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PubMed2006

Population structure and gene flow among wild populations of the black muntjac (Muntiacus crinifrons) based on mitochondrial DNA control region sequences.

The black muntjac (Muntiacus crinifrons) is a rare species endemic to China and its current distribution is confined to partial mountain ranges in eastern China. To assess the population structure and gene flow among the extant populations, we sequenced a portion of the mitochondrial control region (424 bp) for 47 samples collected from its current three large populations (Huangshan, Tiammushan and Suichang). A total of 18 unique haplotypes were defined based on 22 polymorphic sites. Of these haplotypes, 15 ones were population-specific and only one haplotype was shared among the three populations. Significant genetic differentiation was detected between Suichang and Huangshan populations (ø(ST)=0.1677, P<0.001) or between Suichang and Tianmushan populations (ø(ST)=0.2002, P<0.001), indicating that the Suichang population may be spatially structured from other two populations along matriline. The Mantel test revealed that this significant differentiation was not driven by geographic distance (P=0.14), implying that genetic divergence of Suichang population might result from recent human disturbances. Phylogenetic analyses suggested the mitochondrial control region haplotypes were split into two well divergent clades (Clade I and Clade II). Interestingly, the two distinct haplotype clades were found to coexist in Suichang area. The nested clade analysis revealed a significant phylogeographic structure among the black muntjac populations (total cladogram: chi2=18.68; P<0.001), which was inferred to result from past fragmentation followed by range expansion. The population expansion was supported by the analysis of mismatch distribution and the tests of neutrality. Therefore, we suggest that the coexistence of distinct haplotypes in Suichang population was induced by historical population expansion after fragmentation and that the current genetic differentiation should be attributed to the reduction of female-mediated gene flow due to recent habitat fragmentation and subsequent loss.

Animals↗

PubMed2003

Genomic organization of the S core region and the S flanking regions of a class-II S haplotype in Brassica rapa.

The nucleotide sequence of an 86.4-kb region that includes the SP11, SRK, and SLG genes of Brassica rapa S-60 (a class-II S haplotype) was determined. In the sequenced region, 13 putative genes were found besides SP11-60, SRK-60, and SLG-60. Five of these sequences were isolated as cDNAs, five were homologues of known genes, cDNAs, or ORFs, and three are hypothetical ORFs. Based on their nucleotide sequences, however, some of them are thought to be non-functional. Two regions of colinearity between the class-II S-60 and Brassica class-I S haplotypes were identified, i.e., S flanking region 1 which shows partial colinearity of non-genic sequences and S flanking region 2 which shows a high level of colinearity. The observed colinearity made it possible to compare the order of SP-11, SRK, and SLG genes in the S locus between the five sequenced S haplotypes. It emerged that the order of SRK and SLG in class-II S-60 is the reverse of that in the four class-I S haplotypes reported so far, and the order of SP11, SRK and SLG is the opposite of that in the class-I haplotype S-910. The possible gene designated as SAN1 (S locus Anther-expressed Non-coding RNA like-1), which is located in the region between SP11-60 and SRK-60, has features reminiscent of genes for non-coding RNAs (ncRNAs), but no homologous sequences were found in the databases. This sequence is transcribed in anthers but not in stigmas or leaves. These features of the genomic structure of S-60 are discussed with special reference to the characteristics of class-II S haplotypes.

Amino Acid Sequence↗

PubMed2003

Molecular evolution of a plastid tandem repeat locus in an orchid lineage.

The molecular evolution of a chloroplast minisatellite locus in the Anacamptis palustris (Orchidaceae) lineage and haplotype variation in two Italian A. palustris populations were investigated. A phylogenetic analyses of the chloroplast tRNA(LEU) intron, where the minisatellite locus is located, revealed that a deletion in the ancestor of the A. palustris lineage led to the formation of two noncontiguous, complementary sequence motifs. We propose a model to explain the initial formation of the minisatellite repeat motif, starting with the two noncontiguous, complementary sequence motifs. A survey of minisatellite variation in four species of the A. palustris lineage revealed several haplotypes that differed not only in repeat number, but also in repeat organization. A haplotype network suggests that three different minisatellite loci evolved independently at the same position in the tRNA(LEU) intron. A secondary structure model revealed that the A. palustris minisatellite repeat forms a stem region of the tRNA(LEU) intron, which allows its notable expansion without negatively affecting splicing. Minisatellite variation was high in the two examined A. palustris populations where 20 haplotypes were detected, whereas no length variation was detected in a neighboring poly (A) microsatellite locus. We estimated a chloroplast minisatellite mutation rate of 3.2 x 10(-3) mutations per generation. Southern blot analyses did not find evidence for chloroplast heteroplasmy. Based on the analysis of the largest known, extant A. palustris population, a stepwise mutation model (SMM) was inferred.

Evolution, Molecular↗

PubMed1982

Subtyping of phosphoglucomutase locus 1 (PGM1) polymorphism in some populations of Rwanda: description of variant phenotypes, "haplotype" frequencies, and linkage disequilibrium data.

Some populations of Rwanda (South Twa Pygmies, Hutu, and Tutsi) have been analyzed by acid starch gel electrophoresis for the subtyping of PGM1 polymorphism. The new polymorphic third PGM11 allele, the PGM1(1Twa), which we recently detected in Twa Pygmies from North Rwanda, has not been found in this survey, whereas the rare PGM1(6) allele attains subpolymorphic frequencies in all groups. Comparison between the various populations of Rwanda shows that they differ significantly from each other with the exception of South Twa Pygmies and Tutsi. A relatively low frequency (9.6%) of the PGM1(2S) allele appears to be typical of North Twa Pygmies; a low frequency of PGM1(2F) (1.2%-3.6%) has been found in all these groups but not in the Hutu (6.4%); and a particularly high incidence of the PGM1(1F) allele (the highest so far reported) has been observed in the South Twa Pygmies (20%) and in the Tutsi (18%). The PGM1(1Twa) and PGM1(6) enzymes, which in acid starch gel are not distinguishable, can be clearly differentiated by isoelectric focusing. In addition, the same technique has shown that the rare PGM1(7) allele observed in one Hutu is different from that found at polymorphic frequency in the Japanese and from a rare PGM1(7) allele found in Germany. On the very likely hypothesis that the PGM1(1S), PGM1(1F), PGM1(2S), and PGM1(2F) result from variations at two different polymorphic sites, 1/2 and F/S, within the PGM1 structural gene, all the available population data have been analyzed to investigate whether preferential combinations (haplotypes) were identifiable. Whereas Caucasians show a prevalence of 2F and 1S combination with an 8.02% mean value of linkage disequilibrium expressed as % Dmax, from the very few and scattered African data, it is impossible to draw any inference at present.

Alleles↗

PubMed1990

Organization of a functional chicken class II B gene.

Five class II (B-L) B genes are encoded in the major histocompatibility complex (MHC) of chickens of the B12 haplotype. We report here the nucleotide sequence of one of these genes, B-LBII, as well as the primary structure of a corresponding cDNA. The organization of B-LBII, its 5' flanking region including the promotor region, and the amino acid sequence of its product are compared to mammalian class II B genes and to the previously described B-LBIII gene, which probably is a pseudogene since no B-LBIII transcript could be identified. The 5' flanking region of B-LBII exhibits homologs of transcription-controlling sequence motifs, namely S, X, X2, and Y boxes, of class II A and B genes of rodents and man. However, the promotor region of B-LBIII lacks an equivalent of the S box, displays two nucleic acid substitutions in the core sequence of the Y box, and exhibits a 16 base pair (bp) deletion upstream of the site of initiation of transcription. Therefore, an aberrant promotor region is likely to account for the pseudogene-like nature of B-LBIII, which displays open-reading frames in all exons. The data obtained with the functional B-LBII gene are in line with our previous interpretation that both genomic organization and tertiary structure of class II beta molecules are remarkably conserved between birds and mammals.

Amino Acid Sequence↗

PubMed2003

Association of positional and functional candidate genes FGF1, FBN2, and LOX on 5q31 with intracranial aneurysm.

We previously performed a genome-wide linkage study of intracranial aneurysm (IA) and found positive evidence of linkage at chromosomes 5q22-31, 7q11, and 14q22. In the present study, we focus on 5q31, where three candidate genes, fibroblast growth factor 1 (FGF1), fibrillin 2 (FBN2), and lysyl oxidase gene ( LOX) lie, and evaluate associations with IA. Genomic DNAs were obtained from 172 IA patients and 192 controls. Association analysis was performed with ten, five, and four single-nucleotide polymorphisms (SNPs) identified in FGF1, FBN2, and LOX, respectively. A difference in allelic frequency was observed for only the SNP at intron 4 in FGF1 (chi(2)=4.44, df=1, P=0.035). Although a haplotype association was observed with the combination of ten SNPs in FGF1 (chi(2)=16.04, df=1, P=0.00006), significant haplotype associations were not observed when haplotypes were constructed with the three, two, and four SNPs in FGF1 according to the linkage disequilibrium structure. No associations of FBN2 and LOX with IA were detected in the present study.

Aged↗

PubMedDate not supplied

Spatial heterogeneity of mitochondrial DNA and allozymes among populations of white-tailed deer and mule deer.

A white-tailed deer (Odocoileus virginianus) population in northeastern Minnesota and a mule deer (O. hemionus) population in the Bridger Mountains Montana, have previously been shown to be spatially subdivided into contiguous subpopulations. We assessed the degree of genetic differentiation among subpopulations and tested the hypothesis that differentiation will be greater for mitochondrial DNA (mtDNA) than for nuclear-encoded allozymes. Differentiation of the white-tailed deer subpopulations was significant for two allozyme loci but not for mtDNA, and the overall degree of differentiation was low. Gene flow, recent founding of the subpopulations, and polygamous breeding structure may all have contributed to this pattern. Greater differentiation was evident among disjunct populations than between the contiguous subpopulations of white-tailed deer. The contiguous mule deer subpopulations were significantly differentiated for mtDNA and one allozyme locus. Differentiation was greater for mtDNA than for allozymes. These results are consistent with demographic data that indicate mule deer males disperse more than do females. Disjunct mule deer populations may be similar or dramatically different in mtDNA haplotype frequencies that do not necessarily vary with geographic distance. Current and historical gene flow and breeding structure will influence population genetic patterns.

Animals↗

PubMed1996

Phylogeography of an asexual marine clam complex, Lasaea, in the northeastern Pacific based on cytochrome oxidase III sequence variation.

Northeastern Pacific populations of the intertidal marine clam Lasaea are exclusively composed of polyploid asexual clones that lack pelagic larval development. We investigated the phylogeographic structure of this clonal assemblage by assaying genetic divergence in 4 populations along 2000 km of the west coast of North America. In each population a 462-nt portion of the mitochondrial Cytochrome Oxidase III gene was amplified and sequenced for 30 individuals. A total of 21 haplotypes were detected and phylogenetic analyses resolved this variation into 5 main branches that differ in sequence composition by 8.9-14.5%. Two of the branches each encompass a single haplotype, the other 3 terminate in clades containing 3-11 lineages and within clade divergence ranges from 0.4 to 2.3%. Obvious geographic structuring was evident in that 19 of the 21 lineages were restricted in their distributions to single populations and 3 of the main phylogenetic branches were limited to specific marine biogeographic provinces. Two of the clades were encountered in multiple, geographically distant populations; however, the absence of shared haplotypes indicates that long distance gene flow is rare among these direct-developing populations. Northeastern Pacific Lasaea clones form a robust monophyletic grouping relative to other studied populations of the cosmopolitan genus. We estimate divergence times among northeastern Pacific clones to range from 3 to 6 myr. If the latest common ancestor of these exclusively asexual, genetically diverse, regionally monophyletic Lasaea lineages was also asexual, this represents a minimal age estimate for asexuality in the genus. The most plausible alternate hypothesis requires that at least 5 northeastern Pacific sexual parental species have recently become extinct.

Animals↗

PubMedDate not supplied

The major histocompatibility complex: the value of extended haplotypes in the analysis of associated immune diseases and disorders.

Major histocompatibility complex antigens are critical to an animal's immune response. In most animals, the extreme polymorphism of MHC molecules complicates studies of the role of this complex in the immune response. In mice, however, MHC haplotype-homozygous inbred strains have been developed which are invaluable in the study of the immune system and the search for immune response genes. The human MHC bears many similarities to its murine equivalent with regard to antigen structure and polymorphism; furthermore, a number of combinations of specific MHC alleles between HLA-B and HLA-DR/DQ (extended haplotypes) are found in people more commonly than predicted by individual allele frequencies. Over 30 percent of Caucasian haplotypes are extended haplotypes, and over 55 percent of individuals have at least one extended haplotype. Examples of the same extended haplotype, even in unrelated individuals, should either all have or lack any gene within the MHC region. The value of considering extended haplotypes in searching for associations between the MHC and diseases, or immune response, is shown in three examples: congenital adrenal hyperplasia, hepatitis B immunization, and transfusion-associated graft-versus-host disease.

Animals↗

PubMed1987

A deductive method of haplotype analysis in pedigrees.

Derivation of haplotypes from pedigree data by means of likelihood techniques requires large computational resources and is thus highly limited in terms of the complexity of problems that can be analyzed. The present paper presents 20 rules of logic that are both necessary and sufficient for deriving haplotypes by means of nonstatistical techniques. As a result, automated haplotype analysis that uses these rules is fast and efficient, requiring computer memory that increases only linearly (rather than exponentially) with family size and the number of factors under analysis. Some error analysis is also possible. The rules are completely general with regard to any system of completely linked, discrete genetic markers that are autosomally inherited. There are no limitations on pedigree structure or the amount of missing data, although the existence of incomplete data usually reduces the fraction of haplotypes that can be completely determined.

Genetic Markers↗

PubMed1992

Amino acid substitutions at position 38 of the DR beta polypeptide confer susceptibility to and protection from primary sclerosing cholangitis.

Previous studies based on serological HLA phenotyping have implicated genes in the HLA class II region in susceptibility to and protection from primary sclerosing cholangitis. In a recent report, the HLA DRw52a antigen was present in all 29 patients who had been referred for liver transplantation. In this study, HLA DRB, DQA and DQB genotypes were studied using gene amplification and sequence-specific oligonucleotide probing in 71 patients with primary sclerosing cholangitis and 68 healthy controls to determine the frequency among the patients of the DRB3*0101 allele that encodes DRw52a and whether other class II alleles are involved in susceptibility or protection. DRB3*0101 was the most strongly associated allele, being present in 55% of the patients and 22% of the controls. Survival among the DRB3*0101-positive patients was reduced compared with the DRB3*0101-negative patients. Both DRB3*0101 and DRB5*0101, a possible second DRB susceptibility allele, encode a leucine residue at position 38 of the DR beta molecule. The DRB4*0101 allele, which encodes DRw53 and may be protective, encodes an alanine residue at this position. Susceptibility to and protection from primary sclerosing cholangitis may result from amino acid substitutions at position 38 of the DR beta molecule because maximum relative risk was conferred by two leucine-38-containing DR beta molecules, whereas minimum relative risk was conferred by two alanine-38-containing molecules.

Alleles↗

PubMed1992

Definition of microsatellite size variants for Tnfa and Hsp70 in autoimmune and nonautoimmune mouse strains.

We have cloned and sequenced the upstream regulatory region of tumor necrosis factor alpha (Tnfa) gene in 12 different mouse strains and identified an allelic polymorphism in the upstream regulatory region of the mouse Tnfa gene. The TNF allele found in the NZW strain is distinct from those of all other H-2 haplotypes, supporting our previous suggestion that this allele may be associated with a regulatory or structural defect. In addition, simple tandem repeat sequences (microsatellites) within the promoter region of the Tnfa gene and the 3' untranslated region of one of the members of the HSP70 family (Hsp68c clone) were utilized as genetic markers. Ten TNF size variants and twelve HSP70 variants were identified in over forty mouse strains. Using these markers in a set of congenic mice, we mapped this member of the HSP70 family to the central portion of the H-2 complex, centromeric to the Tnfa gene. The NOD and NZW strains carry unique HSP70 alleles based on the variability in the length of this marker. These findings raise the possibility that this protein may play a role in the association of the major histocompatibility complex with these autoimmune diseases.

Animals↗

PubMed2000

An unexpected recurrence of Angelman syndrome suggestive of maternal germ-line mosaicism of del(15)(q11q13) in a Finnish family.

Angelman syndrome is a neuro-developmental disorder caused by genetic abnormalities affecting the maternal gene expression in the chromosome region 15q11-q13. In a study group of 45 Finnish Angelman patients, a recurrence of a del(15)(q11q13) was detected in one family. The mother's chromosomes 15 were structurally normal, whereas the patients and their unaffected brother shared an identical maternally derived haplotype outside the deletion region. These findings are suggestive of maternal germ-line mosaicism of del(15)(q11q13).

Adolescent↗

PubMed2002

Mannan-binding lectin: clinical significance and applications.

Mannan-binding lectin (MBL) is a collectin (protein with both collagen-like and C-type lectin domains) synthesised in the liver and secreted into the bloodstream. Its plasma concentration is for the most part genetically determined by a series of allelic dimorphisms located both in the structural gene and in the promoter region. Genotypes made up of combinations of seven haplotypes are mainly responsible for a 1000-fold concentration variation found in human beings. MBL is a pattern recognition molecule able to bind repeating sugar arrays on many microbial surfaces, and can activate complement via associated serine proteases. A poorly defined proportion (roughly 10%) of the population with the lowest MBL concentrations is thought to be MBL insufficient and more vulnerable to a variety of infectious and noninfectious disorders. The evidence that MBL makes an important contribution to innate immunity, by increasing susceptibility to disease and/or affecting the course of disease, is discussed in detail. Preliminary results from MBL replacement therapy are encouraging, and extension of this approach to large-scale randomised clinical trials would provide solid evidence concerning the physiological significance of this protein.

Alleles↗

PubMed1997

Human diversity in killer cell inhibitory receptor genes.

The presence and expression of killer inhibitory receptor (KIR) and CD94:NKG2 genes from 68 donors were analyzed using molecular typing techniques. The genes encoding CD94:NKG2 receptors were present in each person, but KIR gene possession varied. Most individuals expressed inhibitory KIR for the three well-defined HLA-B and -C ligands, but noninhibitory KIR genes were more variable. Twenty different KIR phenotypes were defined. Two groups of KIR haplotypes were distinguished and occurred at relatively even frequency. Group A KIR haplotypes consist of six genes: the main inhibitory KIR, one noninhibitory KIR, and a structurally divergent KIR. Allelic polymorphism within five KIR genes was detected. Group B comprises more noninhibitory KIR genes and contains at least one additional gene not represented in group A. The KIR locus therefore appears to be polygenic and polymorphic within the human population.

Antigens, CD↗

PubMed2003

The clonal structure of Quercus geminata revealed by conserved microsatellite loci.

The scrub oak communities of the southeastern USA may have existed at their present locations for thousands of years. These oaks form suckers, and excavations of root systems suggest that clones may occupy very large areas. Resolution of the clonal nature of scrub oaks is important both to manage the tracts of this ecosystem that remain, and in conducting long-term ecological studies, where the study area must substantially exceed the area occupied by any single clone. Microsatellites were used to determine the genetic diversity of a dominant oak species within a 2-ha long-term experimental site on Merritt Island at the Kennedy Space Center. This area contains a long-term study of the effects of elevated CO2 on the ecosystem. Conservation of seven microsatellite loci, previously identified in the sessile oak, Quercus petraea, was tested in two Florida scrub oak species, Q. geminata and Q. myrtifolia. Sequence analysis revealed that all seven microsatellite loci were conserved in Q. geminata and five loci were conserved in Q. myrtifolia. Six microsatellite loci were polymorphic in Q. geminata and these were subsequently used to investigate the clonal structure of the Q. geminata population. Twenty-one unique combinations of microsatellites, or haplotypes, occurred only once, whereas the remaining 26 individuals belonged to a total of seven different haplotypes. Trees with identical haplotypes were in close proximity, supporting the interpretation that they were clones. The results showed that there is significant genetic diversity within the 2-ha experimental site. Microsatellites provided a powerful and noninvasive tool for distinguishing individual genotypes and determining an adequate area for long-term ecosystem studies.

Base Sequence↗

PubMed1975

The HL-A gene structure of Twareg populations. II. The Kel Dinig.

The HL-A groups of 138 Kel Diniq Twaregs were determined by the platelet complement fixation microtechnique. Their HL-A characteristics, compared to those of Caucasoid populations, are: decrease in HL-A2, 9, W17 and W15; increase in W28, W32, HL-A7, W5, W10 and second locus blank; absence of Da25 (W30 plus W31), HL-A13, W15, W18, W27. This genetic structure is in accordance with the isolated condition of this population. The most frequent haplotypes are W28,HL-A7, common to both the Kel Diniq and the Kel Kummer Twaregs previously studied; W32,W10 and HL-A3, HL-A5, Kel Diniq only. These two populations are both isolates, with a common origin the seventeenth century, but separated as from that date. Genealogical studies have enabled the haplotype W28,HL-A7 to be attributed to the two brothers who founded the populations in the seventeenth century. A comparison of these two populations constitutes a model for the study of genetic drift and the founder effect.

Complement Fixation Tests↗

PubMed1984

Approximate linkage equilibrium between two polymorphic sites within the gene for human complement component 3.

Haplotypes have been determined for alleles at two separate polymorphic sites within the human structural gene for complement component 3, identified as a protein polymorphism and as a restriction fragment length polymorphism by hybridization using a cloned gene probe. No evidence was found for appreciable disequilibrium between alleles at these sites, despite their very close linkage.

Alleles↗