probes were arrayed on a silylated glass slide. The length of the probes was 19-24 bps. The COI sequences amplified from the tissues of the selected birds were labeled with a fluorescent probe for microarray hybridization, and unique hybridization patterns were detected for each selected species. These patterns may be considered diagnostic patterns for species identification. This microarray system will provide a sensitive and a high-throughput method for identification of Korean birds.     

Molecular phylogenetic relationship of Eplnephelus based on sequences of mtDNA Cty b

The mtDNA Cyt b gene was sequenced partially for Variola louti of Serranidae,Epinephelinae and seven endemic species of groupers-Epinephelus awoara,E.brunneus,E.coioides,E.longispinis,E.sexfasciatus,E.spilotoceps and E.tauvina in China.The seven endemic species and other seven foreign species of groupers--E,aeneus,E.caninus,E.drummondhayi,E,haifensis,E.labriformis,E.marginatus and E.multinotatus from the GenBank were combined and analysed as ingroup,while Variola louti was used as outgroup.We compared the 420 bp sequences of Cyt b among the 15 species and constructed two types of molecular phylogenetic trees with maximum parsimony method (MP)and neighbor-joining method (NJ) respectively.The results were as follows:(1) As to the base composition of mtDNA Cyt b sequence (402 bp) of 14 species of Epinepkelus,the content of (A + T) was 53.6%,higher than that of (G + C) (46.4%).The transition/transversion ratio was 4.78 with no mutation saturation.(2) The duster relationships between E.awoara and E.sexfasciatus,E.coioides and E.tauvina,E.longispinis and E.spilotoceps were consistent with phenotypes in taxonomy.(3) In the phylogenetic tree,the species in the Atlantic Ocean were associated closely with those in the Pacific Ocean,which suggested that the Cyt b sequences of Epinephelus were highly conserved.This may be attributed to the coordinate evolution.(4) In well-bred mating or heredity management,mating Epinephelus of the same branch should be avoided.It is likely to be an effective way to mate the species of the Atlantic Ocean with those of the Pacific Ocean to improve the inheritance species.     

Molecular phylogenetic relationship of Epinephelus based on sequences of mtDNA Cty b

The mtDNA Cyt b gene was sequenced partially for Variola louti of Serranidae, Epinephelinae and seven endemic species of groupers—Epinephelus awoara, E. brunneus, E. coioides, E. longispinis, E. sexfasciatus, E. spilotoceps and E. tauvina in China. The seven endemic species and other seven foreign species of groupers—E. aeneus, E. caninus, E. drummondhayi, E. haifensis, E. labriformis, E. marginatus and E. multinotatus from the GenBank were combined and analysed as ingroup, while Variola louti was used as outgroup. We compared the 420 bp sequences of Cyt b among the 15 species and constructed two types of molecular phylogenetic trees with maximum parsimony method (MP) and neighbor-joining method (NJ) respectively. The results were as follows: (1) As to the base composition of mtDNA Cyt b sequence (402 bp) of 14 species of Epinephelus, the content of (A + T) was 53.6%, higher than that of (G + C) (46.4%). The transition/transversion ratio was 4.78 with no mutation saturation. (2) The cluster relationships between E. awoara and E. sexfasciatus, E. coioides and E. tauvina, E. longispinis and E. spilotoceps were consistent with phenotypes in taxonomy. (3) In the phylogenetic tree, the species in the Atlantic Ocean were associated closely with those in the Pacific Ocean, which suggested that the Cyt b sequences of Epinephelus were highly conserved. This may be attributed to the coordinate evolution. (4) In wel1-bred mating or heredity management, mating Epinephelus of the same branch should be avoided. It is likely to be an effective way to mate the species of the Atlantic Ocean with those of the Pacific Ocean to improve the inheritance species.     

从细胞色素b部分序列探讨石斑鱼属的分子系统发育关系

石斑鱼的分类在学术界尚存在很多争议。本文采用PCR技术,测定了分布于中国的点带石斑鱼(Epinepheluscoioiaes)、青石斑鱼(E.awoara)、六带石斑鱼(E.sexfasciatus)、褐石斑鱼(E.brunneus),长棘石斑鱼(E.longispinis),吻斑石斑鱼(E.spilotoceps),巨石斑鱼(E.tauvina)以及石斑鱼亚科侧牙鲈属的侧牙鲈(Variola louti)的线粒体细胞色素b基因402bp的序列,结合GenBank提供的7种中国无记录的石斑鱼:青铜石斑鱼(E.aeneus)、海丰石斑鱼(E.haifensis)、犬牙石斑鱼(E.caninus)、东大西洋石斑鱼(E.marginatus)、白斑石斑鱼(E.multinotatus)、德氏石斑鱼(E.drummondhayi)、淡点石斑鱼(E.labriformis),把这14种石斑鱼作为内群,对他们的序列组成和结构特点进行了分析;并以同为科(Serranidae)、石斑鱼亚科(Epinephelinae)的侧牙鲈属(Variola)的侧牙鲈作外群,分别用MP法、NJ法对内、外群构建了分子系统树,结果表明:(1)14种石斑鱼402bp的mtDNA Cytb部分序列的碱基组成上,A+T的含量为53.6%高于G+C含量(46.4%),序列中转换颠换比为4.78,没有突变饱和;(2)青石斑鱼与六带石斑鱼、点带石斑鱼与巨石斑鱼、长棘石斑鱼与吻斑石斑鱼分别聚在一起,与形态分类结果一致;(3)系统树中,大西洋与太平洋种类各枝交替汇合,表明石斑鱼的Cytb序列有严格的保守性,也可能是协同进化的结果;(4)揭示在良种选配或遗传管理时,避免居于同枝的石斑鱼混交,将大西洋种类与太平洋种类杂交可能是遗传改良的一种途径。       

Molecular phylogeny and taxonomy of wood mice (genus Apodemus Kaup, 1829) based on complete mtDNA cytochrome b sequences, with emphasis on Chinese species

Phylogenetic relationships among 15 species of wood mice (genus Apodemus) were reconstructed to explore some long-standing taxonomic problems. The results provided support for the monophyly of the genus Apodemus, but could not reject the hypothesis of paraphyly for this genus. Our data divided the 15 species into four major groups: (1) the Sylvaemus group (A. sylvaticus, A. flavicollis, A. alpicola, and A. uralensis), (2) the Apodemus group (A. peninsulae, A. chevreri, A. agrarius, A. speciosus, A. draco, A. ilex, A. semotus, A. latronum, and A. mystacinus), (3) A. argenteus, and (4) A. gurkha. Our results also suggested that orestes should be a valid subspecies of A. draco rather than an independent species; in contrast, A. ilex from Yunnan may be regarded as a separate species rather than a synonym of orestes or draco. The species level status of A. latronum, tscherga as synonyms of A. uralensis, and A. chevrieri as a valid species and the closest sibling species of A. agrarius were further corroborated by our data. Applying a molecular clock with the divergences of Mus and Rattus set at 12 million years ago (Mya) as a calibration point, it was estimated that five old lineages (A. mystacinus and four major groups above) diverged in the late Miocene (7.82-12.74 Mya). Then the Apodemus group (excluding A. mystacinus) split into two subgroups: agrarius and draco, at about 7.17-9.95 Mya. Four species of the Sylvaemus group were estimated to diverge at about 2.92-5.21 Mya. The Hengduan Mountains Region was hypothesized to have played important roles in Apodemus evolutionary histories since the Pleistocene.