Ancient DNA analysis of human populations.

The use of ancient DNA (aDNA) in the reconstruction of population origins and evolution is becoming increasingly common. The resultant increase in number of samples and polymorphic sites assayed and the number of studies published may give the impression that all technological hurdles associated with aDNA technology have been overcome. However, analysis of aDNA is still plagued by two issues that emerged at the advent of aDNA technology, namely the inability to amplify a significant number of samples and the contamination of samples with modern DNA. Herein, we analyze five well-preserved skeletal specimens from the western United States dating from 800-1600 A.D. These specimens yielded DNA samples with levels of contamination ranging from 0-100%, as determined by the presence or absence of New World-specific mitochondrial markers. All samples were analyzed by a variety of protocols intended to assay genetic variability and detect contamination, including amplification of variously sized DNA targets, direct DNA sequence analysis of amplification products and sequence analysis of cloned amplification products, analysis of restriction fragment length polymorphisms, quantitation of target DNA, amino acid racemization, and amino acid quantitation. Only the determination of DNA sequence from a cloned amplification product clearly revealed the presence of both ancient DNA and contaminating DNA in the same extract. Our results demonstrate that the analysis of aDNA is still an excruciatingly slow and meticulous process. All experiments, including stringent quality and contamination controls, must be performed in an environment as free as possible of potential sources of contaminating DNA, including modern DNA extracts. Careful selection of polymorphic markers capable of discriminating between ancient DNA and probable DNA contaminants is critical. Research strategies must be designed with a goal of identifying all DNA contaminants in order to differentiate convincingly between contamination and endogenous DNA.

Identification of Treponema pallidum subspecies pallidum in a 200-year-old skeletal specimen.

Treponema pallidum subsp. pallidum, the causative agent of venereal syphilis, was detected in a 200-year-old skeletal specimen from Easter Island. An initial diagnosis of treponemal infection was confirmed by extensive purification of immunoglobulin that reacted strongly with T. pallidum antigen. Extracted DNA exhibited a single-base polymorphism that distinguished T.p. subsp. pallidum from 4 other human and nonhuman treponemes. Extensive precautions against contamination of the subject matter with modern treponemal DNA were employed, including analysis of archaeological and modern specimens in 2 geographically separate laboratories. Molecular determination of historical disease states by using skeletal material can significantly enhance our understanding of the pathology and spread of infectious diseases.

Further diversification of the HLA-B locus in Central American Amerindians: new B*39 and B*51 alleles in the Kuna of Panama.

Several new HLA-B locus alleles have been discovered in South American Amerindians. By contrast, analysis of the MHC class I alleles of North American native populations has revealed few new HLA-B alleles. This suggests that the HLA-B locus is evolving rapidly in South American populations. Here we describe the HLA-B locus alleles present in individuals from a Central American tribe, the Kuna of Panama. Using a sequence-based typing technique that separates alleles by denaturing gradient gel electrophoresis (DGGE) followed by direct sequencing, we determined the HLA-B alleles from eight Kunas. Two of the HLA-B alleles present in the Kuna have been previously described in other South American Amerindian populations; one allele has been characterized in a Mexican-American. We characterized two new HLA-B alleles in the Kuna, HLA-B*3911 and HLA-B*5110. HLA-B*3911 differed from HLA-B*3905 by only a single nucleotide substitution in exon 3. This substitution resulted in an amino acid replacement of leucine by arginine at residue 156 in the alpha 2 domain. Such a change may affect the repertoire of peptides that are bound by this molecule. HLA-B*5110 differed significantly from other HLA-B*51 alleles in that it is the result of an unusually large intra-locus recombination event of minimally 216 nucleotides. This recombination results in an allele that is part HLA-B*51 and part HLA-B*40. Thus, more dramatic recombination events may also play a role in the rapid evolution of the HLA-B locus in Amerindians.

Mitochondrial and nuclear DNA diversity in the Chocó and Chibcha Amerinds of Panamá.

Mitochondrial and nuclear DNA diversities were determined for two Chocó-speaking Amerind populations, the Emberá and Wounan, sampled widely across their geographic range in eastern Panamá. These data were compared with mitochondrial and nuclear diversities determined here and previously for neighboring Chibcha-speaking Ngöbé and Kuna populations. Chocoan groups exhibited mitochondrial diversity levels typical for Amerind populations while Chibchan groups revealed reduced mitochondrial diversity. A slight reduction in autosomal levels of heterozygosity was determined for the Chibcha while X and Y variation appeared equivalent in all populations. Genetic distinctiveness of the two linguistic groups contradicts the anthropological theory that Paleoindians migrated repeatedly through the isthmian region and, instead, supports the idea of cultural adaptation by endogenous populations. Reduced genetic diversity in Chibchan populations has been proposed to represent a population bottleneck dating to Chibchan ethnogenesis. The relative sensitivities of haplotype pairwise difference distributions and Tajima's D to detect demographic events such as population bottlenecks are examined. Also, the potential impact of substitution rate heterogeneity, population subdivision, and genetic selection on pairwise difference distributions are discussed. Evidence is presented suggesting that a larger effective population size may obscure the historical signal obtained from nuclear genes while the single mitochondrial locus may provide a moderately strong signal.

Mitochondrial DNA analysis of Mongolian populations and implications for the origin of New World founders.

High levels of mitochondrial DNA (mtDNA) diversity were determined for Mongolian populations, represented by the Mongol-speaking Khalkha and Dariganga. Although 103 samples were collected across Mongolia, low levels of genetic substructuring were detected, reflecting the nomadic lifestyle and relatively recent ethnic differentiation of Mongolian populations. mtDNA control region I sequence and seven additional mtDNA polymorphisms were assayed to allow extensive comparison with previous human population studies. Based on a comparative analysis, we propose that indigenous populations in east Central Asia represent the closest genetic link between Old and New World populations. Utilizing restriction/deletion polymorphisms, Mongolian populations were found to carry all four New World founding haplogroups as defined by WALLACE and coworkers. The ubiquitous presence of the four New World haplogroups in the Americas but narrow distribution across Asia weakens support for GREENBERG and coworkers' theory of New World colonization via three independent migrations. The statistical and geographic scarcity of New World haplogroups in Asia makes it improbable that the same four haplotypes would be drawn from one geographic region three independent times. Instead, it is likely that founder effects manifest throughout Asia and the Americas are responsible for differences in mtDNA haplotype frequencies observed in these regions.

Mitochondrial DNA diversity in the Kuna Amerinds of Panamá.

Mitochondrial DNA (mtDNA) haplotype diversity was determined for 63 Chibcha-speaking Kuna Amerinds sampled widely across their geographic range in eastern Panamá. The Kuna data were compared with mtDNA control region I sequences from two neighboring Chibchan groups, the Ngöbé and the Huetar; two Amerind groups located at the northern and southern extremes of Amerind distribution, the Nuu-Chah-Nulth of the Pacific Northwest and the Chilean Mapuche; and with a single Na-Dene group, the Haida of the Pacific Northwest. The Kuna exhibited low levels of mitochondrial diversity as had been reported for the other two Chibchan groups and, furthermore, carried only two of the four Amerind founding lineages first reported by Schurr and coworkers (Am. J. Hum. Genet. 1990; 46: 613-623). We posit that speakers of modern Chibchan languages (henceforth referred to as the Chibcha) passed through a population bottleneck caused either by ethnogenesis from a small founding population and/or subsequent European conquest and colonization. Using the approach of Harpending et al. (Curr. Anthropol. 1993; 34: 483-496), we estimated a Chibchan population bottleneck and subsequent expansion approximately 10,000 years before present, a date consistent with a bottleneck at the time of Chibchan ethnogenesis. The low mtDNA diversity of Kuna Amerinds, as opposed to the generally high levels of mtDNA variation detected in other Amerind groups, demonstrates the need for adequate sampling of cultural or racial groups when attempting to genetically characterize human populations.

Reduced mtDNA diversity in the Ngöbé Amerinds of Panamá.

Mitochondrial DNA (mtDNA) haplotype diversity was determined for 46 Ngöbé Amerinds sampled widely across their geographic range in western Panamá. The Ngöbé data were compared with mtDNA control region I sequences from two additional Amerind groups located at the northern and southern extremes of Amerind distribution, the Nuu-Chah-Nulth of the Pacific Northwest and the Chilean Mapuche and from one Na-Dene group, the Haida of the Pacific Northwest. The Ngöbé exhibit the lowest mtDNA control region sequence diversity yet reported for an Amerind group. Moreover, they carry only two of the four Amerind founding lineages first described by Wallace and coworkers. We posit that the Ngöbé passed through a population bottleneck caused by ethnogenesis from a small founding population and/or European conquest and colonization. Dating of the Ngöbé population expansion using the Harpending et al. approach to the analysis of pairwise genetic differences indicates a Ngöbé expansion at roughly 6800 years before present (range: 1850-14,000 years before present), a date more consistent with a bottleneck at Chibcha ethnogenesis than a conquest-based event.

Marked variation in the size of genomic plasmids among members of a family of related Epstein-Barr viruses.

Epstein-Barr virus (EBV) genomes in the P3J-HR-1 (HR-1) Burkitt lymphoma cell line rearrange at a high rate. Previously described deletions and rearrangements in HR-1 cells have been found at sites of EBV replication in vivo, suggesting that DNA rearrangement may be an integral aspect of EBV biology and pathogenesis. We examined the structure of linear EBV genomes in subcultures of HR-1 cells using contour-clamped homogenous electric field gel electrophoresis. We developed a second pulsed electrophoretic technique to separate intracellular circular EBV plasmids. The standard, linear HR-1 EBV genome was approximately 155 kilobases in length. Linear molecules of less than unit length, presumably defective genomes, were seen in numerous subcultures. Linear intracellular genomes greater than 155 kilobases were also detected, but only linear genomes of 155 kilobases or less were packaged into virions. The size of circular EBV plasmids also varied greatly among HR-1 subcultures, some of which contained two plasmids of different size. The progeny of the unusual circular plasmids could be either standard or nonstandard linear genomes. No aberrant linear or circular form was detected in a subculture carrying the previously described het fragments. Pulsed-gel electrophoresis has provided two additional characteristics of mutant EBVs: abnormal linear and circular genome configurations.

Identification of a portable determinant of cell cycle function within the carboxyl-terminal domain of the yeast CDC34 (UBC3) ubiquitin conjugating (E2) enzyme.

The ubiquitin conjugating (E2) enzyme encoded by CDC34 (UBC3) in Saccharomyces cerevisiae is required for the G1 to S transition of the cell cycle. CDC34 consists of a 170 residue amino-terminal domain that is homologous to that found in other E2s, followed by a 125 residue carboxyl-terminal domain that is specific to CDC34. We found that a truncation mutant of CDC34 which lacked the CDC34 carboxyl-terminal domain could not support the essential function of CDC34 in the cell cycle in vivo. To explore further the role of the carboxyl-terminal domain in determining the cell cycle function of CDC34, we constructed and characterized genes encoding chimeric E2s incorporating sequences from CDC34 and the related but functionally distinct E2 RAD6 (UBC2). We found that a construct encoding a chimeric RAD6-CDC34 ubiquitin conjugating enzyme, in which the 21 residue acidic carboxyl-terminal domain of RAD6 has been replaced with the 125 residue carboxyl-terminal domain of CDC34, performed the essential functions of CDC34 in vivo. This chimeric E2 also complemented the growth deficiency, UV sensitivity and sporulation deficiency of rad6 mutant strains. Deletion analysis of the CDC34 carboxyl-terminal domain in both CDC34 and the RAD6-CDC34 chimeric E2 identified a region comprising residues 171-244 of CDC34 that was sufficient to confer CDC34 function on the amino-terminal domains of CDC34 and RAD6. We suggest that this region interacts with substrates of CDC34 or with trans-acting factors (such as CDC34-specific ubiquitin protein ligases) that govern the substrate selectivity of CDC34. Congruent results demonstrating a positive role for the carboxyl-terminal domain of CDC34 in the essential function of CDC34 have also been obtained by Silver et al. (1992) and are reported in the accompanying paper.

Genomic organization of tRNA and aminoacyl-tRNA synthetase genes for two amino acids in Saccharomyces cerevisiae.

The genomic organization in Saccharomyces cerevisiae of the tRNA and aminoacyl-tRNA synthetase genes for two amino acids was investigated. Aspartic acid and serine were chosen for the study because of the number and diversity of their tRNA gene sequences and the availability of cloned tRNA and aminoacyl-tRNA synthetase genes. Chromosome assignments were determined by hybridization to DNA gel blots of chromosomal DNA resolved by contour-clamped homogeneous electric field gel electrophoresis. Our results show that the tRNA and the cognate synthetase genes in such a family are dispersed and, therefore, cannot be regulated via a mechanism dependent on close proximity of genes. In general, the genome of S. cerevisiae contains randomly dispersed tRNA genes that are transcribed individually. We have supported and expanded this view by applying the facile method of contour-clamped homogeneous electric field gel electrophoresis to the investigation of these small multigene families.

Alcohol and dietary intake in the development of chronic pancreatitis and liver disease in alcoholism.

Alcohol and dietary intake were determined in alcoholic patients with chronic pancreatitis and alcoholic liver disease. Patients with chronic pancreatitis, alcoholic hepatitis, and cirrhosis ingested approximately 50% of their calories as alcohol, and all had low mean intakes of protein, carbohydrate, and fat as compared with control subjects. Patients with severe alcoholic hepatitis had the lowest intake of nonalcohol calories and protein. Women with chronic pancreatitis had ingested alcohol for a shorter period of time than men whereas women with alcoholic hepatitis and cirrhosis had ingested less alcohol per kilogram body weight per day as compared with men. This study does not support the hypothesis that consumption of a high-protein and high-fat diet is a factor in the development of chronic pancreatitis in the alcoholic patient. The increased susceptibility of women as compared with men to alcoholic liver disease is established.