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PubMed2004

Changes in population structure of the soilborne fungus Gaeumannomyces graminis var. tritici during continuous wheat cropping.

A method was developed to assess the genetic structure of Gaeumannomyces graminis var. tritici (Ggt) populations and test the hypothesis of an association between disease level in the field with changes in pathogen populations. A long-term wheat monoculture experiment, established since 1994, generated different take-all epidemics with varying the number of wheat crop successions in the 1999-2000 cropping season. Genetic polymorphism in Ggt populations was investigated over natural, local epidemics. Four populations of 30 isolates were isolated from necrotic wheat roots in a first, third, fourth, and sixth wheat crop in the same year. Each Ggt isolate was characterized with RAPD (Random Amplification Polymorphism DNA) markers and AFLP (Amplified Fragment Length Polymorphism) fingerprinting. Seventeen multilocus genotypes based on the combination of RAPD and AFLP markers were identified among all these populations. The 120 isolates were divided into two main groups, G1 and G2, according to bootstrap values higher than 86%, except for an unique isolate from the third wheat crop. Within each group, populations ranged between 93 and 100% similarity. Both groups included isolates collected from the first, third, fourth or sixth wheat crop. However, G1 group profiles dominated amongst isolates sampled in the first and the sixth wheat crops, whereas G2 group profiles largely dominated amongst isolates collected from the third and fourth wheat crops. Aggressiveness of group G2 (38%) was significantly greater than that of G1 (29.5%). These results suggest that changes in Ggt population structure occur during continuous wheat cropping. The distinction of two Ggt groups provides a simple basis for further spatio-temporal analysis of Ggt population during polyetic take-all decline.

Ascomycota↗

PubMed2001

Comparative analysis of population structure across environments and geographical scales at major histocompatibility complex and microsatellite loci in Atlantic salmon (Salmo salar).

Evidence of selection acting on major histocompatibility complex (MHC) genes has been illustrated with the analysis of their nucleotide sequences and allele frequency distribution. Comparing the patterns of population differentiation at neutral markers and MHC genes in the wild may provide further insights about the relative role of selection and neutrality in shaping their diversity. In this study, we combine both methods to assess the role of selection on a MHC gene in Atlantic salmon. We compare variation at a MHC class II B locus and microsatellites among 14 samples from seven different rivers and seven subpopulations within a single river system covering a variety of habitats and different geographical scales. We show that diversifying selection is acting on the sites involved in antigen presentation and that balancing selection maintains a high level of polymorphism within populations. Despite important differences in habitat type, the comparison of the population structure at MHC and microsatellites on large geographical scales reveals a correlation between patterns of differentiation, indicating that drift and migration have been more important than selection in shaping population differentiation at the MHC locus. In contrast, strong discrepancies between patterns of population differentiation at the two types of markers provides support for the role of selection in shaping population structure within rivers. Together, these results confirm that natural selection is influencing MHC gene diversity in wild Atlantic salmon although neutral forces may also be important in their evolution.

Alleles↗

PubMed2026

Genomic population structure, antimicrobial susceptibility, and clinical features of Mycobacterium xenopi isolates, Frankfurt, Germany, 1995-2020.

Mycobacterium xenopi causes non-tuberculous mycobacterial pulmonary disease (NTM-PD) that is difficult to treat. However, data on the genomic population structure, antimicrobial susceptibility, and the clinical significance of this pathogen remain scarce. We analyzed 76 clinical M. xenopi isolates from 70 patients collected between 1995 and 2020 in Frankfurt am Main, Germany. All isolates underwent phenotypic drug susceptibility testing and whole-genome sequencing. Cluster analysis, including isolates from this study and all hitherto available high-quality M. xenopi genome data sets in the Sequence Read Archive (n = 11), was performed by core genome multilocus sequence typing. In our cohort, only 26.5% of patients met criteria for clinically relevant NTM-PD. Phylogenetic analysis identified three large hospital-associated clusters (≤10 allelic difference), each involving between 7 and 20 patients and persisting for over 18 years, suggesting prolonged transmission chains or a common environmental source. We also defined three major clades (≤50 allelic difference), two of which contained isolates from the United Kingdom. Clofazimine and guideline-recommended antimycobacterial agents showed good in vitro efficacy, except rifampicin, with 23.6% resistance. This study represents a major expansion of M. xenopi genomic resources and provides insights into the genomic population structure, phenotypic susceptibility, and clinical characteristics of M. xenopi. Guideline-recommended antimycobacterials show good in vitro activity, while clofazimine may be a valuable addition to M. xenopi therapy. The identified clusters underscore the need for further investigation into transmission dynamics and globally successful clones.IMPORTANCEMycobacterium xenopi is an increasingly recognized opportunistic lung pathogen that is difficult to treat. Infections often occur in patients with pre-existing health conditions and can present substantial diagnostic and therapeutic challenges. A deeper understanding of its genetic diversity and resistance mechanisms is essential for optimal patient management and for clarifying potential transmission routes. By analyzing 76 whole-genome sequences together with detailed clinical information and phenotypic drug-susceptibility data, this study substantially expands the available genomic repertoire for M. xenopi. While clinical relevance was limited in our cohort, most guideline-recommended antimicrobial agents showed good efficacy in vitro. The detection of closely related strains might point toward a common environmental source of infection. These findings highlight the need for continued surveillance and provide a comprehensive foundation that supports more accurate monitoring, improved understanding of disease behavior, and future investigations into M. xenopi pathogenicity.

Humans↗

PubMed2005

Fragmented population structure of plasmodium falciparum in a region of declining endemicity.

BACKGROUND: The population genetic structure of Plasmodium falciparum differs between endemic regions, but the characteristics of a population recently fragmented by effective malaria control have been unknown. METHODS: Genotypic analysis of 10 microsatellite loci widely separated in the parasite genome was conducted on 288 P. falciparum isolates from 8 foci in Malaysian Borneo, a region in which malaria incidence has been progressively reduced. RESULTS: Within all P. falciparum foci, moderate levels of allelic diversity were found, but levels of multilocus linkage disequilibrium were extremely variable. The population with the highest proportion of mixed-clone infections also had the highest allelic diversity and nonsignificant linkage disequilibrium. In contrast, several populations showed evidence of clonal expansion, and one offshore island population had exceptionally high levels of linkage disequilibrium. Genetic differentiation between many populations was very high and strongly associated with the geographical distance between them. CONCLUSIONS: High levels of differentiation and contrasting population structure among P. falciparum populations in Malaysian Borneo indicate that they are genetically independent. This supports the feasibility of individually eradicating the remaining P. falciparum foci.

Animals↗

PubMed1994

Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales.

Powerful analyses of population structure require information from multiple genetic loci. To help develop a molecular toolbox for obtaining this information, we have designed universal oligonucleotide primers that span conserved intron-exon junctions in a wide variety of animal phyla. We test the utility of exon-primed, intron-crossing amplifications by analyzing the variability of actin intron sequences from humpback, blue, and bowhead whales and comparing the results with mitochondrial DNA (mtDNA) haplotype data. Humpback actin introns fall into two major clades that exist in different frequencies in different oceanic populations. It is surprising that Hawaii and California populations, which are very distinct in mtDNAs, are similar in actin intron alleles. This discrepancy between mtDNA and nuclear DNA results may be due either to differences in genetic drift in mitochondrial and nuclear genes or to preferential movement of males, which do not transmit mtDNA to offspring, between separate breeding grounds. Opposing mtDNA and nuclear DNA results can help clarify otherwise hidden patterns of structure in natural populations.

Animals↗

PubMed2026

Estimating population structure using epigenome-wide methylation data.

Population stratification is one of the source of inflation in epigenome-wide association studies (EWAS) when not properly accounted for. To address this, we developed methylation population scores (MPSs) to predict genetic principal components (GPCs) using a feature selection approach. We used multi-ethnic DNA methylation data from Illumina EPIC arrays across five cohorts, including MESA (n = 929), CARDIA (n = 1123), JHS (n = 1365), ARIC (n = 2338), and HCHS/SOL (n = 1475), randomly splitting participants into training (85%) and test (15%) sets. Within each cohort, associations between GPCs and CpG sites were estimated using linear regression adjusting for age, sex, smoking and alcohol use, race/ethnicity, body mass index, and cell type proportions, followed by meta-analysis and selection of CpGs with FDR <0.05. We then applied a two-stage weighted least squares Lasso regression to construct MPSs, adjusting for the aforementioned covariates. In the test dataset, MPSs showed strong correlation with GPCs, with R² ranging from 0.27 (MPS7 vs. GPC7) to 0.98 (MPS1 vs. GPC1). Visualization demonstrated that MPSs recapitulated the pattern shown by GPCs in differentiating self-reported White, Black, and Hispanic/Latino groups and outperformed methylation-based principal components constructed using alternative published methods. Additionally, MPSs showed comparable performance to GPCs in reducing inflation in EWAS. Overall, MPSs uses supervised learning with covariate adjustment to capture genetic structure across diverse populations, and provide a reliable estimate of population structure in the data and can complement GPCs when genetic data are absent.

Humans↗

PubMed1997

Population structure of harbour porpoises Phocoena phocoena in the seas around the UK and adjacent waters.

The population structure of harbour porpoises from British and adjacent waters was studied by examining variability in a 200 bp (base pair) section of the control region of mitochondrial DNA (mtDNA) extracted from 327 animals. This region contained 20 variable sites giving rise to 24 different haplotypes. Mean nucleotide diversity between all pairs of haplotypes was 0.81% (range 0-4%). The most common haplotype occurred in 63% of the samples and was recorded in all geographical areas; several other haplotypes were present in two or more of the sampling locations. This suggests considerable historical interconnections among populations, probably through gene flow. However, there were significant differences (p < 0.05) as determined by AMOVA (Analysis of Molecular Variance, Excoffier et al. 1992), between porpoises from the northern and southern North Sea, and between the northern North Sea and the Celtic/Irish Sea. The differences were predominantly due to variation among females. This sex-related difference in population genetic structure suggests that males disperse more than females. This has important consequences for evaluating the consequences of incidental catches of porpoises by fisheries in these seas since there may be a greater impact on local populations than is implied by simple calculations of mortality.

Animals↗

PubMed2004

Inverse relationship between F and microsatellite polymorphism in the marine fish, walleye pollock (Theragra chalcogramma): implications for resolving weak population structure.

Microsatellites have proved to be useful for the detection of weak population structure in marine fishes and other species characterized by large populations and high gene flow. None the less, uncertainty remains about the net effects of the particular mutational properties of these markers, and the wide range of locus polymorphism they exhibit, on estimates of differentiation. We examined the effect of varying microsatellite polymorphism on the magnitude of observed differentiation in a population survey of walleye pollock, Theragra chalcogramma. Genetic differentiation at 14 microsatellite loci among six putative populations from across the North Pacific Ocean and Bering Sea was weak but significant on large geographical scales and conformed to an isolation-by-distance pattern. A negative relationship was found between locus variability and the magnitude of estimated population subdivision. Estimates of F(ST) declined with locus polymorphism, resulting in diminished power to discriminate among samples, and we attribute this loss to the effects of size homoplasy. This empirical result suggests that mutation rates of some microsatellite loci are sufficiently high to limit resolution of weak genetic structure typical of many marine fishes.

Animals↗

PubMed1990

Population structure and skeletal variation in the Late Woodland of west-central Illinois.

This paper analyzes nonmetric trait variation in 11 late Late Woodland (ca. AD 700-1000) and one Mississippian (AD 1000-1300) skeletal samples from west-central Illinois from a population-structure perspective. Most of the sites are of the Bluff phase of Late Woodland in the lower Illinois River valley; others are from a nearby, contemporary archaeological phase. Late Woodland as a whole era (ca. AD 250-1000) was a period of marked population growth and expansion into new regional environments, trends that accompanied horticultural intensification in the area. Overall variation between sites was low, but males, females, and the total sample exhibited a significant geographic component to variation due to interregional morphological differences. The Bluff sites tended to group together relative to the non-Bluff sites. However, there was no significant geographic component to variation among the Bluff sites. The results are only partially consistent with archaeological data suggesting population growth and expansion through fissioning. Previous studies have demonstrated significant heterogeneity for nonmetric trait frequencies among Middle Woodland (ca. 100 BC to AD 250) sites, suggesting a Middle to Late Woodland change in population structure that lowered levels of morphological variation. This supports a model of increased intra- and interregional interaction from Middle to Late Woodland times developed from ceramic data by Braun and by Braun and Plog.

Bone and Bones↗

PubMedDate not supplied

Opportunity for natural selection with special reference to population structural measures among the Vadde.

Crow's indices of opportunity for natural selection have been studied among the Vadde, a fishing community of Kolleru Lake, Andhra Pradesh, India. The sample comes from 15 of the 60 fishing villages. The indices were computed both at the level of village and population units. A village sample of Palle, another fishing group in the area, has also been analysed for the purpose of comparison. An attempt has been made to explain variation in selection indices among the villages using population structural measures. A wide variation is found in both the fertility and mortality indices between the villages. The values were compatible with those found for other fishing groups studied previously, and in the middle of the range observed for the Indian populations (about 100) studied so far. Population structural measures are found to explain a significant amount of variation in Im and It but not in the fertility index.

Fertility↗

PubMed2006

Quantifying the influence of sociality on population structure in bottlenose dolphins.

1. The social structure of a population plays a key role in many aspects of its ecology and biology. It influences its genetic make-up, the way diseases spread through it and the way animals exploit their environment. However, the description of social structure in nonprimate animals is receiving little attention because of the difficulty in abstracting social structure from the description of association patterns between individuals. 2. Here we focus on recently developed analytical techniques that facilitate inference about social structure from association patterns. We apply them to the population of bottlenose dolphins residing along the Scottish east coast, to detect the presence of communities within this population and infer its social structure from the temporal variation in association patterns between individuals. 3. Using network analytical techniques, we show that the population is composed of two social units with restricted interactions. These two units seem to be related to known differences in the ranging pattern of individuals. By examining social structuring at different spatial scales, we confirm that the identification of these two units is the result of genuine social affiliation and is not an artefact of their spatial distribution. 4. We also show that the structure of this fission-fusion society relies principally on short-term casual acquaintances lasting a few days with a smaller proportion of associations lasting several years. These findings highlight how network analyses can be used to detect and understand the forces driving social organization of bottlenose dolphins and other social species.

Animals↗

PubMed2006

Relationships between Fusarium population structure, soil nutrient status and disease incidence in field-grown asparagus.

Fusarium species cause important diseases in many crops. Lack of knowledge on how Fusarium species and strains interact with their environment hampers growth management strategies to control root diseases. A field experiment involving asparagus as host plant and three phosphorus fertilization levels was designed to examine the seasonal changes and ecological relationships between Fusarium populations and their soil and plant environments. Fusarium taxa were identified and assessed using PCR-denaturing gradient electrophoresis of the EF1-alpha gene. Resulting profiles were analyzed with respect to 17 ecological parameters measured during the three main asparagus phenological phases across a growing season. Multivariate statistical analysis showed that Fusarium population structure was strongly influenced by soil P level while seasonal variation was less important. A significant relationship between Fusarium population composition and Fusarium crown and root rot incidence was also found in September. Canonical analysis further revealed significant relationships between Fusarium population structure, and plant manganese and iron contents, soil dehydrogenase activity and soil calcium concentration. If higher Fusarium crown and root rot incidence is related to the Fusarium community structure, strategies to reduce the incidence in asparagus plantations may be found through manipulation of the soil fertility.

Asparagus Plant↗

PubMed2005

Population structure in African Drosophila melanogaster revealed by microsatellite analysis.

Tropical sub-Saharan regions are considered to be the geographical origin of Drosophila melanogaster. Starting from there, the species colonized the rest of the world after the last glaciation about 10 000 years ago. Consistent with this demographic scenario, African populations have been shown to harbour higher levels of microsatellite and sequence variation than cosmopolitan populations. Nevertheless, limited information is available on the genetic structure of African populations. We used X chromosomal microsatellite variation to study the population structure of D. melanogaster populations using 13 sampling sites in North, West and East Africa. These populations were compared to six European and one North American population. Significant population structure was found among African D. melanogaster populations. Using a Bayesian method for inferring population structure we detected two distinct groups of populations among African D. melanogaster. Interestingly, the comparison to cosmopolitan D. melanogaster populations indicated that one of the divergent African groups is closely related to cosmopolitan flies. Low, but significant levels of differentiation were observed for sub-Saharan D. melanogaster populations from West and East Africa.

Africa↗

PubMed1990

Isolation by distance and correlation analysis of distance measures in the study of population structure: example from the Island of Hvar.

Assessment of the population structure on the island of Hvar is based on the analysis of Malécot's isolation by distance model. We have tested the fit of the model by regression analysis of different measures of similarity (genetic kinship) and distance [Hamming's HSM distance for linguistic data; Mahalanobis's D2 distances for anthropometric head and body dimensions, radiogrammetric dimensions of metacarpal bones, physiological (cardiorespiratory) traits, and quantitative dermatoglyphic properties of the digitopalmar complex; and Edwards's E2 for frequencies of erythrocyte antigens]. Good fit of the model for linguistic and anthropometric data, which was demonstrated in previous studies on other eastern Adriatic populations, is confirmed. We compared parameters of the model with those already published for various populations in the eastern Adriatic and other parts of the world. We also evaluated the pattern of correlations between different measures of geographic, biological, and sociocultural distances through principal components analysis and interpreted the results within the context of microevolutionary theory and the population's ethnohistorical background.

Adult↗

PubMed2005

Clostridium perfringens: insight into virulence evolution and population structure.

Clostridium perfringens is an important pathogen in veterinary and medical fields. Diseases caused by this organism are in many cases life threatening or fatal. At the same time, it is part of the ecological community of the intestinal tract of man and animals. Virulence in this species is not fully understood and it does seem that there is erratic distribution of the toxin/enzyme genes within C. perfringens population. We used the recently developed multiple-locus variable-number tandem repeat analysis (MLVA) scheme to investigate the evolution of virulence and population structure of this species. Analysis of the phylogenetic signal indicates that acquisition of the major toxin genes as well as other plasmid-borne toxin genes is a recent evolutionary event and their maintenance is essentially a function of the selective advantage they confer in certain niches under different conditions. In addition, it indicates the ability of virulent strains to cause disease in different host species. More interestingly, there is evidence that certain normal flora strains are virulent when they gain access to a different host species. Analysis of the population structure indicates that recombination events are the major tool that shapes the population and this panmixia is interrupted by frequent clonal expansion that mostly corresponds to disease processes. The signature of positive selection was detected in alpha toxin gene, suggesting the possibility of adaptive alleles on the other chromosomally encoded determinants. Finally, C. perfringens proved to have a dynamic population and availability of more genome sequences and use of comparative proteomics and animal modeling would provide more insight into the virulence of this organism.

Animals↗

PubMed2004

Genetic diversity and population structure of Tasmanian devils, the largest marsupial carnivore.

Genetic diversity and population structure were investigated across the core range of Tasmanian devils (Sarcophilus laniarius; Dasyuridae), a wide-ranging marsupial carnivore restricted to the island of Tasmania. Heterozygosity (0.386-0.467) and allelic diversity (2.7-3.3) were low in all subpopulations and allelic size ranges were small and almost continuous, consistent with a founder effect. Island effects and repeated periods of low population density may also have contributed to the low variation. Within continuous habitat, gene flow appears extensive up to 50 km (high assignment rates to source or close neighbour populations; nonsignificant values of pairwise FST), in agreement with movement data. At larger scales (150-250 km), gene flow is reduced (significant pairwise FST) but there is no evidence for isolation by distance. The most substantial genetic structuring was observed for comparisons spanning unsuitable habitat, implying limited dispersal of devils between the well-connected, eastern populations and a smaller northwestern population. The genetic distinctiveness of the northwestern population was reflected in all analyses: unique alleles; multivariate analyses of gene frequency (multidimensional scaling, minimum spanning tree, nearest neighbour); high self-assignment (95%); two distinct populations for Tasmania were detected in isolation by distance and in Bayesian model-based clustering analyses. Marsupial carnivores appear to have stronger population subdivisions than their placental counterparts.

Animals↗

PubMed1990

The coalescent and the genealogical process in geographically structured population.

We shall extend Kingman's coalescent to the geographically structured population model with migration among colonies. It is described by a continuous-time Markov chain, which is proved to be a dual process of the diffusion process of stepping-stone model. We shall derive a system of equations for the spatial distribution of a common ancestor of sampled genes from colonies and the mean time to getting to one common ancestor. These equations are solved in three particular models; a two-population model, the island model and the one-dimensional stepping-stone model with symmetric nearest-neighbour migration.

Genetics, Population↗

PubMed1980

The strong-migration limit in geographically structured populations.

Some strong-migration limits are established for geographically structured populations. A diploid monoecious population is subdivided into a finite number of colonies, which exchange migrants. The migration pattern is fixed and ergodic, but otherwise arbitrary. Generations are discrete and nonoverlapping; the analysis is restricted to a single locus. In all the limiting results, an effective population number Ne (less than or equal to NT) appears instead of the actual total population number NT. 1. If there is no selection, every allele mutates at rate u to types not preexisting in the population, and the (finite) subpopulation numbers Ni are very large, then the ultimate rate and pattern of convergence of the probabilities of allelic identity are approximately the same as for panmixia. If, in addition, the Ni are proportional to 1/u, as NT leads to infinity, the equilibrium probabilities of identity converge to the panmictic value. 2. With a finite number of alleles, any mutation pattern, an arbitrary selection scheme for each colony, and the mutation rates and selection of coefficients proportional to 1/NT, let Pj be the frequency of the allele Aj in the entire population, averaged with respect to the stationary distribution of the backward migration matrix M. As NT leads to infinity, the deviations of the allelic frequencies in each of the subpopulations from Pj converge to zero; the usual panmictic mutation-selection diffusion is obtained for Pj, with the selection intensities averaged with respect to the stationary distribution of M. In both models, Ne = NT and all effects of population subdivision disappear in the limit if, and only if, migration does not alter the subpopulation numbers.

Alleles↗