Article

Mutation patterns of mtDNA: empirical inferences for the coding region.

Center for Research in Natural Resources (CIRN), University of the Azores, 9500 Ponta Delgada, S, Miguel, Azores, Portugal.
BMC Evolutionary Biology (Impact Factor: 3.41). 01/2008; 8:167. DOI: 10.1186/1471-2148-8-167
Source: PubMed

ABSTRACT Human mitochondrial DNA (mtDNA) has been extensively used in population and evolutionary genetics studies. Thus, a valid estimate of human mtDNA evolutionary rate is important in many research fields. The small number of estimations performed for the coding region of the molecule, showed important differences between phylogenetic and empirical approaches. We analyzed a portion of the coding region of mtDNA (tRNALeu, ND1 and tRNAIle genes), using individuals belonging to extended families from the Azores Islands (Portugal) with the main aim of providing empirical estimations of the mutation rate of the coding region of mtDNA under different assumptions, and hence to better understand the mtDNA evolutionary process.
Heteroplasmy was detected in 6.5% (3/46) of the families analyzed. In all of the families the presence of mtDNA heteroplasmy resulted from three new point mutations, and no cases of insertions or deletions were identified. Major differences were found in the proportion and type of heteroplasmy found in the genes studied when compared to those obtained in a previous report for the D-loop. Our empirical estimation of mtDNA coding region mutation rate, calculated taking into account the sex of individuals carrying new mutations, the probability of intra-individual fixation of mutations present in heteroplasmy and, to the possible extent, the effect of selection, is similar to that obtained using phylogenetic approaches.
Based on our results, the discrepancy previously reported between the human mtDNA coding region mutation rates observed along evolutionary timescales and estimations obtained using family pedigrees can be resolved when correcting for the previously cited factors.

0 Bookmarks
 · 
120 Views
  • [Show abstract] [Hide abstract]
    ABSTRACT: This paper describes a site investigation study that has been performed on the Vedsted structure in NW Denmark, where upper Triassic and Lower Jurassic sandy formations are considered potential reservoirs for large-scale CO2 injection. The study presents the updated version 1.0 model using new 2D seismic data from the site and compares to results from the screening stage where only existing vintage data were used for the geological modelling.In this early stage of site investigation, the regional geological model and sequence stratigraphic interpretation are important contributors to the construction of a realistic geo-model. The facies interpretation is critical for understanding the geometry and connectivity of the reservoir layers.The main reservoir is at depths of 1700 to 2000 m, and therefore the CO2 is injected at supercritical conditions. The reservoir rocks are mainly constituted of fluvial to nearshore deposits including shoreface sandstones, interfingering with marine offshore mudstones. The maximum thickness of the sandstone layers of ca. 30 m will restrict the potential for convection of the brine caused by density contrast instability. Therefore the dissolution enhancement normally assumed to be associated with convection must be modified for this geological setting. This is in contrast to the performance predicted for the Sleipner injection site, where convection is interpreted to happen over time, and it therefore illustrates that site specific evaluation is necessary in order to qualify the contribution from enhanced dissolution as storage mechanism. The interpretation of the new 2D seismic data and the resulting revision of the structural model influence the further plans for data collection, drilling planning and injection strategy.
    Energy Procedia 01/2011; 4:4711-4718. DOI:10.1016/j.egypro.2011.02.433
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Determining the levels of human mitochondrial heteroplasmy is of utmost importance in several fields. In spite of this, there are currently few published works that have focused on this issue. In order to increase the knowledge of mitochondrial DNA (mtDNA) heteroplasmy, the main goal of this work is to investigate the frequency and the mutational spectrum of heteroplasmy in the human mtDNA genome. To address this, a set of nine primer pairs designed to avoid co-amplification of nuclear DNA (nDNA) sequences of mitochondrial origin (NUMTs) was used to amplify the mitochondrial genome in 101 individuals. The analysed individuals represent a collection with a balanced representation of genders and mtDNA haplogroup distribution, similar to that of a Western European population. The results show that the frequency of heteroplasmic individuals exceeds 61%. The frequency of point heteroplasmy is 28.7%, with a widespread distribution across the entire mtDNA. In addition, an excess of transitions in heteroplasmy were detected, suggesting that genetic drift and/or selection may be acting to reduce its frequency at population level. In fact, heteroplasmy at highly stable positions might have a greater impact on the viability of mitochondria, suggesting that purifying selection must be operating to prevent their fixation within individuals. This study analyses the frequency of heteroplasmy in a healthy population, carrying out an evolutionary analysis of the detected changes and providing a new perspective with important consequences in medical, evolutionary and forensic fields.
    PLoS ONE 01/2013; 8(10):e74636. DOI:10.1371/journal.pone.0074636 · 3.53 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Background Complete mitochondrial DNA (mtDNA) genome analyses have greatly improved the phylogeny and phylogeography of human mtDNA. Human mitochondrial DNA haplogroup U6 has been considered as a molecular signal of a Paleolithic return to North Africa of modern humans from southwestern Asia. Results Using 230 complete sequences we have refined the U6 phylogeny, and improved the phylogeographic information by the analysis of 761 partial sequences. This approach provides chronological limits for its arrival to Africa, followed by its spreads there according to climatic fluctuations, and its secondary prehistoric and historic migrations out of Africa colonizing Europe, the Canary Islands and the American Continent. Conclusions The U6 expansions and contractions inside Africa faithfully reflect the climatic fluctuations that occurred in this Continent affecting also the Canary Islands. Mediterranean contacts drove these lineages to Europe, at least since the Neolithic. In turn, the European colonization brought different U6 lineages throughout the American Continent leaving the specific sign of the colonizers origin.
    BMC Evolutionary Biology 05/2014; DOI:10.1186/1471-2148-14-109 · 3.41 Impact Factor

Full-text (2 Sources)

Download
53 Downloads
Available from
May 23, 2014