Mitochondrial DNA polymorphisms in Italy. II. Molecular analysis of new and rare morphs from Sardinia and Rome

Evidence of high genetic variation among linguistically diverse populations on a micro-geographic scale: a case study of the Italian Alps

Although essential for the fine-scale reconstruction of genetic structure, only a few micro-geographic studies have been carried out in European populations. This study analyzes mitochondrial variation (651 bp of the hypervariable region plus 17 single-nucleotide polymorphisms) in 393 samples from nine populations from Trentino (Eastern Italian Alps), a small area characterized by a complex geography and high linguistic diversity. A high level of genetic variation, comparable to geographically dispersed European groups, was observed. We found a difference in the intensity of peopling processes between two longitudinal areas, as populations from the west-central part of the region show stronger signatures of expansion, whereas those from the eastern area are closer to the expectations of a stationary demographic state. This may be explained by geomorphological factors and is also supported by archeological data. Finally, our results reveal a striking difference in the way in which the two linguistically isolated populations are genetically related to the neighboring groups. The Ladin speakers were found to be genetically close to the Italian-speaking populations and differentiated from the other Dolomitic Ladins, whereas the German-speaking Cimbri behave as an outlier, showing signatures of founder effects and low growth rate.

Mitochondrial DNA polymorphism in the French population

One hundred unrelated individuals of French origin were screened for mtDNA variation as restriction fragment length polymorphisms (RFLPs) with the restriction enzymes HpaI, BamHI, HaeII, MspI, AvaII and HincII. Twenty enzyme morphs were detected, four of which (AvaII-37Fr, -38Fr, HincII-18Fr and -19Fr) are new. Of the 17 mitotypes detected, five are new and they were named 1-19Fr, 6-18Fr, 100Fr-2 (2-1-2-4-1-2), 101Fr-2 (2-1-1-1-38Fr-2) and 102Fr-2 (2-1-1-4-37Fr-2). All new morphs and mitotypes derive from those already known due to a single nucleotide substitution. The French population was compared with other European, Mediterranean and Caucasian populations. Calculation of the genetic distances showed close genetic affinity with European-Mediterranean populations and especially with Calabrians, Majorcans and northern Italians (at negative values).

mtDNA analysis in ancient Nubians supports the existence of gene flow between sub-Sahara and North Africa in the Nile Valley

The Hpal (np3,592) mitochondrial DNA marker is a selectively neutral mutation that is very common in sub-Saharan Africa and is almost absent in North African and European populations. It has been screened in a Meroitic sample from ancient Nubia through PCR amplification and posterior enzyme digestion, to evaluate the sub-Saharan genetic influences in this population. From 29 individuals analysed, only 15 yield positive amplifications, four of them (26.7%) displaying the sub-Saharan African marker. Hpa 1 (np3,592) marker is present in the sub-Saharan populations at a frequency of 68.7 on average. Thus, the frequency of genes from this area in the Merotic Nubian population can be estimated at around 39% (with a confidence interval from 22% to 55%). The frequency obtained fits in a south-north decreasing gradient of Hpa I (np3,592) along the African continent. Results suggest that morphological changes observed historically in the Nubian populations are more likely to be due to the existence of south-north gene flow through the Nile Valley than to in-situ evolution.

Ancestry and interrelationships of the Indians and their relationship with other world populations: a study based on mitochondrial DNA polymorphisms

Mitochondrial DNA variation was studied in 100 Indians using the same set of six restriction enzymes used in the study of other world ethnic groups in order to compare and discern possible relationships of the Indian populations. Twenty nine mtDNA types were found including the ones from an earlier study (Semino et al. 1991) and unweighted pair-group method (UPGMA) and maximum parsimony trees were constructed using the mtDNA types. The nucleotide diversity values were calculated using the maximum likelihood method. From a study of the shared mitochondrial DNA types and the parsimony tree (Fig. 2) we came to the conclusion that the Indian population is closer to Caucasians and has an admixture with Asians. The North Indian population appears to have a recent admixture of the Caucasian mtDNA types which is absent in the south.

tRNA processing in human mitochondrial disorders

Many human mitochondrial disorders are associated with mutations in tRNA genes or with deletions of regions containing tRNA genes, all of which may be suspected to play a role in recognition by RNase P. Here we describe the analysis of five such mutations. The results presented here demonstrate that none of these mutations result in errors in RNase P function. Further studies of mutations in tRNAs need to be pursued to elucidate the identity elements for RNase P function in mammalian mitochondria.

African, Native American, and European mitochondrial DNAs in Cubans from Pinar del Rio Province and implications for the recent epidemic neuropathy in Cuba. Cuba Neuropathy Field Investigation Team

Genetic predisposition, particularly specific mitochondrial DNA (mtDNA) backgrounds, has been proposed as a contributing factor in the expression of an epidemic of bilateral optic neuropathy that has affected residents of Cuba since 1991. To substantiate or refute the possibility that specific subsets of mtDNAs could participate in disease expression, we took advantage of the heterogeneous ethnic origin of the Cuban population and the recent identification of a number of mtDNA polymorphisms that appear to be specific for Africans, Native Americans, and Europeans. The screening of both carefully selected people with epidemic neuropathy and control subjects from the Pinar del Rio Province for these polymorphisms revealed that African, Native American, and European mtDNA haplotypes were equally represented among case and control subjects, and suggested that approximately 50% of Cuban mtDNAs originated from Europeans, 46% from Africans, and 4% from Native Americans. These findings demonstrate that mutations arising in specific mtDNAs are unlikely to play a role in the epidemic neuropathy and indicate that analysis of mtDNA haplotypes can be a valuable tool for assessing the relative maternal contribution of Africans, Native Americans, and Europeans in a mixed population.

The evolution of two west African populations

The identification of genetically coherent populations is essential for understanding human evolution. Among the culturally uniform ethnic groups of west Africa, there are two geographically distinct populations with high frequencies of sickle-cell hemoglobin (HbS). Although the HbS mutation in each group is found on distinguishable chromosomes 11, these populations have been assumed to be parts of a single population. Analysis of mitochondrial DNA (mtDNA) in these populations demonstrated that the two populations identified by alternative chromosomes 11 bearing HbS have distinct distributions of mitochondrial genotypes, i.e., they are maternally separate. These studies also showed that, contrary to expectation, the mtDNA of some individuals is heteroplasmic. For nuclear loci, a comparison of the frequency of alternative alleles established that these populations are genetically distinct. Both the mitochondrial and nuclear data indicate that these populations have been separate for approximately 50,000 years. Although HbS in the two populations is usually attributed to recent, independent mutations, the duration of the separation and the observed geographic distribution of the population allow for the possibility of an ancient origin of HbS. Assuming an ancient mutation and considering the known biogeography, we suggest that HbS protected selected populations from malaria in rain forest refuges during the most recent ice age.

Duplications of mitochondrial DNA: implications for pathogenesis

This paper describes the mapping data obtained on two patients in whom there was clear evidence for a rearrangement of mitochondrial DNA, using restriction enzyme analysis of DNA from whole blood and of polymerase chain reaction products. This suggested that a direct tandem duplication was present, and this was confirmed by sequence analysis of the junction fragment between duplicated segments. In each case the gene for cytochrome oxidase subunit I (MTCOX1) was interrupted, creating reading frames which, if transcribed and translated, would result in truncated versions of this peptide. Heteroplasmy and mosaicism for the abnormal mtDNA population were apparent. Preliminary data also suggest that high-molecular-weight rearrangements of the duplicated region are present in all tissues. The hypothesis that these duplicated genomes caused the phenotype was investigated by examining the distribution of duplicated genomes in various tissues using Southern hybridization and by RNA analysis. This included Northern blotting and cDNA sequencing. In order to investigate the origins of the duplicated mtDNAs, their distribution in different cells within a tissue was documented using the polymerase chain reaction.

The structure of human mitochondrial DNA variation

Restriction analysis of mitochondrial DNA (mtDNA) of 3065 humans from 62 geographic samples identified 149 haplotypes and 81 polymorphic sites. These data were used to test several aspects of the evolutionary past of the human species. A dendrogram depicting the genetic relatedness of all haplotypes shows that the native African populations have the greatest diversity and, consistent with evidence from a variety of sources, suggests an African origin for our species. The data also indicate that two individuals drawn at random from the entire sample will differ at approximately 0.4% of their mtDNA nucleotide sites, which is somewhat higher than previous estimates. Human mtDNA also exhibits more interpopulation heterogeneity (GST = 0.351 +/- 0.025) than does nuclear DNA (GST = 0.12). Moreover, the virtual absence of intermediate levels of linkage disequilibrium between pairs of sites is consistent with the absence of genetic recombination and places constraints on the rate of mutation. Tests of the selective neutrality of mtDNA variation, including the Ewens-Watterson and Tajima tests, indicate a departure in the direction consistent with purifying selection, but this departure is more likely due to the rapid growth of the human population and the geographic heterogeneity of the variation. The lack of a good fit to neutrality poses problems for the estimation of times of coalescence from human mtDNA data.

Mitochondrial DNA polymorphisms among Hindus: a comparison with the Tharus of Nepal

The polymorphisms of mitochondrial DNA for the restriction enzymes HpaI, BamHI, HaeII, MspI, AvaII and HinecII were studied in a sample of 79 Hindus, 45 from New Delhi (India) and 34 from Terai (Nepal), both to characterize another Caucasian population and to investigate some possible Hindu component in the genetic structure of the Tharus, a Nepalese population, the anthropological position of which is still disputed. 1. A new BamHI polymorphism was detected: about 5% of the Hindu mtDNAs have lost the site at 14258 bp and lack any BamHI site. Once again a BamHI polymorphism was found in a Caucasian population. 2. New site mutations were found to yield morphs previously described (MspI-7, AvaII-18). 3. Variant morphs for two different enzymes were found due to a shared mutation (morphs BamHI-0/AvaII-30 and morphs MspI-7Hindu/AvaII-18Hindu). 4. Comparison between Hindu and Tharu data does not show any evidence of a specific Indian component in the Tharu genetic structure and allows us to conclude that Tharus are clearly differentiated from modern Hindus.

Branching pattern in the evolutionary tree for human mitochondrial DNA

Eighty-eight types of mitochondrial (mt) DNA were found by sequencing the most variable part of the control region from 117 Caucasians. In the tree relating those types, most of the branching events occur about two-thirds of the way from the root of the tree to the tips of the branches. Moreover, the distribution of sequence differences between all possible pairs of individuals is approximately Poisson. Other non-African populations show a similar pattern. Assuming a neutral model, these findings imply that the probability of survival of new lineages has undergone dramatic changes, probably due to population expansion. Conversely, African populations show multimodal distributions fitting with a model of constant population size.

Y chromosome DNA polymorphisms in human populations: differences between Caucasoids and Africans detected by 49a and 49f probes

Several Y-specific TaqI fragments are recognized by 49a and 49f probes in human male DNA digests. The occurrence of polymorphic variations in six of these fragments (A, B, C, D, F and I) has recently been reported, providing a potentially powerful tool for the study of the population genetics of the Y chromosome. The 49a-49f/TaqI polymorphisms were studied in 121 Africans (Senegal and Cameroon) and 125 Caucasians (Italy). In addition to the variability described already, four new bands were observed. Moreover, three patterns were found in which bands constantly present so far (G, O and H-P-R) were missing. At variance with previously reported findings, the coexistence of two different fragments of the same 'allelic' series (A or D) was frequently observed in the Italian sample (10.4%). For some of these 'double-banded' patterns their holoandric transmission could be demonstrated by family studies. In the light of these new findings, the hypothesis of A or D fragments being allelic forms, as advanced by the authors who first described these polymorphisms, has to be reconsidered. A total of 34 haplotypes were encountered, 22 of which are new. The Africans tested all lack C and D fragments. Moreover, about 80% of them are characterized by a band, A1, not present in the Italian group. The combination of A1C0D0 could therefore be a powerful genetic marker of paternal African ancestry. This combination occurs in five haplotypes, one of which, haplotype IV, accounts for 68% of the African sample. In contrast with the results of the mtDNA analysis on the same population samples, the degree of variability displayed by the Y chromosome sequences appears to be much lower in Africans than in Caucasians.

Evolution of human mitochondrial DNA: evidence for departure from a pure neutral model of populations at equilibrium

Human mitochondrial DNA (mt-DNA) data from 18 populations have been carefully reexamined. A phylogeny of 77 mtDNA types found among the 1389 individuals analyzed for restriction fragment length polymorphisms (RFLPs) was established using the parsimony principle and compared to a UPGMA tree of the 18 populations. Both analyses agreed in separating African samples from the other populations, though the mtDNA type phylogeny suggested close relations between Africans and other continental groups. Conformity of observed mtDNA type frequency distributions with the "infinite allele" model was studied for 31 human populations. Several Oriental and Caucasoid populations were found to be overly homogeneous, generally due to an elevated frequency of one particular type. Contrastingly, all African samples conformed to the neutral model of populations at equilibrium and presented more diversified distributions. This suggested that part of the apparent African divergence was due to heterogeneous evolutionary processes and confirmed that some diversity reducing factors were at work in Caucasoids and Orientals. Several nonexclusive hypotheses accounting for the rejection of the neutrality tests were discussed. Alternative hypotheses concerning modern human emergence were also reviewed in the light of present results.

Mitochondrial DNA polymorphism detected with the restriction enzymes BstNI and BclI in a French Canadian population

The enzymes BstNI and BclI were used to detect various human mitochondrial DNA RFLPs in a sample of 104 unrelated French Canadians. These sequence variations were found in total white blood cell DNA probed with whole human mitochondrial DNA. With BstNI, 6 mitochondrial DNA restriction patterns (morphs) were identified. BstNI morphs 2-6 each differ from morph 1 by one single distinct restriction site gain or loss on the mitochondrial DNA molecule. Although BstNI morph 1 was found in most of the subjects (80%), each other morph was observed at a frequency of at least 3%. With the enzyme BclI, 4 different morphs were detected. Morphs 2-4 also result from different single restriction site alteration as compared with BclI morph 1. The morph 1 was clearly the most frequent (95%) while morphs 3 and 4 were present in only 1% of the subjects. These data indicate that the enzyme BstNI and, to a much lesser extent, the enzyme BclI detect mitochondrial DNA polymorphism in Caucasians. They are therefore of interest for population genetics studies.

A mitochondrial DNA mutation as a cause of Leber's hereditary optic neuropathy

Leber's hereditary optic neuropathy is a maternally inherited disease associated with the late onset of bilateral loss of central vision and cardiac dysrhythmias. The maternal inheritance is explained by the mitochondrial origin of the disease. Analysis of the sequence of a mitochondrial DNA has indicated that a single nucleotide change at position 11778 is associated with this disease. This mutation converts the 340th amino acid of NADH dehydrogenase subunit 4 from an arginine to a histidine and eliminates an SfaNI endonuclease restriction site. A survey of restriction-fragment-length polymorphisms in the mitochondrial DNA of three independent families with this disease (an American black and two white European families) and 10 controls confirmed that this SfaNI site is associated with the disease. A phylogenetic tree for mitochondrial DNA polymorphism and sequence variants from three probands with Leber's disease and four controls was constructed, and the mutation at position 11778 was found to be associated with two mitochondrial DNA backgrounds--an American black mitochondrial DNA and a European mitochondrial DNA. Thus, this mutation must have arisen twice independently. Since the mutation correlated with symptoms of Leber's disease in both cases, these findings indicate that the mutation is a cause of the disease. This genetic analysis has identified the specific point mutation in the mitochondrial DNA that results in Leber's hereditary optic neuropathy.

Mitochondrial DNA polymorphisms in Italy. III. Population data from Sicily: a possible quantitation of maternal African ancestry

mtDNA polymorphisms were studied in a sample of 90 individuals of the Sicilian population using six restriction enzymes: HpaI, BamHI, HaeII, MspI, AvaII and HincII. (1) Three new patterns, for MspI, AvaII and HincII, have been detected. (2) At least two different mutations were found to account for both the AvaII morph 3 and the AvaII morph 9 as in many other Caucasian groups so far examined. (3) Seventeen types were found; of these six are new. The frequency (54.5%) of type 1-2 (2.1.1.1.1.2) is lower than in the rest of Italy whereas those of type 6-2 (2.1.2.1.1.2) (10.0%) and type 18-2 (2.3.1.4.9*.2) (12.2%) lie at the upper level of the Italian range. The 18-derivative, type 57-2 (2.3.1.4.13*.2), which is consistently found in all Italian samples, is present also among Sicilians with an incidence of 2.2%. (4) Of particular interest is that the HpaI-3/AvaII-3 complex, which is unique to groups of African ancestry, was found in Sicily at a frequency of 4.4%. For the first time an estimate of the amount of gene flow from Blacks to the Sicilian gene pool could be obtained.

Duplications of mitochondrial DNA in mitochondrial myopathy

Restriction enzyme analysis was done on total cellular DNA extracted from whole blood in two patients with mitochondrial myopathy and multisystem involvement and their families. The two patients had an abnormal mitochondrial genome with a large (about 8 kb) duplication present in several tissues. Normal mitochondrial DNA (mtDNA) was also present, but within each maternal lineage the abnormal mitochondrial genome was confined to clinically affected individuals. This observation, together with the failure of extensive population surveys to identify such abnormalities of mtDNA, suggests that these mutations cause the disease.

Mitochondrial DNA polymorphism in four Sardinian villages

Polymorphism of mitochondrial DNA has been studied in two highland (Desulo, Tonara) and in two lowland (Galtellì, Orosei) Sardinian isolates, formerly subjected to different selective pressure due to malaria, and in 103 individuals from Northern Italy (Bergamo area), where malaria never appeared to be endemic. Two mitochondrial restriction endonuclease patterns (morphs) never described before have been found, one in the Bergamo and Orosei samples, and the other one only in Orosei. Four new mitochondrial types (mitotypes) due to different combinations of morphs have been identified; two of them have been found only in Sardinia, but with such a low frequency that they cannot be defined as typical Sardinian mitotypes. One mitotype (BamHI-morph 3, MspI-morph 4, AvaII-morph 9 and HaeII-morph 1) showed a significantly higher frequency in the highland rather than in the lowland Sardinian villages or in the Bergamo area. Since this mitotype has been found at a relatively high frequency in Central and Southern Italy, while it has been reported to be rare in Caucasians of Central European origin and absent in other ethnic groups (Africans, Chinese, Japanese and Israeli Jews), we suggest it may represent an ancient Mediterranean type. The analysis of these data suggests that drift or other evolutive forces different from malaria might be the major cause of mitochondrial DNA variation in Sardinia.