Polynesian origins and affinities: globin gene variants in eastern Polynesia.

Analysis of copy number variants of the duplicated alpha-, zeta-, and gamma-globin genes in eastern Polynesians revealed a high frequency of both triplicated-zeta-gene chromosomes and a specific alpha thalassemia deletion. This deletion and a novel restriction-enzyme-site polymorphism associated with a zeta zeta zeta chromosome are found only in Melanesians and Polynesians. Analysis of alpha-globin restriction-enzyme haplotypes indicated further similarities to Melanesians but suggested an additional non-Melanesian genetic component in eastern Polynesia. Several globin gene alleles showed evidence of marked frequency fluctuations due to genetic drift.     

Globin genes are useful markers to identify genetic similarities between Fijians and Pacific Islanders from Polynesia and Melanesia.

DNA mapping studies in Fijians have enabled the identification of rearrangements and RFLPs involving the alpha-, zeta-, and gamma-globin genes. Comparisons of these data with corresponding gene markers in Polynesians and Melanesians of Papua New Guinea show considerable overlap between the three population groups. The utility of globin genes as population markers is further confirmed.     

Globin genes in Micronesia: origins and affinities of Pacific Island peoples.

DNA polymorphisms and copy-number variants of alpha-, zeta-, and gamma-globin genes have been studied in seven Micronesian island populations and have been compared with those in populations from Southeast Asia, Melanesia, and Polynesia. Micronesians are not significantly different from Polynesians at these loci and appear to be intermediate between Southeast Asians and Melanesians. There is evidence of significant Melanesian input into the Micronesian gene pool and of substantial proto-Polynesian contact with Melanesia.     

Melanesian origin of Polynesian Y chromosomes

BACKGROUND: Two competing hypotheses for the origins of Polynesians are the 'express-train' model, which supposes a recent and rapid expansion of Polynesian ancestors from Asia/Taiwan via coastal and island Melanesia, and the 'entangled-bank' model, which supposes a long history of cultural and genetic interactions among Southeast Asians, Melanesians and Polynesians. Most genetic data, especially analyses of mitochondrial DNA (mtDNA) variation, support the express-train model, as does linguistic and archaeological evidence. Here, we used Y-chromosome polymorphisms to investigate the origins of Polynesians. RESULTS: We analysed eight single nucleotide polymorphisms (SNPs) and seven short tandem repeat (STR) loci on the Y chromosome in 28 Cook Islanders from Polynesia and 583 males from 17 Melanesian, Asian and Australian populations. We found that all Polynesians belong to just three Y-chromosome haplotypes, as defined by unique event polymorphisms. The major Y haplotype in Polynesians (82% frequency) was restricted to Melanesia and eastern Indonesia and most probably arose in Melanesia. Coalescence analysis of associated Y-STR haplotypes showed evidence of a population expansion in Polynesians, beginning about 2,200 years ago. The other two Polynesian Y haplotypes were widespread in Asia but were also found in Melanesia. CONCLUSIONS: All Polynesian Y chromosomes can be traced back to Melanesia, although some of these Y-chromosome types originated in Asia. Together with other genetic and cultural evidence, we propose a new model of Polynesian origins that we call the 'slow-boat' model: Polynesian ancestors did originate from Asia/Taiwan but did not move rapidly through Melanesia; rather, they interacted with and mixed extensively with Melanesians, leaving behind their genes and incorporating many Melanesian genes before colonising the Pacific.     

Phenylalanine hydroxylase gene haplotypes in Polynesians: evolutionary origins and absence of alleles associated with severe phenylketonuria.

A total of 630 haplotypes for the phenylalanine hydroxylase (PAH) gene locus were established in five groups of Polynesians comprising Samoans, Tongans, Cook Islanders, Maori, and Niueans. Considerable genetic continuity was demonstrated between these widely dispersed populations, since three common haplotypes (4, 1, and 7) constituted over 95% of alleles. A control group of individuals from Southeast Asia shared the same major haplotypes, 4, 1, and 7, with Polynesians. These data provide further support for the theories of genetic homogeneity and of Asian affinities of the Polynesian precursor populations. The absence of severe phenylketonuria (PKU) in both Polynesians and Southeast Asians is consistent with the lack of PAH haplotypes 2 and 3, on which the severe PKU mutants have arisen among Caucasians.     

Genome-wide analysis indicates more Asian than Melanesian ancestry of Polynesians

Analyses of mitochondrial DNA (mtDNA) and nonrecombining Y chromosome (NRY) variation in the same populations are sometimes concordant but sometimes discordant. Perhaps the most dramatic example known of the latter concerns Polynesians, in which about 94% of Polynesian mtDNAs are of East Asian origin, while about 66% of Polynesian Y chromosomes are of Melanesian origin. Here we analyze on a genome-wide scale, to our knowledge for the first time, the origins of the autosomal gene pool of Polynesians by screening 377 autosomal short tandem repeat (STR) loci in 47 Pacific Islanders and compare the results with those obtained from 44 Chinese and 24 individuals from Papua New Guinea. Our data indicate that on average about 79% of the Polynesian autosomal gene pool is of East Asian origin and 21% is of Melanesian origin. The genetic data thus suggest a dual origin of Polynesians with a high East Asian but also considerable Melanesian component, reflecting sex-biased admixture in Polynesian history in agreement with the Slow Boat model. More generally, these results also demonstrate that conclusions based solely on uniparental markers, which are frequently used in population history studies, may not accurately reflect the history of the autosomal gene pool of a population.     

The human T-cell receptor gamma (TRG) genes

The human T-cell receptor gamma (TRG) chain genes, like those encoding the T-cell receptor alpha- and beta-polypeptides, undergo rearrangements specifically in T cells. The human TRG locus, which has been completely mapped, is composed of two constant region genes (TRGC), five joining segments (TRGJ) and at least 14 variable gamma-genes (TRGV). Eight variable genes are functional and belong to four different subgroups. The product of the rearranged TRG gene is the gamma-chain which is expressed, along with the delta-chain, at the surface of a subset of T lymphocytes. Although some gamma delta + cells display a cytolytic activity, their precise function remains to be elucidated.     

Characterization of the class I alpha-mannosidase gene family in the filamentous fungus Aspergillus nidulans

We describe the cloning and sequence characterization of three Class I alpha-1,2-mannosidase genes from the filamentous fungus Aspergillus nidulans. We used degenerate PCR primers to amplify a portion of the alpha-1,2-mannosidase IA gene and used the PCR fragment to isolate the 2495 nt genomic gene plus several hundred bases of flanking region. Putative introns were confirmed by RT-PCR. Coding regions of the genomic sequence were used to identify two additional members of the gene family by BLAST search of the A. nidulans EST sequencing database. Specific PCR primers were designed to amplify portions of these genes which were used to isolate the genomic sequences. The 1619 nt coding region of the alpha-1,2-mannosidase IB gene and the 1759 nt coding region of the alpha-1,2-mannosidase IC gene, plus flanking regions, were fully sequenced. All three genes appeared to encode type-II transmembrane proteins that are typical of Class I alpha-1,2-mannosidases. The deduced protein sequences were aligned with 11 published Class I alpha-1, 2-mannosidases to determine sequence relationships. All three genes exhibited high similarity to other fungal alpha-1,2-mannosidases. The alpha-1,2-mannosidase IB exhibited very high similarity to the Aspergillus satoi and Penicillium citrinum alpha-1,2-mannosidases and likely represents an orthologue of these genes. Phylogenetic analysis suggests that the three A. nidulans Class I alpha-1, 2-mannosidases arose from duplication events that occurred after the divergence of fungi from animals and insects. This is the first report of the existence of multiple Class I mannosidases in a single fungal species.     

Guanylylation and adenylylation of the alpha regulatory proteins of herpes simplex virus require a viral beta or gamma function.

Herpes simplex virus genes form several groups whose expression is coordinately regulated and sequentially ordered in a cascade fashion. Most of the products of the first group, the alpha genes, appear to have regulatory functions. We report that the alpha proteins, infected cell proteins 4, 0, 22, and 27 of herpes simplex virus 1 and 4, 0, and 27 of herpes simplex virus 2, were labeled in the isolated nuclei of infected HeLa cells with [alpha-32P]GTP or [alpha-32P]ATP late in infection and that these proteins represent the largest group of virus-specific proteins labeled in this fashion. Studies with [2-3H]ATP, in which the label is in the purine ring, showed that a portion of the label in alpha proteins and in at least one other infected cell protein is due to nucleotidylylation. Analyses of the labeling reactions in nuclei of (i) cells infected with temperature-sensitive mutants at nonpermissive temperatures, (ii) cells infected with wild-type virus and harvested at different times postinfection, and (iii) cells treated with inhibitors of protein synthesis or of synthesis of viral DNA led to the conclusion that viral gene functions expressed after the synthesis of alpha proteins are required for the labeling of the alpha proteins with [alpha-32P]GTP. We conclude that several of the alpha proteins are extensively posttranslationally modified and that these modifications include nucleotidylylation.     

Transfection of a human alpha-(1,3)fucosyltransferase gene into Chinese hamster ovary cells. Complications arise from activation of endogenous alpha-(1,3)fucosyltransferases

In order to isolate a human gene encoding an alpha-(1,3)fucosyltransferase (alpha-(1,3)Fuc-T), genomic DNA from HL-60 cells was transfected by several methods into Chinese hamster ovary (CHO) cells. Colonies expressing alpha-(1,3)Fuc-T activity were identified by their ability to bind a monoclonal antibody (anti-SSEA-1) that recognizes the carbohydrate product of alpha-(1,3)Fuc-T action. CHO cells do not express alpha-(1,3)Fuc-T activity but contain at least two, silent alpha-(1,3)Fuc-T genes previously identified by their activation in the rare, dominant mutants LEC11 and LEC12. These CHO enzymes were shown to be distinguishable from the alpha-(1,3)Fuc-T activity of HL-60 cells by the latter's comparative inability to transfer fucose to paragloboside and fetuin. Based on these criteria, only 11 isolates from more than 70 putative transfectants examined were found to stably express an alpha-(1,3)Fuc-T activity typical of HL-60 cells. Genomic DNA from two of these isolates was used to generate five independent secondary transfectants with HL-60-like alpha-(1,3)Fuc-T activity. Southern analysis revealed a common DNA fragment that hybridized to an Alu probe in each secondary, providing evidence that a human alpha-(1,3)Fuc-T gene had been transfected. However, in all transfection experiments, isolates that expressed alpha-(1,3)Fuc-T activities similar to CHO-encoded enzymes were also obtained. Several lines of evidence indicated that these cells arose from activation of endogenous CHO alpha-(1,3)Fuc-T genes as a consequence of DNA transfection. These false positives complicated the identification of transfectants expressing a human alpha-(1,3)Fuc-T gene and represent an important consideration in experiments to transfect other glycosyltransferase genes.     

Alpha-globin gene haplotypes in Polynesians: their relationships to population groups and gene rearrangements.

Five hundred two alpha-globin gene haplotypes were established in three Polynesian populations, Samoans, Maoris, and Niueans. Limited diversity of haplotypes was found in Polynesians, in whom six common haplotypes (Ia, IIa, IId, IIe, IIIa, and IVa) predominate. Haplotypes Ia and IIa enable Polynesians to be distinguished from Melanesians. Differences in haplotype profiles between the above Polynesian populations support their separate clustering on the basis of previous globin gene analyses and proposed theories of migration. The -alpha/, alpha alpha alpha/, -zeta/, and zeta zeta zeta/rearrangements are each associated exclusively with a particular haplotype, providing evidence of a single evolutionary origin for each. Therefore, a minimum of four DNA crossover events account for the separate origins of these rearrangements in the Polynesians.     

Concerted evolution of the mouse immunoglobulin gamma chain genes

The nucleotide sequences of the immunoglobulin heavy-chain constant region genes of mouse, C gamma 3, C gamma 1, C gamma 2b and C gamma 2a, together with that of a human equivalent C gamma 4 were compared. All the six pairs of genes within the mouse C gamma gene family contain DNA segments that exhibit marked homology, whereas no such segmental homology was found in interspecies comparisons. This result indicates that the four C gamma genes of the mouse evolved concertedly by exchanging parts of their genetic information with each other either by gene conversion or by double unequal crossing-over. Another example of such concerted evolution was found in gene regions encoding membrane domains of the mouse C gamma chains. We also searched for such segmental homologies in other mammalian C gamma gene families and found at least two more examples in man and guinea-pig. In the mouse C gamma gene family, the silent positions of an exon encoding the third domain of C gamma chains show much greater divergence in sequence than other regions, indicating that the genetic information encoded by this gene region was least scrambled during recent evolution. A phylogenetic tree constructed from the nucleotide differences of this exon demonstrates that at least two C gamma genes had already existed before mammalian radiation. Based on these results, evolution of mammalian C gamma gene families is discussed.     

Limited genetic diversity in polynesians reflected in the highly polymorphic 3'HVR alpha-globin gene marker.

Polynesians from five distinct island groups were studied with DNA probe alpha 3'HVR, a highly polymorphic VNTR (variable number of tandem repeats) minisatellite region associated with the alpha-globin gene cluster. Results showed a paucity of genetic heterozygosity together with clustering of alpha 3'HVR alleles with alpha-globin DNA haplotypes and alpha-globin gene rearrangements. This restricted diversity is consistent with population bottlenecks in the colonization of Polynesia.     

Immunoglobulin CH gene family in hominoids and its evolutionary history.

The organization of the human immunoglobulin CH gene suggests that a gene duplication involving the C gamma-C gamma-C epsilon-C alpha region has occurred during evolution. We previously showed that both chimpanzee and gorilla have two 5'-C epsilon-C alpha-3', as in human, and that orangutan, gibbon, and Old World monkeys have one C epsilon gene and one, two, and one C alpha gene(s), respectively. In addition to these clustered CH genes, there is one processed C epsilon pseudogene in each species. The present study revealed that orangutan and crab-eating macaque (an Old World monkey) both have one 5'-C epsilon-C alpha-3' and that gibbon has two 5'-C epsilon-C alpha-3', one C epsilon gene of which is completely deleted. By Southern analysis, the number of C gamma genes in all the nonhuman hominoids was estimated to be four to five, as in human, in comparison with two for crab-eating macaque. The C mu and C delta genes were estimated to be present as single copies in both hominoids and crab-eating macaque. Furthermore, it was proved that there are two copies of the C epsilon 5'-flanking region in both the orangutan and the gibbon genomes. These results show that gene duplication including the C gamma-C gamma-C epsilon-C alpha genes occurred in the common ancestor of hominoids and that subsequent deletion of the C epsilon gene (in orangutan, including one of the C alpha genes) occurred independently in each hominoid species.     

Regulation of human cardiac myosin heavy chain genes: the effect of catecholamine.

The 5'-flanking regions of the alpha- and beta-cardiac myosin heavy chain (MyHC) genes were excised from the cosmid human genomic clones using Hind III and Xbal for the alpha-MyHC gene, and the Hind III and Hind III sites for the beta-MyHC gene. These fragments were linked to chloramphenicol acetyl transferase (CAT) vector to generate a chimeric fusion gene. These fusion genes were subsequently transfected to neonatal rat cardiac cultured cells to analyze the CAT activity. The alpha-MyHC gene is preferentially expressed as compared to the beta-MyHC. In the presence of norepinephrine (NE) the beta-MyHC gene is remarkably induced (within 24 hours following the addition of norepinephrine to the cardiocyte culture). However, the alpha-MyHC is also induced. Specific alpha andrenergic antagonists such as terazosin (Tz) partially suppressed both the alpha- and beta-MyHC genes as revealed by the CAT activity. These findings suggest that catecholamine does activate the human cardiac MyHC genes but does not differentiate the specific expression of either the alpha- or beta-MyHC genes.     

Obesity and Self‐reported General Health,Hawaii BRFSS: Are Polynesians at Higher Risk?

Objective: This study compared the relationship between fair/poor general health status among overweight and obese Polynesians with that among other overweight and obese persons in Hawaii. Methods and Procedures: Data were pooled from the 1998–2003 Hawaii Behavioral Risk Factor Surveillance System (BRFSS) and logistic regression used to examine the predictors of fair/poor health status. Results: Polynesians were significantly more likely to be obese than non‐Polynesians; overweight Polynesians were more likely than other overweight individuals to report fair/poor health status. After adjusting for confounders, among Polynesians, being obese was no longer associated with fair/poor health. Non‐Polynesians who were obese (odds ratio 1.9; 95% confidence interval: 1.4–2.6), older, less educated, smokers, diabetic, hypertensive, and physically inactive were more likely to report fair/poor health. Discussion: Although Polynesians were significantly more obese than the rest of the Hawaii population, their weight was not independently associated with their odds for fair/poor health as it was with non‐Polynesians. The difference may be that, for Polynesians, hypertension and diabetes overrode the effect of obesity on general health status or this group maintains different cultural perceptions of body size. Regardless, these findings show a major health risk among Polynesians and suggest the need for culturally specific health interventions.     

Melanesian and Asian origins of Polynesians: mtDNA and Y chromosome gradients across the Pacific

The human settlement of the Pacific Islands represents one of the most recent major migration events of mankind. Polynesians originated in Asia according to linguistic evidence or in Melanesia according to archaeological evidence. To shed light on the genetic origins of Polynesians, we investigated over 400 Polynesians from 8 island groups, in comparison with over 900 individuals from potential parental populations of Melanesia, Southeast and East Asia, and Australia, by means of Y chromosome (NRY) and mitochondrial DNA (mtDNA) markers. Overall, we classified 94.1% of Polynesian Y chromosomes and 99.8% of Polynesian mtDNAs as of either Melanesian (NRY-DNA: 65.8%, mtDNA: 6%) or Asian (NRY-DNA: 28.3%, mtDNA: 93.8%) origin, suggesting a dual genetic origin of Polynesians in agreement with the "Slow Boat" hypothesis. Our data suggest a pronounced admixture bias in Polynesians toward more Melanesian men than women, perhaps as a result of matrilocal residence in the ancestral Polynesian society. Although dating methods are consistent with somewhat similar entries of NRY/mtDNA haplogroups into Polynesia, haplotype sharing suggests an earlier appearance of Melanesian haplogroups than those from Asia. Surprisingly, we identified gradients in the frequency distribution of some NRY/mtDNA haplogroups across Polynesia and a gradual west-to-east decrease of overall NRY/mtDNA diversity, not only providing evidence for a west-to-east direction of Polynesian settlements but also suggesting that Pacific voyaging was regular rather than haphazard. We also demonstrate that Fiji played a pivotal role in the history of Polynesia: humans probably first migrated to Fiji, and subsequent settlement of Polynesia probably came from Fiji.     

Assignment of orthologous relationships among mammalian alpha-globin genes by examining flanking regions reveals a rapid rate of evolution

In order to study the relationships among mammalian alpha-globin genes, we have determined the sequence of the 3' flanking region of the human alpha 1 globin gene and have made pairwise comparisons between sequenced alpha-globin genes. The flanking regions were examined in detail because sequence matches in these regions could be interpreted with the least complication from the gene duplications and conversions that have occurred frequently in mammalian alpha-like globin gene clusters. We found good matches between the flanking regions of human alpha 1 and rabbit alpha 1, human psi alpha 1 and goat I alpha, human alpha 2 and goat II alpha, and horse alpha 1 and goat II alpha. These matches were used to align the alpha-globin genes in gene clusters from different mammals. This alignment shows that genes at equivalent positions in the gene clusters of different mammals can be functional or nonfunctional, depending on whether they corrected against a functional alpha-globin gene in recent evolutionary history. The number of alpha-globin genes (including pseudogenes) appears to differ among species, although highly divergent pseudogenes may not have been detected in all species examined. Although matching sequences could be found in interspecies comparisons of the flanking regions of alpha- globin genes, these matches are not as extensive as those found in the flanking regions of mammalian beta-like globin genes. This observation suggests that the noncoding sequences in the mammalian alpha-globin gene clusters are evolving at a faster rate than those in the beta-like globin gene clusters. The proposed faster rate of evolution fits with the poor conservation of the genetic linkage map around alpha-globin gene clusters when compared to that of the beta-like globin gene clusters. Analysis of the 3' flanking regions of alpha-globin genes has revealed a conserved sequence approximately 100-150 bp 3' to the polyadenylation site; this sequence may be involved in the expression or regulation of alpha-globin genes.