Estimating individual mtDNA haplotypes in mixed DNA samples by combining MinION and MiSeq

2022 ◽  
Author(s):  
Hiroaki Nakanishi ◽  
Katsumi Yoneyama ◽  
Masaaki Hara ◽  
Aya Takada ◽  
Kentaro Sakai ◽  
...  
Keyword(s):  
Mtdna Haplotypes

scholarly journals Multiple Origins of a Mitochondrial Mutation Conferring Deafness

Genetics ◽  
1997 ◽  
Vol 145 (3) ◽  
pp. 771-776 ◽  
Author(s):  
Timothy P Hutchin ◽  
Gino A Cortopassi
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Distance ◽  
Ribosomal Subunit ◽  
Sensorineural Deafness ◽  
Nucleotide Substitutions ◽  
Mitochondrial Mutation ◽  
Distance Analysis ◽  
Multiple Origins ◽  
Mtdna Haplotypes ◽  
Mtdna Sequence

A point mutation (1555G) in the smaller ribosomal subunit of the mitochondrial DNA (mtDNA) has been associated with maternally inherited traits of hypersensitivity to streptomycin and sensorineural deafness in a number of families from China, Japan, Israel, and Africa. To determine whether this distribution was the result of a single or multiple mutational events, we carried out genetic distance analysis and phylogenetic analysis of 10 independent mtDNA D-loop sequences from Africa and Asia. The mtDNA sequence diversity was high (2.21%). Phylogenetic analysis assigned 1555G-bearing haplotypes at very divergent points in the human mtDNA evolutionary tree, and the 1555G mutations occur in many cases on race-specific mtDNA haplotypes, both facts are inconsistent with a recent introgression of the mutation into these races. The simplest interpretation of the available data is that there have been multiple origins of the 1555G mutation. The genetic distance among mtDNAs bearing the pathogenic 1555G mutation is much larger than among mtDNAs bearing either evolutionarily neutral or weakly deleterious nucleotide substitutions (such as the 4336G mutation). These results are consistent with the view that pathogenic mtDNA haplotypes such as 1555G arise on disparate mtDNA lineages which because of negative natural selection leave relatively few related descendants. The co-existence of the same mutation with deafness in individuals with very different nuclear and mitochondrial genetic backgrounds confirms the pathogenicity of the 1555G mutation.

scholarly journals Mitochondrial Genome Rearrangements in Glomus Species Triggered by Homologous Recombination between Distinct mtDNA Haplotypes

2013 ◽  
Vol 5 (9) ◽  
pp. 1628-1643 ◽  
Author(s):  
Denis Beaudet ◽  
Yves Terrat ◽  
Sébastien Halary ◽  
Ivan Enrique de la Providencia ◽  
Mohamed Hijri
Keyword(s):  
Homologous Recombination ◽  
Mitochondrial Genome ◽  
Genome Rearrangements ◽  
Mtdna Haplotypes ◽  
Glomus Species

Comparison of Allozyme and Mitochondrial DNA Variation in Populations of Walleye, Stizostedion vitreum

1989 ◽  
Vol 46 (12) ◽  
pp. 2074-2084 ◽  
Author(s):  
Robert D. Ward ◽  
Neil Billington ◽  
Paul D. N. Hebert
Keyword(s):  
Mitochondrial Dna ◽  
Glacial Refugia ◽  
Divergence Times ◽  
Stizostedion Vitreum ◽  
Dna Variation ◽  
Mtdna Variation ◽  
Mtdna Haplotypes ◽  
Total Genetic Diversity ◽  
Allozyme Loci ◽  
Organelle Genes

Twelve populations of walleye (Stizostedion vitreum) from the Great Lakes and three populations from northern Manitoba were screened for allozyme and mitochondrial DNA (mtDNA) variation. Nine enzyme loci known to show genetic variation were screened in all fish: five of them (Prot-4, Prot-2, Mdh-3, Idh-1, Adh) showed appreciable polymorphism. MtDNA was examined in all fish using six endonucleases that detected polymorphic sites and a further 13 endonucleases that detected only monomorphic sites. Only one of the allozyme loci (Prot-4) showed evidence of geographic patterning of allele frequencies. By contrast, the mtDNA haplotypes showed clear geographic variation. The proportion of total genetic diversity attributable to population differentiation (Gst) was three to five times greater for mtDNA than for the allozymes. Gst values for organelle genes are expected on theoretical grounds to be greater than for nuclear genes, and this expected difference may be enhanced in walleye because of the likelihood that, in this species, male-mediated gene flow exceeds that of females. The distributions of mtDNA haplotypes and estimated divergence times are consistent with the derivation of extant walleye populations from three different glacial refugia.

scholarly journals Evidence for non-neutrality of mitochondrial DNA haplotypes in Drosophila pseudoobscura.

Genetics ◽  
1988 ◽  
Vol 120 (2) ◽  
pp. 485-494
Author(s):  
A F MacRae ◽  
W W Anderson
Keyword(s):  
Mitochondrial Dna ◽  
Nuclear Genome ◽  
Drosophila Pseudoobscura ◽  
Initial Population ◽  
Mitochondrial Haplotypes ◽  
Mtdna Haplotypes ◽  
Selective Neutrality ◽  
Frequency Changes ◽  
Apparent Equilibrium ◽  
Neutral Markers

Abstract Mitochondrial DNA (mtDNA) haplotypes usually are assumed to be neutral, unselected markers of evolving female lineages. This assumption was tested by monitoring haplotype frequencies in 12 experimental populations of Drosophila pseudoobscura which were polymorphic for mtDNA haplotypes. Populations were maintained for at least 10 generations, and in one case for 32 generations, while tests of mtDNA selective neutrality were conducted. In an initial population, formed from a mixture of two strains with different mitochondrial haplotypes, the frequency of the Bogota haplotype increased 46% in 3 generations, reaching an apparent equilibrium frequency of 82% after 32 generations. Perturbation of this equilibrium by addition of the less common haplotype resulted in a rapid, dramatic increase in frequency of the second haplotype, and a return to essentially the same equilibrium frequency as before perturbation. This behavior is not consistent with mtDNA neutrality, nor is the equilibrium consistent with a simple model of constant selection on the haploid mtDNAs. Replicate cage experiments with mtDNA haplotypes did not always generate the same result as the initial cage. Several lines of evidence, including manipulations of the nuclear genome, support the idea that both nuclear and mitochondrial genomes are involved in the dramatic mtDNA frequency changes. In another experiment, strong female viability selection was implicated via mtDNA frequency changes. Although the causes of the dramatic mtDNA frequency changes in our populations are not obvious, it is clear that Drosophila mitochondrial haplotypes are not always simply neutral markers. Our findings are relevant to the introduction of a novel mtDNA variant from one species or one population into another. Such introductions could be strongly favored by selection, even if it is sporadic.

New mtDNA Haplotypes of the Sika Deer (Cervus nippon) Found in Hokkaido, Japan Suggest Human-Mediated Immigration

Mammal Study ◽  
2013 ◽  
Vol 38 (2) ◽  
pp. 123-129 ◽  
Author(s):  
Chisato Terada ◽  
Toshiya Yamada ◽  
Hiroyuki Uno ◽  
Takashi Saitoh
Keyword(s):  
Sika Deer ◽  
Cervus Nippon ◽  
Mtdna Haplotypes

scholarly journals Sirt4 Modulates Oxidative Metabolism and Sensitivity to Rapamycin Through Species-Dependent Phenotypes in Drosophila mtDNA Haplotypes

2020 ◽  
Vol 10 (5) ◽  
pp. 1599-1612
Author(s):  
Richard Sejour ◽  
Roger A. Sanguino ◽  
Monika Mikolajczak ◽  
Walishah Ahmadi ◽  
Eugenia Villa-Cuesta
Keyword(s):  
Oxidative Metabolism ◽  
Nuclear Dna ◽  
Metabolic Response ◽  
Symbiotic Relationship ◽  
Tor Signaling ◽  
Epistatic Interactions ◽  
Multifaceted Approach ◽  
Suitable Candidate ◽  
Link Type ◽  
Mtdna Haplotypes

The endosymbiotic theory proposes that eukaryotes evolved from the symbiotic relationship between anaerobic (host) and aerobic prokaryotes. Through iterative genetic transfers, the mitochondrial and nuclear genomes coevolved, establishing the mitochondria as the hub of oxidative metabolism. To study this coevolution, we disrupt mitochondrial-nuclear epistatic interactions by using strains that have mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) from evolutionarily divergent species. We undertake a multifaceted approach generating introgressed Drosophila strains containing D. simulans mtDNA and D. melanogaster nDNA with Sirtuin 4 (Sirt4)-knockouts. Sirt4 is a nuclear-encoded enzyme that functions, exclusively within the mitochondria, as a master regulator of oxidative metabolism. We exposed flies to the drug rapamycin in order to eliminate TOR signaling, thereby compromising the cytoplasmic crosstalk between the mitochondria and nucleus. Our results indicate that D. simulans and D. melanogaster mtDNA haplotypes display opposite Sirt4-mediated phenotypes in the regulation of whole-fly oxygen consumption. Moreover, our data reflect that the deletion of Sirt4 rescued the metabolic response to rapamycin among the introgressed strains. We propose that Sirt4 is a suitable candidate for studying the properties of mitochondrial-nuclear epistasis in modulating mitochondrial metabolism.

scholarly journals mtDNA haplotypes differ in their probability of being eliminated by a mass die-off in an abundant seabird

Heredity ◽  
2012 ◽  
Vol 109 (1) ◽  
pp. 29-33 ◽  
Author(s):  
S V Drovetski ◽  
A S Kitaysky ◽  
N A Mode ◽  
R M Zink ◽  
U Iqbal ◽  
...  
Keyword(s):  
Mtdna Haplotypes

scholarly journals Green turtle Chelonia mydas mixed stocks in the western South Atlantic, as revealed by mtDNA haplotypes and drifter trajectories

2012 ◽  
Vol 447 ◽  
pp. 195-209 ◽  
Author(s):  
MC Proietti ◽  
JW Reisser ◽  
PG Kinas ◽  
R Kerr ◽  
DS Monteiro ◽  
...  
Keyword(s):  
Green Turtle ◽  
Chelonia Mydas ◽  
South Atlantic ◽  
Mtdna Haplotypes

Ghost mtDNA haplotypes generated by fortuitous NUMTs can deeply disturb infra-specific genetic diversity and phylogeographic pattern

2015 ◽  
Vol 53 (2) ◽  
pp. 109-115 ◽  
Author(s):  
Julien Haran ◽  
Fotini Koutroumpa ◽  
Emmanuelle Magnoux ◽  
Alain Roques ◽  
Géraldine Roux
Keyword(s):  
Genetic Diversity ◽  
Phylogeographic Pattern ◽  
Mtdna Haplotypes

What can the geographic distribution of mtDNA haplotypes tell us about the invasion of New Zealand by house mice Mus musculus?

2016 ◽  
Vol 18 (6) ◽  
pp. 1551-1565 ◽  
Author(s):  
Carolyn King ◽  
Alana Alexander ◽  
Tanya Chubb ◽  
Ray Cursons ◽  
Jamie MacKay ◽  
...  
Keyword(s):  
New Zealand ◽  
Geographic Distribution ◽  
Mus Musculus ◽  
House Mice ◽  
Mtdna Haplotypes
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