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Genetic drift and anthropometric variation in Ireland.

The effect of genetic drift on the genetic structure of seven Irish populations was investigated using anthropometric data collected during the 1890s on 259 adult males. These populations ranged in size from 769 to 3757, were relatively stable over time, and were located within 119 km of one another. Two populations are known to have experienced considerable English admixture. Data on ten anthropometric variables (three body measures and seven craniofacial measures) were adjusted for age and used to compute a relationship (R) matrix. The R matrix was converted into a distance measure and compared with a potential genetic drift distance measure, defined as (1/Ni + 1/Nj), where Ni and Nj are the effective population sizes of groups i and j (derivation of this formula is presented). Distances were rank-transformed, and the correlation between their pairwise elements was computed using matrix permutation methods to assess significance. Under the hypothesis that drift affects anthropometric variation, these correlations are expected to be positive. The correlation between anthropometric distance and potential genetic drift distance is 0.123, which is not significantly different from 0 (P = 0.368). When a multiple regression model is used to adjust for geographic distance and English admixture, the partial correlation (0.369) is significant (p = 0.021). As part of further analysis of the genetic structure of these populations, the same analyses were repeated using a distance matrix derived from surname frequencies. The correlation of surname distance and potential genetic drift distance is 0.164, which is not significant (p = 0.264). When the multiple regression model is applied, the correlation is 0.401, which is borderline significant (p = 0.055). These results show the influence of genetic drift, local migration, and admixture on Irish population structure.

Adolescent↗

Evidence for long isolation among populations of a pacific cycad: genetic diversity and differentiation in Cycas seemannii A.Br. (Cycadaceae).

The genetic structure of Cycas seemannii A.Br. (Cycadaceae), sampled throughout its range in Vanuatu, New Caledonia, Fiji, and Tonga, was studied using starch-gel electrophoresis. Twenty enzyme loci in 13 enzyme systems were examined. Low genetic diversity within populations (A = 1.2, P = 21.3, Ho = 0.047, and He = 0.057) and a high degree of differentiation among populations (F(ST) = 0.594) were found. This, together with low gene flow estimates, suggests genetic drift by isolation to have been most critical to the current genetic structure of the species. Inbreeding may occur to some extent (F(IS) = 0.165). The decline in abundance of C. seemannii, coupled with the low level of genetic diversity, suggest that conservation strategies are urgently needed.

Analysis of Variance↗

Structural and genetic characterization of Shigella boydii type 17 O antigen and confirmation of two new genes involved in the synthesis of glucolactilic acid.

Shigella strains are human pathogens and normally identified based on their O antigens. The chemical structure and gene cluster of Shigella boydii type 17 O antigen were studied. As judged by sugar and methylation analyses along with NMR spectroscopy data, the O antigen of S. boydii type 17 has a linear trisaccharide O unit, which consists of two residues of N-acetylgalactosamine (GalNAc) and a 4-O-[(R)-1-carboxyethyl]-d-glucose (glucolactilic acid). The O antigen gene cluster of S. boydii type 17 was sequenced and genes encoding UDP-N-acetylglucosamine C4 epimerase for GalNAc synthesis, O unit flippase, O antigen polymerase, and glycosyltransferases were putatively identified based on sequence similarities and the presence of conserved motifs. Two genes, whose functions could not be clearly indicated by homology search, were confirmed to be involved in the synthesis of glucolactilic acid by mutation and structural verification of the O antigens from the mutants. To our knowledge, this is the first time that genes involved in the synthesis of glucolactilic acid have been reported. Two genes specific to S. boydii type 17 were also identified.

Amino Acid Motifs↗

Geographic patterns of genetic differentiation within the restricted range of the endangered Stephens' kangaroo rat Dipodomys stephensi.

Using mtDNA variation in the kangaroo rat Dipodomys stephensi, we found no support for the hypothesis that a species with an historically restricted range will exhibit low levels of genetic polymorphism and little genetic structure. Dipodomys stephensi has long been restricted to a few interior coastal valleys in southern California encompassing an area of approximately 70 x 40 km; however, we found high levels of genetic variation over much of its range and significant genetic structure both within and between regions. We also found evidence for a recent range expansion. Dipodomys stephensi is a federally endangered species that is separated from D. panamintinus, its presumed sister taxon, by a mountain range to the north. We assessed genetic variation by sequencing 645 bases of the mitochondrial d-loop from 61 individuals sampled from 16 locations across the species range and rooted their relationship using two D. panamintinus individuals. Despite its limited geographic range, the level of mtDNA variation in D. stephensi is comparable to that of other rodents, including that of the more widely distributed D. panamintinus. This variation revealed significant regional differentiation. The northern, central, and southern regions of the range differ in both the level and the distribution of genetic variation. Phylogenetic analysis revealed that the center of the range contains the most diversity of lineages, including the most basal. In this region and in the north, most haplotypes were found at only a single location (25/29), or at a pair of nearby locations (3/29). In addition, related haplotypes clustered geographically. These results are consistent with long-term demographic stability characterized by limited dispersal and high local effective population size. Further support for this conclusion is the finding of unique diversity in two northern peripheral populations, Norco and Potrero Creek (PC). However, in sharp contrast, one haplotype (CC) was found at five of 11 central and northern locations and comprised 18% of individuals sampled. The atypical distribution of the CC haplotype reflected a pattern seen more strongly in the southern region. Here the CC haplotype comprised 69% of the sample and was found at all five sampling locations. Consequently, the southern region had very low genetic variability. We propose that this dominance of CC was probably due to a local population bottleneck that occurred during a recent range expansion into the southern region.

Animals↗

Historical diversification of migration patterns in a passerine bird.

Migratory strategies of birds require complex orientation mechanisms, morphological adaptations, and life-history adjustments. From an evolutionary perspective, it is important to know how fast this complex combination of traits can evolve. We analyzed mitochondrial control-region DNA sequences in 241 blackcaps (Sylvia atricapilla) from 12 populations with different migratory behaviors. The sample included sedentary populations in Europe and Atlantic archipelagos and migratory populations with different distances of migration, from regional to intercontinental migrations, and different heading directions (due to a migratory divide in central Europe). There was no genetic structure between migratory and sedentary populations, or among populations from different biogeographic areas (Atlantic islands, the Iberian Peninsula, or the continent), however we found evidence of a genetic structure when comparing populations located on either side of the migratory divide. These findings support an independent evolution of highly divergent migratory strategies in blackcaps, occurring after a postglacial colonization of the continent along western and eastern routes. Accordingly, mismatch-distribution analyses suggested an expansion of blackcaps from a very small population size, and time estimates dated such an expansion during the last postglacial period. However, the populations in Gibraltar, located in a putative Mediterranean refuge, appeared to be independent of these processes, showing evidence of restricted gene flow with other populations and demonstrating insignificant historical changes in effective population size. Our results show that the interruption of gene flow between migratory and sedentary populations is not necessary for the maintenance of such a polymorphism, and that even the most divergent migratory strategies of a bird species are susceptible to evolution in response to historical environmental changes.

Animal Migration↗

High nuclear genetic diversity, high levels of outcrossing and low differentiation among remnant populations of Quercus petraea at the margin of its range in Ireland.

BACKGROUND AND AIMS: Quercus petraea colonized Ireland after the last glaciation from refugia on mainland Europe. Deforestation, however, beginning in Neolithic times, has resulted in small, scattered forest fragments, now covering less than 12,000 ha. METHODS: Plastid (three fragments) and microsatellite variation (13 loci) were characterized in seven Irish populations sampled along a north-south gradient. Using Bayesian approaches and Wright's F-statistics, the effects of colonization and fragmentation on the genetic structure and mating patterns of extant oak populations were investigated. KEY RESULTS: All populations possessed cytotypes common to the Iberian Peninsula. Despite the distance from the refugial core and the extensive deforestation in Ireland, nuclear genetic variation was high and comparable to mainland Europe. Low population differentiation was observed within Ireland and populations showed no evidence for isolation by distance. As expected of a marker with an effective population size of one-quarter relative to the nuclear genome, plastid variation indicated higher differentiation. Individual inbreeding coefficients indicated high levels of outcrossing. CONCLUSIONS: Consistent with a large effective population size in the historical migrant gene pool and/or with high gene flow among populations, high within-population diversity and low population differentiation was observed within Ireland. It is proposed that native Q. petraea populations in Ireland share a common phylogeographic history and that the present genetic structure does not reflect founder effects.

Gene Frequency↗

Phylogeography of a game species: the red-crested pochard (Netta rufina) and consequences for its management.

Western European populations of red-crested pochard (Netta rufina) are characterized by low size and high fragmentation, which accentuate their sensitivity to hunting. Uncertainties regarding the demographic trends of these populations highlight the need for pertinent hunting regulations. This requires identification of the limits of the populations under exploitation, i.e. delimiting a management unit. We used the left domain of the mitochondrial control region and seven nuclear loci (four microsatellites and three introns) to assess the level of genetic structure and demographic independence between the fragmented Western European and the large Central Asian populations. The second objective was to investigate the colonization history of the Western European populations. This study demonstrated that the Western European populations of red-crested pochard constitute a separate demographic conservation unit relative to the Asian population as a result of very low female dispersal (mitochondrial DNA: PhiST = 0.152). A morphometric analysis further suggested that Central Asian and Western European specimens of both sexes originate from different pools of individuals. Male dispersal seems higher than female dispersal, as suggested by the lack of clear genetic structure for the nuclear markers at this continental scale. Genetic data, in conjunction with historical demographic data, indicate that the current Western European populations probably originate from a recent colonization from Central Asia. As numbers of red-crested pochards in Western Europe cannot be efficiently supplemented by immigration from the larger Asian populations, a management plan regulating the harvest in Western Europe is required.

Animals↗

Molecular characterisation of Haemophilus influenzae type a and untypeable strains isolated simultaneously from cerebrospinal fluid and blood: novel use of quantitative real-time PCR based on the cap copy number to determine virulence.

This study investigated the genetic structure of the cap region of an isolate of Haemophilus influenzae serotype a (Hia) from the cerebrospinal fluid (CSF) of a child with meningitis. In addition, the genetic structure of the cap region of a non-serotypeable H. influenzae isolate, obtained simultaneously from the blood of the same patient, was determined. According to restriction fragment length polymorphism analysis, the CSF and blood isolates were identical, with the exception of a single band shift of c. 35 kb. PCR analyses suggested that the CSF isolate possessed the IS1016-bexA gene and cap region II, whereas the blood isolate only had the IS1016 element. Furthermore, Southern analysis of DNA from both isolates showed that the CSF isolate carried the cap gene(s), while the blood isolate did not. Using a novel quantitative real-time PCR approach for determining the cap copy number, it was demonstrated that the CSF isolate had two intact tandem repeats of the cap gene containing three copies of IS1016, whereas the blood isolate had only one copy of IS1016. This study provided evidence that H. influenzae serotypes other than serotype b can cause serious disease, and that the virulence of these non-serotype b strains relates primarily to the cap gene copy number and the structure of the cap locus. Therefore, the quantitative real-time PCR assay described in this study should be useful for the rapid and definitive identification of strains of H. influenzae type a that represent a risk for serious disease.

Bacterial Capsules↗

The tsetse fly Glossina palpalis palpalis is composed of several genetically differentiated small populations in the sleeping sickness focus of Bonon, Côte d'Ivoire.

Glossina palpalis is the main vector of human African trypanosomosis (HAT, or sleeping sickness) that dramatically affects human health in sub-Saharan Africa. Because of the implications of genetic structuring of vector populations for the design and efficacy of control campaigns, G. palpalis palpalis in the most active focus of sleeping sickness in Côte d'Ivoire was studied to determine whether this taxon is genetically structured. High and statistically significant levels of within population heterozygote deficiencies were found at each of the five microsatellite loci in two temporally separated samples. Neither null alleles, short allele dominance, nor trap locations could fully explain these deviations from random mating, but a clustering within each of the two samples into different genetic sub-populations (Wahlund effect) was strongly suggested. These different genetic groups, which could display differences in infection rates and trypanosome identity, were composed of small numbers of individuals that were captured together, leading to the observed Wahlund effect. Implications of this population structure on tsetse control are discussed.

Animals↗

Structural and genetic analyses of O polysaccharide from Actinobacillus actinomycetemcomitans serotype f.

The oral bacterium Actinobacillus actinomycetemcomitans is implicated as a causative agent of localized juvenile periodontitis (LJP). A. actinomycetemcomitans is classified into five serotypes (a to e) corresponding to five structurally and antigenically distinct O polysaccharide (O-PS) components of their respective lipopolysaccharide molecules. Serotype b has been reported to be the dominant serotype isolated from LJP patients. We determined the lipopolysaccharide O-PS structure from A. actinomycetemcomitans CU1000, a strain isolated from a 13-year-old African-American female with LJP which had previously been classified as serotype b. The O-PS of strain CU1000 consisted of a trisaccharide repeating unit composed of L-rhamnose and 2-acetamido-2-deoxy-D-galactose (molar ratio, 2:1) with the structure -->2)-alpha-L-Rhap-(1-3)-2-O-(beta-D-GalpNAc)-alpha-L-Rhap-(1-->* O-PS from strain CU1000 was structurally and antigenically distinct from the O-PS molecules of the five known A. actinomycetemcomitans serotypes. Strain CU1000 was mutagenized with transposon IS903phikan, and three mutants that were deficient in O-PS synthesis were isolated. All three transposon insertions mapped to a single 1-kb region on the chromosome. The DNA sequence of a 13.1-kb region surrounding these transposon insertions contained a cluster of 14 open reading frames that was homologous to gene clusters responsible for the synthesis of A. actinomycetemcomitans serotype b, c, and e O-PS antigens. The CU1000 gene cluster contained two genes that were not present in serotype-specific O-PS antigen clusters of the other five known A. actinomycetemcomitans serotypes. These data indicate that strain CU1000 should be assigned to a new A. actinomycetemcomitans serotype, designated serotype f. A PCR assay using serotype-specific PCR primers showed that 3 out of 20 LJP patients surveyed (15%) harbored A. actinomycetemcomitans strains carrying the serotype f gene cluster. The finding of an A. actinomycetemcomitans serotype showing serological cross-reactivity with anti-serotype b-specific antiserum suggests that a reevaluation of strains previously classified as serotype b may be warranted.

Actinobacillus Infections↗

Substrate properties of C1 inhibitor Ma (alanine 434----glutamic acid). Genetic and structural evidence suggesting that the P12-region contains critical determinants of serine protease inhibitor/substrate status.

The serine protease inhibitor (serpin) C1 inhibitor inactivates enzymes involved in the regulation of vascular permeability. A patient from the Ma family with the genetic disorder hereditary angioedema inherited a dysfunctional C1 inhibitor allele. Relative to normal plasma, the patients's plasma contained an additional C1 inhibitor immunoreactive band, which comigrated with normal C1 inhibitor cleaved by plasma kallikrein, C1s, or factor XIIa. C1 inhibitor Ma did not react with a monoclonal antibody to a neoepitope that is present in complexed and cleaved normal C1 inhibitor, suggesting conformational differences between cleaved normal C1- inhibitor and cleaved C1 inhibitor Ma. Molecular cloning and sequencing of exon 8 of the C1 inhibitor Ma allele revealed a single C to A mutation, changing alanine 434 to glutamic acid. Ala 434 of C1 inhibitor aligns with the P12 residue of the prototypical serpin alpha 1-antitrypsin. The P12 amino acid of all inhibitory serpins is alanine, and it is present in a highly conserved region on the amino-terminal side of the serpin-reactive center loop. Whereas normal C1 inhibitor expressed by transfected COS-1 cells formed complexes with and was cleaved by kallikrein, fXIIa, and C1s, COS-1-expressed Ala434---Glu C1 inhibitor was cleaved by these enzymes but did not form complexes with them. These results, together with evidence from other studies, suggest that serpin protease inhibitor activity is the result of protein conformational change that occurs when the P12 region of a serpin moves from a surface location, on the reactive site loop of the native molecule, to an internal location within sheet A of the complexed inhibitor.

Amino Acid Sequence↗

Antigen structure and genetic basis of histo-blood groups A, B and O: their changes associated with human cancer.

Three areas of research involved in blood group (or histo-blood group) ABO antigens and their genes, developed by our research group, are reviewed: (1) Antigen structures. The structural basis of A and H, A(1) and A(2), i and I antigens expressed in erythrocyte membranes. Major carriers of A and H determinants in erythrocytes are type 2 chain poly-LacNAc, short vs. long and unbranched vs. branched structures termed A(a), A(b), A(c), A(d) and H(1), H(2), H(3), H(4). Regular A (A(1)) and weak A (A(2)) were identified respectively as repetitive A (type 3 chain A) and A-associated H. A(1)- and A(2)-specific type 3 chain A and H, type 1 chain (representing Lewis blood group antigens), and type 4 chain (globo-series antigen; an extremely minor component in erythrocytes) are all glycosphingolipids. A and H determinants in fetal and newborn erythrocytes are carried by unbranched poly-LacNAc, whereas these determinants in adult erythrocytes are carried by branched poly-LacNAc. (2) ABO genes. A few cDNAs encoding A enzyme (UDP-GalNAc: H-a-GalNAc transferase) were cloned based on the amino acid sequence of purified A enzyme and their structures were compared with those of homologous cDNA from blood cells of B and O individuals (genotype BB, OO). Four nucleotide substitutions and four corresponding amino acid sequences essential for expression of A(1) allele and B allele, and differences between A and B enzymes, were identified. Amino acids 266 and 268, i.e. Leu and Gly for A enzyme vs. Met and Ala for B enzyme, were dominant in determining A vs. B activity (presumably recognizing UDP-GalNAc vs. UDP-Gal). The A(2) allele was characterized by deletion of the termination codon, extending nucleotides up to 1128 and thus encoding 21 extra amino acids at the C terminus, which may affect (diminish) the dominant function of amino acids 266 and 268. Typical O allele (O(1)) is characterized by deletion of nucleotide 261 G, causing frame shift and encoding of an entirely different, short polypeptide, due to appearance of early termination codon at nucleotide 354. Structures of other O alleles (O(1 v), O(2)) and other weak A alleles (A(3), A(el)) are also described. The genomic structure of ABO genes consists of seven exons which span approximately 19 kb of genomic DNA on chromosome 9, band q34. Most of the coding sequence is located in exon 7. Analysis of the 5' upstream region revealed the presence of the binding site for transcription factors and enhancer element. (3) Antigens and genes in cancer. A and B phenotypes aberrantly expressed in various types of human cancer, and their genetic basis, have been studied. One widely-occurring change observed in a large variety of human cancers is deletion of A or B epitope, associated with accumulation of their precursor H (Le(y), Le(b)), which causes enhanced malignancy. A less-commonly observed change is expression of incompatible A, identified as real type 1 chain A, in tumors of O or B individuals. A possible molecular genetic mechanism leading to such phenotypic changes is discussed.

ABO Blood-Group System↗

Detection and pattern of interspecific hybridization between Gliricida sepium and G. maculata in Meso-America revealed by PCR-based assays.

Gliricidia sepium provides a variety of products important for rural communities in tropical countries. Native populations in Meso-America currently form an important source of seed for distribution to farmers, but concerns centre on mechanisms which may lead to their genetic erosion, including anthropogenic dispersal and subsequent introgression from the related species, G. maculata. Populations of Gliricidia were examined genetically using approaches based on the polymerase chain reaction to test for interspecific hybridization and introgression between G. sepium and G. maculata. Analysis involved 13 RAPD and two RFLP-PCR markers which were identified to have species-diagnostic distributions. Data from both approaches corresponded and indicated three locations where multilocus genotypes were consistent with an hybrid origin. Data at one of these sites was consistent with introgression following hybridization. The hybrid origin of populations was supported by the intermediate geographical location of these sites to 'pure' populations of each species. Analysis of maternally inherited organellar DNA, which involved the detection of SSCPs in mitochondrial DNA amplification products, allowed further delineation of genetic structure among Gliricidia populations. Mitochondrial data indicated a high degree of organelle differentiation between sampled locations and identified G. sepium- and G. maculata-diagnostic haplotypes. This data supported the interpretation of genetic structure based on RAPDs and RFLP-PCR. In addition, cytonuclear analysis allowed the directionality of gene transfer during the formation of hybrid populations to be described. Despite evidence for the occurrence of interspecific hybridization and introgression in Gliricidia, important resource populations of G. sepium on the Pacific coast appear to have retained their genetic integrity. Implications in terms of the conservation and utilization of genetic resources within the genus are discussed.

Base Sequence↗

Spatial distribution of allozyme polymorphisms following clonal and sexual reproduction in populations of Rhus javanica (Anacardiaceae).

Rhus javanica L. (Anacardiaceae), a dioecious tree with both sexual reproduction and clonal growth, is widely distributed in warm temperate, subtropical, and tropical regions in east Asia. We used allozyme loci and spatial autocorrelation statistics to examine clonal structure and the spatial distribution of allozyme polymorphisms in two Korean populations. Populations of the species maintain moderate levels of allozyme variability (mean He=0.175, GST=0.060), and high levels of multilocus genotypic diversity (mean DG=0.971). Clone-pair distances ranged from 1.4 m to 57.4 m, and had high mean values of 24.0 m and 25.6 m in the two study populations. Approximate genetic patch widths were inferred to be 23-25 m. The results indicated that within populations there is moderate (one study population) or no (other study population) spatial genetic structure among sexually reproduced individuals, and vegetatively reproduced genotypes also are almost randomly distributed. The spatial genetic structure among sexually reproduced trees in the one case is probably caused by limited pollen dispersal in that population, and the lack of structure in the other probably results from the short time elapsed since founding. It appears that clonal reproduction also does not contribute substantially to genetic isolation by distance neither among the sexually reproduced individuals nor the total population. Ramets often establish long distances from their progenitors and thus do not substantially increase the degree of local consanguineous matings.

Genetic Markers↗

Geographic and temporal genetic patterns of Aedes aegypti populations in Rio de Janeiro, Brazil.

Rio de Janeiro is considered as the most important entry point for dengue viruses in Brazil. Using isoenzyme markers, we investigated the genetic structure of the mosquito vector Aedes aegypti sampled at three-month intervals in 14 districts in Rio de Janeiro from December 2002 to December 2003. We detected high levels of genetic differentiation (i.e. high F(ST) values and significant P values), which tended to persist throughout the year. The species does not take advantage of routes and railways to disperse. Genetic structuring was higher in the rainy season, suggesting low dispersion of Ae. aegypti at this time of year when all dengue epidemics have been reported in the city.

Aedes↗

Allozyme diversity in Macbridea alba (Lamiaceae), an endemic florida mint.

Macbridea alba is a herbaceous perennial mint endemic to the panhandle region of Florida. We used starch gel electrophoresis to describe allozyme diversity and genetic structure in this federally threatened plant. Ten populations were analyzed, with an average sample size of 47 plants (range 41-48 plants) per population. Of the 22 loci analyzed, 11 (50%) were polymorphic, with an average of 36.2% of the loci polymorphic within populations. Gene diversity measures for the species (Hes = 0.121) and for the populations (Hep = 0.099) were slightly higher than means found for other surveyed endemic plants. Compared to nine previously analyzed woody mints, however, M. alba is genetically depauperate. Little genetic structure was evident within the species, with 92% of the total genetic variation found within populations. Genetic identities between population pairs were high (mean I = 0.98). The perennial life habit of M. alba and long-distance pollination by bumblebees may contribute to the maintenance of genetic diversity within this threatened species.

Electrophoresis, Starch Gel↗

Patterns and levels of genetic differentiation in North American populations of the Alaskan wheatgrass complex.

Levels and distribution of genetic variation were assessed using six allozymes in 27 populations of Alaskan wheatgrass (Elymus alaskanus) from different locations in Canada, USA, Greenland and Russia to obtain information on the genetic structure of these populations. The enzyme systems were ACO, DIA, GPI, MDH, PGM and SKD. Allozyme variation at the species level was high, with 64.3% (Ps) of the loci being polymorphic, an average number of alleles per locus of 1.9 (As), and an average genetic diversity of 0.17 (Hes). Differentiation was found in the populations studied, with the following findings: (1) statistically significant differences were found in allele frequencies among populations for every polymorphic locus (P < 0.001); (2) 63% of the total allozyme variation at polymorphic loci was partitioned among populations (GST = 0.63); (3) relatively low mean genetic distances between the populations were obtained (mean D = 0.029); (4) the genetic structure of Russian populations are clearly distinct from the other populations, the cluster and principal component analyses revealed the same genetic patterns of relationships among populations. This study also indicates that E. alaskanus contains different levels of allozyme variation in its populations. Furthermore, some banding patterns at the loci Aco-1, Aco-2, Gpi-2, Mdh-1, Skd-1, Skd-2 can be used as markers to identify individual populations.

Canada↗