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Mitochondrial Sequences (mitochondrial + sequence)
Terms modified by Mitochondrial Sequences Selected AbstractsNovel method for analyzing proteomeINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2007Bo Liao Abstract We propose a 6D representation of protein sequences consisting of 20 amino acids. Based on this 6D representation, we propose a proteome distance measure for constructing phylogenic tree. And we make use of the corresponding similarity matrix to construct phylogenic tree. The examination of phylogenic tree belong to 30 mitochondrial sequence illustrates the utility of our approach. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Molecular genetic structure and relationship of Chinese and Hungarian common carp (Cyprinus carpio L.) strains based on mitochondrial sequenceAQUACULTURE RESEARCH, Issue 9 2010Chenghui Wang Abstract China and Hungary are major providers of the common carp (Cyprinus carpio L.) in East Asia and Europe respectively. However, the genetic variation and relationship of this species in the two countries have been poorly understood. In this study, mitochondrial COII-tRNALys and D-loop sequences were analysed to investigate the genetic structure and relationships of the representative wild and domesticated common carps distributed in China and Hungary. The results indicated that the genetic diversities of the Chinese common carps are higher than those of Hungarian common carps, and the diversities of the wild common carps are higher than those of domesticated common carps in both the countries. Analysis of molecular variance and pairwise FST demonstrated a significant genetic divergence between the Chinese and the Hungarian common carps, and between the wild and the domesticated common carps. Bayesian phylogenetic analysis and statistical parsimony network showed an obvious genetic differentiation between the Chinese and the Hungarian common carps, between the wild and the domesticated common carps. However, a few specimens and haplotypes from the Chinese wild common carps appeared in the Hungarian common carps, demonstrating that there was no absolutely isolated and possible genetic linker between the Chinese and the Hungarian common carps. [source] Genetic diversity of endangered brown bear (Ursus arctos) populations at the crossroads of Europe, Asia and AfricaDIVERSITY AND DISTRIBUTIONS, Issue 5 2009Sébastien Calvignac Abstract Aim, Middle East brown bears (Ursus arctos syriacus Hemprich and Ehrenberg, 1828) are presently on the edge of extinction. However, little is known of their genetic diversity. This study investigates that question as well as that of Middle East brown bear relationships to surrounding populations of the species. Location, Middle East region of south-western Asia. Methods, We performed DNA analyses on 27 brown bear individuals. Twenty ancient bone samples (Late Pleistocene to 20th century) from natural populations and seven present-day samples obtained from captive individuals were analysed. Results, Phylogenetic analyses of the mitochondrial sequences obtained from seven ancient specimens identify three distinct maternal clades, all unrelated to one recently described from North Africa. Brown bears from Iran exhibit striking diversity (three individuals, three haplotypes) and form a unique clade that cannot be linked to any extant one. Individuals from Syria belong to the Holarctic clade now observed in Eastern Europe, Turkey, Japan and North America. Specimens from Lebanon surprisingly appear as tightly linked to the clade of brown bears now in Western Europe. Moreover, we show that U. a. syriacus in captivity still harbour haplotypes closely linked to those found in ancient individuals. Main conclusion, This study brings important new information on the genetic diversity of brown bear populations at the crossroads of Europe, Asia and Africa. It reveals a high level of diversity in Middle East brown bears and extends the historical distribution of the Western European clade to the East. Our analyses also suggest the value of a specific breeding programme for captive populations. [source] Identification of shrimp species in raw and processed food products by means of a polymerase chain reaction-restriction fragment length polymorphism method targeted to cytochrome b mitochondrial sequencesELECTROPHORESIS, Issue 15 2008Ananías Pascoal Abstract A novel PCR-RFLP method has been developed for the identification of six commercially relevant penaeid shrimp species in raw and processed food products. The method can be completed within 8,h. To implement the method, PCR amplification with the crustF/crustR primers, targeted to the amplification of a ca. 181,bp region of the cytochrome b (cytb) mitochondrial gene in penaeid shrimps, was coupled to restriction analysis with CviJI, DdeI and NlaIV. The method was also applied successfully to the identification of shrimp species in complex processed foods, including this type of shellfish as an added-value food ingredient. The small size of this molecular target facilitates amplification from fresh, frozen, or precooked samples, where DNA fragmentation may be relevant and fragment size critical. We also report the first cytb mitochondrial sequences described to date for the species Farfantepenaeus notialis, Parapenaeus longirostris and Pleoticus muelleri, and these nearly triplicate current knowledge of reference nucleotide sequences in this mitochondrial region for this group of species. The cytb mitochondrial gene may also be considered as a molecular marker for identification and phylogenetic purposes in penaeid shrimp species. [source] Transcriptome analysis of the salivary glands of the female tick Amblyomma americanum (Acari: Ixodidae)INSECT MOLECULAR BIOLOGY, Issue 2 2009M. N. Aljamali Abstract Ticks infest a wide range of hosts while bypassing their immune, inflammatory and haemostatic responses during their extended feeding, which may last for more than two weeks. Here, we present a transcriptome analysis of 3868 expressed sequence tags (ESTs) from three cDNA libraries generated from the salivary glands of adult female Ambyomma americanum ticks at different stages of feeding. We applied a normalization step for one library, significantly decreasing the abundance of mitochondrial sequences amongst the 2292 sequences from the normalized library. Our ESTs include homologues that may modulate haemostatic, immune and inflammatory responses of the hosts. Other ESTs probably represent important components of the highly efficient secretory pathways for salivary proteins and concomitantly transmitted pathogens. [source] Nuclear mitochondrial-like sequences in ants: evidence from Atta cephalotes (Formicidae: Attini)INSECT MOLECULAR BIOLOGY, Issue 6 2007J. Martins Jr Abstract Nuclear mitochondrial-like sequences (numts) are copies of mitochondrial DNA that have migrated to the genomic DNA. We present the first characterization of numts in ants, these numts being homologues to a mitochondrial DNA fragment containing loci the 3, portion of the cytochrome oxidase I gene, an intergenic spacer, the tRNA leucine gene and the 5, portion of the cytochrome oxidase II gene. All 67 specimens of Atta cephalotes (Hymenoptera: Formicidae: Attini) investigated had these homologues, which are within two monophyletic groups that we called numt1 and numt2. Numt1 and numt2 sequences are less variable than mitochondrial sequences and released from the severe purifying selection constraining the evolution of mitochondrial genes. Their formation probably involved bottlenecks related to two distinct transfer events of ancient and fast evolving mitochondrial DNA fragments to comparative slowly evolving nuclear DNA regions. [source] Sequence and organization of the mitochondrial genome of the Chagas disease vector, Triatoma dimidiataINSECT MOLECULAR BIOLOGY, Issue 3 2001E. M. Dotson Abstract The 17 019 bp mitochondrial genome of Triatoma dimidiata is composed of thirteen protein coding sequences, twenty-two tRNAs, small and large ribosomal units, and a control region. The gene order and orientation are identical to that of Drosophila yakuba. The nucleotide composition is biased toward adenine and thymine (69.5% A + T). The 2.1 kb putative control region, known as the A + T rich region in most insects, has an A + T bias of 66%, but contains a 400 bp sequence that is 77.5% A + T and two other distinct regions: (1) one with a lower A + T bias (60.1%) and (2) a region of eight tandem repeat units. The identified 1.4 kb nuclear copy of mitochondrial sequences encompasses the string of Gs and the beginning of the cytochrome c oxidase 1 gene but lacks the 1.8 kb region spanning the eight tandem repeats and the 5, end of the NADH dehydrogenase subunit II gene. [source] Avian molecular systematics on the rebound: a fresh look at modern shorebird phylogenetic relationshipsJOURNAL OF AVIAN BIOLOGY, Issue 3 2004Marcel Van Tuinen The study of avian molecular systematics currently lags behind that of mammals in several ways. Little phylogenetic resolution is observed among orders and phylogenetic studies below the ordinal level largely remain based on fast evolving mitochondrial sequences. New papers by Paton et al., Ericson et al., and Thomas et al. provide avian molecular systematics with a badly needed boost. These studies indicate that sampling more taxa and slower evolving nuclear genes yields strong phylogenetic resolution among the major shorebird (order Charadriiformes) families. The new data show surprising overall consensus and converge on certain novel clades. If correct, this newly obtained phylogenetic framework has tremendous implications for our understanding of the evolution of shorebird morphology, ecology and behaviour. [source] Phylogeographic structuring and volant mammals: the case of the pallid bat (Antrozous pallidus)JOURNAL OF BIOGEOGRAPHY, Issue 7 2007Sarah E. Weyandt Abstract Aim, To examine the phylogeographic pattern of a volant mammal at the continental scale. The pallid bat (Antrozous pallidus) was chosen because it ranges across a zone of well-studied biotic assemblages, namely the warm deserts of North America. Location, The western half of North America, with sites in Mexico, the United States, and Canada. Methods, PCR amplification and sequencing of the mitochondrial control region was performed on 194 pallid bats from 36 localities. Additional sequences at the cytochrome- b locus were generated for representatives of each control-region haplotype. modeltest was used to determine the best set of parameters to describe each data set, which were incorporated into analyses using paup*. Statistical parsimony and measurements of population differentiation (amova, FST) were also used to examine patterns of genetic diversity in pallid bats. Results, We detected three major lineages in the mitochondrial DNA of pallid bats collected across the species range. These three major clades have completely non-overlapping geographic ranges. Only 6 of 80 control-region haplotypes were found at more than a single locality, and sequences at the more conserved cytochrome- b locus revealed 37 haplotypes. Statistical parsimony generated three unlinked networks that correspond exactly to clades defined by the distance-based analysis. On average there was c. 2% divergence for the combined mitochondrial sequences within each of the three major clades and c. 7% divergence between each pair of clades. Molecular clocks date divergence between the major clades at more than one million years, on average, using the faster rates, and at more than three million years using more conservative rates of evolution. Main conclusions, Divergent haplotypic lineages with allopatric distributions suggest that the pallid bat has responded to evolutionary pressures in a manner consistent with other taxa of the American southwest. These results extend the conclusions of earlier studies that found the genetic structuring of populations of some bat species to show that a widespread volant species may comprise a set of geographically replacing monophyletic lineages. Haplotypes were usually restricted to single localities, and the clade showing geographic affinities to the Sonoran Desert contained greater diversity than did clades to the east and west. While faster molecular clocks would allow for glacial cycles of the Pleistocene as plausible agents of diversification of pallid bats, evidence from co-distributed taxa suggests support for older events being responsible for the initial divergence among clades. [source] Dispersal and population structure of a New World predator, the army ant Eciton burchelliiJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 4 2008S. M. BERGHOFF Abstract The army ant Eciton burchellii is probably the most important arthropod predator in the Neotropics, and many animal species depend upon it. Sex-biased dispersal with winged males and permanently wingless queens may render this species especially sensitive to habitat fragmentation and natural barriers, which might have severe impacts on population structure and lead to population decline. Using nuclear microsatellite markers and mitochondrial sequences, we investigated genetic differentiation in a fragmented population in the Panama Canal area. While nuclear markers showed little differentiation between subpopulations (FST = 0.017), mitochondrial differentiation was maximal in some cases (,ST = 1). This suggests that, while females are not capable of crossing barriers such as large rivers, flying males are able to promote nuclear gene flow between the studied forest patches. Consistent with this interpretation, we did not find any evidence for inbreeding or genetic deterioration on Barro Colorado Island over the last 90 years since its formation. [source] Variable extent of sex-biased dispersal in a strongly polygynous mammalMOLECULAR ECOLOGY, Issue 15 2010S. PÉREZ-ESPONA Abstract For mammals with a polygynous mating system, dispersal is expected to be male-biased. However, with the increase in empirical studies, discrepancies are arising between the expected and observed direction/extent of the bias in dispersal. In this study, we assessed sex-biased dispersal in red deer (Cervus elaphus) on 13 estates from the Scottish Highlands. A total of 568 adult individuals were genotyped at 21 microsatellite markers and sequenced for 821 bp of the mitochondrial control region. Estimates of population structure with mitochondrial sequences were eight times larger than that obtained with microsatellite data (Fst,-mtDNA = 0.831; Fst,-micros = 0.096) indicating overall male-biased dispersal in the study area. Comparisons of microsatellite data between the sexes indicated a predominance of male-biased dispersal in the study area but values of FST and relatedness were only slighter larger for females. Individual-based spatial autocorrelation analysis generated a similar pattern of relatedness across geographical distances for both sexes, with differences only significant at two distance intervals (25,30 and 70,112 km). Patterns of relatedness differed between estates, male biased-dispersal was detected in eight estates but no sex-biased dispersal was found in the remaining five. Neither population density nor landscape cover was found to be associated with the patterns of relatedness found across the estates. Differences in management strategies that could influence age structure, sex ratio and dispersal behaviour are proposed as potential factors influencing the relatedness patterns observed. This study provides new insights on dispersal of a strongly polygynous mammal at geographical scales relevant for management and conservation. [source] Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversityMOLECULAR ECOLOGY, Issue 8 2009ROSS BARNETT Abstract Lions were the most widespread carnivores in the late Pleistocene, ranging from southern Africa to the southern USA, but little is known about the evolutionary relationships among these Pleistocene populations or the dynamics that led to their extinction. Using ancient DNA techniques, we obtained mitochondrial sequences from 52 individuals sampled across the present and former range of lions. Phylogenetic analysis revealed three distinct clusters: (i) modern lions, Panthera leo; (ii) extinct Pleistocene cave lions, which formed a homogeneous population extending from Europe across Beringia (Siberia, Alaska and western Canada); and (iii) extinct American lions, which formed a separate population south of the Pleistocene ice sheets. The American lion appears to have become genetically isolated around 340 000 years ago, despite the apparent lack of significant barriers to gene flow with Beringian populations through much of the late Pleistocene. We found potential evidence of a severe population bottleneck in the cave lion during the previous interstadial, sometime after 48 000 years, adding to evidence from bison, mammoths, horses and brown bears that megafaunal populations underwent major genetic alterations throughout the last interstadial, potentially presaging the processes involved in the subsequent end-Pleistocene mass extinctions. [source] Origin and genetic diversity of Western European populations of the potato cyst nematode (Globodera pallida) inferred from mitochondrial sequences and microsatellite lociMOLECULAR ECOLOGY, Issue 9 2008O. PLANTARD Abstract Native to South America, the potato cyst nematode Globodera pallida is one of the principal pests of Andean potato crops and is also an important global pest following its introduction to Europe, Africa, North America, Asia and Oceania. Building on earlier work showing a clear south to north phylogeographic pattern in Peruvian populations, we have been able to identify the origin of Western European populations with high accuracy. They are all derived from a single restricted area in the extreme south of Peru, located between the north shore of the Lake Titicaca and Cusco. Only four cytochrome b haplotypes are found in Western Europe, one of them being also found in some populations of this area of southern Peru. The allelic richness at seven microsatellite loci observed in the Western European populations, although only one-third of that observed in this part of southern Peru, is comparable to the allelic richness observed in the northern region of Peru. This result could be explained by the fact that most of the genetic variability observed at the scale of a field or even of a region is already observed at the scale of a single plant within a field. Thus, even introduction via a single infected potato plant could result in the relatively high genetic variability observed in Western Europe. This finding has important consequences for the control of this pest and the development of quarantine measures. [source] Genetic continuity of brood-parasitic indigobird speciesMOLECULAR ECOLOGY, Issue 5 2005KRISTINA M. SEFC Abstract Speciation in brood-parasitic indigobirds (genus Vidua) is a consequence of behavioural imprinting in both males and females. Mimicry of host song by males and host fidelity in female egg laying result in reproductive isolation of indigobirds associated with a given host species. Colonization of new hosts and subsequent speciation require that females occasionally lay eggs in the nests of novel hosts but the same behaviour may lead to hybridization when females parasitize hosts already associated with other indigobird species. Thus, retained ancestral polymorphism and ongoing hybridization are two alternative explanations for the limited genetic differentiation among indigobird species. We tested for genetic continuity of indigobird species using mitochondrial sequences and nuclear microsatellite data. Within West Africa and southern Africa, allopatric populations of the same species are generally more similar to each other than to sympatric populations of different species. Likewise, a larger proportion of genetic variation is explained by differences between species than by differences between locations in alternative hierarchical amovas, suggesting that the rate of hybridization is not high enough to homogenize sympatric populations of different species or prevent genetic differentiation between species. Broad sharing of genetic polymorphisms among species, however, suggests that some indigobird species trace to multiple host colonization events in space and time, each contributing to the formation of a single interbreeding population bound together by songs acquired from the host species. [source] BARCODING: Assessing the effect of varying sequence length on DNA barcoding of fungiMOLECULAR ECOLOGY RESOURCES, Issue 3 2007XIANG JIA MIN Abstract DNA barcoding shows enormous promise for the rapid identification of organisms at the species level. There has been much recent debate, however, about the need for longer barcode sequences, especially when these sequences are used to construct molecular phylogenies. Here, we have analysed a set of fungal mitochondrial sequences , of various lengths , and we have monitored the effect of reducing sequence length on the utility of the data for both species identification and phylogenetic reconstruction. Our results demonstrate that reducing sequence length has a profound effect on the accuracy of resulting phylogenetic trees, but surprisingly short sequences still yield accurate species identifications. We conclude that the standard short barcode sequences (,600 bp) are not suitable for inferring accurate phylogenetic relationships, but they are sufficient for species identification among the fungi. [source] Mitochondrial DNA diversity and origins of South and Central American goatsANIMAL GENETICS, Issue 3 2009M. Amills Summary We have analysed the genetic diversity of South and Central American (SCA) goats by partially sequencing the mitochondrial control region of 93 individuals with a wide geographical distribution. Nucleotide and haplotype diversities reached values of 0.020 ± 0.00081 and 0.963 ± 0.0012 respectively. We have also observed a rather weak phylogeographic structure, with almost 69% of genetic variation included in the within-breed variance component. The topology of a median-joining network analysis including 286 European, Iberian, Atlantic and SCA mitochondrial sequences was very complex, with most of the haplotypes forming part of independent small clusters. SCA sequences showed a scattered distribution throughout the network, and clustering with Spanish and Portuguese sequences occurred only occasionally, not allowing the distinguishing of a clear Iberian signature. Conversely, we found a prominent cluster including Canarian, Chilean, Argentinian and Bolivian mitochondrial haplotypes. This result was independently confirmed by constructing a Bayesian phylogenetic tree (posterior probability of 0.97). Sharing of mitochondrial haplotypes by SCA and Canarian goats suggests that goat populations from the Atlantic archipelagos, where Spanish and Portuguese ships en route to the New World used to stow food and supplies, participated in the foundation of SCA caprine breeds. [source] Genetic relationship between Litopenaeus setiferus (L.) and L. schmitti (Burkenroad) determined by using 16S mitochondrial sequences and enzymatic analysisAQUACULTURE RESEARCH, Issue 12 2003L Arena Abstract Genetic differentiation and variability data of two populations of two species of shrimp (Litopenaeus setiferus (L.) and L. schmitti (Burkenroad)) have been obtained by electrophoretic analysis and by analysis of 16S mitochondrial DNA. Using eight polymorphic enzymes, the genetic distance (GD) between the two species was 0.165. The GD between L. setiferus populations was 0.0057 and between L. schmitti populations it was 0.0034. The greatest differentiation was found within, rather than between, populations, although the differentiation value between Mexican and Cuban populations varied in accordance with the geographic distance and ecological characteristic of each. We found a high similarity between these two species with a bimodal distribution of the loci with respect to genetic identity. The homology percentages for gene 16S fragments were compared with those from six different shrimp species (L. vannamei, L. stylirostris, Farfantepenaeus notialis, Metapeneopsis lamellata) and Artemia salina. Ninety-seven percent of identity was found by analysis of a 409 bp of 16S mitochondrial DNA. With these values a phylogenetic tree was made using parsimony criteria. The GDs obtained with this method confirm the classification proposed by Pérez-Farfante & Kensley (1997). [source] | ||||||||||