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PubMed1996

Pre-Caucasoid and Caucasoid genetic features of the Indian population, revealed by mtDNA polymorphisms.

About 70 individuals from Punjab were examined for some mtDNA polymorphisms, namely, the RFLPs of the six classical enzymes (HpaI, BamHI, HaeII, MspI, AvaII, and Hin-cII) and for the sites AluI(7,025), DdeI(10,394), and AluI(10,397). The AluI(7,025) polymorphic site was also investigated in 96 Indians from Uttar Pradesh and Andhra Pradesh and in 163 Mediterranean Caucasoids. Moreover, 30 Indian DdeI(10,394)Alu(10,397) (++) mtDNAs were typed by the "high-resolution restriction analysis" with 14 endonucleases to estimate their divergence time. The results obtained are the following: (1) The RFLPs analysis has displayed some Caucasoid types as in Indians of Uttar Pradesh; (2) the AluI(7,025) (-) allele, which defines the most frequent Caucasoid-specific lineage (haplogroup H), ranges from 18% to 45% in the Mediterranean Caucasoids, whereas it has shown low frequencies in Punjab (6.0%) and in Uttar Pradesh (1.8%) and was not found in Andhra Pradesh; (3) the DdeI(lO,394)AluI(10,397) (+ +) haplotype, which although previously was considered an East Asian marker (haplogroup M) and was found very frequently in India, is also frequent in Punjab (27%); this frequency is, however, much lower than in Uttar Pradesh (49%) and in Andhra Pradesh (74%), and a gradient decreasing from south to north is therefore observed; (4) the divergence time of the Indian DdeI(10,394)AluI(10,397) (++) mtDNAs has been estimated to be 30,250-60,500 years, a value that is compatible with that of the homologous East Asian lineage. These results strongly support the hypothesis that the DdeI(10,394)AluI(10,397) (++) haplotype predated the Indo-European invasion and probably the split between proto-Indians and proto-Orientals. Its frequency cline well reflects the major influence of Indo-Europeans in the north and in the center of India.

DNA, Mitochondrial↗
PubMed1997

Haplotype and phylogenetic analyses suggest that one European-specific mtDNA background plays a role in the expression of Leber hereditary optic neuropathy by increasing the penetrance of the primary mutations 11778 and 14484.

mtDNAs from 37 Italian subjects affected by Leber hereditary optic neuropathy (LHON) (28 were 11778 positive, 7 were 3460 positive, and 2 were 14484 positive) and from 99 Italian controls were screened for most of the mutations that currently are associated with LHON. High-resolution restriction-endonuclease analysis also was performed on all subjects, in order to define the phylogenetic relationships between the mtDNA haplotypes and the LHON mutations observed in patients and in controls. This analysis shows that the putative secondary/intermediate LHON mutations 4216, 4917, 13708, 15257, and 15812 are ancient polymorphisms, are associated in specific combinations, and define two common Caucasoid-specific haplotype groupings (haplogroups J and T). On the contrary, the same analysis shows that the primary mutations 11778, 3460, and 14484 are recent and are due to multiple mutational events. However, phylogenetic analysis also reveals a different evolutionary pattern for the three primary mutations. The 3460 mutations are distributed randomly along the phylogenetic trees, without any preferential association with the nine haplogroups (H, I, J, K, T, U, V, W, and X) that characterize European populations, whereas the 11778 and 14484 mutations show a strong preferential association with haplogroup J. This finding suggests that one ancient combination of haplogroup J-specific mutations increases both the penetrance of the two primary mutations 11778 and 14484 and the risk of disease expression.

DNA Primers↗
PubMedDate not supplied

[MtDNA-like sequences and the coordination of the functioning of mammalian nuclear and mitochondrial genomes].

Mitochondrial DNA-like sequences in the nuclear genome of mammals are classified in two types: ontogenetic and evolutionary. Mechanisms of the transfer of DNA from mitochondria into nucleus and transformation of the ontogenetic mtDNA-like sequences to evolutionary ones are discussed. The origin of short sequences of DNA common to nuclear and mitochondrial genome and the role of these sequences in the coordination of gene expression have received much attention.

Animals↗
PubMed1997

Study of the populations of the Balearic Islands (Spain) using mtDNA RFLPs.

The Balearic archipelago (Spain) is composed of three major islands, Majorca, Minorca, and Ibiza. Majorca is the largest and most populous island. Minorca is the second largest in area and third in population, and Ibiza is the smallest of the three and has the second largest population. Ibiza also shows differences from the other two islands in its landscape, vegetation, and especially origins of the founding settlements. The three islands also have been settled by people of different cultures. We have carried out a genetic analysis at the level of mtDNA RFLPs in these populations and found that the three populations are genetically structured, with differences in the RFLP haplotype frequencies reflecting the different population substrata of the three islands. In this structure Ibiza is genetically more different from Majorca and Minorca. In addition, we found a new haplotype in Minorca, named haplotype 150, which seems to originate from haplotype 56.

DNA, Mitochondrial↗
PubMed1998

Yield of mtDNA mutation analysis in 2,000 patients.

The multiplex polymerase chain reaction-allele specific oligonucleotides (PCR/ASO) dot blot hybridization method was used to detect 44 mitochondrial DNA point mutations in 2,000 patients suspected as having mitochondrial DNA disorders. These point mutations are classified into four categories. Category I consists of primary disease-causing, heteroplasmic point mutations. Homoplasmic nucleotide substitutions that have been reported to be possibly disease associated are in Category II. Homoplasmic nucleotide substitutions that are thought to be benign polymorphism are included in category III. The novel nucleotide substitutions recently discovered in our laboratory by single strand conformation polymorphism analysis are in category IV. Frequencies of these 44 nucleotide substitutions in 2,000 patients and 262 control individuals were studied. The results indicated that analysis of 12 recurrent disease-causing point mutations in category I identified 5.4% of the patients suspected as having mitochondrial DNA disorders. Since the mitochondrial disorders are a group of complex, heterogeneous, and multisystemic diseases, it is often difficult to confirm clinical diagnosis without molecular studies. Thus, the multiplex PCR/ASO method is an effective approach for initial screening of mtDNA mutations in patients suspected as having mitochondrial DNA disorders.

DNA Mutational Analysis↗
PubMed1998

[Sequencing of the mtDNA cytochrome b gene and reconstruction of the matriarchal relationships between wood and field mice of the genus Apodemus (Muridae, Rodentia)].

The primary sequence of a 402-bp part of the cytochrome b gene was determined in nine species of wood and field mice of the genus Apodemus. The majority of mutations were synonymous. The total number of transitions exceeded than of transversions. Among all substitutions, C-T transitions prevailed (51%); the most common substitution type in genus-specific sites was C-A transversions (42%). In interpopulation analysis, only transitions were recorded. A phylogenetic tree, constructed with the use of the neighbor-joining method, showed that the genus Apodemus is divided into three highly divergent groups: south Asian (Apodemus argenteus, A. semotus), east Asian (A. speciosus, A. agrarius), and Eurocaucasian (A. sylvaticus, A. flavicollis, A. uralensis, A. ponticus, A. flavipectis). The mean genetic distances within each group were 12.6, 11.2, and 8.8%, respectively. The species of the first group are more remote genetically and ancestrally with regard to the other groups. The interspecies divergence estimated for A. speciosus ranged from 0.25 to 3.75%. Thus, the evolutionary age of the genus Apodemus is about 6 Myr, and time of divergence of A. speciosus populations is 0.1-1.5 Myr. The phylogeny inferred from the data on the sequence of the cytochrome b gene in Apodemus mtDNA is somewhat different from similar phylogenies based on other genetic data and from the zoological taxonomy of wood and field mice. However, the above classification of species is confirmed by features of their karyotypes and segmentation of satDNA, and by the RFLP of total nDNA and isozyme polymorphism. Our results are in good agreement with the new classification of wood and field mice recently proposed by Russian zoologists.

Animals↗
PubMed1998

Technical note: chromosomal and mtDNA analysis of Oliver.

Oliver is an African ape whose species identity has been debated in the popular media and by various scientists since the early 1970s. Although decisive morphological data has never been adduced on Oliver, many reports indicated that Oliver was morphologically unusual for a chimpanzee, particularly in his habitual bipedal posture. In addition, his diploid chromosome number was reported to be inconsistent with either human or chimpanzee, but instead intermediate between those species. We performed standard chromosomal studies which demonstrated that Oliver had the diploid number expected for a chimpanzee (2N = 48) and that the banding patterns of his chromosomes were typical for a chimpanzee and different from both humans and bonobos. We also sequenced a 312 bp region of his mitochondrial DNA D-loop region. Results indicated a high sequence homology to the Central African variety of chimpanzee, Pan troglodytes troglodytes. The highest percent homology was observed with a previously characterized specimen from Gabon, strongly suggesting that Oliver originated from this region.

Animals↗
PubMed2001

Phylogenetic history of sifakas (Propithecus: lemuriformes) derived from mtDNA sequences.

The sifakas (Propithecus) include three species containing up to 10 described subspecies, whose evolutionary relationships remain contentious. In particular, it is unclear whether P. verreauxi deckeni and P.v. coronatus populations are differentiated at the subspecific level. Furthermore, the taxonomic status of the recently discovered P. tattersalli and its phylogenetic position also require further examination. About 2,400 bp of mitochondrial DNA sequence data from part of the COIII gene, together with complete genes for ND3, ND4L, ND4, and five tRNAs, were used to clarify relationships among Propithecus species and subspecies. All analyses group Avahi as the sister group to all sifakas. P. diadema is placed as a sister group to all other Propithecus. Among the remaining sifakas, one subclade is formed by Puv. coquereli and P. tattersalli, while P.v. verreauxi, P.v. deckeni, and P.v. coronatus form the second subclade. All analyses fail to resolve P.vu. coronatus and P.v. deckeni into separate monophyletic lineages. Based on pairwise distance comparisons and tree topology, we conclude that P. tattersalli does not represent a distinct species and that P.v. deckeni and P.v. coronatus do not deserve subspecific rank. On the other hand, our analyses indicate that P.v. coquereli may well represent a separate species.

Animals↗
PubMed1999

Exercise intolerance due to a nonsense mutation in the mtDNA ND4 gene.

We report the first molecular defect in an NADH-dehydrogenase gene presenting as isolated myopathy. The proband had lifelong exercise intolerance but no weakness. A muscle biopsy showed cytochrome c oxidase (COX)-positive ragged-red fibers (RRFs), and analysis of the mitochondrial enzymes revealed complex I deficiency. Sequence analysis of the mitochondrial genes encoding the seven NADH-dehydrogenase subunits showed a G-to-A transition at nucleotide 11832 in the subunit 4 (ND4) gene, which changed an encoded tryptophan to a stop codon. The mutation was heteroplasmic (54%) in muscle DNA. Defects in mitochondrially encoded complex I subunits should be added to the differential diagnosis of mitochondrial myopathies.

Adult↗
PubMed2001

A novel mtDNA mutation in the ND5 subunit of complex I in two MELAS patients.

We identified a novel heteroplasmic mutation in the mitochodrial DNA gene encoding the ND5 subunit of complex I. This mutation (13514A-->G) hits the same codon affected by a previously reported mitochondrial encephalomyopathy, lactic acidosis, and strokelike episodes (MELAS)-associated mutation (13513G-->A), but the amino acid replacement is different (D393G vs D393N). The 13514A-->G mutation was found in two unrelated MELAS-like patients. However, in contrast to typical MELAS, lactic acidosis was absent or mild and the muscle biopsy was morphologically normal. Strongly positive correlation between the percentage of heteroplasmy and defective activity of complex I was found in cybrids. We found an additional 13513G-->A-positive case, affected by a progressive mitochondrial encephalomyopathy. Our results clearly demonstrate that the amino acid position D393 is crucial for the function of complex I. Search for D393 mutations should be part of the routine screening for mitochondrial disorders.

Adolescent↗
PubMed1995

Screening for mtDNA diabetes mutations in Pima Indians with NIDDM.

More than half of the Pima Indians over age 35 years have non-insulin-dependent (type II) diabetes mellitus (NIDDM). Extensive data indicate the importance of maternal diabetes in determining their risk for diabetes. Generally, the risk of having NIDDM is higher in patients with affected mothers than affected fathers. This has been attributed to intrauterine factors, but recently mitochondrial inheritance has been raised as an alternative hypothesis. In other populations, several families and individuals with diabetes due to a mitochondrial DNA point mutation at nucleotide 3243 in the tRNA(leu(UUR)) gene have been described, as has one family with a 10.4 kb mitochondrial DNA duplication/deletion. We tested whether these specific mitochondrial gene mutations could explain a portion of the excess maternal transmission seen in the Pima Indians. Mitochondrial DNA obtained from blood lymphocytes of 148 Pima Indians with NIDDM was screened both for the point mutation at nt 3243, and the 10.4 kb duplication/deletion. Neither of these mutations was detected, and although a small proportion of the excess maternal transmission in Pima Indians could still be due to yet undescribed mitochondrial mutations or imprinted nuclear genes, our data support the role of the intrauterine environment in this population.

Adolescent↗
PubMed2007

Patterns of dispersal in Sumatran siamangs (Symphalangus syndactylus): preliminary mtDNA evidence suggests more frequent male than female dispersal to adjacent groups.

Gibbons of both sexes have been observed emigrating from their natal groups, but the consequences of dispersal in gibbons are poorly understood, and it is unclear whether these are the same for both sexes. I sequenced a 350-bp fragment of mitochondrial DNA from 18 adults in seven siamang (Symphalangus syndactylus) groups at the Way Canguk Research Station in southern Sumatra to assess patterns of matrilineal relatedness among and within siamang groups, and to assess their fit with different patterns of sex-specific dispersal. A total of 11 haplotypes were identified in the seven study groups; 50% of adult males in five contiguous groups shared a haplotype with a member of an immediately adjacent group, whereas only 16.7% of females shared a haplotype with a neighbor. The apparent difference persisted if only same-sex individuals were considered (37.5% of males vs. 0% of females). Four of the seven study groups contained two adult males and a single adult female. In three multimale groups, the three adults all had different haplotypes, suggesting that neither male was the retained adult offspring of the female, whereas in the fourth group, the haplotype of one male was identical with that of the adult female. The high diversity of haplotypes and the absence of clustering among female haplotypes in the study neighborhood suggest that female dispersal to territories adjacent to the natal group may be relatively rare. The presence of some clustering of male haplotypes suggests that shorter dispersal distances may be more common in males.

Animals↗
PubMed2005

Reconstructing the population history of Puerto Rico by means of mtDNA phylogeographic analysis.

The haplogroup identities of 800 mtDNAs randomly and systematically selected to be representative of the population of Puerto Rico were determined by restriction fragment length polymorphism (RFLP), revealing maternal ancestries in this highly mixed population of 61.3% Amerindian, 27.2% sub-Saharan African, and 11.5% West Eurasian. West Eurasian frequencies were low in all 28 municipalities sampled, and displayed no geographic patterns. Thus, a statistically significant negative correlation was observed between the Amerindian and African frequencies of the municipalities. In addition, a statistically highly significant geographic pattern was observed for Amerindian and African mtDNAs. In a scenario in which Amerindian mtDNAs prevailed on either side of longitude 66 degrees 16' West, Amerindian mtDNAs were more frequent west of longitude 66 degrees 16' West than east of it, and the opposite was true for African mtDNAs. Haplogroup A had the highest frequency among Amerindian samples (52.4%), suggesting its predominance among the native Taínos. Principal component analysis showed that the sub-Saharan African fraction had a strong affinity to West Africans. In addition, the magnitudes of the Senegambian and Gulf of Guinea components in Puerto Rico were between those of Cape Verde and São Tomé. Furthermore, the West Eurasian component did not conform to European haplogroup frequencies. HVR-I sequences of haplogroup U samples revealed a strong North African influence among West Eurasian mtDNAs and a new sub-Saharan African clade.

DNA, Mitochondrial↗
PubMed2005

mtDNA analysis of human remains from an early Danish Christian cemetery.

One of Denmark's earliest Christian cemeteries is Kongemarken, dating to around AD 1000-1250. A feature of early Scandinavian Christian cemeteries is sex segregation, with females buried on the northern sides and males on the southern sides. However, such separation was never complete; in the few early Christian cemeteries excavated in Scandinavia, there were always a few males placed on the north side, and some females on the south side. At Kongemarken, several males with juxtaposed females were found on the north side of the cemetery. Thus, to evaluate possible kinship relationships, and more general questions of population affinity, we analyzed mitochondrial DNA extracted from nine individuals excavated in two different areas within the cemetery: one male and four females from Area 1, and one male and three females from Area 2. Using stringent laboratory protocols, each individual was unequivocally assigned to a mitochondrial haplogroup. A surprising amount of haplogroup diversity was observed (Area 1: 1 U7 (male), 1 H, 1 I, 1 J, and 1 T2; Area 2: 2 H, 1 I, and 1 T, with one H being male); even the three subjects of haplogroup H were of different subtypes. This indicates that no subjects within each area were maternally related. The observed haplogroup, U7, while common in India and in western Siberian tribes, was not previously observed among present-day ethnic Scandinavians, and haplogroup I is rare (2%) in Scandinavia. These observations suggest that the individuals living in the Roskilde region 1,000 years ago were not all members of a tightly knit local population and comprised individuals with genetic links with populations that were from much farther away.

Age Determination by Skeleton↗