A preliminary phylogenetic analysis of Metapenaeopsis (Decapoda : Penaeidae) based on mitochondrial dna sequences of selected species from the Indo-West Pacific

Phylogenetic relationships within Metapenaeopsis remain largely unknown. The modern revision of the genus suggests that the shape of the petasma, followed by the presence of a stidulating organ, are the most important distinguishing taxonomic features. In the present study, phylogenetic relationships were studied among seven Metapenaeopsis species from the Indo-West Pacific based on partial sequences of mitochondrial 16S rRNA and cytochrome c oxidase I (COI) genes. Mean sequence divergence was 6.4% for 16S and 15.8% for COI. A strikingly large nucleotide distance (10.0% for 16S and 16.9% for COI) was recorded between M. commensalis, the only Indo-West Pacific species with a one-valved petasma, and the other species with a two-valved petasma. Phylogenetic analyses using neighbor-joining, maximum parsimony, and maximum likelihood generated mostly identical tree topologies in which M. commensalis is distantly related to the other species. Two clades were resolved for the remaining species, one with and the other without a stridulating organ, supporting the main groupings of the recent taxonomic revision. Results of the present study also indicate that the deep-water forms represent a relatively recent radiation in Metapenaeopsis.

Interactions of the human telomeric DNA with terbium-amino acid complexes

The human telomeric DNA can form four-stranded structures: the G-rich strand adopts a G-quadruplex conformation stabilized by G-quartets and the C-rich strand may fold into an I-motif based on intercalated C (.) C+ base pairs. There is intense interests in the design and synthesis of compounds which can target telomeric DNA and inhibit the telomerase activity. Here we report the thermodynamic studies of the two newly synthesized terbium-amino acid complexes bound to the human telomeric G-quadruplex and I-motif DNA which were studied by means of UV-Visible, DNA meltings, fluorescence and circular dichroism. These two complexes can bind to the human telomeric DNA and have shown different features on DNA stability, binding stoichiometry, and sequence-dependent fluorescence enhancement. To our knowledge, this is the first report to show terbium-amino acid complexes can interact with the human telomeric DNA.

Mitochondrial DNA phylogeny of two morphologically enigmatic fishes in the subfamily Schizothoracinae (Teleostei : Cyprinidae) in the Qinghai-Tibetan Plateau

The complete mitochondrial DNA (mtDNA) cytochrome b gene (1140 bp) was sequenced in Herzenstein macrocephalus and Gymnocypris namensis and in 13 other species and sub-species (n = 22), representing four closely related genera in the subfamily Schizothoracinae. Conflicting taxonomies of H. macrocephalus and G. namensis have been proposed because of the character instability among individuals. Parsimony, maximum likelihood and Bayesian methods produced phylogenetic trees with the same topology and resolved several distinctive clades. Previous taxonomic treatments, which variously placed these two species of separate genera or as sub-species, are inconsistent with the mtDNA phylogeny. Both H. macrocephalus and G. namensis appear in a well-supported clade, which also includes nine species of Schizopygopsis, and hence should be transferred to the genus Schizopygopsis. Morphological changes are further illustrated, and their adaptive evolution in response to the local habitat shifts during the speciation process appears to be responsible for conflicting views on the systematics of these two species and hence the contrasting taxonomic treatments. These species are endemic to the Qinghai-Tibetan Plateau, a region with a history of geological activity and a rich diversity of habitats that may have result in the parallel and reversal evolution of some morphological characters used in their taxonomies. Our results further suggest that speciation and morphological evolution of fishes in this region may be more complex than those previously expected. (c) 2007 The Authors Journal compilation (c) 2007 The Fisheries Society of the British Isles.

Molecular systematics of pikas (genus Ochotona) inferred from mitochondrial DNA sequences

The phylogenetic relationships among worldwide species of genus Ochotona were investigated by sequencing mitochondrial cytochrome b and ND4 genes. Parsimony and neighbor-joining analyses of the sequence data yielded congruent results that strongly indicated three major clusters: the shrub-steppe group, the northern group, and the mountain group. The subgeneric classification of Ochotona species needs to be revised because each of the two subgenera in the present classification contains species from the mountain group. To solve this taxonomic problem so that each taxon is monophyletic, i.e., represents a natural clade, Ochotona could be divided into three subgenera, one for the shrub-steppe species, a second for the northern species, and a third for the mountain species. The inferred tree suggests that the differentiation of this genus in the Palearctic Region was closely related to the gradual uplifting of the Tibet (Qinghai-Xizang) Plateau, as hypothesized previously, and that vicariance might have played a major role in the differentiation of this genus on the Plateau, On the other hand, the North American species, O. princeps, is most likely a dispersal event, which might have happened during the Pliocene through the opening of the Bering Strait. The phylogenetic relationships within the shrub-steppe group are worth noting in that instead of a monophyletic shrub-dwelling group, shrub dwellers and steppe dwellers are intermingled with each other. Moreover, the sequence divergence within the sister tars of one steppe? dweller and one shrub dweller is very low. These findings support the hypothesis that pikes have entered the steppe environment several times and that morphological similarities within steppe dwellers were due to convergent evolution. (C) 2000 Academic Press.

Variation in mitochondrial DNA and phylogeny of six species of pikas (Ochotona)

Phylogenetic relationships of six species of Ochotona were investigated using mitochondrial DNA (mtDNA) restriction-site analysis. The phylogenetic tree constructed using PAUP was based on 62 phylogenetically informative sites with O. erythrotis designated as an outgroup. Two clades were evident. One contained O. curzoniae, O. huangensis, and O. thibetana. in the second, O. daurica was a sister taxon of O. cansus. The five species appear to come from different maternal lineages. The branching structure of the tree and sequence divergence confirm that huangensis and cansus are distinct species, and that mol-osa is a synonym of O. cansus rather than O. thibetana. Divergence time, estimated from genetic distances, indicates that the ancestors of the two maternal lineages diverged ca. 6.5 x 10(6) years ago. O. curzoniae diverged from O. huangensis, and O. daurica diverged from O. cansus, at about the same time (ca. 3.4 x 10(6) years ago). These data suggest a period of rapid radiation of the genus Ochotona in China, perhaps during the late Pliocene. These calculations correspond roughly to tectonic events and environmental changes in China throughout this period, and appear to be substantiated by the fossil record.

Phylogenetic relationships of five pika species (genus Ochotona) based on mitochondrial DNA restriction maps

Restriction site mapping of mitochondrial DNA (mtDNA) with 16 restriction endonucleases was used to examine the phylogenetic relationships of Ochotona cansus, O. huangensis, O. thibetana, O. curzoniae and O. erythrotis. A 1-kb length variation between O. erythrotis of subgenus Pika and other four species of subgenus Ochotona was observed, which may be a useful genetic marker for identifying the two subgenera. The phylogenetic tree constructed using PAUP based on 61 phylogenetically informative sites suggests that O. erythrotis diverged first, followed by O. cansus, while O. curzoniae and O. huangensis are sister taxa related to O. thibetana, The results indicate that both O. cansus and O. huangensis should be treated as independent species. If the base substitution rate of pikas mtDNA was 2% per million years, then the divergence time of the two subgenera, Pika and Ochotana, is about 8.8 Ma ago of late Miocence, middle Bao-dian of Chinese mammalian age, and the divergence of the four species in subgenus Ochotona would have occurred about 2.5 - 4.2 Ma ago, Yushean of Chinese mammalian age. This calculation appears to be substantiated by the fossil record.

Frequency of the mtDNA 9-bp deletion in Chinese ethnic groups

The 9-bp deletion in the COII/tRNA(Lys) intergenic region (region V) of human mitochondrial DNA was screened in 1521 Chinese from 16 ethnic groups and 9 Hen geographic groups. The highest frequency was found in populations of Miao (32.4%) and Bouyei (30.8

Updating the East Asian mtDNA phylogeny: a prerequisite for the identification of pathogenic mutations

Knowledge about the world phylogeny of human mitochondrial DNA (mtDNA) is essential not only for evaluating the pathogenic role of specific mtDNA mutations but also for performing reliable association studies between mtDNA haplogroups and complex disorder

Assessment of cattle genetic introgression into domestic yak populations using mitochondrial and microsatellite DNA markers

Hybridization between yak Poephagus grunniens and taurine Bos taurus or indicine B. indicus cattle has been widely practiced throughout the yak geographical range, and gene flow is expected to have occurred between these species. To assess the impact of cattle admixture on domestic yak, we examined 1076 domestic yak from 29 populations collected in China, Bhutan, Nepal, India, Pakistan, Kyrgyzstan, Mongolia and Russia using mitochondrial DNA and 17 autosomal microsatellite loci. A cattle diagnostic marker-based analysis reveals cattle-specific mtDNA and/or autosomal microsatellite allele introgression in 127 yak individuals from 22 populations. The mean level of cattle admixture across the populations, calculated using allelic information at 17 autosomal microsatellite loci, remains relatively low (mY(cattle) = 2.66 +/- 0.53% and Q(cattle) = 0.69 +/- 2.58%), although it varies a lot across populations as well as among individuals within population. Although the level of cattle admixture shows a clear geographical structure, with higher levels of admixture in the Qinghai-Tibetan Plateau and Mongolian and Russian regions, and lower levels in the Himalayan and Pamir Plateau region, our results indicate that the level of cattle admixture is not significantly correlated with the altitude across geographical regions as well as within geographical region. Although yak-cattle hybridization is primarily driven to produce F-1 hybrids, our results show that the subsequent gene flow between yak and cattle took place and has affected contemporary genetic make-up of domestic yak. To protect yak genetic integrity, hybridization between yak and cattle should be tightly controlled.

The Acquisition of an Inheritable 50-bp Deletion in the Human mtDNA Control Region Does Not Affect the mtDNA Copy Number in Peripheral Blood Cells

The mitochondrial DNA (mtDNA) control region is believed to play an important biological role in mtDNA replication. Large deletions in this region are rarely found, but when they do occur they might be expected to interfere with the replication of the molecule, thus leading to a reduction of mtDNA copy number. During a survey for mtDNA sequence variations in 5,559 individuals from the general Chinese population and 2,538 individuals with medical disorders, we identified a 50-bp deletion (m.298_347del50) in the mtDNA control region in a member of a healthy Han Chinese family belonging to haplogroup B4c1b2, as suggested by complete mtDNA genome sequencing. This deletion removes the conserved sequence block II (CSBII; region 299-315) and the replication primer location (region 317-321). However, quantification of the mtDNA copy number in this subject showed a value within a range that was observed in 20 healthy subjects without the deletion. The deletion was detected in the hair samples of the maternal relatives of the subject and exhibited variable heteroplasmy. Our current observation, together with a recent report for a benign 154-bp deletion in the mtDNA control region, suggests that the control of mtDNA replication may be more complex than we had thought. Hum Mutat 31:538-543, 2010. (C) 2010 Wiley-Liss, Inc.

Mitochondrial and chloroplast phylogeography of Picea crassifolia Kom. (Pinaceae) in the Qinghai-Tibetan Plateau and adjacent highlands

The disjunct distribution of forests in the Qinghai-Tibetan Plateau (QTP) and adjacent Helan Shan and Daqing Shan highlands provides an excellent model to examine vegetation shifts, glacial refugia and gene flow of key species in this complex landscape region in response to past climatic oscillations and human disturbance. In this study, we examined maternally inherited mitochondrial DNA (nad1 intron b/c and nad5 intron 1) and paternally inherited chloroplast DNA (trnC-trnD) sequence variation within a dominant forest species, Picea crassifolia Kom. We recovered nine mitotypes and two chlorotypes in a survey of 442 individuals from 32 populations sampled throughout the species' range. Significant mitochondrial DNA population subdivision was detected (G(ST) = 0.512; N-ST = 0.679), suggesting low levels of recurrent gene flow through seeds among populations and significant phylogeographical structure (N-ST > GST, P < 0.05). Plateau haplotypes differed in sequence from those in the adjacent highlands, suggesting a long period of allopatric fragmentation between the species in the two regions and the presence of independent refugia in each region during Quaternary glaciations. On the QTP platform, all but one of the disjunct populations surveyed were fixed for the same mitotype, while most populations at the plateau edge contained more than one haplotype with the mitotype that was fixed in plateau platform populations always present at high frequency. This distribution pattern suggests that present-day disjunct populations on the QTP platform experienced a common recolonization history. The same phylogeographical pattern, however, was not detected for paternally inherited chloroplast DNA haplotypes. Two chlorotypes were distributed throughout the range of the species with little geographical population differentiation (G(ST) = N-ST = 0.093). This provides evidence for highly efficient pollen-mediated gene flow among isolated forest patches, both within and between the QTP and adjacent highland populations. A lack of isolation to pollen-mediated gene flow between forests on the QTP and adjacent highlands is surprising given that the Tengger Desert has been a geographical barrier between these two regions for approximately the last 1.8 million years.