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Mitochondrial DNA (mtDNA) has formed the backbone of phylogeographic research for many years, however, recent trends focus on genome-wide analyses. One method proposed for calibrating inferences from noisy Next-Generation data, such as RAD sequencing, is to compare these results with analyses of mitochondrial sequences. Most researchers using this approach appear to be unaware that many Single Nucleotide Polymorphisms (SNPs) identified from genome-wide sequence data are themselves mitochondrial, or assume that these are too few to bias analyses. Here we demonstrate two methods for mining mitochondrial markers using RAD sequence data from three South African species of yellowfish, Labeobarbus. First, we use a rigorous SNP discovery pipeline using the program Stacks, to identify variant sites in mtDNA, which we then combine into haplotypes. Secondly, we directly map sequence reads against a mitochondrial genome reference. This method allowed us to reconstruct up to 98% of the Labeobarbus mitogenome. We validated these mitogenome reconstructions through BLAST database searches and by comparisons with cytochrome b gene sequences obtained through Sanger sequencing. Finally, we investigate the organismal consequences of these data including ancient genetic exchange and a recent translocation among populations of L. natalensis, as well as interspecific hybridisation between L. aeneus and L. kimberleyensis. This article is protected by copyright. All rights reserved.
This article was published in the following journal.
Name: Molecular ecology resources
In this paper, we examined relationships and differences between personal and vicarious life stories, i.e., the life stories one knows of others. Personal and vicarious life stories of both members of...
Mitochondria perform crucial roles in many biochemical processes, and mitochondrial depolarization is an early sign of platelet apoptosis. The mitochondrial membrane potential is usually evaluated thr...
Noise annoyance may reflect a pro-participatory attitude towards public information and consultation according to the European Environmental Noise Directive. However, noise annoyance is also indicativ...
An analysis of the measured ocean noise during the tropical cyclone period is presented. While the observed noise is highly correlated with wind, this study reveals the dispersion of noise spectra. A ...
Environmental noise pollution is an important social problem. Noise is known to have an adverse effect on human emotions and bodies. However, the methodology of previous studies did not consider selec...
The effect of noise is often underestimated but it is one of the most common occupational health hazards. Its health effects include; noise-induced hearing loss, sleep disturbance, interfe...
It has been suggested that mitochondrial dysfunction might play a role in the development of diabetic cardiomyopathy. From animal studies, it has been suggested that an altered PPAR and PG...
Many patients complain to clinicians that they have difficulty sleeping appears to be due to environmental noise. There is a common perception that acute noises are more troublesome than c...
Finding a predictive biomarker for IAI could improve the clinical outcome for the mother and the neonate. The aim of this study is to quantify the copy number of circulating cell-free mito...
Patients and caregivers undergoing hematopoietic stem cell transplantation often continue to experience anxiety, depression, isolation, and other psychosocial distress. A narrative-based d...
The comparison of the quantity of meaningful data to the irrelevant or incorrect data.
Signal and data processing method that uses decomposition of wavelets to approximate, estimate, or compress signals with finite time and frequency domains. It represents a signal or data in terms of a fast decaying wavelet series from the original prototype wavelet, called the mother wavelet. This mathematical algorithm has been adopted widely in biomedical disciplines for data and signal processing in noise removal and audio/image compression (e.g., EEG and MRI).
Books containing photographs, prints, drawings, portraits, plates, diagrams, facsimiles, maps, tables, or other representations or systematic arrangement of data designed to elucidate or decorate its contents. (From The ALA Glossary of Library and Information Science, 1983, p114)
Works consisting of photographs, prints, drawings, portraits, plates, diagrams, facsimiles, maps, tables, or other representations or systematic arrangements of data designed to elucidate or decorate the contents of a publication. (From The ALA Glossary of Library and Information Science, 1983, p114)
Noise present in occupational, industrial, and factory situations.
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. During DNA sequencing, the bases of a small fragment of DNA are sequentially identified from signals emitted as each fragment is re-synthesized from a ...