Molecular phylogenetic systematics of twelve species of acipenseriformes based on mtDNA ND4L-ND4 gene sequence analysis

Acipenseriformes is an endangered primitive fish group, which occupies a special place in the history of ideas concerning fish evolution, even in vertebrate evolution. However, the classification and evolution of the fishes have been debated. The mitochondrial DNA (mtDNA) ND4L and partial ND4 genes were first sequenced in twelve species of the order Acipenseriformes, including endemic Chinese species. The following points were drawn from DNA sequences analysis: (i) the two species of Huso can be ascribed to Acipenser; (ii) A. dabryanus is the mostly closely related to A. sinensis, and most likely the landlocked form of A. sinensis; (iii) genus Acipenser in trans-Pacific region might have a common origin; (iv) mtDNA ND4L and ND4 genes are the ideal genetic markers for phylogenetic analysis of the order Acipenseriformes.

Molecular phylogenetic systematics of twelve species of acipenseriformes based on mtDNA ND4L-ND4 gene sequence analysis

Acipenseriformes is an endangered primitive fish group, which occupies a special place in the history of ideas concerning fish evolution, even in vertebrate evolution. However, the classification and evolution of the fishes have been debated. The mitochondrial DNA (mtDNA) ND4L and partial ND4 genes were first sequenced in twelve species of the order Acipenseriformes, including endemic Chinese species. The following points were drawn from DNA sequences analysis: (i) the two species of Huso can be ascribed to Acipenser; (ii) A. dabryanus is the mostly closely related to A. sinensis, and most likely the landlocked form of A. sinensis; (iii) genus Acipenser in trans-Pacific region might have a common origin; (iv) mtDNA ND4L and ND4 genes are the ideal genetic markers for phylogenetic analysis of the order Acipenseriformes.

12种鳃形目鱼类mt DNA NI4 L- NI4基因的序列变异及其分子系统学

鳃形目鱼类是一类在鱼类乃至脊椎动物进化史上占有很重要地位的古老濒 危鱼类，长期悬而未决的系统演化关系为世人瞩目.采用DNA测序技术首次测定了 包括中国特有鳃形目鱼类在内的12种鳃形目鱼类的mtDNA ND4L和ND4基因(703 by)的序列，并进行了分子系统学分析.从分子系统学的角度得出了如下结论:(1) 鲤属可以归并到鳃属;(2)达氏鳃与中华鳃的亲缘关系最近，很有可能为中华鳃的 一陆封类型;(3)环太平洋地区的鳃科鱼类可能有共同的起源;(4) ND4L和ND4基 因是进行鳃形目鱼类系统演化研究很好的遗传标记.

Phylogeny and evolution of the Drosophila nasuta subgroup based on mitochondrial ND4 and ND4L gene sequences

The sequences of the mitochondrial ND4 gene (1339 bp) and the ND4L gene (290 bp) were determined for all the 14 extant taxa of the Drosophila nasuta subgroup The average A + T content of ND4 genes is 76.5% and that of ND4L genes is 83.5%. A total of 114 variable sites were scored. The ND4 gene sequence divergence ranged from 0 to 5.4% within the subgroup. The substitution rate of the ND4 gene is about 1.25% per million years. The base substitution of the genesis strongly transition biased. Neighbor-joining and parsimony were used to construct a phylogeny based on the resultant sequence data set. According to these trees, five, distinct mtDNA clades can be identified. D. niveifrons represents the most diverged lineage. D, sulfurigaster bilimbata and D. kepulauana form two independent lineages. The other two clades are the kohkoa complex and the albomicans complex. The Kohkoa complex consists of D. sulfurigaster sulfurigaster, D. pulaua, D. kohkoa, and Taxon-F. The albomicans complex can be divided into two groups: D. nasuta, D. sulfurigaster neonasuta, D. sulfurigaster albostrigata, and D.. albomicans from Chiangmai form one group; and D. pallidifrons, Taxon-I, Taxon-J, and D. albomicans from China form the other group. High genetic differentiation was found among D. albomicans populations. Based on our phylogenetic results, we hypothesize that D. niveifrons diverged first from the D, nasuta subgroup in Papua New Guinea about 3.5 Mya. The ancestral population spread to the north and when it reached Borneo, it diversified sequentially into the kohkoa complex, D. s. bilimbata, and D. kepulauana. About 1 Mya, another radiation occurred when the ancestral populations reached the Indo-China Peninsula, forming the albomicans complex. Discrepancy between morphological groupings and phylogenetic results suggests that the male morphological traits may not be orthologous. (C) 1999 Academic Press.

High connectivity in rastrelliger kanagurta: Influence of historical signatures and migratory behaviour inferred from mtDNA Cytochrome b

Phylogeographic patterns and population structure of the pelagic Indian mackerel, Rastrelliger kanagurta were examined in 23 populations collected from the Indonesian-Malaysian Archipelago (IMA) and the West Indian Ocean (WIO). Despite the vast expanse of the IMA and neighbouring seas, no evidence for geographical structure was evident. An indication that R. kanagurta populations across this region are essentially panmictic. This study also revealed that historical isolation was insufficient for R. kanagurta to attain migration drift equilibrium. Two distinct subpopulations were detected between the WIO and the IMA (and adjacent populations); interpopulation genetic variation was high. A plausible explanation for the genetic differentiation observed between the IMA and WIO regions suggest historical isolation as a result of fluctuations in sea levels during the late Pleistocene. This occurrence resulted in the evolution of a phylogeographic break for this species to the north of the Andaman Sea.

Mitochondrial helicase Twinkle in mtDNA copy number regulation and a late-onset disease model

Mitochondrial diseases are caused by disturbances of the energy metabolism. The disorders range from severe childhood neurological diseases to muscle diseases of adults. Recently, mitochondrial dysfunction has also been found in Parkinson s disease, diabetes, certain types of cancer and premature aging. Mitochondria are the power plants of the cell but they also participate in the regulation of cell growth, signaling and cell death. Mitochondria have their own genetic material, mtDNA, which contains the genetic instructions for cellular respiration. Single cell may host thousands of mitochondria and several mtDNA molecules may reside inside single mitochondrion. All proteins needed for mtDNA maintenance are, however, encoded by the nuclear genome, and therefore, mutations of the corresponding genes can also cause mitochondrial disease. We have here studied the function of mitochondrial helicase Twinkle. Our research group has previously identified nuclear Twinkle gene mutations underlying an inherited adult-onset disorder, progressive external ophthalmoplegia (PEO). Characteristic for the PEO disease is the accumulation of multiple mtDNA deletions in tissues such as the muscle and brain. In this study, we have shown that Twinkle helicase is essential for mtDNA maintenance and that it is capable of regulating mtDNA copy number. Our results support the role of Twinkle as the mtDNA replication helicase. No cure is available for mitochondrial disease. Good disease models are needed for studies of the cause of disease and its progression and for treatment trials. Such disease model, which replicates the key features of the PEO disease, has been generated in this study. The model allows for careful inspection of how Twinkle mutations lead to mtDNA deletions and further causes the PEO disease. This model will be utilized in a range of studies addressing the delay of the disease onset and progression and in subsequent treatment trials. In conclusion, in this thesis fundamental knowledge of the function of the mitochondrial helicase Twinkle was gained. In addition, the first model for adult-onset mitochondrial disease was generated.

Demographic history of India and mtDNA-sequence diversity

The demographic history of India was examined by comparing mtDNA sequences obtained from members of three culturally divergent Indian subpopulations (endogamous caste groups). While an inferred tree revealed some clustering according to caste affiliation, there was no clear separation into three genetically distinct groups along caste lines. Comparison of pairwise nucleotide difference distributions, however, did indicate a difference in growth patterns between two of the castes. The Brahmin population appears to have undergone either a rapid expansion or steady growth. The low-ranking Mukri caste, however, may have either maintained a roughly constant population size or undergone multiple bottlenecks during that period. Comparison of the Indian sequences to those obtained from other populations, using a tree, revealed that the Indian sequences, along with ah other non-African samples, form a starlike cluster. This cluster may represent a major expansion, possibly originating in southern Asia, taking place at some point after modern humans initially left Africa.

The Expanded mtDNA Phylogeny of the Franco-Cantabrian Region Upholds the Pre-Neolithic Genetic Substrate of Basques

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Origin of immature loggerhead sea turtles (Caretta caretta) at Hutchinson Island, Florida: evidence from mtDNA markers

Loggerhead sea turtles (Caretta caretta) are migratory, long-lived, and slow maturing. They are difficult to study because they are seen rarely and their habitats range over vast stretches of the ocean. Movements of immature turtles between pelagic and coastal developmental habitats are particularly difficult to investigate because of inadequate tagging technologies and the difficulty in capturing significant numbers of turtles at sea. However, genetic markers found in mitochondrial DNA (mtDNA) provide a basis for predicting the origin of juvenile turtles in developmental habitats. Mixed stock analysis was used to determine which nesting populations were contributing individuals to a foraging aggregation of immature loggerhead turtles (mean 63.3 cm straight carapace length [SCL]) captured in coastal waters off Hutchinson Island, Florida. The results indicated that at least three different western Atlantic loggerhead sea turtle subpopulations contribute to this group: south Florida (69%), Mexico (20%), and northeast Florida-North Carolina (10%). The conservation and management of these immature sea turtles is complicated by their multinational genetic demographics.

麻栗坡县家马mtDNA多态性研究

对采自麻栗坡县的晋通马矮马各３匹的材料，所用２０种限制性内切酶中，有１６种可产生切点，平均每个个体获得５６条限制性片段。与其它家畜家一不同，家马有高度的ｍｔＤＮＡ多态性，６匹马均有自己独特的ｍｔＤ－ＮＡ基因型，提示该地家马可能为多起源，至少有多重母系，这些母系可追溯到１～１０万年前，与化石记载相一致。本次实验未找到将两种马区分开的特异性多态标记，这可能是同栖于同一生态环境中，相互交配，血液相融，而不是各自起源于自己原母系。由于所测样本数较少，尚不能得到区分两种马的一个统计学上的规律性来。云南地理地貌十分复杂，马的品种或类群较多，亦可能是多起源，其遗传多样性很丰富。因此，云南马是值得保护和重视的种质资源库。自８０年代以来，动物线粒体ＤＮＡ（ｍｔＤ－ＮＡ）在群体遗传及进化生物学研究中起着重要作用，由于其组成序列简单，母体遗传，且不存在重组，所以是追踪母系血统的理想标记和能对漂移血统进行识别￣［１］（Ｈａｒｒｉｓｏｎｌ９８９年）．在家养动物中，对ｍｔＤＮＡ多态性研究以前多在鸡、黄牛、猪中进行，它们的ｍｔＤＮＡ多态频率相当低￣［２］。Ｍａｒｔｈｅｗ和Ｒｙｄｅｒ（１９８６）的研究已涉及家马ｍｔＤＮＡ种内特异性的情况.

一种从鱼类卵巢制备地高辛标记 mtDNA 探针的简易方法

线粒体 DNA 限制性片段长度多态性(RFLP)分析, 已被广泛地应用于动物的系统进化和遗传多样性研究, 取得了许多有意义的结果. 线粒体 DNA RFLP 分析一般有两条途径: 一是从动物组织中提取 mtDNA 后, 酶切, 紫外灯下观察, 或放射性自显影. 这要求所提取的 mtDNA 量足够多, 或纯度相当高; 二是将基因组DNA酶切后, 用 mtDNA 探针进行 Southern 杂交. 该途径不需要专门提纯 mtDNA, 特别适合于微量 mtDNA 的 RFLP 分析进行 Southern 杂交分析, 关键在于要有高质量的探针. 用于制备探针的 mtDNA, 纯度要求较高, 一般采用氯化铯密度梯度离心或制备 mtDNA 克隆等方法获得. 这些方法, 不仅操作步骤繁锁, 而且设备条件要求高, 在一般实验室难以实施。

The origin of Mosuo people as revealed by mtDNA and Y chromosome variation

The Mosuo, living in the Lugu Lake area in northwest Yunnan Province, China, is the only matriarchal population in China. The Mosuo was officially identified as Naxi nationality although its relationship with Naxi remains controversial. We studied the gen

The mitochondrial genome organization of the rice frog, Fejervarya limnocharis (Amphibia : Anura): a new gene order in the vertebrate mtDNA

The mitochondrial DNA of the rice frog, Fejervarya limnocharis (Amphibia, Anura), was obtained using long-and-accurate polymerase chain reaction (LA-PCR) combining with subcloning method. The complete nucleotide sequence (17,717 bp) of mitochondrial genome was determined subsequently. This mitochondrial genome is characterized by four distinctive features: the translocation of ND5 gene, a cluster of rearranged tRNA genes (tRNA(Thr), tRNA(Pro), tRNA(Leu) ((CUN))) a tandem duplication of tRNA(Mer) gene, and eight large 89-bp tandem repeats in the control region, as well as three short noncoding regions containing two repeated motifs existing in the gene cluster of ND5/tRNA(Thr)/tRNA(Pro)/tRNA(Leu)/tRNA(Phe). The tandem duplication of gene regions followed by deletions of supernumerary genes can be invoked to explain the shuffling of tRNAM(Met) and a cluster of tRNA and ND5 genes, as observed in this study. Both ND5 gene translocation and tandem duplication of tRNA(Met) were first observed in the vertebrate mitochondrial genomes. (c) 2004 Elsevier B.V. All rights reserved.

Gene admixture in the Silk Road region of China: Evidence from mtDNA and melanocortin 1 receptor polymorphism

Mitochondrial DNA control region segment I sequences and melanocortin 1 receptor (MC1R) gene polymorphism were examined in ethnic populations in the silk road region of China. Both the frequencies of the MC1R variants and the results of mtDNA data in this region presented intermediate values between those of Europe and East and Southeast Asia, which suggested extensive gene admixture in this area and was in general agreement with previous studies. Phylogenetic analysis of the ethnic populations in the Silk Road region that based on mtDNA data didn't show expected cluster pattern according to their ethnogenesis. We suspect that a high migration rate in female among these closely related populations and other three demographic events might account for it.

古老人群 mtDNA 研究中存在的问题和对策

由于多种原因, 古老人类标本中的DNA 一般都有不同程度的降解, 在分析时只能得到短片段的 序列. 如何对这些序列片段的真实性进行甄别, 最大限度地挖掘出其中包含的信息, 是目前对古代人 群遗传结构分析及其他古DNA 研究中普遍存在的一个难题. 本文对近期国内古老人群mtDNA 研究中 存在的问题进行了评述, 并从mtDNA 世系的系统发育关系角度, 对新疆(包括邻近的中亚地区)古老人 群数据进行了重新分析. 结果显示, 这些古老DNA 数据的可靠性存在或多或少的问题; 结合现代不同 地理人群中的mtDNA 变异情况, 能够对获得的距今数千年前的mtDNA 的真实性进行判别和自检, 并 能有效地对序列信息进行解码. 同时, 对中亚地区古老人群mtDNA 数据重新分析的结果, 支持该地区 欧亚人群基因交流融合由来已久的推测.