The position of the retinal area centralis changes with age in Champsocephalus gunnari (Channichthyidae), a predatory fish from coastal Antarctic waters

Histological examinations of the topographical distribution and the area of highest density (the area centralis: AC) of presumed retinal ganglion cells found in the retina in 0- to 6-year-old Champsocephalus gunnari revealed differences between younger and older fish. Individuals of up to 2 years of age had the AC in the temporal retina, whereas in 3-, 4-, 5- and 6-year-old fish it was positioned in the ventro-temporal region of the retina. The main visual axis in the pitch plane of C. gunnari was shown to shift from facing forward to an upward-forward direction during growth, corresponding to the habitat change in this species from pelagic to benthic. Moreover, the AC in 0- to 3-year-old fish was near the retinal periphery, but displaced towards the inner retina in 4- to 6-year-old fish. This means that the visual axis in the horizontal plane of the younger fish was directed towards the frontal sector of vision, while in the older fish a slightly more lateral position was favoured. Therefore, younger fish can be expected to possess superior binocular vision when it comes to prey closely in front of them, but in older fish it seems more important to have a wider visual field to detect prey (and possibly predators) within a greater volume of water.     

Speciation in North American black basses,Micropterus (Actinopterygii: Centrarchidae)

Abstract.— The Pleistocene Epoch has been frequently cited as a period of intense speciation for a significant portion of temperate continental biotas. To critically assess the role of Pleistocene glaciations on the evolution of the freshwater fish clade Micropterus , we use a phylogenetic analysis of complete gene sequences from two mitochondrial genes (cytochrome b and ND2), and a fossil calibration of the molecular clock to estimate ages of speciation events and rates of diversification. The absence of substantial morphological and ecological divergence together with endemism of five of the eight species in North American tributaries of the Gulf of Mexico may be interpreted as the result of a recent Pleistocene origin for these species. Speciation dates in Micropterus range from 1.01 ± 0.32 to 11.17 ± 1.02 million years ago. Only one speciation event is dated to the Pleistocene, and rates of diversification are not significantly variable in Micropterus. The premise that the Pleistocene was an exceptional period of speciation in Micropterus is not supported. Instead, a Gulf Coast allopatric speciation model is proposed, and predicts periods of dynamic speciation driven by sea level fluctuations in the Late Miocene and Pliocene. The Pleistocene, however, was a period of significant intraspecific mitochondrial lineage diversification. The application of the Gulf Coast allopatric speciation model to the remaining aquatic fauna of the Gulf of Mexico coast in North America will rely on robust phylogenetic hypotheses and accurate age estimations of speciation events.     

蚕类昆虫线粒体DNA研究及其在起源与进化研究中的应用

线粒体DNA(mtDNA)属母系遗传,进化速率较核基因快且基因组结构相对简单,已作为理想的分子标记广泛应用于昆虫群体遗传学及分子系统学等研究。本文对蚕类昆虫线粒体DNA在分子水平上的最新研究进展进行了较详细的阐述,重点介绍了蚕类昆虫线粒体基因组的组成及特征、mtDNA克隆与多态性及在蚕类昆虫分子系统学研究中的应用等。     

The perils of single gene trees — mitochondrial versus single-copy nuclear DNA variation in white-eyes (Aves: Zosteropidae)

Phylogenetic relationships among animal populations and species commonly have been inferred from patterns of variation observed within a single gene system, most often the mitochondrial genome. Analysis of restriction site variation in the mitochondrial DNA of two species of white-eye ( Zosterops lateralis and Z. lutea ) in Australia produced a single gene tree that does not accurately represent the organismal tree. In contrast, patterns of variation at two anonymous, single-copy nuclear DNA loci revealed a phylogeography consistent with traditional classification of the species. Discordance between mitochondrial DNA and single-copy nuclear DNA variation is probably the result of past hybridization between Z. lateralis and Z. lutea , evidence of which has been lost from the nuclear genome by recombination. This study provides a clear empirical demonstration that single gene genealogies cannot be assumed to accurately represent the true phylogenies, and emphasizes the need for composite genetic analyses.     

Complete mitochondrial genomes of three skippers in the tribe Aeromachini (Lepidoptera: Hesperiidae: Hesperiinae) and their phylogenetic implications

The mitochondrial genome is now widely used in the study of phylogenetics and molecular evolution due to its maternal inheritance, fast evolutionary rate, and highly conserved gene content. To explore the phylogenetic relationships of the tribe Aeromachini within the subfamily Hesperiinae at the mitochondrial genomic level, we sequenced and annotated the complete mitogenomes of 3 skippers: Ampittia virgata, Halpe nephele, and Onryza maga (new mitogenomes for 2 genera) with a total length of 15,333 bp, 15,291 bp, and 15,381 bp, respectively. The mitogenomes all contain 13 protein‐coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a noncoding A + T‐rich region and are consistent with other lepidopterans in gene order and type. In addition, we reconstructed the phylogenetic trees of Hesperiinae using maximum likelihood (ML) and Bayesian inference (BI) methods based on mitogenomic data. Results show that the tribe Aeromachini in this study robustly constitute a monophyletic group in the subfamily Hesperiinae, with the relationships Coeliadinae + (Euschemoninae + (Pyrginae + ((Eudaminae + Tagiadinae) + (Heteropterinae + ((Trapezitinae + Barcinae) + Hesperiinae))))). Moreover, our study supports the view that Apostictopterus fuliginosus and Barca bicolor should be placed out of the subfamily Hesperiinae.     

眼镜王蛇线粒体基因组全序列分析

参照近缘物种线粒体基因序列共设计和合成了8对引物, 结合Ex Taq-PCR、TA克隆和步移测序技术, 文章首次获得眼镜王蛇线粒体基因组全序列(GenBank登录号: EU_921899)。该基因组全长17 267 bp, 共编码13个蛋白、2个rRNA、23个tRNA-- 其中tRNA-Ile基因发生了复制, 属于一种新的蛇类物种线粒体基因排列模式, 另外还含有2个非编码的富含AT的控制区。除了8个tRNA基因和1个蛋白基因由L链编码外, 其余均由H链编码, 其中H链编码基因的A和T含量接近, 而L链上A的含量则明显高于T。基于21种蛇合并的“12S＋16S”rRNA基因序列的系统发育分析表明, 眼镜王蛇属与眼镜蛇属亲缘关系较近, 两者与环蛇属共同构成一个单系群。作为国内外眼镜王蛇线粒体基因组全序列的首次报道, 上述结果对于蛇类物种分子系统发育和进化研究具有重要意义。     

蜱螨线粒体基因组研究进展

蜱螨亚纲包括蜱类和螨类, 是节肢动物中物种多样性最高的类群之一。本文综述了当前已测序的28种蜱螨线粒体基因组的研究成果。概括起来, 蜱螨线粒体基因组具有以下特点： （1）大小变异显著, 其中柑橘全爪螨Panonychus citri线粒体基因组在目前已测节肢动物中最小（13 077 bp）; （2）一般碱基组成偏向A和T, 但6种蜱螨具有相反的GC-偏斜（正值）; （3）基因组的碱基组成及A+T富集区的位置、 长度和拷贝数等变异显著, 其中4种叶螨的A+T含量最高, 其A+T富集区在目前已测节肢动物中最短（44~57 bp）; （4）基因高度重排, 特别是真螨总目的种类, 但重排与高分类阶元无相关性; （5）真螨总目部分螨类的tRNA基因极度缩短, 不能形成经典的三叶草二级结构。作者建议要进一步测定更多蜱螨的线粒体基因组, 验证蜱螨非典型tRNA基因的生物学功能性, 分析蜱螨线粒体基因组的分子进化机制, 开展蜱螨线粒体转录组研究等。     

The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae

The currently available yeast mitochondrial DNA (mtDNA) sequence is incomplete, contains many errors and is derived from several polymorphic strains. Here, we report that the mtDNA sequence of the strain used for nuclear genome sequencing assembles into a circular map of 85 779 bp which includes 10 kb of new sequence. We give a list of seven small hypothetical open reading frames (ORFs). Hot spots of point mutations are found in exons near the insertion sites of optional mobile group I intron-related sequences. Our data suggest that shuffling of mobile elements plays an important role in the remodelling of the yeast mitochondrial genome.     

The complete nucleotide sequence of the mitochondrial DNA genome of the rainbow trout,Oncorhynchus mykiss

The complete nucleotide sequence of the mitochondrial DNA of the rainbow trout, Onchorynchus mykiss, has been determined. The total length of the molecule is 16,660 bp. The rainbow trout mitochondrial DNA has the same organization described in eutherian mammals, the clawed frog (Xenopus laevis), and the two fish species, Oriental stream loach (Crossotoma lacustre) and carp (Cyprinus carpio). Alignment and comparison of the deduced amino acid sequences of the 13 proteins encoded by rainbow trout and other vertebrate mitochondrial genomes allowed us to estimate that COI is the most conserved mitochondrial subunit (amino acid identity ranging from 85.6% to 94.8%) whereas ATPase 8 is the most variable one (amino acid identity ranging from 30.8% to 70.4%). Putative secondary structures for the 22 tRNAs found in the molecule are given along with an extensive comparison of tRNA sequences among representative species of each major group of vertebrates. In this sense, an unusual cloverleaf structure for the tRNA^Ser(AGY) is proposed. A stem-loop structure inferred for the origin of the L-strand replication (O_L) and the presence of a large polycytidine tract in the O_L loop is described. The existence of this stretch instead of the usual T-rich sequence reported so far in mammal mtDNAs is explained in terms of a less-strict template dependence of the RNA primase involved in the initiation of L-strand replication. Correspondence to: J.M. Bautista     

林氏按蚊线粒体全基因组序列的测定及基于线粒体基因组的按蚊属系统发育分析(英文)

【目的】对林氏按蚊Anopheles lindesayi完整的线粒体基因组进行测序及分析,依据已知的线粒体基因组构建并讨论按蚊属蚊虫的分子系统发育关系。【方法】对林氏按蚊线粒体基因组进行测序、注释,并对其基本特征和基本组成进行分析。基于串联的13个蛋白质编码基因的核苷酸序列和氨基酸序列,用ML法和贝叶斯法构建林氏按蚊和按蚊属其他32种蚊虫的系统发育树,据此探讨按蚊属蚊虫的系统发育关系和系统分类。【结果】林氏按蚊线粒体基因组全长为15 366 bp,包含13个蛋白质编码基因,22个tRNA基因,2个rRNA基因和一段控制区。林氏按蚊线粒体基因组呈现明显的AT偏斜和GC偏斜,AT偏斜为正,GC偏斜为负。除了COX1使用TCG和ND5使用GTG作为起始密码子以外,其他蛋白质编码基因的起始密码子均遵循ATN原则;终止密码子为TAA或者T。除了tRNA^Ser(AGN)以外,其他的tRNA基因均呈现典型的三叶草二级结构。控制区AT含量最高,为94.54%。滑窗分析显示蛋白质编码基因是用于构建亚属或属水平系统发育关系的最佳分子标记。系统发育树强烈支持塞蚊亚属Cellia、按蚊亚属Anopheles、徕蚊亚属Nyssorhynchus和柯特蚊亚属Kerteszia均为单系群。小五斑按蚊An. atroparvus和四斑按蚊An. quadrimaculatus A这两个种聚到一起,从传统的形态分类上讲,它们和林氏按蚊均属于按蚊亚属按蚊系蚊虫。但本研究构建的4个系统发育树均显示,(小五斑按蚊An. atroparvus+四斑按蚊An. quadrimaculatus A)和林氏按蚊被属于迈蚊系的中华按蚊分开,这为两个系的分类提供了新的论点。【结论】本研究获得了林氏按蚊的完整的线粒体基因组,探析了按蚊属的线粒体基因组特征和系统发育关系,为进一步研究蚊科线粒体基因组和系统发育关系提供了依据。     

Characterization of the complete mitochondrial genome of Phodopus roborovskii (Rodentia: Cricetidae) and systematic implications for Cricetinae phylogenetics

Phodopus roborovskii (subfamily Cricetinae) is widely distributed in the northern arid regions of China. This study reports its complete mitochondrial genome (mitogenome) for the first time. The complete sequence was 16,273 bp long, including 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and 1 major noncoding region. The base composition and codon usage were described. The putative origin of replication for the light strand (O_L) of P. roborovskii was approximately 45 bp long and was highly conserved in the stem-loop and adjacent sequences, but the starting sequence of replication varied between genera among Rodentia. We analyzed the three domains of the D-loop region, and the results indicated that the central domain had higher G + C content and lower A + T content than two peripheral domains. Phylogenetic analyses indicated high resolution in four main divergent clades using mitogenomes data within Cricetidae. Within Cricetinae clade, P. roborovskii was at basal position which was in line with previous researches, and it shared a common ancestor with other extant hamsters. This work validated previous molecular and karyotype researches using mitogenomes data, and provided a set of useful data on phylogeny and molecular evolution in Cricetidae species.     

The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plants

The phylogenetic positions of bryophytes and charophytes, together with their genome features, are important for understanding early land plant evolution. Here we report the complete nucleotide sequence (105,340 bp) of the circular-mapping mitochondrial DNA of the moss Physcomitrella patens. Available evidence suggests that the multipartite structure of the mitochondrial genome in flowering plants does not occur in Physcomitrella. It contains genes for 3 rRNAs (rnl, rns, and rrn5), 24 tRNAs, and 42 conserved mitochondrial proteins (14 ribosomal proteins, 4 ccm proteins, 9 nicotinamide adenine dinucleotide dehydrogenase subunits, 5 ATPase subunits, 2 succinate dehydrogenase subunits, apocytochrome b, 3 cytochrome oxidase subunits, and 4 other proteins). We estimate that 5 tRNA genes are missing that might be encoded by the nuclear genome. The overall mitochondrial genome structure is similar in Physcomitrella, Chara vulgaris, Chaetosphaeridium globosum, and Marchantia polymorpha, with easily identifiable inversions and translocations. Significant synteny with angiosperm and chlorophyte mitochondrial genomes was not detected. Phylogenetic analysis of 18 conserved proteins suggests that the moss-liverwort clade is sister to angiosperms, which is consistent with a previous analysis of chloroplast genes but is not consistent with some analyses using mitochondrial sequences. In Physcomitrella, 27 introns are present within 16 genes. Nine of its intron positions are shared with angiosperms and 4 with Marchantia, which in turn shares only one intron position with angiosperms. The phylogenetic analysis as well as the syntenic structure suggest that the mitochondrial genomes of Physcomitrella and Marchantia retain prototype features among land plant mitochondrial genomes.     

绿眼赛茧蜂线粒体基因组全序列测定和分析

【目的】测定绿眼赛茧蜂Zele chlorophthalmus线粒体基因组全序列,分析其基因组结构及茧蜂科(Braconidae)部分类群的系统发育关系。【方法】利用Illumina MiSeq二代测序技术对绿眼赛茧蜂的线粒体基因组进行测序,对基因组序列进行拼装、注释,分析其结构特点和碱基组成;基于22种茧蜂科昆虫的COX1蛋白编码基因序列,应用最大似然法(ML)和邻接法(NJ)构建系统发育树,分析绿眼赛茧蜂与茧蜂科其他昆虫的系统发育关系。【结果】绿眼赛茧蜂线粒体基因组全长16 661 bp(GenBank登录号: MG822749),包含13个蛋白质编码基因、22个tRNA基因和2个rRNA基因,共37个基因,以及1个控制区。线粒体基因组有明显的核苷酸组成的偏倚,AT偏正,GC偏负,其A+T含量为82.83%。基因排列顺序与推测的昆虫祖先的序列不完全一致,tRNA基因7处发生重排。13个蛋白质编码基因均以ATN为起始密码子,以TAA为终止密码子。在22个tRNA基因二级结构中,除tRNA^His(H)缺失TΨC环和tRNA^Cys(C)仅剩二氢尿嘧啶(DHU)臂和反密码子臂外,其余tRNA基因均能形成典型的三叶草结构。基于COX1蛋白编码序列的系统发育分析结果显示,与绿眼赛茧蜂亲缘关系最近的是同属于赛茧蜂属的雪跗赛茧蜂Z. niveitarsis。【结论】本研究首次获得绿眼赛茧蜂线粒体基因组全序列。结果表明绿眼赛茧蜂隶属于优茧蜂亚科(Euphorinae)赛茧蜂属,并支持赛茧蜂属的单系性。     

Phylogeographic analysis of mitochondrial gene flow and introgression in the salamander, Plethodon shermani

Plethodon shermani comprises a series of geographically disjunct populations occupying high-elevation mountain isolates. These populations hybridize at their borders with salamanders of the Plethodon glutinosus species complex, and past range expansions inferred from Pleistocene climatic cycles may have increased the possible genetic interactions between P. shermani and species of the P. glutinosus complex. Because mitochondrial DNA haplotypes often show introgression across species borders, we survey mtDNA variation for evidence of past and ongoing genetic interactions between P. shermani, its close relative Plethodon cheoah, and species of the P. glutinosus complex. Ongoing hybridization with the P. glutinosus-complex species Plethodon teyahalee is accompanied by extensive mitochondrial introgression in some Unicoi populations of P. shermani, but it has little genetic impact on P. shermani populations outside hybrid zones at three other isolates (Tusquitee, Wayah Bald, Standing Indian). Some Unicoi populations of P. shermani exhibit mtDNA evidence of past hybridization with diverse lineages from P. aureolus and P. glutinosus. The Tusquitee isolate of P. shermani is also characterized by mtDNA haplotypes most closely related to Plethodon aureolus and P. glutinosus, presumably introduced by past genetic contact with these species or with introgressed populations of Unicoi P. shermani. The mtDNA variation in sampled populations of the Wayah Bald and Standing Indian isolates of P. shermani appears largely unaffected by ongoing hybridization. Principal components analyses of allozymic data indicate that P. shermani isolates collectively form a genetically homogeneous unit clearly demarcated from species with which they have had current or past genetic interactions. Rapid mtDNA introgression associated with transient contacts between P. shermani and other species permits a fine-level resolution of evolutionary lineages not evident from allozymic data.     

The mitochondrial genome of the firefly, Pyrocoelia rufa: complete DNA sequence, genome organization, and phylogenetic analysis with other insects

The complete nucleotide sequences of the mt genome from the firefly, Pyrococelia rufa (Coeleoptera: Lampyridae) was determined. The circular genome is 17,739-bp long, and contains a typical gene complement, order, and arrangement identical to Drosophila yacuba. The presence of 1,724-bp long intergenic spacer in the P. rufa mt genome is unique. The putative initiation codon for ND1 gene appears to be TTG, instead of frequently found ATN. All tRNAs showed stable canonical clover-leaf structure of other mt tRNAs, except for tRNA(Ser) (AGN), DHU arm of which could not form stable stem-loop structure. Phylogenetic analysis among insect orders confirmed a monophyletic Endopterygota, a monophyletic Mecopterida, a monophyletic Diptera, a monophyletic Lepidoptera, and a monophyletic Coleoptera, suggesting that the complete insect mt genome sequence has a resolving power in the diversification events within Endopterygota. However, internal relationships among three coleopteran species are not clear, and the inclusion of some insect orders (i.e., apterygotan T. gertschi) in the analysis provided inconsistent results compared to other molecular studies.     

Evolutionary implications of analyses of complete mitochondrial genomes across order Zoantharia (Cnidaria: Hexacorallia)

Cnidarians are early-diverging metazoans, but evolutionary aspects of some taxa are still poorly understood, as in the order Zoantharia (Anthozoa: Hexacorallia). Zoantharians have been divided into two suborders based on the arrangement of the fifth septae as complete (Macrocnemina) or incomplete (Brachycnemina). Previous molecular phylogenetic analyses have indicated the need for re-evaluation as Macrocnemina has been found to be paraphyletic. Despite many phylogenetic studies, the recovery of complete mitochondrial genomes (mt-genomes) for systematic and evolutionary studies of zoantharians has been limited. The present study represents the first to sequence the complete mt-genomes of members of eight of nine zoantharian families. Although all examined mt-genomes had the same gene order arrangement, there were variations among mt-genomes' sizes, nucleotide substitution rates, and introns. Only two species did not have the cox1 intron, which harbors a gene coding a homing endonuclease of the LAGLIDADG type. Our mitogenomic analyses also showed relatively high nucleotide diversity in mt-DNA regions other than the standard regions traditionally considered for DNA barcoding of this group. Phylogenetic analyses using 13 mt-genome protein-coding genes recovered a fully resolved tree with clear separation between macrocnemic representatives. Ancestral state reconstruction analyses revealed three main transitions in arrangement of the marginal musculature through the evolutionary history of the order. An “early” transition from reticulate mesogleal to a cteniform endodermal arrangement was followed by transitions that occurred in the common ancestor of the Brachycnemina and family Hydrozoanthidae. Our results indicate the need for clarification of higher-level phylogeny and taxonomy of Zoantharia.     

The dazzling array of basal branches in the mtDNA macrohaplogroup M from India as inferred from complete genomes

Many efforts based on complete mitochondrial DNA (mtDNA) genomeshave been made to depict the global mtDNA landscape, but thephylogeny of Indian macrohaplogroup M has not yet been resolvedin detail. To fill this lacuna, we took the same strategy asin our recent analysis of Indian mtDNA macrohaplogroup N andselected 56 mtDNAs from over 1,200 samples across India forcomplete sequencing, with the intention to cover all Indianautochthonous M lineages. As a result, the phylogenetic statusof previously identified haplogroups based on control-regionand/or partial coding-region information, such as M2, M3, M4,M5, M6, M30, and M33, was solidified or redefined here. Moreover,seven novel basal M haplogroups (viz., M34–M40) were identified,and yet another five singular branches of the M phylogeny werediscovered in the present study. The comparison of matrilinealcomponents among India, East Asia, Southeast Asia, and Oceaniaat the deepest level yielded a star-like and nonoverlappingpattern, reflecting a rapid mode of modern human dispersal alongthe Asian coast after the initial "out-of-Africa" event.     

黑尾地鸦线粒体基因组序列测定与分析

采用长PCR扩增的线粒体DNA和引物步移法, 测定并注释了中国特有鸟类-黑尾地鸦(Podoces hendersoni)的线粒体基因组全序列。黑尾地鸦的mtDNA序列全长16 867 bp, GenBank登录号GU592504。基因含量和排列次序与原鸡的一致, 包含13个蛋白编码基因、22个tRNA、2个rRNA和1个控制区(D-loop)。除COI基因以GTG作为起始密码子外, 其余12个蛋白质编码基因均以典型ATG密码子起始。11个蛋白编码基因以完全终止密码子TAA、AGG或AGA终止, COIII和ND4基因终止密码子为不完整的T。tRNA^Ser(AGY)的DHU臂缺失, tRNA^Leu(CUN)的反密码子环由9个碱基构成, 而不是标准的7个碱基。其余的20个tRNA基因的二级结构均属典型的三叶草结构。预测了rRNA的二级结构, 其中, 12S rRNA二级结构包含4个结构域, 43个茎环结构; 16S rRNA的二级结构包含6个结构域, 55个茎环结构。此外, 在其他鸟类控制区中所发现的F-box、D-box、C-box、B-box、Bird similarity-box和CSB1-box也同样存在于黑尾地鸦中。     

高桥仁蚧线粒体全基因组测序与分析

【目的】测定和分析半翅目(Hemiptera)仁蚧科(Aclerdidae)首个线粒体全基因组——高桥仁蚧Aclerda takahashii线粒体全基因组序列,并探讨与其他蚧虫类群的系统发育关系。【方法】基于Illumina测序技术进行高桥仁蚧线粒体全基因组测序,并进行生物信息学分析;基于已报道的15科31种半翅目昆虫的线粒体全基因组序列运用最大似然法(ML)和贝叶斯推断法(BI)构建半翅目系统发育树。【结果】高桥仁蚧线粒体基因组全长16 599 bp, AT含量高达84.51%。在该线粒体基因组中,缩减tRNA非常普遍, 10个tRNA缺失二氢尿嘧啶(DHU)臂或TΨC臂, tRNAser(S1)和tRNAser(S2)缺失DHU臂和TΨC臂。系统发育树显示, 与仁蚧科亲缘关系最近的是蚧科(Coccidae)。【结论】本研究报道了首个仁蚧科的线粒体基因组, 发现在高桥仁蚧线粒体基因组中存在普遍的tRNA缺臂现象, 为进一步系统地研究蚧虫线粒体基因组提供了数据支持。