Identifying changes in viral fitness using population genetic structure.
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Genetics, Population↗
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The genetic structure of adders (Vipera berus) in Fennoscandia: congruence between different kinds of genetic markers.
In order to elucidate the colonization history of Fennoscandian adders (Vipera berus), the phylogeographical patterns of two nuclear sets of DNA markers (random amplified polymorphic DNA and microsatellite) are compared with that previously obtained from mitochondrial DNA. An eastern and a western lineage within Fennoscandian adders is readily distinguishable using both sets of nuclear markers, corroborating the hypothesis that the lineages stem from separate glacial refugia. Moreover, the same contact zones as were derived from mitochondrial data are clearly identifiable. Both sets of nuclear markers detect a high level of admixture across one zone in northern Finland, with introgression reaching far west into Sweden.
Analysis of Variance↗
Genetic structure of the population with rheumatoid arthritis in north east England: a genetic approach to define different subtypes.
Clinically and immunologically rheumatoid arthritis (RA) is possibly a heterogeneous disorder. Despite numerous efforts clearer definition of this heterogeneity has been of limited success. Measurements of rheumatoid factor (RF) and antinuclear antibodies (ANA) by conventional methods define subpopulations of patients with RA and in a few recent studies an association of human leucocyte antigens (HLA) undoubtedly indicates the immunogenetic differences in the susceptibility of RA patients with different status of autoantibodies. The studies on a few isolated non-HLA genetic markers in RA are controversial. To understand the role of genetic factors in susceptibility 24 single gene characters other than HLA were investigated in 225 patients with RA classified by humoral status (presence or absence of RF and ANA) into three groups and in 104 healthy control individuals from the north east of England. Locus by locus comparison suggested associations of MN, Lewis, and Bf system with RF positive patients. Although the associations with MN and Lewis blood groups require further investigations, the involvement of the Bf locus is in agreement with the immunological component of the disease suggested by HLA associations and it could be due to the phenomenon of linkage disequilibrium. Measures of genetic distance applied to the subpopulations of patients with RA, divided according to the presence or absence of humoral factors, suggest that RF+ ANA+, RF- ANA-, and RF+ ANA- subgroups are distinct genetic diseases, each affecting a different subsection of the population which is genetically distinct. Such genetic heterogeneity may suggest a different pathogenetic mechanism for each of these subpopulations of rheumatoid arthritis.
Antibodies, Antinuclear↗
[The effects of longterm selection on the genetic structure of populations--a simulation study. II. The effects of selection on genetic variances].
Monte Carlo simulation has been done to study the effects of longterm artificial selection on genetic variances under additive, dominant, and over-dominant models. The effects of population size, linkage, and heritability have been considered. Just as under the additive model, the additive variance under the dominant and over-dominant models has also been decomposed into three components which represent changes in gene frequencies (VT), departure from Hardy-Weinberg equilibrium (VHW) and from linkage equilibrium (VLD) respectively. These present a resonable approach to study the association among multiple genes. In small populations, genetic variance fluctuates wildly over generations and replicates due to the establishment of linkage disequilibrium. Rapid decrease of VT observed. Intense linkage retained a greater additive variance in the small populations while slowing down responses, which makes it difficult to predict responses during longterm selection.
Animals↗
Population genetic structure of Pacific white shrimp (Litopenaeus vannamei) from Mexico to Panama: microsatellite DNA variation.
Genetic variation and population structure of wild white shrimp (Litopenaeus vannamei) from 4 geographic locations from Mexico to Panama were investigated using 5 microsatellite DNA loci. The genetic diversity between populations was indicated by the mean number of alleles per locus and mean observed heterozygosity, which ranged from 7.4 to 8.6 and from 0.241 to 0.388, respectively. Significant departures from Hardy-Weinberg equilibrium were found at most locations at each locus, with the exception Guatemala at Pvan0013, and were caused by high heterozygote deficiencies. Genetic differences between localities were detected by pairwise comparison based on allelic and genotypic frequencies, with the exception of locus Pvan1003. Significant pairwise F (ST) values between locations and total F (ST) showed that the white shrimp population is structured into subpopulations. However, population differentiation does not follow an isolation-by-distance model. Knowledge of the genetic diversity and structure of L.vannamei populations will be of interest for aquaculture and fisheries management to utilize and preserve aquatic biodiversity.
Animals↗
Genetic structure of populations of Ostertagia ostertagi.
Most genetic work to distinguish strains of parasitic helminths focuses on searching for genetic markers to correlate with phenotypes of interest, but in this study genetic diversity among individual Ostertagia ostertagi adults is partitioned into components within and between populations. Restriction fragment polymorphism data on mitochondrial DNA from ten individual worms from each of five different parasite populations are analyzed. Three of these populations are characterized by arrested larval development (hypobiosis) over the summer months, and the other two by hypobiosis over the winter months. Sequence divergence is scored by the presence or absence of 37 different restriction sites. Although the populations are genetically differentiated with respect to the timing of hypobiosis, greater than 98% of the total mitochondrial DNA sequence diversity is partitioned within a single population, and the geographic distribution of individual mitochondrial DNA haplotypes suggests high gene flow among populations. Further, estimates of within-population mitochondrial DNA diversity are five to ten times greater in O. ostertagi than typical estimates reported for species in other taxa.
Animals↗
DNA fingerprinting data and the analysis of population genetic structure by comparing band-sharing patterns.
Genetic isolation among populations can be effectively investigated by multilocus DNA fingerprinting. If populations have diverged, it is expected that the mean proportion of bands shared by individuals from the same population, Bw, exceeds the corresponding mean, Bb, calculated from pairs of individuals from distinct populations. A problem arises in deciding whether any difference between Bw and Bb is statistically significant. In fact, any two band-sharing data (bij), contributing to Bw or Bb, are not independent if they share a common individual (like bij and bjl). This prevents a correct application of parametric tests, such as the Student's t-test. Recently, a modification of this test has been proposed that should avoid the independence problem. Using a large number of samples of fingerprints, simulated from an appropriate 'genetic' model, under a wide range of conditions, we compared the performances of the Student's t-test, the modified t-test and five new permutation tests, where individuals, rather than bij values, are permuted. We found that: (i) the Student's t-test can be very permissive, rejecting too often the null hypothesis when true, but is correct or conservative in certain cases; (ii) the modified t-test is extremely conservative when the null hypothesis is true and very inefficient otherwise; (iii) all five permutation tests are strictly correct, provided that individuals are ordered randomly on gels; and (iv) in this case, the permutation tests are equally efficient, and are not inferior to the Student's t-test when the latter is approximately correct and provides a fair benchmark.
DNA Fingerprinting↗
Effects of traffic pollution on the genetic structure of Poa annua L. populations.
The genetic composition of Poa annua L. populations with a series of traffic pollution was studied by starch electrophoresis. Five enzyme systems were stained. The results showed that: (1) Traffic pollution can dramatically change genotypic frequencies at some loci of P. annua populations. Significant deviations from Hardy-Weinberg equilibrium were observed on loci Fe-1 and Me due to the excess of heterozygotes in some populations. (2) The effective number of alleles per locus and the observed and expected heterozygosity were higher in the pollution series than in the clear control site (Botanic Park population), but the increase was not related with the pollution extent. (3) Most genetic variation was found within populations, and only 6.21% was among populations of the polluted series. Slightly higher differentiation (FST = 7.98%) was observed when the control population was included. (4) The calculated gene flow (Nm) is 2.8841 per generation. The mean of genetic identity is 0.9864 and the genetic distance average to 0.0138.
Air Pollutants↗
Genetic structure and differentiation in cultivated grape, Vitis vinifera L.
222 cultivated (Vitis vinifera) and 22 wild (V. vinifera ssp. sylvestris) grape accessions were analysed for genetic diversity and differentiation at eight microsatellite loci. A total of 94 alleles were detected, with extensive polymorphism among the accessions. Multivariate relationships among accessions revealed 16 genetic groups structured into three clusters, supporting the classical eco-geographic grouping of grape cultivars: occidentalis, pontica and orientalis. French cultivars appeared to be distinct and showed close affinity to the wild progenitor, ssp. sylvestris from south-western France (Pyrenees) and Tunisia, probably reflecting the origin and domestication history of many of the old wine cultivars from France. There was appreciable level of differentiation between table and wine grape cultivars, and the Muscat types were somewhat distinct within the wine grapes. Contingency chi2 analysis indicated significant heterogeneity in allele frequencies among groups at all loci. The observed heterozygosities for different groups ranged from 0.625 to 0.9 with an overall average of 0.771. Genetic relationships among groups suggested hierarchical differentiation within cultivated grape. The gene diversity analysis indicated narrow divergence among groups and that most variation was found within groups (approximately 85%). Partitioning of diversity suggested that the remaining variation is somewhat structured hierarchically at different levels of differentiation. The overall organization of genetic diversity suggests that the germplasm of cultivated grape represents a single complex gene pool and that its structure is determined by strong artificial selection and a vegetative mode of reproduction.
Genetic Variation↗
Testing for genetic structure in different urban Argentinian populations.
Fifteen autosomal short tandem repeat (STR) markers (D3S1358, HUMTH01, D21S11, D18S51, PENTA E, D5S818, D13S317, D7S820, D16S539, CSF1PO, PENTA D, HUMvWA, D8S1179, HUMTPOX, FGA) were analyzed in 1734 individuals living in urban areas of cities from six different Argentinian provinces (Buenos Aires, Neuquén, Tucumán, La Pampa, San Luis, Santa Cruz) in order to determine if a common urban database could be used in Argentina for forensic purposes. Frequencies estimates, Hardy-Weinberg equilibrium (HWE), and other parameters of forensic interest were computed. Comparisons between the six populations, and with published data from one Native American population from Argentina and other urban populations from Argentina and Europe were also performed. Our results reveal evidences for population structure, both when testing for genetic differentiation and when comparing frequencies distributions between different pairs of populations. Therefore, caution should be taken when using a common pooled database with general forensic purposes in Argentina.
Argentina↗
Phylogeography and spatial genetic structure of the Southern torrent salamander: implications for conservation and management.
The Southern torrent salamander (Rhyacotriton variegatus) was recently found not warranted for listing under the US Endangered Species Act due to lack of information regarding population fragmentation and gene flow. Found in small-order streams associated with late-successional coniferous forests of the US Pacific Northwest, threats to their persistence include disturbance related to timber harvest activities. We conducted a study of genetic diversity throughout this species' range to 1) identify major phylogenetic lineages and phylogeographic barriers and 2) elucidate regional patterns of population genetic and spatial phylogeographic structure. Cytochrome b sequence variation was examined for 189 individuals from 72 localities. We identified 3 major lineages corresponding to nonoverlapping geographic regions: a northern California clade, a central Oregon clade, and a northern Oregon clade. The Yaquina River may be a phylogeographic barrier between the northern Oregon and central Oregon clades, whereas the Smith River in northern California appears to correspond to the discontinuity between the central Oregon and northern California clades. Spatial analyses of genetic variation within regions encompassing major clades indicated that the extent of genetic structure is comparable among regions. We discuss our results in the context of conservation efforts for Southern torrent salamanders.
Animals↗
Population genetic structure in European populations of Spiranthes romanzoffiana set in the context of other genetic studies on orchids.
Spiranthes romanzoffiana Cham. is restricted in Europe to the British Isles, where it is recognised as a conservation priority species due to frequent extirpation of populations along with no evidence of seed set; vegetative reproduction has been invoked as the sole means of perpetuation and dispersal. To investigate the reproductive ecology of this species, 17 populations have been sampled for chloroplast microsatellites and amplified fragment length polymorphisms (AFLPs). These markers revealed a previously unsuspected genetic-geographic split in the species, which correlates with differences in patterns of within-population variation. Northern populations were fixed for one chloroplast haplotype but showed high levels of AFLP genotypic diversity consistent with sexual reproduction (proportion of genotypes distinguishable, PD = 0.98). More southerly populations showed fixed differences from the northern populations in their chloroplast haplotype and for 10 AFLP markers. They harboured only 12 unique multilocus genotypes among 113 individuals from six populations (PD = 0.11). These genotypes differed mostly by single bands, and none by more than 4/138 loci, with identical multilocus genotypes occurring in widely separated populations. This uniformity in southern populations is consistent with agamospermous or autogamous reproduction, and/or an extreme population bottleneck. Finally, the observed patterns of population differentiation in S. romanzoffiana are compared with other studies of orchids, revealing a wide range of values that belie recent contrasting published generalisations that claim that orchids show either higher, or lower, levels of population differentiation than other plant families.
Chloroplasts↗
Genetic structure of populations of Porphyromonas gingivalis associated with periodontitis and other oral infections.
One hundred isolates of the oral pathogenic bacterium Porphyromonas gingivalis were genetically characterized by determining the electrophoretic mobilities of 16 metabolic enzymes and the presence or absence of catalase activity. A total of 78 distinct electrophoretic types (ETs), representing multilocus genotypes, were identified, and cluster analysis placed them in three major phylogenetic divisions. Division I (71 ETs) included all 88 human isolates examined, most of which had been recovered from patients with periodontitis, together with 4 monkey isolates. The strains in division II (four ETs) and division III (three ETs) are strongly differentiated from those in division I and apparently represent two previously unclassified (cryptic) species. The mean genetic diversity per enzyme locus among the 92 isolates of division I (P. gingivalis, strict sense) was 0.321, and the strains were distributed among 14 phylogenetic clusters and single-ET lineages. The population structure is basically clonal, with some clonal genotypes being widespread, and even global, in distribution. There was no evidence of association between specific genetic lineages or clusters of ETs and the type of disease (periodontitis or root canal infections), invasive potential, serogroup, or fimbrial restriction fragment length polymorphism group. The finding that dental patients are infected by strains of a wide variety of chromosomal genotypes suggests that interstrain variation in pathogenicity is small. On the basis of the observed genetic structure of natural populations of P. gingivalis, we hypothesize that the role of this microorganism in the pathogenesis of periodontitis and other dental infections is largely opportunistic.
Alleles↗
On the origin of high negative interference over short segments of the genetic structure of bacteriophage T4.
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Bacteriophage T4↗
Temporal change in genetic structure and effective population size in steelhead trout (Oncorhynchus mykiss).
There is a wealth of published molecular population genetic studies, however, most do not include historic samples and thus implicitly assume temporal genetic stability. We tested for changes in genetic diversity and structure in three populations of steelhead trout (Oncorhynchus mykiss) from a northern British Columbia watershed using seven microsatellite loci over 40 years. We found little change in genetic diversity (mean allele numbers and observed and expected heterozygosity), despite large variation in the estimated numbers of steelhead returning to the watershed over the same time period. However, the temporal stability in genetic diversity is not reflected in population structure, which appears to be high among populations, yet significantly variable over time. The neighbour-joining tree showed that, overall, two of the populations (Zymoetz and Kispiox) clustered separately from the third (Babine); a finding which was not consistent with their geographical separation. The clustering pattern was also not temporally consistent. We used the temporal method to estimate the effective number of breeders (Nb ) for the three populations; our values (Nb = 17-102) were low for the large and presumed vigorous populations of steelhead trout sampled. The low Nb values were also not consistent with the generally high genetic diversity estimates, suggesting the possibility of intermittent gene flow among the three populations. The use of temporal analyses in population genetic samples should be a priority; first, to verify observed patterns in contemporary data, and second, to build a dataset of temporal analyses to allow generalizations to be made concerning temporal genetic stability and effective population size in natural populations.
Animals↗
GENETIC STRUCTURE OF THE D-SERINE DEAMINASE SYSTEM OF ESCHERICHIA COLI.
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Escherichia coli↗
Genetic structure in wild populations of black tiger shrimp (Penaeus monodon) using randomly amplified polymorphic DNA analysis.
Randomly amplified polymorphic DNA (RAPD) analysis was used to examine genetic variation in wild black tiger shrimp, Penaeus monodon. Specimens were collected from five geographically separated locations (Satun-Trang, Phangnga, and Medan in the Andaman Sea and Chumphon and Trad in the Gulf of Thailand). A total of 100 P. monodon individuals were investigated using seven arbitrarily selected primers. Fifty-eight (72.5%) of eighty reproducible RAPD fragments ranging in size from 200 to 2200 bp were polymorphic. The percentages of polymorphic bands of the five geographic populations investigated varied from 51.5 to 57.7%. The genetic distance between populations and UPGMA dendrograms indicated that the Medan population was genetically different from Thai P. monodon (Dij = 14.976%). Within Thailand, the Satun-Trang P. monodon was separated from the remaining geographic populations with a genetic distance of 2.632%. RAPD analysis in the present study yielded a total of 252 genotypes. A Monte Carlo analysis illustrated geographic heterogeneity in genotype frequencies within this species, suggesting that genetic population structure does exist in this taxon (P < 0.001 for all primers). Signficant differences in genotype frequencies between Thai and Indonesian (Medan) P. monodon were observed (P < 0.0001). Within Thailand, the Andaman Sea P. monodon was significantly different from that of the Gulf of Thailand (P values between 0.0000 and 0.0387), indicating population differentiation between P. monodon from these two main fishery regions of Thailand.
Journal Article↗
Population genetic structure of and inbreeding in an insular cattle breed, the Jersey, and its implications for genetic resource management.
The Jersey is a ubiquitous and successful breed of cattle that originates from the UK Channel Island of Jersey. While the breed has been exported extensively, no imports have taken place to the island since 1789, leading to a concern regarding possible losses of genetic diversity and increased inbreeding. We have conducted the first large-scale genetic analysis of the Jersey cattle using only samples from the island. A total of 223 cattle from all parishes except one were genotyped for 12 microsatellite loci. The average number of alleles per locus and expected heterozygosity were found to be comparatively high (n(A)=4, H(e)=0.64) with respect to that observed in a number of continental breeds. Only breeds that have been upgraded and are therefore the result of admixture are clearly more variable than the Jersey. We also found a significant but limited amount of genetic differentiation between parishes (F(st)=0.013), or even between farms (F(st)=0.035) despite an apparent lack of movement. This is confirmed by the application of two recent statistical methods. A Bayesian partition analysis shows that the most probable value of K, the number of possible hidden partitions, is 1 (P approximately 0.98). K=2 has a much lower probability (P approximately 0.02) while other values are essentially zero. Similarly, we were able to show that there was no support for departure from panmixia other than due to population structure, and thus that there is sufficient background gene flow across the island to overcome local drift. Overall, it appears that the current level of genetic diversity and its distribution within the island means it is unnecessary to import unrelated genetic material to the island for management purposes.
Alleles↗