The role of ultrasonography in the diagnosis of pyloric stenosis: a decision analysis

Sequence variants of the hypervariable region I of human mitochondrial DNA (mtDNA) of 125 individuals from three aboriginal population groups of northern Asia (Yakuts, Evens, and Koryaks) were analyzed. Unique types of mtDNA (mitotypes) were discovered in 80% of Koryaks, 78% of Evens, and 59% of Yakuts. The mitotypes observed were clustered into nine phylogenetically related groups, two of which, according to the data on the comparative analysis of Siberian and east Asian populations, were Koryak-specific, and one was Even-specific. Koryaks and Evens exhibited mtDNAs that were highly frequent in Ainu. The results are discussed in terms of genetic differentiation and the ethnogenesis of ethnic groups of northern Asia.     

Mitochondrial and nuclear genetic relationships among Pacific Island and Asian populations

Mitochondrial and autosomal short tandem-repeat (STR) genetic distances among 28 Pacific Island and Asian populations are significantly correlated (r=.25, P<.01) but describe distinct patterns of relationships. Maternally inherited-mtDNA data suggest that Remote Oceanic Islanders originated in island Southeast Asia. In contrast, biparental STR data reveal substantial genetic affinities between Remote Oceanic Islanders and Near Oceanic populations from highland Papua New Guinea and Australia. The low correlation between maternal and biparental genetic markers from the same individuals may reflect differences in genome-effective population sizes or in sex-biased gene flow. To explore these possibilities, we have examined genetic diversity, gene flow, and correlations among genetic, linguistic, and geographic distances within four sets of populations representing potential geographic and cultural spheres of interaction. GST estimates (a measure of genetic differentiation inversely proportional to gene flow) from mtDNA sequences vary between 0.13 and 0.39 and are typically five times greater than GST estimates from STR loci (0.05-0.08). Significant correlations (r>.5, P<.05) between maternal genetic and linguistic distances are coincident with high mtDNA GST estimates (>0.38). Thus, genetic and linguistic distances may coevolve, and their correspondence may be preserved under conditions of genetic isolation. A significant correlation (r=.65, P<.01) between biparental genetic and geographic distances is coincident with a low STR GST estimate (0.05), indicating that isolation by distance is observed under conditions of high nuclear-gene flow. These results are consistent with an initial settlement of Remote Oceania from island Southeast Asia and with extensive postcolonization male-biased gene flow with Near Oceania.     

Phylogeography of Bufo marinus from its natural and introduced ranges

The marine toad, Bufo marinus, has a broad natural distribution extending from the south-west of the USA to southern Peru and the central Amazon. It was introduced to several localities in the Caribbean and Pacific Oceans to control sugar cane pests. We sequenced 468 bp of mitochondrial DNA (mtDNA) containing the ND3 gene, and flanking tRNA genes from toads spanning the broad natural and introduced ranges. Consistent with the known history of introductions and expected effects of serial bottlenecks, mtDNA within introduced populations in Hawaii and Australia was uniform and most closely related to samples from eastern Venezuela and French Guiana. However, mtDNA nucleotide diversity in the geographic region spanning the source areas is also relative low (0.18-0.46%) and the absence of variation in the introduced populations precludes quantitative assessment of the reduction in genetic diversity. Unexpectedly, there was a large phylogeographic break (5.4% sequence divergence) within the natural range separating populations east and west of the Venezuelan Andes. We hypothesize that the two major lineages of B. marinus were isolated by the uplift of the eastern Andean cordillera which was completed approximately 2.7 Ma. Another species of the marinus group, B. paracnemis, had mtDNA paraphyletic, with marinus, being nested within the eastern lineage. Thus, at least one speciation event within the marinus group postdates the split within marinus. These findings suggest that the taxonomy of B. marinus should be re-evaluated and that the search for pathogens to control Australian populations should be conducted in populations from both lineages in the natural range.     

Testing migration patterns and estimating founding population size in Polynesia by using human mtDNA sequences

The hypervariable 1 region of human mtDNA shows markedly reduced variability in Polynesians, and this variability decreases from western to eastern Polynesia. Fifty-four sequences from New Zealand Maori show that the mitochondrial variability with just four haplotypes is the lowest of any sizeable human group studied and that the frequency of haplotypes is markedly skewed. The Maori sequences, combined with 268 published sequences from the Pacific, are consistent with a series of founder effects from small populations settling new island groups. The distributions of haplotypes were used to estimate the number of females in founding population of New Zealand Maori. The three-step simulation used a randomly selected founding population from eastern Polynesia, an expansionary phase in New Zealand, and finally the random selection of 54 haplotypes. The results are consistent with a founding population that includes approximately 70 women (between 50 and 100), and sensitivity analysis shows that this conclusion is robust to small changes in haplotype frequencies. This size is too large for models postulating a very small founding population of "castaways," but it is consistent with a general understanding of Maori oral history as well as the results of recent canoe voyages recreating early trans-oceanic voyages.     

Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales

Powerful analyses of population structure require information from multiple genetic loci. To help develop a molecular toolbox for obtaining this information, we have designed universal oligonucleotide primers that span conserved intron-exon junctions in a wide variety of animal phyla. We test the utility of exon-primed, intron-crossing amplifications by analyzing the variability of actin intron sequences from humpback, blue, and bowhead whales and comparing the results with mitochondrial DNA (mtDNA) haplotype data. Humpback actin introns fall into two major clades that exist in different frequencies in different oceanic populations. It is surprising that Hawaii and California populations, which are very distinct in mtDNAs, are similar in actin intron alleles. This discrepancy between mtDNA and nuclear DNA results may be due either to differences in genetic drift in mitochondrial and nuclear genes or to preferential movement of males, which do not transmit mtDNA to offspring, between separate breeding grounds. Opposing mtDNA and nuclear DNA results can help clarify otherwise hidden patterns of structure in natural populations.     

Genetic evidence for the proto-Austronesian homeland in Asia: mtDNA and nuclear DNA variation in Taiwanese aboriginal tribes

Previous studies of mtDNA variation in indigenous Taiwanese populations have suggested that they held an ancestral position in the spread of mtDNAs throughout Southeast Asia and Oceania (Melton et al. 1995; Sykes et al. 1995), but the question of an absolute proto-Austronesian homeland remains. To search for Asian roots for indigenous Taiwanese populations, 28 mtDNAs representative of variation in four tribal groups (Ami, Atayal, Bunun, and Paiwan) were sequenced and were compared with each other and with mtDNAs from 25 other populations from Asia and Oceania. In addition, eight polymorphic Alu insertion loci were analyzed, to determine if the pattern of mtDNA variation is concordant with nuclear DNA variation. Tribal groups shared considerable mtDNA sequence identity (P>.90), where gene flow is believed to have been low, arguing for a common source or sources for the tribes. mtDNAs with a 9-bp deletion have considerable mainland-Asian diversity and have spread to Southeast Asia and Oceania through a Taiwanese bottleneck. Only four Taiwanese mtDNA haplotypes without the 9-bp deletion were shared with any other populations, but these shared types were widely dispersed geographically throughout mainland Asia. Phylogenetic and principal-component analyses of Alu loci were concordant with conclusions from the mtDNA analyses; overall, the results suggest that the Taiwanese have temporally deep roots, probably in central or south China, and have been isolated from other Asian populations in recent history.     

Field trial to evaluate the immunogenicity of pseudorabies virus vaccines with deletions for glycoproteins G and E

This study is a geographically systematic genetic survey of the easternmost subspecies of chimpanzee, Pan troglodytes schweinfurthii. DNA was noninvasively collected in the form of shed hair from chimpanzees of known origin in Uganda, Rwanda, Tanzania, and Za?re. Two hundred sixty-two DNA sequences from hypervariable region 1 of which of the mitochondrial control region were generated. Eastern chimpanzees display levels of mitochondrial genetic variation which are low and which are similar to levels observed in humans (Homo sapiens). Also like humans, between 80% and 90% of the genetic variability within the eastern chimpanzees is apportioned within populations. Spatial autocorrelation analysis shows that genetic similarity between eastern chimpanzees decreases clinically with distance, in a pattern remarkably similar to one seen for humans separated by equivalent geographic distances. Eastern chimpanzee mismatch distributions (frequency distributions of pairwise genetic differences between individuals) are similar in shape to those for humans, implying similar population histories of recent demographic expansion. The overall pattern of genetic variability in eastern chimpanzees is consistent with the hypothesis that the subject has responded demographically to paleoclimatically driven changes in the distribution of eastern African forests during the recent Pleistocene.     

Dorset and Thule divergence from East Central Asian roots

The history of the immigration of East Asians to America during the last glacial period remains controversial. In an attempt to add critical data to this problem, a large sample of whole teeth derived from Southeast Asian, Mongolian, Thule, Western Inuit, and pre-Inca (Huari) people was quantified (N = 4,507 teeth from 495 individuals; approximately 30 variables per tooth). Multivariate analysis helped establish that all Native Americans were likely derived from one ancient, extinct population that resided in the region of Mongolia (east Central Asia), and that Mongolians and Southeast Asians are two independent groups. A controversial and enigmatic Central Canadian Arctic "Thule culture Inuit" group on Southampton Island that survived until 1902 was identified as a relic, mainly Paleoeskimo Dorset community. Surprisingly, there was little, or no, indication of Dorset-to-Thule gene flow. Cumulatively, the data suggest that a small population of Paleoindian founders remained resident in Beringia, may have blocked further immigration, and were the antecedents to the Thule/Inuit. With the confluence of the Arctic and Pacific oceans at the breakup of Beringia, the resulting increased availability of marine animal food sources allowed this population to increase in size and expand throughout the eastern Arctic.     

Paternal directional mating in two Amerindian subpopulations located at different altitudes in northwestern Argentina

We used mitochondrial DNA (mtDNA) and Y-chromosome DNA polymorphisms to analyze the ethnic origin of maternal and paternal lineages in two Amerindian subpopulations from northwestern Argentina. One of the subpopulations was from San Salvador de Jujuy, located 1200 m above sea level. The second subpopulation inhabits the Quebrada de Humahuaca area at altitudes ranging from 2500 to 3500 m. Both subpopulations have the same ethnic background. All mtDNA haplotypes were identified as Amerindian with a frequency of 64.6% of the B form (9-bp deletion in mtDNA region V). Because all Central Andean Amerindian populations studied so far exhibit high frequencies of the B haplotype, we propose that they probably are derived from a common ancestral population that inhabited the Central Andes 6000-8000 years B.P. The presence of paternal directional mating (asymmetric contribution of one parental lineage to interethnic gene mixtures) was demonstrated by the finding of an average introgression of 40.5% Spanish Y chromosomes into our Amerindian sample. This introgression was more evident at low altitude than at high altitude, with frequencies of 64.3% in San Salvador de Jujuy (low altitude) and 27.6% in Quebrada de Humahuaca (high altitude) (p < 0.05). The San Salvador de Jujuy subpopulation also showed a significantly higher Y-chromosome gene variability than the Quebrada de Humahuaca subpopulation. These findings are in good agreement with historical reports indicating that the colonization of South America was undertaken by men who usually practiced polygamous unions with Amerindian women and that San Salvador de Jujuy was the main northwestern Argentinian region of European to Amerindian gene admixture. We found 16.7% of cases with Spanish Y chromosomes and Amerindian family names, and the same percentage with Amerindian Y chromosomes and Hispanic names. The former group probably is the result of unions between Hispanic men, who transmitted the Y chromosome, and Amerindian women, who transmitted the family name to the progeny. The latter group likely illustrates the practice of changing names from Amerindian to Hispanic during the baptism of native Americans in colonial times.     

A comparison of mtDNA restriction sites vs. control region sequences in phylogeographic assessment of the musk turtle (Sternotherus minor)

A total of nearly 800 base pairs of mitochondrial DNA sequence was assayed in each of 52 musk turtles (Sternotherus minor) collected across the species' range in the south-eastern USA. About one-half of the sequence information in effect was accessed by conventional recognition-site assays of the entire mtDNA molecule; the remainder came from direct sequence assays of a normally hypervariable 5' section of the noncoding control region. The two assay methods produced essentially nonoverlapping sets of variable character states that were compared with respect to magnitudes and phylogeographic patterns of mtDNA variation. The two assay procedures yielded nearly identical outcomes with regard to: (a) total levels of species-wide mtDNA genetic variation; (b) mean levels of within-locale variation; (c) extremely high population genetic structure; (d) a phylogenetically significant separation of samples from the north-western half of the species' range vs. those in the south-eastern segment; and (e) considerably lower genetic variability within the north-western clade. The micro- and macro-phylogeographic mtDNA patterns in the musk turtle are consistent with a low-dispersal natural history, and with a suspected longer-term biogeographic history of the species, respectively.     

HLA-B35 frequency variations correlate with malaria infection in Sardinia

The hypothesis of a possible selective role of malaria in HLA allele frequency variations was investigated in Sardinia by typing completely 1,039 individuals for HLA: 536 from six lowland villages exposed to malaria until 1948, and 503 from six highland villages with no history of malaria. Another 1,928 individuals from 136 villages scattered all over the island were studied to establish if the HLA allele frequencies among villages correlated with the malaria incidence and/or altitude above sea level. Only the HLA-B35 allele yielded significantly higher frequencies in the lowland versus the highland villages (P<1 x 10(-5)). The observed B35 variance was 9.5 times higher than expected in the absence of selection, showing an adaptive origin. The highly significant positive correlation found between HLA-B35 frequency and malaria in 136 villages suggests that malaria has been the selective factor for HLA-B35 in Sardinia.     

Mitochondrial DNA variation in Koryaks and Itel'men: population replacement in the Okhotsk Sea-Bering Sea region during the Neolithic

In this study, we analyzed the mitochondrial DNA (mtDNA) variation in 202 individuals representing one Itel'men and three Koryak populations from different parts of the Kamchatka peninsula. All mtDNAs were subjected to high resolution restriction (RFLP) analysis and control region (CR) sequencing, and the resulting data were combined with those available for other Siberian and east Asian populations and subjected to statistical and phylogenetic analysis. Together, the Koryaks and Itel'men were found to have mtDNAs belonging to three (A, C, and D) of the four major haplotype groups (haplogroups) observed in Siberian and Native American populations (A-D). In addition, they exhibited mtDNAs belonging to haplogroups G, Y, and Z, which were formerly called "Other" mtDNAs. While Kamchatka harbored the highest frequencies of haplogroup G mtDNAs, which were widely distributed in eastern Siberian and adjacent east Asian populations, the distribution of haplogroup Y was restricted within a relatively small area and pointed to the lower Amur River-Sakhalin Island region as its place of origin. In contrast, the pattern of distribution and the origin of haplogroup Z mtDNAs remained unclear. Furthermore, phylogenetic and statistical analyses showed that Koryaks and Itel'men had stronger genetic affinities with eastern Siberian/east Asian populations than to those of the north Pacific Rim. These results were consistent with colonization events associated with the relatively recent immigration to Kamchatka of new tribes from the Siberian mainland region, although remnants of ancient Beringian populations were still evident in the Koryak and Itel'men gene pools.     

Microsatellite instability in the mitochondrial DNA of colorectal carcinomas: evidence for mismatch repair systems in mitochondrial genome

The role, if any, that mitochondrial (mt) DNA alterations play in the carcinogenic process remains unclear. To determine whether mtDNA instability occurs in cancers, nine microsatellite sequences in the mtDNA were examined in 45 sporadic colorectal carcinomas. Alteration in a polycytidine (C)n tract within a non-coding displacement-loop (D-loop) region was detected in 20 carcinomas (44%), three of which also exhibited frameshift mutations in a polyadenosine (A)8 or polycytidine (C)6 tract within NADH dehydrogenase (ND) genes. Interestingly, all three mutant genes were predicted to encode truncated ND proteins, which lacked a large portion of the C-terminus. These results suggested that certain repair systems, like the mismatch repair systems in the nuclear genome, are required for mtDNA maintenance and that defects in these systems can lead to target mitochondrial gene mutations in colorectal carcinomas.     

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 Ng?bé 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.     

Evolution of the mitochondrial DNA control region in the mbuna (Cichlidae) species flock of Lake Malawi, East Africa

Considerable controversy has surrounded the application of mitochondrial DNA data to reconstruction of evolutionary relationships among the endemic cichlids of Lake Malawi. Central to this debate has been the issue of whether lineage sorting is complete, and thus whether these data actually reflect species phylogeny, or simply gene genealogy. Review of all mtDNA control region sequences available for members of one monophyletic subset of this species flock, the Malawi rockfishes, or mbuna, strongly indicates that lineage sorting is incomplete: Character-based analyses of these sequences reconstruct gene, not species, interrelationships. Analysis of the pattern of nucleotide substitutions differentiating these mtDNA alleles suggests that pyrimidine residues undergo transition substitutions more often than do purines. Estimation of the magnitude of derived sequence differentiation in light of the reconstructed gene genealogy suggests that the mbuna may be of considerably more recent vintage than previous molecular characterizations have indicated.     

The genetic relationship between the Finns and the Finnish Saami (Lapps): analysis of nuclear DNA and mtDNA

The genetic relationships between two Finno-Ugric-speaking populations, the Finns and the Finnish Saami (Lapps), were studied by using PCR for six nuclear-DNA marker loci, mitochondrial restriction-site polymorphism, and sequence variation of a 360-bp segment of the mitochondrial control region. The allele frequencies of each of the nuclear-DNA marker loci and the frequencies of mtDNA restriction haplotypes were significantly different between the populations. The Saami showed exceptionally low variation in their mtDNA restriction sites. The 9-bp deletion common in East Asian populations was not observed, nor did the haplotype data fit into the haplogroup categorization of Torroni et al. The average number of nucleotide substitutions from the mtDNA haplotype data indicated that the Finnish Saami may be closer to the Finns than to the other reference populations, whereas nuclear DNA suggested that the Finns are more closely related to the European reference populations than to the Finnish Saami. The similarity of the Finns to the other Europeans was even more pronounced according to the sequence data. We were unable to distinguish between the Finns and either the Swiss or Sardinian reference populations, whereas the Finnish Saami clearly stood apart. The Finnish Saami are distinct from other Circumarctic populations, although two of the lineages found among the Saami showed closer relationship to the Circumarctic than to the European lineages. The sequence data indicated an exceptionally high divergence for the Saami mtDNA control lineages. The distribution of the pairwise nucleotide differences in the Saami suggested that this population has not experienced an expansion similar to what was indicated for the Finns and the reference populations.     

Departure from neutrality at the mitochondrial NADH dehydrogenase subunit 2 gene in humans, but not in chimpanzees

To test whether patterns of mitochondrial DNA (mtDNA) variation are consistent with a neutral model of molecular evolution, nucleotide sequences were determined for the 1041 bp of the NADH dehydrogenase subunit 2 (ND2) gene in 20 geographically diverse humans and 20 common chimpanzees. Contingency tests of neutrality were performed using four mutational categories for the ND2 molecule: synonymous and nonsynonymous mutations in the transmembrane regions, and synonymous and nonsynonymous mutations in the surface regions. The following three topological mutational categories were also used: intraspecific tips, intraspecific interiors, and interspecific fixed differences. The analyses reveal a significantly greater number of nonsynonymous polymorphisms within human transmembrane regions than expected based on interspecific comparisons, and they are inconsistent with a neutral equilibrium model. This pattern of excess nonsynonymous polymorphism is not seen within chimpanzees. Statistical tests of neutrality, such as TAJIMA's D test, and the D and F tests proposed by FU and LI, indicate an excess of low frequency polymorphisms in the human data, but not in the chimpanzee data. This is consistent with recent directional selection, a population bottleneck or background selection of slightly deleterious mutations in human mtDNA samples. The analyses further support the idea that mitochondrial genome evolution is governed by selective forces that have the potential to affect its use as a "neutral" marker in evolutionary and population genetic studies.     

Comparison between the complete mtDNA sequences of the blue and the fin whale, two species that can hybridize in nature

The sequence of the mitochondrial DNA (mtDNA) molecule of the blue whale (Balaenoptera musculus) was determined. The molecule is 16,402 bp long and its organization conforms with that of other eutherian mammals. The molecule was compared with the mtDNA of the congeneric fin whale (B. physalus). It was recently documented that the two species can hybridize and that male offspring are infertile whereas female offspring may be fertile. The present comparison made it possible to determine the degree of mtDNA difference that occurs between two species that are not completely separated by hybridization incompatibility. The difference between the complete mtDNA sequences was 7.4%. Lengths of peptide coding genes were the same in both species. Except for a small portion of the control region, disruption in alignment was usually limited to insertion/deletion of a single nucleotide. Nucleotide differences between peptide coding genes ranged from 7.1 to 10.5%, and difference at the inferred amino acid level was 0.0-7.9%. In the rRNA genes the mean transition difference was 3.8%. This figure is similar in degree to the difference (3.4%) between the 12S rRNA gene of humans and the chimpanzee. The mtDNA differences between the two whale species, involving both peptide coding and rRNA genes, suggest an evolutionary separation of > or = 5 million years. Although hybridization between more distantly related mammalian species may not be excluded, it is probable that the blue and fin whales are nearly as different in their mtDNA sequences as hybridizing mammal species may be.     

Applications of microsatellite-based Y chromosome haplotyping

Y-chromosomal microsatellites have been investigated for the purposes of application to male identification, population genetics and population history. With nine markers, every male in a German population sample (n = 70) could be identified by an individual-specific Y microsatellite haplotype. The analysis of 474 unrelated males of nine human populations with seven markers revealed 301 different Y haplotypes. The analysis of molecular variance (AMOVA) approach was used to detect male population characteristics of Y microsatellite haplotypes. With pairwise comparisons of inter-population variance, most of the populations could be distinguished significantly. Sixty individuals from different male populations in Asia and Northern Europe carrying a novel Y-chromosomal T-->C transition show reduced microsatellite variability together with haplotype similarities. Microsatellite data suggest that the mutation occurred recently in Asia, supporting the hypothesis of Asian ancestry of some northern European populations.