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Results for “Haplotype structures”

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PubMed2003

Phylogenetic relationships between the tideland snails Batillaria flectosiphonata in the Ryukyu Islands and B. multiformis in the Japanese Islands.

Phylogenetic relationships between two sibling species of Japanese tideland snails, namely, Batillaria multiformis from the Japanese Islands and B. flectosiphonata from the Ryukyu Islands, were analyzed on the basis of the nucleotide sequences of the mitochondrial gene for cytochrome oxidase I. Populations of B. multiformis were genetically distinct from those of B. flectosiphonata with the exception of a population from Amami-Oshima Island, which corresponded to the boundary between the distributions of these two species. Individuals with the mitochondrial gene of B. multiformis and those with the mitochondrial gene of B. flectosiphonata were collected from the same tidal flat on Amami-Oshima Island. All the snails with the mitochondrial gene of B. multiformis could be divided into two genetically distinct groups but there was no geographical structure to the distribution of these two groups. Individual populations of B. flectosiphonata in the Amami, Okinawa, Miyako and Yaeyama insular groups each consisted exclusively of a unique set of haplotypes, with the exception of a population at a northern site on Okinawajima Island, which included a few individuals with sequences related to those of individuals in the Amami insular group. All individuals from South Ryukyu formed a well-supported monophyletic group, while the monophyly of individuals from Central Ryukyu was not supported. The monophyly of B. multiformis was clearly demonstrated but there was no evidence to support that of B. flectosiphonata. Batillaria multiformis might have been derived from immigrants from the Ryukyu Islands, which became isolated and diverged genetically on the Japanese Islands.

Animals↗

PubMed1992

Enhancing the immunogenicity of a permissive binding T cell epitope derived from the simian immunodeficiency virus-encoded negative regulatory factor.

Using the murine system we have analyzed an immunogenic T cell peptide epitope corresponding to amino acids 96-112 of the simian immunodeficiency virus-negative regulatory protein sequence. This epitope was unusual in that it was strongly immunogenic in mice of five of the six H-2 haplotypes tested. We generated a T cell hybridoma (SVNF) specific for this peptide in order to determine how manipulating the peptide might alter its immunogenicity. Substitution analysis showed that His 103, Pro 104, Val 106, and Pro 107 were important amino acids for stimulating SVNF because substitutions at these positions diminished the reactivity of SVNF. However, we also found that substituting an Ala for a Val at position 100 or a Val for an Ala at position 110 enhanced reactivity of SVNF. We were able to further enhance the immunogenicity of this epitope by extending the carboxyl terminus two amino acids and making the resulting carboxyl-terminal Lys an amide and by adding a Glu to the amino terminus. These modifications shifted the in vitro activity of SVNF at least two orders of magnitude. We also compared the ability of this modified peptide and the wild-type SIV nef 96-112 to prime a T cell response in vivo. We primed mice with various doses of either the wild-type or the modified peptide and looked at the ability of the draining lymph node cells to proliferate to wild-type peptide. We found that the modified peptide was 10- to 100-fold better at priming a T cell response than the wild-type peptide. Therefore, we were able to create a peptide that was more immunogenic than the wild-type peptide in vivo as well as in vitro. Manipulations such as these that enhance the immunogenicity of T cell epitopes must be considered in developing peptide vaccines against HIV or other infectious agents.

Amino Acid Sequence↗

PubMed2005

Phylogeographic structure of the fire ant Solenopsis invicta in its native South American range: roles of natural barriers and habitat connectivity.

We generated mitochondrial DNA (mtDNA) sequence data from 402 individuals of the fire ant Solenopsis invicta collected from 11 native populations and analyzed these data using a combination of demographic, phylogenetic, and phylogeographic methods to infer features of the evolutionary history of this species. Prior expectations regarding high levels of genetic structure and isolation by distance among populations were supported by the data, but we also discovered several unanticipated patterns. Our analyses revealed a major genetic break between S. invicta mtDNA haplotypes that coincides with the Mesopotamia wetlands region of South America, resulting in two higher level nested clade groupings. In addition, we identified contrasting patterns of genetic differentiation within these two major groups, which may reflect differences in connectivity of suitable habitat in different parts of the native range of S. invicta. Our study represents the first attempt to understand the phylogeographic history of S. invicta across its native range.

Animals↗

PubMed1997

[Gm and Km allotypes in a Chilean urban population sample].

BACKGROUND: The knowledge of the genic structure of a population is of great importance for evolutive studies. AIM: To estimate in a Chilean population sample from the low-middle and low socioeconomic strata of Santiago, haplotypes and allele frequencies for Gm and Km loci. SUBJECTS AND METHODS: The sample included 460 controls of a case-control study of typhoid fever. RESULTS: The G1m-G2m-G3m most frequent haplotypes were: za;..;g or 1,17;(-);21 = 0.4493;fn;b or 3;23;5,13 = 0.2522; f-,..;b or 3;(-);5,13 = 0.1389; zax;..;g or 1,2,17;(-);21 = 0.0685; za;..;b or 1,17;(-);5,13 = 0.0454; za;n;g or 1,17;23;21 = 0.0207; f;..;g or 3;(-);21 = 0.0129. The frequencies of Km alleles were 0.2391 and 0.7609 for Km1 and Km3 respectively. CONCLUSIONS: These frequencies are within those found in Amerindian and Caucasian populations as expected from the origin of the Chilean population. Gm haplotypes did not differ from Hardy-Weinberg equilibrium, while a significant lack of homozygous Km1/km1 was found in Km.

Adolescent↗

PubMed1998

[Characteristics of the gene pool of Russian Old Believers in Siberia based on polymorphism of blood groups, isoenzymes, and blood proteins].

The frequency distributions of A1A2B0, Rhesus, MNSs, P, Duffy, Kell, Hp, Tf, AcP, PGM1 alleles, and haplotypes were studied in Siberian populations of Old Believers (Burnyi village, Krasnoyarskii krai, and Isetskii raion, Tyumenskaya oblast) and in ethnic Russians from Tyumenskaya oblast. Features characteristic of the genetic structure of these groups were revealed. The Siberian groups of Russians were shown to be genetically removed from European Russian populations (Tverskaya and Vologodskaya oblasts). The Burnyi population of Old Believers was significantly removed from the other groups of Russians due to peculiarities in the sample.

Blood Group Antigens↗

PubMed2006

A "silent" polymorphism in the MDR1 gene changes substrate specificity.

Synonymous single-nucleotide polymorphisms (SNPs) do not produce altered coding sequences, and therefore they are not expected to change the function of the protein in which they occur. We report that a synonymous SNP in the Multidrug Resistance 1 (MDR1) gene, part of a haplotype previously linked to altered function of the MDR1 gene product P-glycoprotein (P-gp), nonetheless results in P-gp with altered drug and inhibitor interactions. Similar mRNA and protein levels, but altered conformations, were found for wild-type and polymorphic P-gp. We hypothesize that the presence of a rare codon, marked by the synonymous polymorphism, affects the timing of cotranslational folding and insertion of P-gp into the membrane, thereby altering the structure of substrate and inhibitor interaction sites.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2006

Haplotype spanning TTC12 and ANKK1, flanked by the DRD2 and NCAM1 loci, is strongly associated to nicotine dependence in two distinct American populations.

Nicotine dependence (ND) is a moderately heritable trait. We ascertained a set of 1615 subjects in 632 families [319 African-American (AA) and 313 European-American (EA)] based on affected sibling pairs with cocaine or opioid dependence. Subjects were interviewed with the Semi-Structured Assessment for Drug Dependence and Alcoholism (SSADDA). Previously, we identified a modest linkage peak (LOD score =1.97) for ND in the EA part of the sample on chromosome 11q23, a region that includes the NCAM1-TTC12-ANKK1-DRD2 gene cluster. DRD2 and NCAM1 are functional candidate genes for substance dependence; the TTC12 and ANKK1 loci are not well characterized. We genotyped a set of 43 single nucleotide polymorphisms (SNPs) spanning this region, and performed family-based association and haplotype analysis. There was relatively weak evidence for association of the flanking DRD2 and NCAM1 markers to ND, but very strong evidence of association of multiple SNPs at TTC12 and ANKK1 in both populations (minimal P=0.0007 in AAs and minimal P=0.00009 in EAs), and in the pooled sample, as well as strong evidence for highly significant association of a single haplotype spanning TTC12 and ANKK1 to ND in the pooled sample (P=0.0000001). We conclude that a risk locus for ND, important both in AAs and EAs, maps to a region that spans TTC12 and ANKK1. Functional studies of these loci are warranted. These results provide additional information useful in evaluating the many earlier discrepant findings regarding association of DRD2 with substance dependence.

Adult↗

PubMedDate not supplied

Genetic variation of southern hemisphere fur seals (Arctocephalus spp.): investigation of population structure and species identity.

We have examined phylogenetic and geographic patterns of variation in the mitochondrial cytochrome b gene of Southern Hemisphere fur seals (Arctocephalus spp.). Our survey of 106 individuals from four putative species reveals three distinct patterns of variation reflecting ancient, recent historic, and contemporary gene flow. For the combined samples of Subantarctic (Arctocephalus tropicalis) and Antarctic (Arctocephalus gazella) fur seals, we find low levels of sequence diversity and reciprocal paraphyly of hapiotypes (where representative haplotypes of a species are found to occur infrequently in another species and vice versa). For the Australian and Cape fur seal subspecies (Arctocephalus pusillus doriferus and A. p. pusillus, respectively), we find low levels of sequence diversity but significant differences in the regional distribution of haplotypes that are consistent with, but not conclusive of, the current subspecies definition based on nonmolecular data. For the New Zealand fur seal (Arctocephalus forsteri), we find high levels of average sequence diversity because of the survival of two divergent lineages of mitochondrial hapiotypes with differences approaching that found in interspecific comparisons of other mammals. The two divergent clades are distributed sympatrically in some regions, but the overall geographic structure of the variation is significant across the range of this species. These new molecular data are inconsistent with current taxonomic definitions of species within the Southern Hemisphere fur seals and argue for reevaluation of these "species" definitions. For management purposes, the definition of evolutionarily significant units (Ryder 1986) and genetic management units (Moritz 1994) in relation to these species may also be evaluated in light of this molecular genetic information.

Animals↗

PubMed2005

Mitochondrial DNA analysis of the bark beetle predator Thanasimus dubius F. (Coleoptera: Cleridae) reveals regional genetic differentiation.

The checkered beetle, Thanasimus dubius F., is an important predator of scolytid bark beetles that attack conifers. Relatively few studies exist that have addressed the population genetics of predatory beetles, especially those with potential as biological control agents. This study was conducted to investigate the population genetics of T. dubius across a large part of its range in the eastern United States. A 464-base pair portion of the mitochondrial cytochrome c oxidase subunit I was sequenced for 85 individuals resulting in 60 haplotypes. Analysis of molecular variance was conducted on the resulting haplotypes for all populations and as a hierarchical analysis between populations defined as broad-scale northern and southern groups. Results indicate a significant overall Phi ST = 0.220 (P < 0.001) for all populations with the hierarchical analysis revealing that this significant Phi ST is due to structuring of the populations between northern and southern regions (Phi CT = 0.388, P < 0.009). The observed genetic structure is possibly due to the discontinuous distribution of pine trees, which act as hosts for the prey of T. dubius, which has occurred historically in the central region of the United States that has been covered by prairie.

Animals↗

PubMed2005

Signature of recent historical events in the European Y-chromosomal STR haplotype distribution.

Previous studies of human Y-chromosomal single-nucleotide polymorphisms (Y-SNPs) established a link between the extant Y-SNP haplogroup distribution and the prehistoric demography of Europe. By contrast, our analysis of seven rapidly evolving Y-chromosomal short tandem repeat loci (Y-STRs) in over 12,700 samples from 91 different locations in Europe reveals a signature of more recent historic events, not previously detected by other genetic markers. Cluster analysis based upon molecular variance yields two clearly identifiable sub-clusters of Western and Eastern European Y-STR haplotypes, and a diverse transition zone in central Europe, where haplotype spectra change more rapidly with longitude than with latitude. This and other observed patterns of Y-STR similarity may plausibly be related to particular historical incidents, including, for example, the expansion of the Franconian and Ottoman Empires. We conclude that Y-STRs may be capable of resolving male genealogies to an unparalleled degree and could therefore provide a useful means to study local population structure and recent demographic history.

Chromosomes, Human, Y↗

PubMed1999

No association between D2 dopamine receptor (DRD2) "A" system alleles, or DRD2 haplotypes, and posttraumatic stress disorder.

BACKGROUND: Association studies between marker alleles at the D2 dopamine receptor gene (DRD2) and various psychiatric illnesses have produced conflicting results. Reports of allelic associations were originally made with alcoholism, but were then extended to other psychiatric disorders, including posttraumatic stress disorder (PTSD). METHODS: We studied allele frequency of the DRD2 TaqI "A," "B," and "D" system markers in 52 European-American subjects with diagnoses of PTSD (based on structured interviews). RESULTS: Frequency of the A1 allele in this sample was .15, not significantly different from the .19 allele frequency seen in 87 control subjects. We were thus unable to replicate the previous reports of allelic association between the DRD2 TaqI "A1" allele and PTSD. There were also no significant differences in allele frequency for the "B" or "D" systems. We then computed three marker (TaqI "A," "B," and "D" system) haplotypes for the sample; DRD2 haplotype frequencies also did not differ between control subjects and subjects with PTSD. CONCLUSIONS: We conclude that DRD2 alleles are not associated with PTSD in this sample, and that genetic variation at the DRD2 locus is not likely to be an important contributor to risk for this disorder.

Adult↗

PubMed2004

Long-distance gene flow and cross-Andean dispersal of lowland rainforest bees (Apidae: Euglossini) revealed by comparative mitochondrial DNA phylogeography.

Euglossine bees (Apidae; Euglossini) exclusively pollinate hundreds of orchid species and comprise up to 25% of bee species richness in neotropical rainforests. As one of the first studies of comparative phylogeography in a neotropical insect group, we performed a mitochondrial DNA (mtDNA)-based analysis of 14 euglossine species represented by populations sampled across the Andes and/or across the Amazon basin. The mtDNA divergences within species were consistently low; across the 12 monophyletic species the mean intraspecific divergence among haplotypes was 0.9% (range of means, 0-1.9%). The cytochrome oxidase 1 (CO1) divergence among populations separated by the Andes (N = 11 species) averaged 1.1% (range 0.0-2.0%). The mtDNA CO1 data set displayed homogeneous rates of nucleotide substitution, permitting us to infer dispersal across the cordillera long after the final Andean uplift based on arthropod molecular clocks of 1.2-1.5% divergence per million years. Gene flow across the 3000-km breadth of the Amazon basin was inferred from identical cross-Amazon haplotypes found in five species. Although mtDNA haplotypes for 12 of the 14 euglossine species were monophyletic, a reticulate CO1 phylogeny was recovered in Euglossa cognata and E. mixta, suggesting large ancestral populations and recent speciation. Reference to closely related outgroups suggested recent speciation for the majority of species. Phylogeographical structure across a broad spatial scale is weaker in euglossine bees than in any neotropical group previously examined, and may derive from a combination of Quaternary speciation, population expansion and/or long-distance gene flow.

Animals↗

PubMed1985

Polymorphisms within the HLA-DRw6 haplotype. I. Restriction fragment length variation and its correlation with serology.

The Dw6/DRw6 complex, one of the MHC class II specificities that can be defined by cellular techniques and by serology, probably has one or more immunoregulatory functions. To obtain information on the molecular structure of the DRw6 region, we studied several DRw6 homozygous cell lines, of which three were of consanguineous origin. DNA-DNA hybridization comprised the use of seven restriction enzymes in combination with three DR beta cDNA probes. The obtained results were compared with similar analyses of an HLA homozygous cell panel, expressing DR1-w8 specificities. This comparison indicated that in DRw6 homozygous individuals the coding potential for DR beta chains resembles closely that of all other DR specificities, thus identifying DRw6 as a regular DR region. In addition, we found a restriction fragment length pattern unique for DRw6, indicating the possibility to type for DRw6 by DNA-DNA hybridization. Comparisons within the DRw6 cell panel revealed the occurrence of several HLA class II DNA subtypes. These subdivisions partly correlated with serologically obtained reaction patterns. No correlation, however, could be observed between the different DNA subtypes and cellular reaction patterns as obtained by MLC and T cell cytotoxicity.

Antigen-Antibody Reactions↗

PubMed2005

Population study of Y-chromosome STR haplotypes in Japanese from the Tokushima.

The Y-chromosome short tandem repeat (STR) systems including DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS385 and YCAII were investigated in 121 Japanese males (Tokushima area). Analysis of the nine loci permitted classification of the samples into 107 haplotypes, and the haplotype diversity was estimated to be 0.989. DYS385 showed the highest gene diversity (GD) value (GD=0.946), while DYS391 showed the lowest GD value (GD=0.27). Furthermore, in DYS392, we found a new mutant allele that added a T within the repeat region (a mutation in the repetitive region), and the allele was designated 13.1 according to the sequence structure. We also detected allele 20 in DYS392 as a new allele. In DYS385, a new allele 26 that has not been previously reported was observed.

Asian People↗

PubMed2004

Mitochondrial DNA differentiation between two forms of trout Salmo letnica, endemic to the Balkan Lake Ohrid, reflects their reproductive isolation.

Mitochondrial haplotype diversity in sympatric populations of Ohrid trout, Salmo letnica was investigated by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the mtDNA control region and ND1, ND3/4, ND5/6 segments. A 310 bp fragment at the 5' end, and a 340-572 bp fragment at the 3' end of the control region were sequenced from representatives of the populations studied. Based on pairwise comparison of the sequences, five new haplotypes were identified plus one identical with the brown trout Andalusian haplotype from the southern Iberian Peninsula. The combination of both RFLP and sequence data sets yielded a total of 10 composite haplotypes. A high degree of genetic subdivision between S. letnica typicus and S. letnica aestivalis populations was observed. The notion of a sympatric origin for the two morphs is discussed. Length variation of the mtDNA control region due to the presence of an 82 bp unit, tandemly repeated one to four times, in the region between the conserved sequence block-3 (CSB-3) and the gene for phenylalanine tRNA is reported. Further, we demonstrate that a single duplication of the approximately 82 bp repeat unit is a common element of the salmonid mitochondrial control region. The unique genetic structure of Ohrid trout represents a highly valuable genetic resource that deserves appropriate management and conservation.

Animals↗

PubMed1996

Prenatal diagnosis for recessive dystrophic epidermolysis bullosa in 10 families by mutation and haplotype analysis in the type VII collagen gene (COL7A1).

BACKGROUND: Epidermolysis bullosa (EB) is a group of heritable diseases that manifest as blistering and erosions of the skin and mucous membranes. In the dystrophic forms of EB (DEB), the diagnostic hallmark is abnormalities in the anchoring fibrils, attachment structures beneath the cutaneous basement membrane zone. The major component of anchoring fibrils is type VII collagen, and DEB has been linked to the type VII collagen gene (COL7A1) at 3p21, with no evidence for locus heterogeneity. Due to life-threatening complications and significant long-term morbidity associated with the severe, mutilating form of recessive dystrophic EB (RDEB), there has been a demand for prenatal diagnosis from families with affected offspring. MATERIALS AND METHODS: Intragenic polymorphisms in COL7A1 and flanking microsatellite markers on chromosome 3p21, as well as detection of pathogenetic mutations in families, were used to perform PCR-based prenatal diagnosis from DNA obtained by chorionic villus sampling at 10-15 weeks or amniocentesis at 12-15 weeks gestation in 10 families at risk for recurrence of RDEB. RESULTS: In nine cases, the fetus was predicted to be normal or a clinically unaffected carrier of a mutation in one allele. These predictions have been validated in nine cases by the birth of a healthy child. In one case, an affected fetus was predicted, and the diagnosis was confirmed by fetal skin biopsy. CONCLUSIONS: DNA-based prenatal diagnosis of RDEB offers an early, expedient method of testing which will largely replace the previously available invasive fetal skin biopsy at 18-20 weeks gestation.

Amniocentesis↗

PubMed2005

Fast and cheap genome wide haplotype construction via optical mapping.

We describe an efficient algorithm to construct genome wide haplotype restriction maps of an individual by aligning single molecule DNA fragments collected with Optical Mapping technology. Using this algorithm and small amount of genomic material, we can construct the parental haplotypes for each diploid chromosome for any individual. Since such haplotype maps reveal the polymorphisms due to single nucleotide differences (SNPs) and small insertions and deletions (RFLPs), they are useful in association studies, studies involving genomic instabilities in cancer, and genetics, and yet incur relatively low cost and provide high throughput. If the underlying problem is formulated as a combinatorial optimization problem, it can be shown to be NP-complete (a special case of K-population problem). But by effectively exploiting the structure of the underlying error processes and using a novel analog of the Baum-Welch algorithm for HMM models, we devise a probabilistic algorithm with a time complexity that is linear in the number of markers for an epsilon-approximate solution. The algorithms were tested by constructing the first genome wide haplotype restriction map of the microbe T. pseudoana, as well as constructing a haplotype restriction map of a 120 Mb region of Human chromosome 4. The frequency of false positives and false negatives was estimated using simulated data. The empirical results were found very promising.

Algorithms↗

PubMed2004

[Population genetic structure of Pelophylax nigromaculata in Chinese mainland based on mtDNA control region sequences].

Molecular genetic data were used to investigate population genetic structure and differentiation of Pelophylax nigromaculata (Anura: Ranidae). Frogs were collected from 12 localities across Chinese mainland. Sample sizes of up to 10 frogs per population were assayed for mitochondrial control region sequence variation. The aligned 685 bp of the 5'CR include 111 variable sites. Sixty-seven haplotypes were defined. Most of the haplotypes are unique to local populations, only 7 of the 67 are shared among a few local populations. The overall species haplotype diversity is quite high (h = 0.98 +/- 0.005), and the nucleotide diversity is also high (pi = 0.0303 +/- 0.0029). This is corresponding to huge population size and extensive distribution of Pelophylax nigromaculata throughout Palaearctic and Oriental Regions. Phylogenetic tree of mtDNA control region haplotypes based on maximum parsimony algorithm and reconstructed phylogenetic relationships among the local populations based on neighbor joining algorithm all suggest that the haplotypes of Jiling and Liaoning populations in northeastern China have a sister relationship with 10 local populations in northern, central, southern and southwestern China. The analysis of molecular variance (AMOVA), the pairwise FST values and nucleotide divergence all support significant population subdivision between the Jilin-Liaoning group and multi-population group. The most possible cause of the significant genetic subdivision between the two groups might be referred to the effect of Quaternary glaciation. The possible reasons for the lack of obvious geographic structure on the whole in the multi-population group and the genetic differentiation in some local populations of the multi-population group were also discussed.

Animals↗