The use of restriction endonucleases to measure mitochondrial DNA sequence relatedness in natural populations. III. Techniques and potential applications

Phylogenetic relationships of bitterling fishes (Teleostei: Cypriniformes: Acheilognathinae), inferred from mitochondrial cytochrome B sequences

Bitterling (Teleostei: Acheilognathinae) are small cyprinid fishes with a discrete distribution in East Asia and Europe. We used a complete mitochondrial cytochrome b sequence (1141 bp) from 49 species or subspecies in three genera (Tanakia, Rhodeus, and Acheilognathus), sampled across the major part of their distribution, to elucidate their phylogeny and biogeography, focusing particularly on their origin and dispersal. Based on high support value, the monophyletic Acheilognathinae separated into two major clades, Acheilognathus and Tanakia-Rhodeus. In the latter clade, the monophyly of Rhodeus was poorly supported, though it was topologically nested in Tanakia. On the basis of molecular-clock calibration, both clades diverged in the middle Miocene, with Tanakia-Rhodeus diverging slightly earlier than Acheilognathus. The Tanakia-Rhodeus clade expanded its distribution westward from the Far East, eventually reaching Europe, while Acheilognathus dispersed in the temperate regions of East Asia. A feature common to both clades is that most extant species, including Japanese endemics, appeared by the end of the Pliocene, corresponding with the present delineation of the Japanese archipelago. Autumn-spawning species with an embryonic diapause, unique to bitterling among cyprinid fishes, formed two distinct lineages (barbatulusrhombeus and longipinnis-typus) within Acheilognathus. The estimated time of divergence of the two lineages was approximately from the late Pliocene, a period characterized by glaciations. The timing of divergence suggests that the shift of spawning from spring to autumn, coupled with embryonic diapause, convergently emerged twice in the evolution of bitterling, possibly as an adaptation to the climate of the late Pliocene.

Mitochondrial DNA diversity of honey bees (Apis mellifera) from unmanaged colonies and swarms in the United States

To study the genetic diversity of honey bees (Apis mellifera L.) from unmanaged colonies in the United States, we sequenced a portion of the mitochondrial DNA COI-COII region. From the 530 to 1,230 bp amplicon, we observed 23 haplotypes from 247 samples collected from 12 states, representing three of the four A. mellifera lineages known to have been imported into the United States (C, M, and O). Six of the 13 C lineage haplotypes were not found in previous queen breeder studies in the United States. The O lineage accounted for 9% of unmanaged colonies which have not yet been reported in queen breeder studies. The M lineage accounted for a larger portion of unmanaged samples (7%) than queen breeder samples (3%). Based on our mitochondrial DNA data, the genetic diversity of unmanaged honey bees in the United States differs significantly from that of queen breeder populations (p < 0.00001). The detection of genetically distinct maternal lineages of unmanaged honey bees suggests that these haplotypes may have existed outside the managed honey bee population for a long period.

Relationship between two androgenetic clam species, Corbicula leana and Corbicula fluminea, inferred from mitochondrial cytochrome b and nuclear 28S rRNA markers

Two shell color types, yellow (type I) and brown (type II), of hermaphrodite Corbicula fluminea clams from Ritto, Shiga Prefecture, Japan, are sympatric with both male and hermaphrodite Corbicula leana. In the present study, the mitochondrial DNA (mtDNA) cytochrome b and nuclear 28S rRNA genes of C. fluminea were sequenced to construct a haplotype network in order to investigate the genetic relationship with C. leana. Ninety C. fluminea samples revealed only two cytb haplotypes; the majority (97.8%) were CB7, while the remainder were CB1. In C. leana, only CB1 was detected in hermaphrodites, but both CB1 and CB7 were detected in males. Nuclear 28S rRNA haplotypes of C. fluminea type I individuals were divergent from those of hermaphrodite C. leana. However, C. fluminea type I clams shared haplotypes with male C. leana individuals, whereas C. fluminea type II individuals shared haplotypes with both hermaphrodite and male C. leana samples. These results suggest that it may be difficult to define a clear genetic border between these species.

Molecular approaches to Taenia asiatica

Taenia solium, T. saginata, and T. asiatica are taeniid tapeworms that cause taeniasis in humans and cysticercosis in intermediate host animals. Taeniases remain an important public health concerns in the world. Molecular diagnostic methods using PCR assays have been developed for rapid and accurate detection of human infecting taeniid tapeworms, including the use of sequence-specific DNA probes, PCR-RFLP, and multiplex PCR. More recently, DNA diagnosis using PCR based on histopathological specimens such as 10% formalin-fixed paraffin-embedded and stained sections mounted on slides has been applied to cestode infections. The mitochondrial gene sequence is believed to be a very useful molecular marker for not only studying evolutionary relationships among distantly related taxa, but also for investigating the phylo-biogeography of closely related species. The complete sequence of the human Taenia tapeworms mitochondrial genomes were determined, and its organization and structure were compared to other human-tropic Taenia tapeworms for which complete mitochondrial sequence data were available. The multiplex PCR assay with the Ta4978F, Ts5058F, Tso7421F, and Rev7915 primers will be useful for differential diagnosis, molecular characterization, and epidemiological surveys of human Taenia tapeworms.

Dietary fatty acids modulate liver mitochondrial cardiolipin content and its fatty acid composition in rats with non alcoholic fatty liver disease

No data are reported on changes in mitochondrial membrane phospholipids in non-alcoholic fatty liver disease. We determined the content of mitochondrial membrane phospholipids from rats with non alcoholic liver steatosis, with a particular attention for cardiolipin (CL) content and its fatty acid composition, and their relation with the activity of the mitochondrial respiratory chain complexes. Different dietary fatty acid patterns leading to steatosis were explored. With high-fat diet, moderate macrosteatosis was observed and the liver mitochondrial phospholipid class distribution and CL fatty acids composition were modified. Indeed, both CL content and its C18:2n-6 content were increased with liver steatosis. Moreover, mitochondrial ATP synthase activity was positively correlated to the total CL content in liver phospholipid and to CL C18:2n-6 content while other complexes activity were negatively correlated to total CL content and/or CL C18:2n-6 content of liver mitochondria. The lard-rich diet increased liver CL synthase gene expression while the fish oil-rich diet increased the (n-3) polyunsaturated fatty acids content in CL. Thus, the diet may be a significant determinant of both the phospholipid class content and the fatty acid composition of liver mitochondrial membrane, and the activities of some of the respiratory chain complex enzymes may be influenced by dietary lipid amount in particular via modification of the CL content and fatty acid composition in phospholipid.

28S rDNA haplotypes of males are distinct from those of androgenetic hermaphrodites in the clam Corbicula leana

The clam Corbicula leana exists in two forms, hermaphrodites and males. Our previous study on mitochondrial DNA suggested that the male nuclear DNA might have derived from hermaphrodite C. leana relatively recently. To clarify the origin of males in the clam, sequences of the nuclear 28S rDNA divergent domain (which is 441-444 bp long) in androgenetic hermaphrodites and males and dioecious (bisexual) species were analyzed. Unexpectedly, the nuclear 28S rDNA haplotypes of males and hermaphrodites were distinct. Haplotype network analysis indicated that males and hermaphrodites are reproductively isolated from each other without sharing the same nuclear haplotype. These results support a hypothesis that the egg nuclear genome of androgenetic hermaphrodites is replaced by the male sperm genome, and only males develop after fertilization by a male spermatozoon.

Origin and possible role of males in hermaphroditic androgenetic Corbicula clams

Hermaphroditic Corbicula leana clams reproduce by androgenesis and have been regarded as simultaneous hermaphrodites. To date, there has been no report on the occurrence of male clams in hermaphroditic Corbicula. In an irrigation ditch in Shiga Prefecture, we found that 78.2% of C. leana specimens were males and 21.8% were hermaphrodites. Microfluorometric analysis revealed that males were diploids and hermaphrodites were triploids. All males produced nonreductional and biflagellate spermatozoa. The sequence analysis of mitochondrial DNA (cytochrome b, 621 bp) for 31 specimens of C. leana showed that four male and nine hermaphrodites shared the same H2 mtDNA haplotype; H1 was detected from 17 males and H3 was detected from one hermaphrodite. Coexisting C. fluminea clams also have haplotypes H1 and H2. Phylogenetic tree by a neighborjoining method based on the partial sequence of cytochrome b revealed that the haplotypes (H1- 3) of C. leana were evidently different from those of dioecious C. sandai (S1 and S2) and C. japonica (J1 and J2). These results suggest that males may be derived from hermaphrodite C. leana clams. The role of males in hermaphroditic populations is unknown. However, if the spermatozoon from a male is able to fertilize an egg from a hermaphrodite and the nuclear genome of the egg is expelled as polar bodies, the sperm nucleus could form a zygote nucleus. This mode of reproduction would allow the replacement of the nuclear genome.

The role of propagule pressure in the invasion success of bluegill sunfish, Lepomis macrochirus, in Japan

The bluegill sunfish, Lepomis macrochirus, is a widespread exotic species in Japan that is considered to have originated from 15 fish introduced from Guttenberg, Iowa, in 1960. Here, the genetic and phenotypic traits of Japanese populations were examined, together with 11 native populations of the USA using 10 microsatellite markers and six meristic traits. Phylogenetic analysis reconfirmed a single origin of Japanese populations, among which populations established in the 1960s were genetically close to Guttenberg population, keeping high genetic diversity comparable to the ancestral population. In contrast, genetic diversity of later-established populations significantly declined with genetic divergence from the ancestral population. Among the 1960s established populations, that from Lake Biwa showed a significant isolation-by-distance pattern with surrounding populations in which genetic bottlenecks increased with geographical distance from Lake Biwa. Although phenotypic divergence among populations was recognized in both neutral and adaptive traits, P(ST)-F(ST) comparisons showed that it is independent of neutral genetic divergence. Divergent selection was suggested in some populations from reservoirs with unstable habitats, while stabilizing selection was dominant. Accordingly, many Japanese populations of L. macrochirus appear to have derived from Lake Biwa population, expanding their distribution with population bottlenecks. Despite low propagule pressure, the invasion success of L. macrochirus is probably because of its drastic population growth in Lake Biwa shortly after its introduction, together with artificial transplantations. It not only enabled the avoidance of a loss in genetic diversity but also formed a major gene pool that supported local adaptation with high phenotypic plasticity.

Atypical mitochondrial DNA from the deep-sea scallop Placopecten magellanicus

The mitochondrial DNA of most metazoan animals is highly conserved in size, averaging about 17 kilobase paris (kbp). The mitochondrial DNA from the deep-sea scallop Placopecten magellanicus, in contrast, has been found to be approximately 34 kbp long. It is also highly variable in size from individual to individual and is unusual in the extent of its size variation. Mitochondrial DNAs from individuals collected at the same site differ by as much as 7 kbp. The size variation is due largely to differences in the number of copies of a tandemly repeated 1.2-kbp element.

Evolution of mitochondrial DNA in Drosophila subobscura

The colonization of the New World by the Palearctic species Drosophila subobscura was first detected in 1978 in South America and around 1982 in western North America. The ensuing dramatic expansion of the species, in territory as well as numbers, provides an opportunity for studying evolution in a scale rarely possible. We have used 10 restriction endonucleases to analyze the mitochondrial DNA (mtDNA) of individuals from 23 widely dispersed localities. Only two mtDNA composite morphs have been detected in the Americas. None of the two morphs has been found in Africa, and only one in the Atlantic islands; but both are widespread in Europe, which provides no clue of the precise geographic origin of the colonizers. The amount of nucleotide-substitution polymorphism detected in D. subobscura is typical for animals, but it is greater in the Old than in the New World, presumably due to the recent colonization by a limited number of colonizers. Assuming standard evolutionary rates of mtDNA base substitution, the mtDNA morphs found in D. subobscura can be traced to a single one that existed no less than one million years ago. We argue against the inference that the D. subobscura flies now living descend from only one or a few females that lived at that time. This type of inference, which we call the "Mother Eve hypothesis," has been made to conclude that the human population went through a severe constriction about 200,000 years ago, so that all living humans descend from only one or a few women who lived at that time. The Mother Eve hypothesis is fallacious.

Extensive variation and heteroplasmy in size of mitochondrial DNA among geographic populations of Drosophila melanogaster

Size variation and heteroplasmy in mitochondrial DNA (mtDNA) are relatively common in natural populations of Drosophila melanogaster. Of 92 isofemale lines of flies obtained from various geographic regions throughout the world, 75 lines were homoplasmic and showed a total of 12 different mtDNA size classes. The remaining 17 lines were heteroplasmic, each line carrying two different mtDNAs, and, in all but one case, the mtDNAs in these heteroplasmic lines differed in size; a total of nine size classes was represented among them. In cases where one type was predominant within an individual, it was usually the smaller mtDNA. This finding parallels what was observed in homoplasmic lines, in that the smaller mtDNAs were much more common than the larger variants in most populations. The data suggest a high rate of mutational occurrence of mtDNA size variants and some natural selection against them.

Directional introgression of mitochondrial DNA in a hybrid population of tree frogs: The influence of mating behavior

A total of 305 individuals from a hybrid population of North American tree frogs was characterized for allozyme and mitochondrial DNA (mtDNA) genotype. Species-specific mating behaviors had suggested the potential for directional hybridization, in which matings between Hyla cinerea males and Hyla gratiosa females numerically predominate over the reciprocal combination. Such directional bias leads to predictions about expected distributions of the female-transmitted mtDNA markers in F(1), backcross, and later-generation hybrids. These predictions were fully confirmed by the observed distributions of mtDNA genotypes among these allozymically inferred hybrid classes. Results exemplify the significance of stereotyped mating behaviors in determining the genetic architecture of a hybrid population.

Phylogeographic population structure of Red-winged Blackbirds assessed by mitochondrial DNA

A continent-wide survey of restriction-site variation in mitochondrial DNA (mtDNA) of the Red-winged Blackbird (Agelaius phoeniceus) was conducted to assess the magnitude of phylogeographic population structure in an avian species. A total of 34 mtDNA genotypes was observed among the 127 specimens assayed by 18 restriction endonucleases. Nonetheless, population differentiation was minor, as indicated by (i) small genetic distances in terms of base substitutions per nucleotide site between mtDNA genotypes (maximum P approximately 0.008) and by (ii) the widespread geographic distributions of particular mtDNA clones and phylogenetic arrays of clones. Extensive morphological differentiation among redwing populations apparently has occurred in the context of relatively little phylogenetic separation. A comparison between mtDNA data sets for Red-winged Blackbirds and deermice (Peromyscus maniculatus) also sampled from across North America shows that intraspecific population structures of these two species differ dramatically. The lower phylogeographic differentiation in redwings is probably due to historically higher levels of gene flow.

Mitochondrial DNA differentiation in North Atlantic eels: Population genetic consequences of an unusual life history pattern

A survey of restriction site polymorphism in the mitochondrial DNA (mtDNA) of the American eel Anguilla rostrata showed no genetic divergence among samples from a 4000-km stretch of North America coastline. Lack of geographic differentiation in mtDNA over such a large area contrasts sharply with results for terrestrial and freshwater vertebrates and is most likely attributable to the extraordinary life history of these catadromous fishes, which involves perhaps a single spawning population in the western tropical mid-Atlantic Ocean and subsequent widespread dispersal of larvae by ocean currents. However, samples of the European eel (nominally Anguilla anguilla) are highly distinct from A. rostrata in mtDNA genotype (distinguishable by 11 of 14 restriction endonucleases), contradicting some previous suggestions that the two forms belong to the same panmictic population. Results of this study emphasize the importance of life history in shaping population genetic structure.

An odyssey of the green sea turtle: Ascension Island revisited

Green turtles (Chelonia mydas) that nest on Ascension Island, in the south-central Atlantic, utilize feeding grounds along the coast of Brazil, more than 2000 km away. To account for the origins of this remarkable migratory behavior, Carr and Coleman [Carr, A. & Coleman, P. J. (1974) Nature (London) 249, 128-130] proposed a vicariant biogeographic scenario involving plate tectonics and natal homing. Under the Carr-Coleman hypothesis, the ancestors of Ascension Island green turtles nested on islands adjacent to South America in the late Cretaceous, soon after the opening of the equatorial Atlantic Ocean. Over the last 70 million years, these volcanic islands have been displaced from South America by sea-floor spreading, at a rate of about 2 cm/year. A population-specific instinct to migrate to Ascension Island is thus proposed to have evolved gradually over tens of millions of years of genetic isolation. Here we critically test the Carr-Coleman hypothesis by assaying genetic divergence among several widely separated green turtle rookeries. We have found fixed or nearly fixed mitochondrial DNA (mtDNA) restriction site differences between some Atlantic rookeries, suggesting a severe restriction on contemporary gene flow. Data are consistent with a natal homing hypothesis. However, an extremely close similarity in overall mtDNA sequences of surveyed Atlantic green turtles from three rookeries is incompatible with the Carr-Coleman scenario. The colonization of Ascension Island, or at least extensive gene flow into the population, has been evolutionarily recent.

Do Mediterranean crickets Gryllus bimaculatus De Geer (Orthoptera: Gryllidae) come from the Mediterranean? Largescale phylogeography and regional gene flow

We investigate the degree of between-population genetic differentiation in the Mediterranean field cricket Gryllus bimaculatus, as well as the possible causes of such differentiation. Using cytochrome b mtDNA sequences, we estimate genetic variation in G. bimaculatus from seven South African and two Mediterranean populations. Within-population genetic variation in Europe (two haplotypes, one unique to a single individual) suggest low effective population size and strong bottlenecks with associated founder effects, probably due to cold winter environments in Europe that limit reproduction to a short part of the summer. The likely cause for this is the daily maxima in winter temperatures that fall below the critical level of 16 degrees C (enabling normal calling and courtship behaviour) in Mediterranean Europe, whereas the equivalent temperatures in southern Africa are above this limit and enable reproduction over a large part of the year. European genetic variants were either shared with Africa or closely related to African haplotypes. For survival, European populations are probably dependent on immigration from other areas, including Africa. South African populations have low but measurable gene flow with Europe and show significant between-population genetic differentiation (30 haplotypes). Isolation-by-distance is not sufficient to explain the degree of between-population genetic differences observed, and a large degree of dispersal is also required in order to account for the observed patterns. Differences in morphology and calling behaviour among these populations are underlied by these genetic differences.

Genetic divergence in mitochondrial DNA between the wood mouse (Apodemus sylvaticus) and the yellow necked mouse (A. flavicollis)

Genetic variability and the relationships between clones of mitochondrial DNA (mtDNA) provide data which can be used to construct hypotheses about the biogeographical and postglacial colonization history of Fennoscandian species. We have investigated fragment differences in mtDNA among 24 Wood mice (Apodemus sylvaticus) from 8 localities, and 9 Yellow necked mice (A. flavicollis) from four North European localities. The greatest intraspecific sequence divergence found between mtDNA clones was 1.40% within A. sylvaticus and 1.00% within A. flavicollis. The mean pairwise divergence in samples from a local population (n = 14) of A. sylvaticus was only 0.003%. Interspecific fragment comparison of mtDNA from A. sylvaticus and A. flavicollis give a sequence divergence close to 10%. However, comparison of genetic distances based on mtDNA between the two Apodemus species shows that they are more distantly related than suggested by nuclear distances. The observed discrepancy between distances estimated from mitochondrial and nuclear DNA suggests that mtDNA divergence predated divergence in nuclear genes or that there was an influx of nuclear variation during the speciation process or in connection with the expansion and contractions of populations during interglacial and glacial periods.

Sequencing and phylogenomic analysis of whole mitochondrial genomes of animals

Mitochondrial genomes (mtDNA) of animals are circular molecules of relatively small size, compactly organized, and generally encoding genes for 2 rRNAs, 22 tRNAs, and 13 proteins that are required for mitochondrial function. Methods of mtDNA isolation take advantage of its physical localization apart from the nuclear genome (centrifugation at low speed efficiently separates mitochondria from nuclei) and of its structure (alkaline lysis differentially precipitates linear nuclear DNA, but not circular mtDNA). Furthermore, the recent development of robust long-PCR techniques has boosted high-throughput determination of complete sequences of animal mtDNAs. The exponentially growing number of complete animal mitochondrial genomes deposited in GenBank allows a phylogenomic approach to disentangle phylogenetic relationships among main animal phyla, and provides extensive new data to gain insights on the molecular mechanisms underlying genome evolution.

Inheritance of two M type mitochondrial DNA from sperm and unfertilized eggs to offspring in Mytilus galloprovincialis

In Mytilus mussels, paternal mitochondrial DNA (mtDNA) from sperm is known to be transmitted to offspring. This phenomenon is called doubly uniparental inheritance (DUI). Under DUI, sperm mtDNA (M type) is inherited only by males. Female mussels receive maternal mtDNA (F type). However, in our previous study, we showed female and unfertilized eggs have both F and M types. We hypothesized that the two M types both from sperm and unfertilized eggs were transmitted to offspring. To test the hypothesis, we examined the number of M type haplotypes in mature M. galloprovincialis. The M type in larvae was compared with those of the parents. Cross experiments were carried out to test the inheritance of M type. In six of 20 mature mussels, two M types were detected by sequence analysis and polymerase chain reaction-restriction fragment length polymorphism. In cross experiments of larval samples from five of 12 crosses, double peak wave was observed by single nucleotide polymorphisms analysis. In these larval samples, the higher peak wave was identical to the parental M type. Larvae received much more paternal M type than the maternal ones. We demonstrated that two M types from sperm and unfertilized eggs were transmitted to offspring in M. galloprovincialis.

A novel dicyclodextrinyl diselenide compound with glutathione peroxidase activity

A 6A,6A'-dicyclohexylamine-6B,6B'-diselenide-bis-beta-cyclodextrin (6-CySeCD) was designed and synthesized to imitate the antioxidant enzyme glutathione peroxidase (GPX). In this novel GPX model, beta-cyclodextrin provided a hydrophobic environment for substrate binding within its cavity, and a cyclohexylamine group was incorporated into cyclodextrin in proximity to the catalytic selenium in order to increase the stability of the nucleophilic intermediate selenolate. 6-CySeCD exhibits better GPX activity than 6,6'-diselenide-bis-cyclodextrin (6-SeCD) and 2-phenyl-1,2-benzoisoselenazol-3(2H)-one (Ebselen) in the reduction of H(2)O(2), tert-butyl hydroperoxide and cumenyl hydroperoxide by glutathione, respectively. A ping-pong mechanism was observed in steady-state kinetic studies on 6-CySeCD-catalyzed reactions. The enzymatic properties showed that there are two major factors for improving the catalytic efficiency of GPX mimics. First, the substrate-binding site should match the size and shape of the substrate and second, incorporation of an imido-group increases the stability of selenolate in the catalytic cycle. More efficient antioxidant ability compared with 6-SeCD and Ebselen was also seen in the ferrous sulfate/ascorbate-induced mitochondria damage system, and this implies its prospective therapeutic application.

A fused selenium-containing protein with both GPx and SOD activities

As a safeguard against oxidative stress, the balance between the main antioxidant enzymes including superoxide dismutase (SOD), glutathione peroxidase (GPx), and catalase (CAT) was believed to be more important than any single one, for example, dual-functional SOD/CAT enzyme has been proved to have better antioxidant ability than either single enzyme. By combining traditional fusion protein technology with amino acid auxotrophic expression system, we generated a bifunctional enzyme with both GPx and SOD activities. It displayed better antioxidant ability than GPx or SOD. Such dual-functional enzymes could facilitate further studies of the cooperation of GPx and SOD and generation of better therapeutic agents.

Quantitation of the male and female types of mitochondrial DNA in a blue mussel, Mytilus galloprovincialis, using real-time polymerase chain reaction assay

The system termed doubly uniparental inheritance (DUI) of mitochondrial transmission to progeny has been reported in Mytilus. Under DUI, it has been thought that males have both paternally (M type) and maternally (F type) transmitted mitochondrial DNA (mtDNA), and females have only F type. However, the presence of M type in females has been reported. To clarify the ratio of M type to F type mtDNA in female and male tissues to further our understanding of mitochondrial transmission, we developed a procedure to measure the copy numbers of the two types of mtDNA in Mytilus galloprovincialis using a real-time polymerase chain reaction assay. The following results were obtained by this method. In females, the copy numbers of M type mtDNA detected in adductor muscle, gonad and eggs were approximately 10 000-fold lower than those of F type. In males, F type dominated in adductor muscle, as in the female tissue. However, copy numbers of M type mtDNA were approximately 1000-fold higher than those of F type in gonad and 100 000-fold higher than those of F type in sperm. We examined the quantity relationship between the two types of mtDNA and the transmission mechanism of mtDNA in M. galloprovincialis.

Defeating numts: Semi-pure mitochondrial DNA from eggs and simple purification methods for field-collected wildlife tissues

Mitochondrial DNA (mtDNA) continues to play a pivotal role in phylogeographic, phylogenetic, and population genetic studies. PCR amplification with mitochondrial primers often yields ambiguous sequences, in part because of the coamplification of nuclear copies of mitochondrial genes (numts) and true mitochondrial heteroplasmy arising from mutations, hybridization with paternal leakage, gene duplications, and recombination. Failing to detect numts or to distinguish the origin of such homologous sequences results in the incorrect interpretation of data. However, few studies obtain purified mtDNA to confirm the mitochondrial origin of the first reference sequences for a species. Here, we demonstrate the importance and ease of obtaining semi-pure mtDNA from wildlife tissues, preserved under various typical field conditions, and investigate the success of 3 commercial extraction kits, cesium-chloride gradient mtDNA purification, long-template PCR amplification, cloning, and more species-specific degenerate primers. Using more detailed avian examples, we illustrate that unfertilized or undeveloped eggs provide the purest sources of mtDNA; that kits provide an alternative to cesium-chloride gradient methods; and that long-template PCR, cloning, and degenerate primers cannot be used to produce reliable mitochondrial reference sequences, but can be powerful tools when used in conjunction with purified mtDNA stocks to distinguish numts from true heteroplasmy.

Sperm mitochondrial DNA transmission to both male and female offspring in the blue mussel Mytilus galloprovincialis

In Mytilus mussels, paternal mitochondrial DNA (M type) from sperm is known to be transmitted to offspring. This phenomenon is called doubly uniparental inheritance (DUI). Under DUI, it has been reported that female mussels generally have only maternal mtDNA (F type). In this study, we examined the mode of mtDNA transmission in Mytilus galloprovincialis using M and F type-specific primer sets. The ratio of M and F types were measured in each sample by SNaPshot. The M type was detected in the adductor muscle and female gonad of all females. In unfertilized eggs spawned by 84.6% of females (22/26), M type was also detected. The F type was more abundant than the M type in all females. Although the ratio of M type in females was very low, all females contained the M type. From these results, we propose a new possibility about DUI inheritance. The presence of M type in unfertilized eggs indicates that the M type of eggs may also contribute to M type inheritance.

Taenia asiatica and Taenia saginata: Genetic divergence estimated from their mitochondrial genomes

We conducted a differential identification of Taenia asiatica and Taenia saginata, through the mapping of mitochondrial genomes and the sequencing of the cox1 and cob genes. The entire mitochondrial genomes of T. asiatica and T. saginata were amplified by long-extension PCR and cloned; each was approximately 14 kb in size. Restriction maps of T. asiatica and T. saginata mitochondrial genomes were then constructed using 13 restriction enzymes. The resulting restriction patterns enable us to estimate their genetic divergence at 4.8%. The actual sequence divergence was computed 4.5% from the cox1 gene, and 4.1% from the cob gene. These results support the designation of T. asiatica as a separate species from T. saginata.

Origin and dispersal of bluegill sunfish, Lepomis macrochirus, in Japan and Korea

The bluegill sunfish, Lepomis macrochirus, is a notorious exotic species in many freshwater ecosystems, currently expanding its distribution worldwide. In 1960, a small group of bluegills captured in the Mississippi River at Guttenberg in Iowa were imported to Japan as a gift from the mayor of Chicago to the Japanese government. The offspring of these fish were released into the wild in Japan and also in Korea. Over 40 years after this first introduction, L. macrochirus now occupies all the freshwater ecosystems of both countries. We compared invading populations of L. macrochirus in Japan and Korea with native populations in the USA, using PCR-RFLP (polymerase chain reaction-restricted fragment length polymorphism) analyses of mitochondrial DNA, to estimate the origin and dispersal of L. macrochirus in Japan and Korea. Five haplotypes of mitochondrial DNA detected in Japanese and Korean populations completely coincided with the haplotypes of the Guttenberg population. Haplotype diversity of invading populations was shown to be highest in populations established in the 1960s, while genetic variability was lower in more recently established populations. Our results suggest that all L. macrochirus in Japan and Korea have originated from the 15 fish first introduced in 1960. Low haplotype diversity in newly established populations is probably due to genetic drift arising from repeated population bottlenecks, while the high similarity of haplotypes among neighbouring populations is considered to reflect the history of transplantation by humans.

Low Genetic Variation and Inbreeding Depression in Small Isolated Populations of the Japanese Rosy Bitterling, Rhodeus ocellatus kurumeus

The Japanese rosy bitterling, Rhodeus ocellatus kurumeus, has been affected not only by the invasion of another subspecies, R. o. ocellatus, from China, but also by habitat fragmentation. In this study, the effects of habitat fragmentation on the fitness of R. o. kurumeus were investigated. Owing to exclusion by R. o. ocellatus, R. o. kurumeus in Honshu and Shikoku has disappeared entirely, except for small populations in isolated man-made ponds in Osaka and Kagawa. In Kyushu it still occupies open water systems, into which R. o. ocellatus has only recently invaded. Meristic and genetic data show that the diversity of R. o. kurumeus is significantly lower in the isolated Osaka and Kagawa populations than the non-isolated Fukuoka population. The Osaka population is inferior to the Fukuoka population in terms of viability and growth. The viability of reciprocal inter-population hybrids between the Osaka and Fukuoka populations was, however, as high as that of the Fukuoka population. In addition to the high scores of band sharing index (BSI) in RAPD-PCR analysis, acceptance of transplanted scales among individuals, irrespective of natal pond, indicates that the Osaka population forms a highly inbred line. These results suggest that low genetic variation is associated with inbreeding depression in the small isolated Osaka populations. Consequently, the management of ponds, including the free movement of individuals, in addition to measures to prevent the invasion of R. o. ocellatus, is necessary for the conservation of R. o. kurumeus.

A selenium-containing single-chain abzyme with potent antioxidant activity

Reactive oxygen species (ROS) are products of normal metabolic activities and are thought to be the cause of many diseases. A selenium-containing single-chain abzyme 2F3 (Se-2F3-scFv) that imitates glutathione peroxidase has been produced which has the capacity to remove ROS. To evaluate the antioxidant ability of Se-2F3-scFv, we constructed a ferrous sulfate/ascorbate (Vc/Fe2+)-induced mitochondrial damage model system and investigated the capacity of Se-2F3-scFv to protect mitochondria from oxidative damage. Se-2F3-scFv markedly decreased mitochondrial swelling, inhibited lipid peroxidation, and maintained the activity of cytochrome c oxidase, in comparison with Ebselen, a well-studied glutathione peroxidase mimic, indicating that Se-2F3-scFv has potential for treating diseases mediated by ROS.

Yolk platelets in artemia embryos: are they really storage sites of immature mitochondria?

We have used semi-quantitative polymerase chain reaction (PCR) technology to determine the mitochondrial DNA (mtDNA) content of yolk platelets isolated from embryos of the brine shrimp, Artemia franciscana, and ultrastructural analysis of yolk platelet formation to determine whether these organelles contain mitochondria as reported previously. Using six different isolation and purification protocols, we found one yolk platelet preparation to be devoid of mtDNA, while four yolk platelet preparations contained mtDNA ranging from 16.4 to 85 pg/10(6) yolk platelets. One preparation contained 600 pg mtDNA per 10(6) yolk platelets. Based on our PCR analyses, the mtDNA component of Artemia yolk platelets represented 0.16-4.5% of the total DNA isolated from the platelets. We calculated that Artemia yolk platelets contain, on average, approximately 1.78 molecules of mtDNA/platelet. Direct analysis of mtDNA in "free" mitochondria isolated from yolk platelet-free preparations of Artemia embryos and newly hatched larvae yielded 0.76-0.80 ng/animal. Based on these values, the mtDNA content of yolk platelets was approximately 0.2% of total mtDNA in Artemia embryos. Microscopic analysis of yolk platelet formation during oogenesis in Artemia failed to show the inclusion of mitochondria during the assemblage of yolk platelets. The "mitochondria-like" structures that appear in yolk platelets during their utilization lack the well defined inner and outer membranes characteristic of mitochondria making it unlikely that the yolk platelet inclusions are mitochondria. Our results from PCR technology and ultrastructure analysis demonstrate that mtDNA in yolk platelets of Artemia franciscana embryos is a minor component of the total mtDNA in the embryo, and they fail to support the notion that yolk platelets in Artemia are a major source of immature mitochondria for development.

A novel cyclodextrin-derived tellurium compound with glutathione peroxidase activity

A novel dicyclodextrinyl ditelluride (2-TeCD) compound was devised as a functional mimic of the glutathione peroxidase (GPX) enzymes that normally remove hydroperoxides from the cell. The GPX activity of the mimic was found to be 46.7 U microM(-1), which is 46 times as active as Ebselen, a well-known GPX mimic. A detailed steady-state kinetic study was undertaken to probe the reason for the high catalytic efficiency of 2-TeCD. This high efficiency can be explained based on both the binding of the substrate to the cyclodextrin and the catalytic mechanism of 2-TeCD, which is different from that of diselenide compounds. 2-TeCD exhibits good water solubility and is chemically and biologically stable. The biological effect of 2-TeCD was evaluated by its ability to protect mitochondria from oxidative damage. 2-TeCD exhibited excellent antioxidant capacity in comparison with Ebselen.

Phylogenetic relationships of North American garter snakes (Thamnophis) based on four mitochondrial genes: how much DNA sequence is enough?

The clade of garter snakes (Thamnophis) includes some of the most abundant and well-studied snakes in North America. However, phylogenetic relationships within this group have been little studied. We used DNA sequences of four mitochondrial genes (cytochrome b and NADH dehydrogenase subunits 1, 2, and 4) to estimate relationships among 29 of the 31 recognized species of Thamnophis plus the related species Adelophis foxi. Both maximum parsimony (MP) and maximum-likelihood (ML) analyses of all these genes combined produced well-resolved trees with moderate (70-89%) to strong (90-100%) bootstrap support for most clades. MP and ML trees were very similar, with no strongly supported conflict between the two analyses. These analyses identify a clade of 12 species largely restricted to México (the "Mexican clade"), and a clade containing 15 species that collectively range from Central America to southern Canada (the "widespread clade"). These two groups are identified as sister taxa in both MP and ML analyses. A clade consisting of the ribbon snakes (T. sauritus and T. proximus) and the common garter snake (T. sirtalis) is placed as the sister group to all other Thamnophis (i.e., the Mexican + widespread clades) in our analyses. High bootstrap proportions at several levels in the tree support the inclusion of both Thamnophis validus, which has traditionally been placed in the genus Nerodia, and the poorly known species Adelophis foxi within Thamnophis. We used randomly sampled characters (i.e., standard bootstrapping) and randomly sampled contiguous blocks of characters to examine the effect of number of characters on resolution of and support for relationships within Thamnophis using MP. In general, these analyses indicate that we have reached a point of strongly diminishing returns with respect to the effect of adding mtDNA sequence characters for the current set of taxa; our sample of 3809 mtDNA characters is apparently "enough." The next steps to improve the phylogenetic estimate may be to add nuclear DNA sequences, morphology, or behavior, or to sequence additional mtDNA lineages within species.