Somatic mutations of mtDNA are implicated in the aging process, but there is no universally accepted method for their accurate quantification. We have used ultra-deep sequencing to study genome-wide ...mtDNA mutation load in the liver of normally- and prematurely-aging mice. Mice that are homozygous for an allele expressing a proof-reading-deficient mtDNA polymerase (mtDNA mutator mice) have 10-times-higher point mutation loads than their wildtype siblings. In addition, the mtDNA mutator mice have increased levels of a truncated linear mtDNA molecule, resulting in decreased sequence coverage in the deleted region. In contrast, circular mtDNA molecules with large deletions occur at extremely low frequencies in mtDNA mutator mice and can therefore not drive the premature aging phenotype. Sequence analysis shows that the main proportion of the mutation load in heterozygous mtDNA mutator mice and their wildtype siblings is inherited from their heterozygous mothers consistent with germline transmission. We found no increase in levels of point mutations or deletions in wildtype C57Bl/6N mice with increasing age, thus questioning the causative role of these changes in aging. In addition, there was no increased frequency of transversion mutations with time in any of the studied genotypes, arguing against oxidative damage as a major cause of mtDNA mutations. Our results from studies of mice thus indicate that most somatic mtDNA mutations occur as replication errors during development and do not result from damage accumulation in adult life.
To study the evolutionary history of the Australian and New Guinean indigenous peoples, we analyzed 101 complete mitochondrial genomes including populations from Australia and New Guinea as well as ...from Africa, India, Europe, Asia, Melanesia, and Polynesia. The genetic diversity of the Australian mitochondrial sequences is remarkably high and is similar to that found across Asia. This is in contrast to the pattern seen in previously described Y-chromosome data where an Australia-specific haplotype was found at high frequency. The mitochondrial genome data indicate that Australia was colonized between 40 and 70 thousand years ago, either by a single migration from a heterogeneous source population or by multiple movements of smaller groups occurring over a period of time. Some Australian and New Guinea sequences form clades, suggesting the possibility of a joint colonization and/or admixture between the two regions.
The mitochondrial genome, contained in the subcellular mitochondrial network, encodes a small number of peptides pivotal for cellular energy production. Mitochondrial genes are highly polymorphic and ...cataloguing existing variation is of interest for medical scientists involved in the identification of mutations causing mitochondrial dysfunction, as well as for population genetics studies. Human Mitochondrial Genome Database (mtDB) (http://www.genpat.uu.se/mtDB) has provided a comprehensive database of complete human mitochondrial genomes since early 2000. At this time, owing to an increase in the number of published complete human mitochondrial genome sequences, it became necessary to provide a web-based database of human whole genome and complete coding region sequences. As of August 2005 this database contains 2104 sequences (1544 complete genome and 560 coding region) available to download or search for specific polymorphisms. Of special interest to medical researchers and population geneticists evaluating specific positions is a complete list of (currently 3311) mitochondrial polymorphisms among these sequences. Recent expansions in the capabilities of mtDB include a haplotype search function and the ability to identify and download sequences carrying particular variants.
It has been proposed that as a result of human adaptation to different climates, mitochondrial genes have been affected by natural selection. To further study the selective pressure on human ...mitochondrial DNA, we have analysed polymorphism at the gene, domain and nucleotide site level in four geographic regions. The ratio of non-synonymous relative to synonymous substitutions is elevated for ATP6 in North Asia, ND3 in Africa and cytb in Europe relative to other mitochondrial genes. In addition, non-synonymous substitutions appear nearly five times more frequently outside core functional domains as compared with within functional domains. Therefore, a large part of the rate variation between mitochondrial genes is explained by differences in the length of the functional domain relative to the length of the gene. The accumulation of non-synonymous substitutions in the ATP6 gene among sequences from North Asia has been a gradual process over many thousands of years, consistent with relaxed purifying selection rather than recent strong selective sweeps. It is not necessary to invoke adaptive selection to explain the pattern of polymorphism in mitochondrial genes, when the most parsimonious explanation is relaxed purifying selection and the action of genetic drift.
Resequencing of genomic regions that have been implicated by linkage and/or association studies to harbor genetic susceptibility loci represents a necessary step to identify causal variants. ...Massively parallel sequencing (MPS) offers the possibility of SNP discovery and frequency determination among pooled DNA samples. The strategies of pooling DNA samples and pooling PCR amplicons generated from individual DNA samples were evaluated, and both were found to return accurate estimates of SNP frequencies across varying levels of sequence coverage.
Domestic animals are excellent models for genetic studies of phenotypic evolution. They have evolved genetic adaptations to a new environment, the farm, and have been subjected to strong human-driven ...selection leading to remarkable phenotypic changes in morphology, physiology and behaviour. Identifying the genetic changes underlying these developments provides new insight into general mechanisms by which genetic variation shapes phenotypic diversity. Here we describe the use of massively parallel sequencing to identify selective sweeps of favourable alleles and candidate mutations that have had a prominent role in the domestication of chickens (Gallus gallus domesticus) and their subsequent specialization into broiler (meat-producing) and layer (egg-producing) chickens. We have generated 44.5-fold coverage of the chicken genome using pools of genomic DNA representing eight different populations of domestic chickens as well as red jungle fowl (Gallus gallus), the major wild ancestor. We report more than 7,000,000 single nucleotide polymorphisms, almost 1,300 deletions and a number of putative selective sweeps. One of the most striking selective sweeps found in all domestic chickens occurred at the locus for thyroid stimulating hormone receptor (TSHR), which has a pivotal role in metabolic regulation and photoperiod control of reproduction in vertebrates. Several of the selective sweeps detected in broilers overlapped genes associated with growth, appetite and metabolic regulation. We found little evidence that selection for loss-of-function mutations had a prominent role in chicken domestication, but we detected two deletions in coding sequences that we suggest are functionally important. This study has direct application to animal breeding and enhances the importance of the domestic chicken as a model organism for biomedical research.
The genetic origin of the Sami is enigmatic and contributions from Continental Europe, Eastern Europe and Asia have been proposed. To address the evolutionary history of northern and southern Swedish ...Sami, we have studied their mtDNA haplogroup frequencies and complete mtDNA genome sequences. While the majority of mtDNA diversity in the northern Swedish, Norwegian and Finnish Sami is accounted for by haplogroups V and U5b1b1, the southern Swedish Sami have other haplogroups and a frequency distribution similar to that of the Continental European population. Stratification of the southern Sami on the basis of occupation indicates that this is the result of recent admixture with the Swedish population. The divergence time for the Sami haplogroup V sequences is 7600 YBP (years before present), and for U5b1b1, 5500 YBP amongst Sami and 6600 YBP amongst Sami and Finns. This suggests an arrival in the region soon after the retreat of the glacial ice, either by way of Continental Europe and/or the Volga-Ural region. Haplogroup Z is found at low frequency in the Sami and Northern Asian populations but is virtually absent in Europe. Several conserved substitutions group the Sami Z lineages strongly with those from Finland and the Volga-Ural region of Russia, but distinguish them from Northeast Asian representatives. This suggests that some Sami lineages shared a common ancestor with lineages from the Volga-Ural region as recently as 2700 years ago, indicative of a more recent contribution of people from the Volga-Ural region to the Sami population.
The analysis of mitochondrial DNA (mtDNA) has been a potent tool in our
understanding of human evolution, owing to characteristics such as high copy
number, apparent lack of recombination, high ...substitution rate and maternal mode of inheritance. However, almost
all studies of human evolution based on mtDNA sequencing have been confined
to the control region, which constitutes less than 7% of the mitochondrial
genome. These studies are complicated by the extreme variation in substitution
rate between sites, and the consequence of parallel mutations
causing difficulties in the estimation of genetic distance and making phylogenetic
inferences questionable. Most comprehensive studies of the
human mitochondrial molecule have been carried out through restriction-fragment
length polymorphism analysis, providing data that are ill suited
to estimations of mutation rate and therefore the timing of evolutionary events.
Here, to improve the information obtained from the mitochondrial molecule
for studies of human evolution, we describe the global mtDNA diversity in
humans based on analyses of the complete mtDNA sequence of 53 humans of diverse
origins. Our mtDNA data, in comparison with those of a parallel study of the
Xq13.3 region in the same individuals, provide a concurrent
view on human evolution with respect to the age of modern humans.
Somatic mutations of mtDNA are implicated in the aging process, but there is no universally accepted method for their accurate quantification. We have used ultra-deep sequencing to study genome-wide ...mtDNA mutation load in the liver of normally- and prematurely-aging mice. Mice that are homozygous for an allele expressing a proof-reading-deficient mtDNA polymerase (mtDNA mutator mice) have 10-times-higher point mutation loads than their wildtype siblings. In addition, the mtDNA mutator mice have increased levels of a truncated linear mtDNA molecule, resulting in decreased sequence coverage in the deleted region. In contrast, circular mtDNA molecules with large deletions occur at extremely low frequencies in mtDNA mutator mice and can therefore not drive the premature aging phenotype. Sequence analysis shows that the main proportion of the mutation load in heterozygous mtDNA mutator mice and their wildtype siblings is inherited from their heterozygous mothers consistent with germline transmission. We found no increase in levels of point mutations or deletions in wildtype C57Bl/6N mice with increasing age, thus questioning the causative role of these changes in aging. In addition, there was no increased frequency of transversion mutations with time in any of the studied genotypes, arguing against oxidative damage as a major cause of mtDNA mutations. Our results from studies of mice thus indicate that most somatic mtDNA mutations occur as replication errors during development and do not result from damage accumulation in adult life.
The analysis of mitochondrial DNA (mtDNA) sequences has been a potent tool in our understanding of human evolution. However, almost all studies of human evolution based on mtDNA sequencing have ...focused on the control region, which constitutes less than 7% of the mitochondrial genome. The rapid development of technology for automated DNA sequencing has made it possible to study the complete mtDNA genomes in large numbers of individuals, opening the field of mitochondrial population genomics. Here we describe a suitable methodology for determining the complete human mitochondrial sequence and the global mtDNA diversity in humans. Also, we discuss the implications of the results with respect to the different hypotheses for the evolution of modern humans.
PDF
