Identifying genetic traces of historical expansions: Phoenician footprints in the Mediterranean

The Phoenicians were the dominant traders in the Mediterranean Sea two thousand to three thousand years ago and expanded from their homeland in the Levant to establish colonies and trading posts throughout the Mediterranean, but then they disappeared from history. We wished to identify their male genetic traces in modern populations. Therefore, we chose Phoenician-influenced sites on the basis of well-documented historical records and collected new Y-chromosomal data from 1330 men from six such sites, as well as comparative data from the literature. We then developed an analytical strategy to distinguish between lineages specifically associated with the Phoenicians and those spread by geographically similar but historically distinct events, such as the Neolithic, Greek, and Jewish expansions. This involved comparing historically documented Phoenician sites with neighboring non-Phoenician sites for the identification of weak but systematic signatures shared by the Phoenician sites that could not readily be explained by chance or by other expansions. From these comparisons, we found that haplogroup J2, in general, and six Y-STR haplotypes, in particular, exhibited a Phoenician signature that contributed > 6% to the modern Phoenician-influenced populations examined. Our methodology can be applied to any historically documented expansion in which contact and noncontact sites can be identified.     

Recent human evolution in northwestern Africa.

The first modern humans in the Maghreb are said to be associated with the Aterian industries which appeared at least 40 ka BP in the northwest. Their predecessors are mainly represented by the Jebel Irhoud (Morocco) specimens. Palaeontological evidence, as well as electron spin resonance (ESR) dating, suggests that this series is older than previously published, and should belong to oxygen isotope stage 5 or even 6. There is no evidence of any Neanderthal apomorphy in this group which can no longer be considered as 'African Nanderthals'. Clear synapomorphies with modern man combined with some plesiomorphic retentions indicate a slightly more primitive (and older?) grade than the Qafzeh-Skhul sample in southwestern Asia. The Northwestern evidence demonstrates that the mediterranean sea was a major biological barrier during the upper Middle and lower Upper Pleistocene and that the rise of anatomically modern features cannot be restricted to a sub-Saharan of eastern African area.     

Seroepidemiology of human immunodeficiency virus in Africa.

Serum samples from 6015 African subjects without symptoms of the acquired immune deficiency syndrome (AIDS) or contact with the disease were examined for antibodies to the human immunodeficiency virus by a combination of an enzyme linked immunosorbent assay and radioimmunoprecipitation (2567 samples) or by immunofluorescence (3448 samples). Serum samples had been collected between 1976 and 1984 in Senegal (n = 789), Liberia (935), Ivory Coast (1195), Burkina Faso (299), Nigeria (536), Gabon (1649), Zaire (15), Uganda (164), and Kenya (433). Only four samples contained antibodies. Three of these were from attenders at the Lambarene clinic in Gabon and one from a villager in Senegal. By contrast, two out of six AIDS suspects from Guinea-Bissau, all 13 patients with AIDS from Kinshasa (Zaire), and two out of three of their contacts were seropositive, all these specimens having been collected in 1985. These data show that fewer than one in a 1000 subjects were seropositive for AIDS at the time of sampling before 1985 and do not support the hypothesis of the disease originating in Africa.     

Mitochondrial biogenesis in human fibroblasts

It is not known whether limitation of lifespan represents a programmed genetic event or is a result of environmental factors imposed by the conditions of culture. An investigation of the factors surrounding the limitedin vitro lifespan of human diploid fibroblasts has been undertaken. We have investigated the role of mitochondria in the finite lifespan of WI-38 human lung fibroblasts. Mitochondrial function was depressed in a controlled manner by treating cells with ethidium bromide and chloramphenicol both of which inhibit normal biogenesis. These antibiotics decrease cytochrome oxidase activity, change cell ultrastructure, and inhibit growth at high concentration. At lower concentrations the antibiotics do not affect cell proliferation for several generations. However, their effect is cumulative and after several generations the cells enlarge, stop dividing and die. Removal of antibiotics from the culture media before death restores proliferative capacity. At still lower concentrations cytochrome oxidase activity was decreased but continuous growth in the presence of the antibiotics caused no decrease inin vitro lifespan. Thus, the potential for oxidative metabolism appears to be in excess of that needed for cell proliferation at all stages of thein vitro lifespan of a culture. The importance of cytoplasmic protein synthesis was evaluated using cycloheximide, a specific inhibitor of this process. Cycloheximide was used to try to distinguish between the effects due to general inhibition and that due to specific inhibition of mitochondrial biogenesis. Exposure of cultures to concentrations of cycloheximide which inhibited growth drastically caused no decrease in cytochrome oxidase activity.     

Mitochondrial DNA reveals multiple introductions of domestic chicken in East Africa

Chicken were possibly domesticated in South and Southeast Asia. They occur ubiquitously in East Africa where they show extensive phenotypic diversity. They appeared in the region relatively late, with the first undisputed evidence of domestic chicken in Sudan, around ~ 700 BC. We reveal through a detailed analysis of mitochondrial DNA D-loop sequence diversity of 512 domestic village chickens, from four East African countries (Kenya, Ethiopia, Sudan, Uganda), the presence of at least five distinct mitochondrial DNA haplogroups. Phylogeographic analyses and inclusion of reference sequences from Asia allow us to address the origin, ways of introduction and dispersion of each haplogroup. The results indicate a likely Indian subcontinent origin for the commonest haplogroup (D) and a maritime introduction for the next commonest one (A) from Southeast and/or East Asia. Recent introgression of commercial haplotypes into the gene pool of village chickens might explain the rare presence of two haplogroups (B and C) while the origin of the last haplogroup (E) remains unclear being currently observed only outside the African continent in the inland Yunnan Province of China. Our findings not only support ancient historical maritime and terrestrial contacts between Asia and East Africa, but also indicate the presence of large maternal genetic diversity in the region which could potentially support genetic improvement programmes.     

Mitochondrial DNA topoisomerase I from human platelets.

An anucleated cell system has been used for the first time to study mitochondrial topoisomerase activity. Mitochondrial extracts from human blood platelets contained type I topoisomerase. The type I classification was based on ATP-independent activity, inhibition by ATP or camptothecin, and the lack of inhibition by novobiocin. Platelet mitochondrial topoisomerase I relaxation activity was inhibited linearly by increasing concentrations of EGTA. Topoisomerase activity greater than 90% inhibited by 175 microM EGTA was partially restored to 16 and 50% of the initial level of activity by the subsequent addition of 50 and 100 microM Ca2+, respectively. Additionally, results from studies of partially purified platelet mitochondrial topoisomerase I were consistent with the crude extract data. This work supports the hypothesis that platelet mitochondria contain a type I topoisomerase that is biochemically distinct from that previously isolated and characterized from cell nuclei.     

Mitochondrial and submitochondrial localization of human deoxyguanosine kinase.

Deoxyguanosine kinase and thymidine kinase 2 are responsible for catalysing the first step in the salvage of deoxynucleosides in mitochondria. These enzymes also play an important role in activating several antiviral and anticancer nucleoside analogs, which may lead to unwanted side-effects when the resulting nucleotides are incorporated into the mitochondrial genome. We studied deoxyguanosine kinase in submitochondrial fractions from human placental mitochondria. It was localized in the mitochondrial matrix fraction by Western blotting using a purified polyclonal antibody. This antibody was also used in an immunohistochemical in situ experiment with human embryonic kidney 293 cells, in which the deoxyguanosine kinase antibody colocalized with a mitochondrion-specific fluorescent probe and there was no significant cytosolic staining.     

Mitochondrial DNA mutations in human diseases: a review.

Human mitochondrial diseases have been associated recently with mitochondrial DNA mutations, duplications and deletions which impair the protein synthesis of the mitochondrial subunits of the respiratory chain complexes. A constant feature is the coincident presence of the mutated and wild type genomes which provide heteroplasmy. The clinical expression of these diseases depends on the relative expression of each kind of mitochondrial DNA in the various tissues, which in turn affects the production of ATP in these tissues. Research on nuclear gene products interfering with mtDNA or with its gene products is the next step towards understanding the etiology of these diseases.     

Pleistocene human footprints from the Willandra Lakes, Southeastern Australia

Human and other hominid fossil footprints provide rare but important insights into anatomy and behavior. Here we report recently discovered fossil trackways of human footprints from the Willandra Lakes region of western New South Wales, Australia. Optically dated to between 19-23 ka and consisting of at least 124 prints, the trackways form the largest collection of Pleistocene human footprints in the world. The prints were made by adults, adolescents, and children traversing the moist surface of an ephemeral soak. This site offers a unique glimpse of humans living in the arid inland of Australia at the height of the last glacial period.     

Trinucleotide repeat expansions and human genetic disease

Trinucleotide repeat expansions are now a well-established mutational mechanism in human genetic disease. An unstable CAG repeat is known to be responsible for three neurodegenerative disorders: Huntington's disease, spinal and bulbar musclar atrophy and spinocerebellar ataxia type 1. Similarities in the genetics of these diseases, the size of the repeat expansions and the position of the unstable repeat within the gene (when known) suggest a common basis to the observed phenotypes. The cloning of two regions at which chromosome breakage can be induced (FRAXA and FRAXE) has in each case uncovered an unstable CG-rich triplet repeat which becomes methylated when fully expanded. In addition to these two classes of mutation, the presence of an expanded CTG repeat in the 3′ untranslated region of a protein kinase causes myotonic dystrophy. The size of the respective expansions, repeat stability, mutational origins and possible mechanisms of action are discussed.     

Southern Africa and modern human origins.

This paper argues that southern Africa was a remote part of the Old World in the late Pleistocene (125-10 ka ago). Because of this isolated position there was continuity without significant replacement in the resident population. Isolation and the relatively recent spread of agriculture to the region has allowed a section of this population to survive into the present. They are the Bushmen (San). Studies of geographic patterning in conventional genetic markers and mitochondrial DNA indicate that the Bushman clade has a long evolutionary history in southern Africa. Estimates of more than 100 ka for the continued presence of this population in the region are supported in archaeological investigations of sites with long sequences such as Klasies River main site and Border Cave. Human remains dating to the earlier part of the late Pleistocene have been recovered from these sites and the samples form a morphological series with the Klasies River remains possibly 20 ka older than those from Border Cave. There is no fossil record for the later Pleistocene, however, at a period when selection for a gracile morphology may have been pronounced. The cultural associations in the earlier late Pleistocene are with the Middle Stone Age. Expressions of cultural 'style' and the occurrence of similar artefact design types in the Middle and Later Stone Ages can be interpreted with reference to the ethnographic present. Temporal continuity can be shown in the geographical distribution of stylistic markers and this suggests participation in a shared cognitive system.(ABSTRACT TRUNCATED AT 250 WORDS)     

Florisbad and human population succession in Southern Africa.

The human cranium recovered at Florisbad in 1932 is compared with other Sub-Saharan African hominid remains from Broken Hill, the Omo and Klasies River Mouth. The Florisbad frontal is very broad, but despite this breadth and differences in zygomatic form, there is a definite resemblance to archaic Homo sapiens from Broken Hill. There is also some similarity to both Omo I and Omo II, while fragmentary remains from Klasies River are more lightly built and hence more modern in appearance. These impressions are strengthened by measurement and statistical analysis, which demonstrates that Florisbad and Broken Hill are distant from recent African populations. Even if Florisbad is less archaic than the earlier (Middle Pleistocene?) hominid, it is not noticeably Bushman-like. New dates suggestive of early Upper Pleistocene antiquity also place Florisbad securely in a lineage containing Broken Hill, and there is no evidence to support special ties with any one group of living Africans.     

Gonococcal infection and human fertility in sub-Saharan Africa.

An analysis is presented of the influence of Neisseria gonorrhoeae on human population growth in regions of sub-Saharan Africa where gonococcal infections are prevalent in sexually active adults. Combining epidemiological and demographic data within the framework of a mathematical model, we show that gonorrhoea has a major impact on fertility and, concomitantly, on net population growth in areas with a high prevalence of untreated infections. Specifically, a 20% prevalence in sexually active adults is predicted to induce a 50% reduction in net population growth. Model predictions are in good agreement with observed data from Uganda, and the sensitivity of the prediction to various complications, such as heterogeneity in sexual behaviour, is assessed. The analysis suggests that the predicted increase in fertility arising from expanded sexually transmitted disease (STD) control programmes in Africa to help combat the spread of human immunodeficiency viruses (HIV-1 and HIV-2) will help to offset the predicted demographic impact of AIDS in the worst afflicted areas. In other areas the rise in fertility associated with effective STD control will need to be countered by the linkage of STD control programmes with family planning initiatives.     

Mitochondrial genome instability in human cancers

Malfunction of mismatch repair (MMR) genes produces nuclear genome instability (NGI) and plays an important role in the origin of some hereditary and sporadic human cancers. The appearance of non-inherited microsatellite alleles in tumor cells (microsatellite instability, MSI) is one of the expressions of NGI. We present here data showing mitochondrial genome instability (mtGI) in most of the human cancers analyzed so far. The mtDNA markers used were point mutations, length-tract instability of mono- or dinucleotide repeats, mono- or dinucleotide insertions or deletions, and long deletions. Comparison of normal and tumoral tissues from the same individual reveals that mt-mutations may show as homoplasmic (all tumor cells have the same variant haplotype) or as heteroplasmic (tumor cells are a mosaic of inherited and acquired variant haplotypes). Breast, colorectal, gastric and kidney cancers exhibit mtGI with a pattern of mt-mutations specific for each tumor. No correlation between NGI and mtGI was found in breast, colorectal or kidney cancers, while a positive correlation was found in gastric cancer. Conversely, germ cell testicular cancers lack mtGI. Damage by reactive oxygen species (ROS), slipped-strand mispairing (SSM) and deficient repair are the causes explaining the appearance of mtGI. The replication and repair of mtDNA are controlled by nuclear genes. So far, there is no clear evidence linking MMR gene malfunction with mtGI. Polymerase gamma (POLgamma) carries out the mtDNA synthesis. Since this process is error-prone due to a deficiency in the proofreading activity of POLgamma, this enzyme has been assumed to be involved in the origin of mt-mutations. Somatic cells have hundreds to thousands of mtDNA molecules with a very high rate of spontaneous mutations. Accordingly, most somatic cells probably have a low frequency of randomly mutated mtDNA molecules. Most cancers are of monoclonal origin. Hence, to explain the appearance of mtGI in tumors we have to explain why a given variant mt-haplotype expands and replaces part of (heteroplasmy) or all (homoplasmy) wild mt-haplotypes in cancer cells. Selective and/or replicative advantage of some mutations combined with a severe bottleneck during the mitochondrial segregation accompanying mitosis are the mechanisms probably involved in the origin of mtGI.     

Mitochondrial malic enzyme in human leukocytes

Leukocyte samples from 316 unrelated blood donors were screened for malic enzyme (MEM). The frequency of the common allele in this investigation was MEM1 = 0.63. There is evidence for the existence of a rare fourth allele MEM4.     

Mitochondrial DNA deletion in human myocardium

Mutation of myocardial mitochondrial DNA was investigated in human left ventricles obtained at autopsy using the polymerase chain reaction (PCR). Seventeen autopsy cases were examined, including patients with diabetes mellitus, myocardial infarction, cardiomyopathy, cancer, and other diseases. Two cases of diabetes mellitus, 2 of myocardial infarction, and 1 of pulmonary fibrosis showed a 7.4 kb deletion of myocardial mitochondrial DNA. Primer shift PCR confirmed that an amplified DNA fragment had not been obtained by misannealing of the primers. It is unclear how much these findings are related to the severity or prognosis of the various diseases, but they indicate that mutation of myocardial mitochondrial DNA can occur in other diseases besides cardiomyopathy, although the influence of aging could not be excluded.     

Mitochondrial DNA mutations in human neoplasia

Many models of tumour formation have been put forth so far. In general they involve mutations in at least three elements within the cell: oncogenes, tumour suppressors and regulators of telomere replication. Recently numerous mutations in mitochondria have been found in many tumours, whereas they were absent in normal tissues from the same individual. The presence of mutations, of course, does not prove that they play a causative role in development of neoplastic lesions and progression; however, the key role played by mitochondria in both apoptosis and generation of DNA-damaging reactive oxygen species might indicate that the observed mutations contribute to tumour development. Recent experiments with nude mice have proven that mtDNA mutations are indeed responsible for tumour growth and exacerbated ROS production. This review describes mtDNA mutations in main types of human neoplasia.     

Mitochondrial DNA mutations in human disease

The human mitochondrial genome is extremely small compared with the nuclear genome, and mitochondrial genetics presents unique clinical and experimental challenges. Despite the diminutive size of the mitochondrial genome, mitochondrial DNA (mtDNA) mutations are an important cause of inherited disease. Recent years have witnessed considerable progress in understanding basic mitochondrial genetics and the relationship between inherited mutations and disease phenotypes, and in identifying acquired mtDNA mutations in both ageing and cancer. However, many challenges remain, including the prevention and treatment of these diseases. This review explores the advances that have been made and the areas in which future progress is likely.