Independent transfer of mitochondrial chromosomes and plasmids during unstable vegetative fusion in Neurospora

The sporadic distribution of similar introns in organelle, nuclear ribosomal RNA and bacteriophage genes suggests that at least some of these introns are mobile genetic elements. Some plasmids in fungal mitochondria contain intron-like sequences and, like introns, they have scattered distributions within and among species. The occurrence and evolutionary importance of such horizontal transfer of DNA, not only between fungi, but among a wide range of organisms have been matters of much discussion. Here, we report experimental evidence for transfer of Neurospora mitochondrial plasmids from one mitochondrial genotype to another at high frequency during unstable vegetative cell fusion. Exchange of mitochondrial and nuclear genomes can also occur. These observations suggest that vegetative fusion may have a more important role in the mitochondrial genetic structure of natural populations than is generally thought, and may provide an explanation for the distribution of certain plasmids and possibly other mobile genetic elements.     

Specific role of mitochondrial electron transport in blood-stage Plasmodium falciparum

The origin of all mitochondria can be traced to the symbiotic arrangement that resulted in the emergence of eukaryotes in a world that was exclusively populated by prokaryotes. This arrangement, however, has been in continuous genetic flux: the varying degrees of gene loss and transfer from the mitochondrial genome in different eukaryotic lineages seem to signify an ongoing 'conflict' between the host and the symbiont. Eukaryotic parasites belonging to the phylum Apicomplexa provide an excellent example to support this view. These organisms contain the smallest mitochondrial genomes known, with an organization that differs among various genera; one genus, Cryptosporidium, seems to have lost the entire mitochondrial genome. Here we show that erythrocytic stages of the human malaria parasite Plasmodium falciparum seem to maintain an active mitochondrial electron transport chain to serve just one metabolic function: regeneration of ubiquinone required as the electron acceptor for dihydroorotate dehydrogenase, an essential enzyme for pyrimidine biosynthesis. Transgenic P. falciparum parasites expressing Saccharomyces cerevisiae dihydroorotate dehydrogenase, which does not require ubiquinone as an electron acceptor, were completely resistant to inhibitors of mitochondrial electron transport. Maintenance of mitochondrial membrane potential, however, was essential in these parasites, as indicated by their hypersensitivity to proguanil, a drug that collapsed the membrane potential in the presence of electron transport inhibitors. Thus, acquisition of just one enzyme can render mitochondrial electron transport nonessential in erythrocytic stages of P. falciparum.     

Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants

A central component of the endosymbiotic theory for the bacterial origin of the mitochondrion is that many of its genes were transferred to the nucleus. Most of this transfer occurred early in mitochondrial evolution; functional transfer of mitochondrial genes has ceased in animals. Although mitochondrial gene transfer continues to occur in plants, no comprehensive study of the frequency and timing of transfers during plant evolution has been conducted. Here we report frequent loss (26 times) and transfer to the nucleus of the mitochondrial gene rps10 among 277 diverse angiosperms. Characterization of nuclear rps10 genes from 16 out of 26 loss lineages implies that many independent, RNA-mediated rps10 transfers occurred during recent angiosperm evolution; each of the genes may represent a separate functional gene transfer. Thus, rps10 has been transferred to the nucleus at a surprisingly high rate during angiosperm evolution. The structures of several nuclear rps10 genes reveal diverse mechanisms by which transferred genes become activated, including parasitism of pre-existing nuclear genes for mitochondrial or cytoplasmic proteins, and activation without gain of a mitochondrial targeting sequence.     

Evolutionary distinctiveness of the endangered Kemp's ridley sea turtle

The endangered Kemp's ridley sea turtle (Lepidochelys kempi) nests almost exclusively at a single locality in the western Gulf of Mexico, whereas the olive ridley (L. olivacea) nests globally in warm oceans. Morphological similarities between kempi and olivacea, and a geographical distribution that "...makes no sense at all under modern conditions of climate and geography", raise questions about the degree of evolutionary divergence between these taxa. Analysis of mitochondrial (mt) DNA restriction sites shows that Kemp's ridley is distinct from the olive ridley in matriarchal phylogeny, and that the two are sister taxa with respect to other marine turtles. Separation of olive and the Kemp's ridley lineages may date to formation of the Isthmus of Panama, whereas the global spread of the olive ridley lineage occurred recently. In contrast to recent examples in which molecular genetic assessments challenged systematic assignments underlying conservation programmes, our mtDNA data corroborate the taxonomy of an endangered form.     

基于12S rRNA 基因序列推断中国及北美部分滑蜥属（有鳞目:石龙子科）物种的生物地理和亲缘关系

许多东亚和北美的生物类群之间呈现较近的亲缘关系,格雷分布即指这种生物洲际间断分布的现象.本文通过线粒体DNA (mtDNA) 12S rRNA基因序列分析,证明北美的滑蜥属Scincella (Squamata: Scincidae)物种Sc. lateralis 与中国的滑蜥属南滑蜥种组呈现典型的格雷分布. 南滑蜥种组包括宁波滑蜥Sc. modesta,秦岭滑蜥Sc. tsinlingensis,南滑蜥Sc. reevesii,和一个采自广东鼎湖山自然保护区的未命名种Scincella indet..这个鼎湖山未命名种并不具备滑蜥属所特有的鉴别性特征“睑窗”,但显示它与Sc. modesta,Sc. tsinlingensis都是由Sc. reevesii演化而来的近缘种.证实了之前认为亚洲的蜓蜥属Sphenomorphus 与滑蜥属Scincella是复系的观点,目前美洲物种Sp. cherriei应隶属于滑蜥属Scincella,具睑窗或不具睑窗的物种分别出现在系统树的不同分支中）.支持前人将Kaestlea travancorica从滑蜥属中划分出去的观点.根据分子钟估算,北美的滑蜥从它们的中国祖先分化出来的时间可追溯到第三纪中新世,约7.3-21.6百万年前,当时白令陆桥还露出海平面而且气候湿润. 该研究为洲际分布的物种的系统发育和生物地理研究提供了理论依据.     

羟基取代双烷烃链苯磺酸盐水气界面单层膜的分子动力学模拟

采用分子动力学模拟方法考察2-羟基-3,5-烷基苯磺酸钠表面活性剂分子在水气界面形成单层膜的过程,通过体系各组分的密度分布分析单层膜的形态,采用径向分布函数和氢键分布考察含有羟基的极性基在界面处的吸附构型,并根据转动时间相关函数对双疏水链的吸附构型进行分析。结果表明:羟基的存在减弱了极性基之间的静电排斥作用,增加了分子的饱和吸附量;两条烷烃链具有不同的界面吸附构型,烷烃链间的叠加缠绕增强了溶剂对表面活性剂分子的疏水力作用。     

Accelerated evolution of a false-truffle from a mushroom ancestor

THE false-truffles (Hymenogastrales) are a group of basidomycetous fungi that produce underground truffle-like basidiocarps. They are generally believed to be independently derived from several mushroom lineages, but extensive morphological divergence often obscures recognition of these phylogenetic connections. Comparisons of mitochondrial DNA now demonstrate a surprisingly close relationship between species of false-truffles in the genus Rhizopogon (Hymenogastraceae) and the mushroom genus Suillus (Boletaceae). The striking morphological differences separating all Suillus species from Rhizopogon imply an acceleration in the rate of morphological change relative to molecular change during the evolution of these false-truffles from their mushroom ancestors. This acceleration can best be explained by rapid morphological divergence resulting from selective pressures which may have acted on a small number of developmental genes.     

Antiquity of clonal salamander lineages revealed by mitochondrial DNA.

The existence of clonally reproducing vertebrates has often served as a foil in attempts to explain the near-ubiquity of sexual reproduction in eukaryotes, but the absence of recombination, with its attendant limitation of new genotypes to those produced through mutations, restricts the adaptive ability of clonal organisms. It has been argued, therefore, that clonal vertebrate taxa have short lifespans. Variation in mitochondrial DNA (mtDNA) within clonal populations is interpreted instead as reflecting multiple, although limited, independent hybridization events. On the basis of an analysis of an average of 373 nucleotide pairs, we report here that the mtDNA of clonal, hybrid, gynogenetic mole salamanders (Ambystoma, Ambystomatidae) differs by 5% or more from mtDNA of their closest possible sexual relatives (A. jeffersonianum, A. laterale and A. texanum). Assuming usual rates of mtDNA divergence, these lineages have persisted for about 5 million years, far longer than estimated for other clonal vertebrate populations. The low mtDNA variability in the clonal lineages suggests that they have undergone population reductions during the Pleistocene.     

Complex hybrid origin of genetic caste determination in harvester ants

Caste differentiation and division of labour are the hallmarks of insect societies and at the root of their ecological success. Kin selection predicts that caste determination should result from environmentally induced differences in gene expression, a prediction largely supported by empirical data. However, two exceptional cases of genetically determined caste differentiation have recently been found in harvester ants. Here we show that genetic caste determination evolved in these populations after complex hybridization events. We identified four distinct genetic lineages, each consisting of unique blends of the genomes of the parental species, presumably Pogonomyrmex barbatus and P. rugosus. Crosses between lineages H1 and H2 and between J1 and J2 give rise to workers, whereas queens develop from within-lineage matings. Although historical gene flow is evident, genetic exchange among lineages and between lineages and the parental species no longer occurs. This unusual system of caste determination seems to be evolutionarily stable.     

Genetic evidence for female host-specific races of the common cuckoo

The common cuckoo Cuculus canorus is divided into host-specific races (gentes). Females of each race lay a distinctive egg type that tends to match the host's eggs, for instance, brown and spotted for meadow pipit hosts or plain blue for redstart hosts. The puzzle is how these gentes remain distinct. Here, we provide genetic evidence that gentes are restricted to female lineages, with cross mating by males maintaining the common cuckoo genetically as one species. We show that there is differentiation between gentes in maternally inherited mitochondrial DNA, but not in microsatellite loci of nuclear DNA. This supports recent behavioural evidence that female, but not male, common cuckoos specialize on a particular host, and is consistent with the possibility that genes affecting cuckoo egg type are located on the female-specific W sex chromosome. Our results also support the ideas that common cuckoos often switched hosts during evolution, and that some gentes may have multiple, independent origins, due to colonization by separate ancestral lineages.     

Influence of seasonal migration on geographic distribution of mitochondrial DNA haplotypes in humpback whales

Humpback whales (Megaptera novaeangliae) migrate nearly 10,000 km each year between summer feeding grounds in temperate or near-polar waters and winter breeding grounds in shallow tropical waters. Observations of marked individuals suggest that major oceanic populations of humpback whales are divided into a number of distinct seasonal subpopulations which are not separated by obvious geographic barriers. To test whether these observed patterns of distribution and migration are reflected in the genetic structure of populations, we looked for variation in the mitochondrial DNA of 84 individual humpback whales on different feeding and wintering grounds of the North Pacific and western North Atlantic oceans. On the basis of restriction-fragment analysis, we now report a marked segregation of mitochondrial DNA haplotypes among subpopulations as well as between the two oceans. We interpret this segregation to be the consequence of maternally directed fidelity to migratory destinations.     

Attribute level lineage in uncertain data with dependencies

In uncertain data management, lineages are often used for probability computation of result tuples. However, most of existing works focus on tuple level lineage, which results in imprecise data derivation. Besides, correlations among attributes cannot be captured. In this paper, for base tuples with multiple uncertain attributes, we define attribute level annotation to annotate each attribute. Utilizing these annotations to generate lineages of result tuples can realize more precise derivation. Simultaneously, they can be used for dependency graph construction. Utilizing dependency graph, we can represent not only constraints on schemas but also correlations among attributes. Combining the dependency graph and attribute level lineage, we can correctly compute probabilities of result tuples and precisely derivate data. In experiments, comparing lineage on tuple level and attribute level, it shows that our method has advantages on derivation precision and storage cost.     

Evidence from mitochondrial DNA that African honey bees spread as continuous maternal lineages

African honey bees have populated much of South and Central America and will soon enter the United States. The mechanism by which they have spread is controversial. Africanization may be largely the result of paternal gene flow into extant European populations or, alternatively, of maternal migration of feral swarms that have maintained an African genetic integrity. We have been using both mitochondrial and nuclear DNA restriction fragment length polymorphisms to follow the population dynamics between European and African bees. In earlier reports, we suggested that if African honey bees had distinctive mitochondrial (mt) DNA, then it could potentially distinguish the relative contributions of swarming and mating to the Africanization process. Because mtDNA is maternally inherited, it would not be transmitted by mating drones and only transported by queens accompanying swarms. Furthermore, the presence of African mtDNA would reflect unbroken maternal lineages from the original bees introduced from Africa. The value of mtDNA for population studies in general has been reviewed recently. Here we report that 19 feral swarms, randomly caught in Mexico, all carried African mtDNA. Thus, the migrating force of the African honey bee in the American tropics consists of continuous African maternal lineages spreading as swarms. The mating of African drones to European queens seems to contribute little to African bee migration.     

Subcellular localization of several heavy metals of Hg, Cd and Pb in human liver

Liver, as an important metabolic and detoxicological organ of human body, can be used as a good bioindicator for evaluating body burden of environmental pollutants. Its elemental contents and their chemical forms are closely related to the status of human health and disease. In this paper, the liver samples collected from normal subjects were separated to different subcellular fractions of nuclei, mitochondria, lysosome, microsome and cytosol by differential centrifugation. Then their concentrations of heavy metals of As, Pb, Cd, and Hg were determined by atomic absorption and atomic fluorescent spectroscopy. Our results show no significant difference with literature ones when comparing their gross concentrations. In the case of their subcellular distribution, the Hg concentrations are higher in mitochondrial, microsomal and cytosolic fractions; the Cd concentrations are higher in cytosolic and mitochondrial fractions, while As highest in nuclear fraction. The highest concentration of Pb is found in microsomal fraction with similarity to Fe. Mercury in liver is mainly in the form of inorganic, and methylmercury ranged from 9% to 50% with the average value of 20.9% 13.3%. These results indicate that the cellular distribution and the accumulated target organelles are quite different among these heavy metals, which suggest their various pathways and toxic mechanism in vivo.     

Diverse transitional giant fleas from the Mesozoic era of China

Fleas are one of the major lineages of ectoparasitic insects and are now highly specialized for feeding on the blood of birds or mammals. This has isolated them among holometabolan insect orders, although they derive from the Antliophora (scorpionflies and true flies). Like most ectoparasitic lineages, their fossil record is meagre and confined to Cenozoic-era representatives of modern families, so that we lack evidence of the origins of fleas in the Mesozoic era. The origins of the first recognized Cretaceous stem-group flea, Tarwinia, remains highly controversial. Here we report fossils of the oldest definitive fleas--giant forms from the Middle Jurassic and Early Cretaceous periods of China. They exhibit many defining features of fleas but retain primitive traits such as non-jumping hindlegs. More importantly, all have stout and elongate sucking siphons for piercing the hides of their hosts, implying that these fleas may be rooted among the pollinating 'long siphonate' scorpionflies of the Mesozoic. Their special morphology suggests that their earliest hosts were hairy or feathered 'reptilians', and that they radiated to mammalian and bird hosts later in the Cenozoic.     

The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes

Angiosperms have dominated the Earth's vegetation since the mid-Cretaceous (90 million years ago), providing much of our food, fibre, medicine and timber, yet their origin and early evolution have remained enigmatic for over a century. One part of the enigma lies in the difficulty of identifying the earliest angiosperms; the other involves the uncertainty regarding the sister group of angiosperms among extant and fossil gymnosperms. Here we report a phylogenetic analysis of DNA sequences of five mitochondrial, plastid and nuclear genes (total aligned length 8,733 base pairs), from all basal angiosperm and gymnosperm lineages (105 species, 103 genera and 63 families). Our study demonstrates that Amborella, Nymphaeales and Illiciales-Trimeniaceae-Austrobaileya represent the first stage of angiosperm evolution, with Amborella being sister to all other angiosperms. We also show that Gnetales are related to the conifers and are not sister to the angiosperms, thus refuting the Anthophyte Hypothesis. These results have far-reaching implications for our understanding of diversification, adaptation, genome evolution and development of the angiosperms.     

Estimating divergence times among subfamilies in Nymphalidae

The mitochondrial cytochrome oxidase subunit Ⅰ （COⅠ） gene and the nuclear elongation factor 1α （EF-1α） gene were sequenced from 13 species of Nymphalidae. Phylogenetic trees of Nymphalidae, which is the largest family in butterflies, were constructed based on the sequences determined from 13 species sequenced in our laboratory and an additional 43 species obtained from GenBank using the maximum likelihood （ML） and Bayesian methods. Relative-rate tests between lineages in these phylogenetic trees were performed. On the basis of the results of the relative-rate tests and fossil information of Satyrinae, Nymphalinae and Biblidinae, the average divergence times among the subfamilies are estimated as 44.2-87.1 million years ago （Ma）. These results will be helpful for better understanding of the origin and evolution of this family, as well as the divergence time of butterflies and other complex taxa.     

Ancestry of unisexual salamanders.

In eastern North America there are populations of all-female salamanders that incorporate the nuclear genomes of two or three of four sympatric bisexual species. The hybrids can be diploid, triploid, tetraploid or pentaploid, and 18 different combinations have been reported. All hybrids require sperm from a sympatric male of one of the bisexual species to reproduce, but the sperm may or may not be incorporated in the egg. Some of the hybrids are believed to represent separate, clonal species, but little is known of the origin of this hybrid complex. Vertebrate mitochondrial DNA is inherited maternally, allowing identification of the female parent that gave rise to hybrid lineages. A portion of the cytochrome b gene was sequenced from diploid and triploid hybrids that represent combinations of all four species. Nearly all hybrids had a similar mitochondrial genome sequence, independent of nuclear genome composition and ploidy, and the sequence was distinct from that of any of the four bisexual species. The hybrids maintain a mitochondrial lineage that has evolved independently of their nuclear genome and represent the most ancient known unisexual vertebrate lineage.