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PubMed2003

The impact of data structure on genetic (co)variance components of early growth in sheep, estimated using an animal model with maternal effects.

Several studies have noted high negative correlations between maternal genetic and direct additive effects and their influence on additive and maternal heritability of early growth traits in sheep. Multigeneration data from the Suffolk Sire Reference Scheme (SSRS) were used to investigate the effect of data structure on estimates of direct and maternal (co)variances for lamb 8-wk weight. In all analyses the additive, maternal genetic, maternal environmental, and residual effects were fitted along with the covariance between direct and maternal additive effects. The contributions of particular genetic relationships to the estimates were studied by analyzing subsets of the SSRS data. A further eight subsets were formed having 10% or 50% of the dams with their own records and having one or two, three or four, five or six, and more than six offspring per dam. Analysis of data having only 10% of the dams with their own record and one or two offspring records yielded a high negative correlation (-0.99) between direct and maternal genetic effects. However, the seven other data sets with more records per dam or a higher proportion of dams with their own records produced values of -0.35 to -0.51. Data structure and the number of dams and granddams with records are important determinants of estimated direct and maternal effects in early growth traits.

Analysis of Variance↗
PubMed2006

Comparative population genetic study of two oligophagous insects associated with the same hosts.

A parallel study of the genetic structure of two oligophagous species associated with the same hosts was conducted to determine the main factors shaping the distribution of genetic diversity. The bark beetle Tomicus piniperda and the pine processionary moth (PPM) Thaumetopoea pityocampa are both associated with the genus Pinus and belong to different guilds (xylophagous vs defoliating species). The PPM is an ectophagous species that feeds on the needles of living trees, whereas T. piniperda is endophagous and bores galleries in the inner bark of weakened trees. Both species were sampled in the main regions of France, and their genetic structure was assessed after genotyping with five microsatellite markers. Populations of the PPM were significantly structured. A pattern of isolation by distance was found when distances were calculated as bypassing the Massif Central, whereas no such pattern could be found with raw geographic distances. On the contrary, most populations of T. piniperda were not differentiated. No effect of host species could be detected in either of the two species. We conclude that the two taxa have contrasting effective dispersal rates per generation, and we hypothesize that this reflects the different selection pressures acting on individual fitness via different strategies of host use.

Animals↗
PubMed2006

Genetic population structure and call variation in a passerine bird, the satin bowerbird, Ptilonorhynchus violaceus.

Geographic variation in vocalizations is widespread in passerine birds, but its origins and maintenance remain unclear. One hypothesis to explain this variation is that it is associated with geographic isolation among populations and therefore should follow a vicariant pattern similar to that typically found in neutral genetic markers. Alternatively, if environmental selection strongly influences vocalizations, then genetic divergence and vocal divergence may be disassociated. This study compared genetic divergence derived from 11 microsatellite markers with a metric of phenotypic divergence derived from male bower advertisement calls. Data were obtained from 16 populations throughout the entire distribution of the satin bowerbird, an Australian wet-forest-restricted passerine. There was no relationship between call divergence and genetic divergence, similar to most other studies on birds with learned vocalizations. Genetic divergence followed a vicariant model of evolution, with the differentiation of isolated populations and isolation-by-distance among continuous populations. Previous work on Ptilonorhynchus violaceus has shown that advertisement call structure is strongly influenced by the acoustic environment of different habitats. Divergence in vocalizations among genetically related populations in different habitats indicates that satin bowerbirds match their vocalizations to the environment in which they live, despite the homogenizing influence of gene flow. In combination with convergence of vocalizations among genetically divergent populations occurring in the same habitat, this shows the overriding importance that habitat-related selection can have on the establishment and maintenance of variation in vocalizations.

Animals↗
PubMed2006

Microsatellite variation among diverging populations of Drosophila mojavensis.

Divergence and speciation may occur by various means, depending on the particular history, selective environments, and genetic composition of populations. In Drosophila mojavensis, a good model of incipient speciation, understanding the population genetic structure within this group facilitates our ability to understand the context in which reproductive isolation among populations is developing. Here we report the genetic structure and relationships of D. mojavensis populations at nuclear loci. We surveyed 29 populations throughout the distribution of D. mojavensis for four microsatellite loci to differentiation among populations of this species. These loci reveal four distinct geographical regions of D. mojavensis populations in the south-western United States and north-western Mexico--(i) Baja California peninsula (Baja), (ii) Sonora, Mexico-southern Arizona, United States (Sonora), (iii) Mojave Desert and Grand Canyon (Mojave), and (iv) Santa Catalina Island (Catalina). While all regions show strong isolation, Mojave and Catalina are highly diverged from other regions. Within any region, populations are largely homogenous over broad geographical distances. Based on the population structure, we find clear geographical barriers to gene flow appear to have a strong effect in isolating populations across regions for this species.

Animals↗
PubMed2003

Are the native giant tortoises from the Seychelles really extinct? A genetic perspective based on mtDNA and microsatellite data.

The extinction of the giant tortoises of the Seychelles Archipelago has long been suspected but is not beyond doubt. A recent morphological study of the giant tortoises of the western Indian Ocean concluded that specimens of two native Seychelles species survive in captivity today alongside giant tortoises of Aldabra, which are numerous in zoos as well as in the wild. This claim has been controversial because some of the morphological characters used to identify these species, several measures of carapace morphology, are reputed to be quite sensitive to captive conditions. Nonetheless, the potential survival of giant tortoise species previously thought extinct presents an exciting scenario for conservation. We used mitochondrial DNA sequences and nuclear microsatellites to examine the validity of the rediscovered species of Seychelles giant tortoises. Our results indicate that the morphotypes suspected to represent Seychelles species do not show levels of variation and genetic structuring consistent with long periods of reproductive isolation. We found no variation in the mitochondrial control region among 55 individuals examined and no genetic structuring in eight microsatellite loci, pointing to the survival of just a single lineage of Indian Ocean tortoises.

Animals↗
PubMed1988

A genetic history of Italy.

Statistical techniques for displaying the geographical distribution of many genes in few synthetic images have been used to represent the various patterns of gene frequencies in Europe and in the world (Menozzi et al. 1978; Piazza et al. 1981 a). It has also been shown that such synthetic displays are particularly useful in detecting clines of genetic differentiation associated with movements of populations like those accompanying the Neolithic expansion of farmers from the Near East or, in more recent times, the putative diffusion of Indo-European-speaking populations (Ammerman & Cavalli-Sforza, 1984; Gimbutas, 1973). In this paper we use the same combination of statistical and graphical techniques to study the genetic structure of Italy, a European country whose unity of people and cultures was quite a recent event. The possibility of studying genetic differentiation in a small geographical area is tested and trends of genetic differences are tentatively interpreted in terms of historic and linguistic knowledge. The few demographic pieces of information taken from historical sources and compared with linguistic records support the hypothesis that the genetic structure of Italy still reflects the ethnic stratification of pre-Roman times.

Blood Group Antigens↗
PubMedDate not supplied

The MNSs blood group system in the population of South Backa.

Blood groups represent qualitative characteristics of humans which are controlled by one or a few genetic loci and due to this it is easy to determine various kinds of alleles and their frequencies in certain samples. Analyzing variability of characteristics such as blood groups, it is possible to get an insight in genetic structure of a population and it represents a suitable manner for detecting similarities and differences between populations. The intention of this study was to determine the genetic structure of the population of South Backa in a classic manner by phenotypic characteristics in MNSs blood group system, to assess frequencies of alleles, phenotypes, genotypes, allelic frequencies and genetic distances between the population of South Backa and populations of various geographic regions. Immunohematologic investigation of 1.000 persons included blood group testing in the MNSs system, which was a basis for applying population-genetic analysis based on Hardy-Weinberg equilibrium in populations. Results of investigation revealed that in population of South Backa, s allele has the highest frequence (85.59%); the most frequent genotypes are ss (48.5%), MN (43.4%), Ss (37.4%); the most frequent phenotypes are MNss (19.3%), MNSs (18.4%) and NNss (15.3%). Genetic distances between populations are greatest among geographically most distant populations as Eskimos, Australian Aborigines, populations of Papua-Gvinea, Fiji and low in populations of Turkey, Italy, Albania and Cyprus.

Female↗
PubMed2002

Spatial pattern of chloroplast DNA variation of Cyclobalanopsis glauca in Taiwan and East Asia.

This study examined the spatial pattern of chloroplast DNA (cpDNA) variation in Cyclobalanopsis glauca (Thunb. ex Murray) Oerst. (Fagaceae) in 140 trees from Taiwan (25 populations), Japan (three), Ryukyus (two), Hong Kong (one) and Mainland China (one). By sequencing three cpDNA intergenic spacer fragments using universal primers (trnT-trnL, trnV-trnM, including the trnV intron, and petG-trnP), we found a total of 1,980 bp and 15 polymorphic sites. Among them, 12 sites were caused by point mutation, and three resulted from insertion. This gives rise to a total of 13 cpDNA haplotypes. The level of differentiation among the populations studied is relatively high (GST = 0.612). Two ancestral haplotypes (A and B) are distributed widely in East Asia. Interestingly, all the derived cpDNA variations are found only in Taiwan but not in other areas. The Central Mountain Ridge (CMR) of Taiwan creates an unsurpassed barrier to the east-west gene flow of C. glauca. Among the populations on the west of CMR, only three separated populations, Yangmingshan, Wushe and Chinshuiying, have high haplotype diversity, each consisting of sister haplotypes all mutated from the same ancestral haplotype. Thus, they have probably originated from de novo mutation after the last glaciation. This inference agrees with the observation that no spatial autocorrelation existed on the west side. Two unrelated dominant lineages on the east of the CMR (haplotypes D and F) showed significant spatial genetic structure. Estimate of NST - GST was -0.090 and differed significantly from zero. Thus at the local scale, the phylogeographical component of the genetic structure is significant on the east of the CMR. Accompanied by published palynological records of the last glaciation, this study suggests the possibility that these two types were colonized northward from the southeastern part of Taiwan. 'Star-like' genealogy is characterized, with all the haplotypes coalescing rapidly and as a general outcome of population expansion (Page & Holmes 1998). A neutrality test also suggested a demographic expansion recovered from a bottleneck. We therefore inferred that the southeastern part of Taiwan might be a potential refugium for C. glauca.

DNA, Chloroplast↗
PubMed2002

Geographic structure of genetic variation in the widespread woodland grass Milium effusum L. A comparison between two regions with contrasting history and geomorphology.

Allozyme variation in the forest grass Milium effusum L. was studied in 21-23 populations within each of two equally sized densely sampled areas in northern and southern Sweden. In addition, 25 populations from other parts of Eurasia were studied for comparison. The structure of variation was analysed with both diversity statistics and measures based on allelic richness at a standardised sample size. The species was found to be highly variable, but no clear geographic patterns in the distribution of alleles or in overall genetic differentiation were found, either within the two regions or within the whole sample. Thus, no inferences about the direction of postglacial migration could be made. Obviously, migration and gene flow must have taken place in a manner capable of randomising the distribution of alleles. However, there were clear differences in levels and structuring of the variation between the two regions. Levels of variation, both in terms of genetic diversity and allelic richness, were lower in northern Sweden as compared with southern Sweden. In contrast, different measures of geographic structure all showed higher levels of population differentiation in the northern region. This is interpreted as due to different geomorphological conditions in the two regions, creating a relatively continuous habitat and gene flow in the southern region as compared with the northern region where the species, although common, is confined to narrow and mutually isolated corridors in the landscape.

Alleles↗
PubMed1977

The guinea pig I region. I. A structural and genetic analysis.

The Ia antigens of the guinea pig have been shown to play a central role in the regulation of the immune response. We have previously partially characterized the chemical structure of these antigens. In this communication, we further characterize the structure of the five Ia antigens already described, as well as two new Ia antigens. Evidence is presented which shows that these seven Ia antigens can be organized into three distinct groups, each with a characteristic structure. The Ia.2 determinant of strain 2 and the Ia.3 and Ia.5 determinants of strain 13 animals are found on molecules composed of a 25,000 dalton chain and a 33,000 dalton chain in noncovalent association, or else are individually expressed on nonlinked 33,000 and 25,000 dalton molecules. The Ia.4 and Ia.5 determinants of strain 2 and the Ia.7 determinant of strain 13 are borne on 58,000 dalton molecules in which two chains are linked by disulfide bonds. The Ia.1 and Ia.6 determinants of strain 13 are found on a molecule of 26,000-27,000 daltons. Ia.6 of strain 2 has yet to be definitively assigned. Furthermore, in strain 13 animals the Ia.3 and Ia.5 determinants are borne on the same molecule, as are the Ia.1 and Ia.6 determinants. In strain 2 animals, the Ia.4 and Ia.5 determinants are found on the same molecule. On the basis of chemical structure, we have divided the guinea pig I region into three subregions. The accompanying paper presents evidence of associations between particular Ia genes and Ir genes.

Animals↗
PubMed2005

[Genetic demographic structure of the Lugansk (Ukraine) population: age, ethnicity, education, and occupation].

Data from marriage records from registry office archives of 1960, 1985, 1990, and 2000 have been used to calculate the genetic demographic parameters of the Lugansk city population. The population is mostly Ukrainian and Russian. In the years studied, Ukrainians accounted for 49.4, 44.0, 44.6, and 48.7% of the population and Russians, for 46.0, 52.1, 50.7, and 45.6%, respectively. The total proportion of the two ethnic groups decreased from 97.0 to 94.6% for 40 years. The marriage contingency coefficient (K) with respect to ethnicity decreased from 0.16 to 0.07 in the period between 1960 and 1985 and increased from 0.10 to 0.24 between 1990 and 2000. The frequency of interethnic marriages (48.4, 50.9, 52.0, and 60.0%, respectively, in the years studied) indicate that the outbreeding component has been constantly increasing in the Lugansk population. The marriage assortativeness indices (A') for Ukrainians were 10.2, 4.8, 2.1, and 6.0% in 1960, 1985, 1990, and 2000, respectively. For pooled minor ethnic groups, A' values in these years were 25.6, 12.4, 18.9, and 6.6%, respectively. The marriage contingency coefficient (K) with respect to occupation increased in the period between 1960 and 1990 (0.14, 0.16, and 0.19 in 1960, 1985, and 1990, respectively), and K with respect to education decreased (0.35, 0.30, and 0.26, respectively).

Age Factors↗
PubMed2006

Genetic population structure of the soil bacterium Myxococcus xanthus at the centimeter scale.

Myxococcus xanthus is a gram-negative soil bacterium best known for its remarkable life history of social swarming, social predation, and multicellular fruiting body formation. Very little is known about genetic diversity within this species or how social strategies might vary among neighboring strains at small spatial scales. To investigate the small-scale population structure of M. xanthus, 78 clones were isolated from a patch of soil (16 by 16 cm) in Tübingen, Germany. Among these isolates, 21 genotypes could be distinguished from a concatemer of three gene fragments: csgA (developmental C signal), fibA (extracellular matrix-associated zinc metalloprotease), and pilA (the pilin subunit of type IV pili). Accumulation curves showed that most of the diversity present at this scale was sampled. The pilA gene contains both conserved and highly variable regions, and two frequency-distribution tests provide evidence for balancing selection on this gene. The functional domains in the csgA gene were found to be conserved. Three instances of lateral gene transfer could be inferred from a comparison of individual gene phylogenies, but no evidence was found for linkage equilibrium, supporting the view that M. xanthus evolution is largely clonal. This study shows that M. xanthus is surrounded by a variety of distinct conspecifics in its natural soil habitat at a spatial scale at which encounters among genotypes are likely.

Bacterial Proteins↗
PubMed1990

Genetic and structural characterization of endA. A membrane-bound nuclease required for transformation of Streptococcus pneumoniae.

The endA gene encoding the membrane nuclease of Streptococcus pneumoniae, which is necessary for DNA uptake in genetic transformation, was cloned in a streptococcal vector. This was accomplished by insertional mutagenesis of the gene, cloning of the mutant allele, and substitution of the wild-type allele by chromosomal facilitation of plasmid establishment. Plasmids carrying the endA+ gene complemented cells with endA- in the chromosome to restore DNAase activity and transformability. Determination of its DNA sequence showed the gene to encode a 30 kDa protein, EndA, with a typical signal sequence for membrane transport at its amino end. In vitro synthesis of EndA showed the initial translation product to be enzymatically active without further processing. Comparison with EndA found in cell membranes indicated that the enzyme retained its signal sequence, which apparently anchored the otherwise hydrophilic protein to the membrane. From the nucleotide sequence in the vicinity of endA and the effect of various insertions and deletions, it appears that endA is the last gene in an operon containing at least two other genes. Neither of these upstream genes, nor the downstream gene, are essential for either cell viability or transformability.

Amino Acid Sequence↗
PubMed2004

Structural and genetic characterization of glycosylation of type a flagellin in Pseudomonas aeruginosa.

Type a flagellins from two strains of Pseudomonas aeruginosa, strains PAK and JJ692, were found to be glycosylated with unique glycan structures. In both cases, two sites of O-linked glycosylation were identified on each monomer, and these sites were localized to the central, surface-exposed domain of the monomer in the assembled filament. The PAK flagellin was modified with a heterogeneous glycan comprising up to 11 monosaccharide units that were O linked through a rhamnose residue to the protein backbone. The flagellin of JJ692 was less complex and had a single rhamnose substitution at each site. The role of the glycosylation island gene cluster in the production of each of these glycosyl moieties was investigated. These studies revealed that the orfA and orfN genes were required for attachment of the heterologous glycan and the proximal rhamnose residue, respectively.

Amino Acid Sequence↗